diff --git a/.gitignore b/.gitignore
index 79ef1c7bef077a3e54fb4d232c05ff82c66cb257..a664ef9a30a875e7f5848056ea4157ff586b5821 100644
--- a/.gitignore
+++ b/.gitignore
@@ -31,7 +31,7 @@ Run/Workspace/*
Run/Jobscripts/*sh
Test/Installation/Convert/VERTICAL.EC
Test/Installation/Convert/fort.15
-For_developers/Sphinx/build_temp
+For_developers/Sphinx/Build_temp
# Temporary ignorance of files!!!!
Source/Fortran/Makefile.ecgate
diff --git a/Documentation/html/.buildinfo b/Documentation/html/.buildinfo
index 48a3106171fbcea641c6e34b77a4390621a2badc..058ef15aca398bb224bc7dcb7dd9ac55ed028bd7 100644
--- a/Documentation/html/.buildinfo
+++ b/Documentation/html/.buildinfo
@@ -1,4 +1,4 @@
# Sphinx build info version 1
# This file hashes the configuration used when building these files. When it is not found, a full rebuild will be done.
-config: fddead496515ad2f1960ed379249d24a
+config: cac76732818e0e42f835f525375110ca
tags: 645f666f9bcd5a90fca523b33c5a78b7
diff --git a/Documentation/html/Developers/gen_docu.html b/Documentation/html/Developers/gen_docu.html
index de9a15c5e7b9fdeb5f6e51b36199d1e517a818ce..a0855447a1b108d673e0966e5e41a187bc21f4a2 100644
--- a/Documentation/html/Developers/gen_docu.html
+++ b/Documentation/html/Developers/gen_docu.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Updating the documentation — flex_extract 7.1.1 documentation</title>
+ <title>Updating the documentation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Api/api_fortran.html b/Documentation/html/Documentation/Api/api_fortran.html
index a4d2f92b578b8d4530809bfba7697a82267b6626..2c77f4bc2158c2054d7fddafbf701d179d4e47c2 100644
--- a/Documentation/html/Documentation/Api/api_fortran.html
+++ b/Documentation/html/Documentation/Api/api_fortran.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Auto-generated documentation for the Fortran programme — flex_extract 7.1.1 documentation</title>
+ <title>Auto-generated documentation for the Fortran programme — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Api/api_python.html b/Documentation/html/Documentation/Api/api_python.html
index b99d3b9a522db7e428f4332bd46ca1630e2679bc..69fc6c5bda714351a9aef03f8cc2095b7d503911 100644
--- a/Documentation/html/Documentation/Api/api_python.html
+++ b/Documentation/html/Documentation/Api/api_python.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Auto-generated documentation for the Python scripts — flex_extract 7.1.1 documentation</title>
+ <title>Auto-generated documentation for the Python scripts — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/changes.html b/Documentation/html/Documentation/Input/changes.html
index 264eda321f21d3cf12bcb3efac7b3f6f80af2d5b..7f6c03c278b91e73e72406ea46ea5d4f8d85561c 100644
--- a/Documentation/html/Documentation/Input/changes.html
+++ b/Documentation/html/Documentation/Input/changes.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>CONTROL file changes — flex_extract 7.1.1 documentation</title>
+ <title>CONTROL file changes — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/compilejob.html b/Documentation/html/Documentation/Input/compilejob.html
index 7e3061faa773208755dc38791943ced55f5abd28..3b9efea4c9bd30e6e41bad74e2381a5ab17d1cf7 100644
--- a/Documentation/html/Documentation/Input/compilejob.html
+++ b/Documentation/html/Documentation/Input/compilejob.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The compilation job script compilejob.ksh — flex_extract 7.1.1 documentation</title>
+ <title>The compilation job script compilejob.ksh — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -194,11 +194,11 @@
<div class="section" id="the-compilation-job-script-compilejob-ksh">
<h1>The compilation job script <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code><a class="headerlink" href="#the-compilation-job-script-compilejob-ksh" title="Permalink to this headline">¶</a></h1>
-<p>The compile job is a Korn-shell script which will be created during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong> from a template called <code class="docutils literal notranslate"><span class="pre">compilejob.template</span></code> in the template directory.</p>
+<p>The compile job is a Korn-shell script which will be created during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong> from a template called <code class="docutils literal notranslate"><span class="pre">installscript.template</span></code> in the template directory.</p>
<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by a doubled <code class="docutils literal notranslate"><span class="pre">$</span></code> sign in <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>.</p>
-<p>The job script has a number of settings for the batch system which are fixed, and it differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
+These individual parameters are marked by a doubled <code class="docutils literal notranslate"><span class="pre">$</span></code> sign in <code class="docutils literal notranslate"><span class="pre">installscript.template</span></code>.</p>
+<p>The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
server system to load the necessary modules for the environment when submitted to the batch queue.</p>
<p>The submission is done by the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> tool from within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-job-submit</span></code>.</p>
<div class="section" id="what-does-the-compilation-script-do">
@@ -210,7 +210,7 @@ server system to load the necessary modules for the environment when submitted t
<li><p>It sets some environment variables for the single session</p></li>
<li><p>It creates the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory in the <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> path of the user</p></li>
<li><p>It untars the tarball into the root directory.</p></li>
-<li><p>It compiles the Fortran program using <code class="docutils literal notranslate"><span class="pre">Makefile</span></code>.</p></li>
+<li><p>It compiles the Fortran program using <code class="docutils literal notranslate"><span class="pre">makefile</span></code>.</p></li>
<li><p>At the end, it checks whether the script has returned an error or not, and emails the log file to the user.</p></li>
</ol>
</div></blockquote>
@@ -247,21 +247,18 @@ server system to load the necessary modules for the environment when submitted t
<span class="k">case</span> <span class="si">${</span><span class="nv">HOST</span><span class="si">}</span> in
*ecg*<span class="o">)</span>
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
<span class="nb">export</span> <span class="nv">FLEXPART_ROOT_SCRIPTS</span><span class="o">=</span><span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>
<span class="nb">export</span> <span class="nv">MAKEFILE</span><span class="o">=</span>makefile_ecgate
<span class="p">;;</span>
*cca*<span class="o">)</span>
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
<span class="nb">echo</span> <span class="si">${</span><span class="nv">GROUP</span><span class="si">}</span>
<span class="nb">echo</span> <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>
<span class="nb">echo</span> <span class="si">${</span><span class="nv">HOME</span><span class="si">}</span> <span class="p">|</span> awk -F / <span class="s1">'{print $1, $2, $3, $4}'</span>
diff --git a/Documentation/html/Documentation/Input/control.html b/Documentation/html/Documentation/Input/control.html
index 4ae1207b75076c8c8532a9df03711ae3e124f689..a8c5b434fdb9a8b4f5981c1f5387a3342e8fea42 100644
--- a/Documentation/html/Documentation/Input/control.html
+++ b/Documentation/html/Documentation/Input/control.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The CONTROL file — flex_extract 7.1.1 documentation</title>
+ <title>The CONTROL file — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/control_params.html b/Documentation/html/Documentation/Input/control_params.html
index 52af3e4f85da7fcde6ad93d0135b6ab98869b1c8..28ab3ba73a397f60f74f34e7894a6f86d5201c6c 100644
--- a/Documentation/html/Documentation/Input/control_params.html
+++ b/Documentation/html/Documentation/Input/control_params.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The CONTROL parameters — flex_extract 7.1.1 documentation</title>
+ <title>The CONTROL parameters — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -278,14 +278,14 @@
<tbody>
<tr class="row-even"><td><p>DEBUG</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>If set to “1” all temporary output files from the mars requests are kept and some extra information is written out to the log file.</p></td>
<td><p>Usually all temporary files except the FLEXPART ready output files are deleted at the end of flex_extract.</p></td>
</tr>
<tr class="row-odd"><td><p>REQUEST</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1,2]</p></td>
+<td><p>0;1;2</p></td>
<td><p>2</p></td>
<td><p>This parameter allows to write out the mars requests in a seperate file.</p></td>
<td><p>The requests are stored in the file “mars_requests.csv”.
@@ -296,34 +296,34 @@ Possible selections are:
</tr>
<tr class="row-even"><td><p>PUBLIC</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>This specifies the selection of the kind of ECMWF Web Api access and therefore the kind of available datasets. Public data sets (1) and Memberstate data sets (0).</p></td>
<td><p>Selecting the public access method, the DATASET parameter has explicitly to be set to select the dataset. (CLASS is not enough.) ATTENTION: For public datasets, the user has to accept the license of the dataset to be retrieved. See here for available datasets and their licenses: https://software.ecmwf.int/wiki/display/WEBAPI/ Available+ECMWF+ Public+Datasets</p></td>
</tr>
<tr class="row-odd"><td><p>OPER</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to prepare the operational job script. Start date, end date and basetime will be prepared with environment variables at ecgate.</p></td>
<td><p>This is only necessary if extraction of half-day retrievals should be done automatically. Specific extra feature which is usually not used by normal flex_extract users.</p></td>
</tr>
<tr class="row-even"><td><p>ECSTORAGE</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to store FLEXPART ready output files in the ECFS file system.</p></td>
<td><p>Mind the data limit.</p></td>
</tr>
<tr class="row-odd"><td><p>ECTRANS</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to transfer FLEXPART ready input files to the gateway server.</p></td>
<td><p>The gateway server has to be up and running. A destination has to be installed. See installation instructions for more information.</p></td>
</tr>
<tr class="row-even"><td><p>PREFIX</p></td>
-<td><p>String [xx]</p></td>
+<td><p>String</p></td>
<td><p>anything</p></td>
<td><p>EN</p></td>
<td><p>Prefix of FLEXPART ready input files</p></td>
@@ -339,7 +339,7 @@ Possible selections are:
<tr class="row-even"><td><p>MAILOPS</p></td>
<td><p>list of String [m1, m2, …]</p></td>
<td><p>any number of mail addresses, seperated by comma</p></td>
-<td><p>[‘”${USER}”]</p></td>
+<td><p>${USER}</p></td>
<td><p>Email list for operational log files on ECMWF servers. The email addresses should be seperated by a comma.</p></td>
<td><p>For the ECMWF server it is enough to give ${USER} as input. On local system an actual email is prefered to operate correctly. </p></td>
</tr>
@@ -369,14 +369,14 @@ Possible selections are:
</thead>
<tbody>
<tr class="row-even"><td><p>START_DATE</p></td>
-<td><p>String [YYYYMMDD]</p></td>
+<td><p>String (YYYYMMDD)</p></td>
<td><p>depends on dataset</p></td>
<td><p>None</p></td>
<td><p>The first day of the retrieval period.</p></td>
<td><p>If END_DATE is set, START_DATE must be greater than END_DATE.</p></td>
</tr>
<tr class="row-odd"><td><p>END_DATE</p></td>
-<td><p>String [YYYYMMDD]</p></td>
+<td><p>String (YYYYMMDD)</p></td>
<td><p>depends on dataset</p></td>
<td><p>None</p></td>
<td><p>The last day of the retrieval period. For a one day retrieval it has to be the same date as START_DATE. If not set, it is automatically equal to START_DATE. </p></td>
@@ -398,7 +398,7 @@ Possible selections are:
</tr>
<tr class="row-even"><td><p>BASETIME</p></td>
<td><p>Integer</p></td>
-<td><p>[0; 12]</p></td>
+<td><p>0; 12</p></td>
<td><p>None</p></td>
<td><p>This parameter is intended for half-day retrievals. Only half a day will be retrieved starting from BASETIME going back 12 hours. E.g. 20180510 with a BASETIME = 00 would lead to a data retrieval of 20180509 12h until 20180510 00h.</p></td>
<td><p>Can be set to 00 or 12 only.</p></td>
@@ -453,14 +453,14 @@ https://software.ecmwf.int/wiki/display/WEBAPI/Available+ECMWF+Public+Datasets</
<tr class="row-odd"><td><p>EXPVER</p></td>
<td><p>String</p></td>
<td><p>1</p></td>
-<td><p>“1”</p></td>
+<td><p>1</p></td>
<td><p>Experiment number, necessary for R&D experiments, E-suites</p></td>
<td><p></p></td>
</tr>
<tr class="row-even"><td><p>NUMBER</p></td>
-<td><p>String [i/to/i]</p></td>
+<td><p>Integer or String [i/to/i]</p></td>
<td><p>depends on availability</p></td>
-<td><p>“OFF”</p></td>
+<td><p>OFF</p></td>
<td><p>In most cases this can be set to “OFF” but for access to individual ensemble members of ensemble forecasts it is necessary to select numbers. Note, however, that model level data are not stored in MARS for individual ensemble members except the control run. They exist only for a few days before they are discarded. </p></td>
<td><p>For retrieving CERA data, a number has to be selected explicitly. Usually “0” is enough.
For operational data just one number or a list of number can be selected. You can use the syntax “1/to/9” for example.</p></td>
@@ -468,7 +468,7 @@ For operational data just one number or a list of number can be selected. You ca
<tr class="row-odd"><td><p>FORMAT</p></td>
<td><p>String</p></td>
<td><p>[GRIB1, GRIB2]</p></td>
-<td><p>“GRIB1”</p></td>
+<td><p>GRIB1</p></td>
<td><p>Output format (either GRIB1 or GRIB2). Use GRIB2
only when using FLEXPART versions >9.2 or FLEXPART hast to be adapted for reading GRIB2</p></td>
<td><p>GRIB2 is only available for 3D model level fields, not for surface fields.</p></td>
@@ -500,7 +500,7 @@ only when using FLEXPART versions >9.2 or FLEXPART hast to be adapted for rea
<tbody>
<tr class="row-even"><td><p>TYPE</p></td>
<td><p>list of String [xx xx … xx]</p></td>
-<td><p>[AN, FC, CV, CF, 4V, PF]</p></td>
+<td><p>AN, FC, CV, CF, 4V, PF</p></td>
<td><p>None</p></td>
<td><p>A list of field types for each retrieving hour per day. E.g. AN FC FC FC AN FC FC FC for a day with 3-hourly retrieval DTIME . At 0 and 12 UTC we retrieve analysis fields and at 3, 6, 9, 15, 18 and 21 UTC forecast fields. </p></td>
<td><p>So far flex_extract is using ANalysis (AN), ForeCast (FC), Control Forecast (CF), Perturbed Forecast (PF), Calibration/Validation forecast (CV) and 4D Variational analysis (4V). Other types might be also possible but were not tested. The analysis fields are usually (depending on data set) available at 00/06/12/18 UTC. For better temporal resolution, the time inbetween the AN fields can be filled with forecasts (FC). Additionally, it is recommended to use analysis fields only at 00 and 12 UTC and fill the rest of the times with other field types, such as forecasts. </p></td>
@@ -554,7 +554,7 @@ With MAXSTEP > 24 the forecasts from different days overlap, the naming schem
<tbody>
<tr class="row-even"><td><p>ACCTYPE</p></td>
<td><p>String</p></td>
-<td><p>[FC, CV, CF, 4V, PF] - just one of them</p></td>
+<td><p>FC, CV, CF, 4V, PF - just one of them</p></td>
<td><p>None</p></td>
<td><p>The type of field for accumulated data retrieval. The accumulated data fields are only available from forecast fields. Therefore it is seperated from the normal TYPE parameter to allow, for example, retrievment solely of hourly analysis fields in the Era5 data set. </p></td>
<td><p>For downward compatibility to older versions: if ACCTYPE is not specified, the default value is taken form the second position of the original TYPE parameter (TYPE[2]). NOTE: This is important at the moment the original TYPE parameter is changed from FC to AN for example.</p></td>
@@ -575,7 +575,7 @@ With MAXSTEP > 24 the forecasts from different days overlap, the naming schem
</tr>
<tr class="row-odd"><td><p>RRINT</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>1</p></td>
<td><p>Switch to select method of disaggregation for precipitation fields. Old method (0) with a simple linear disaggregation or new method (1) with 2 additional subsequent intervals per time interval.</p></td>
<td><p>For more information see article:
@@ -702,7 +702,7 @@ depends on data set</p></td>
<tbody>
<tr class="row-even"><td><p>GAUSS</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>A switch to calculate ETADOT from Lat/Lon grid (0) or from Gaussian grid (1)</p></td>
<td><p></p></td>
@@ -716,7 +716,7 @@ depends on data set</p></td>
</tr>
<tr class="row-even"><td><p>OMEGA</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Retrieve Omega from MARS and put it to file
OMEGAyymmddhh</p></td>
@@ -724,7 +724,7 @@ OMEGAyymmddhh</p></td>
</tr>
<tr class="row-odd"><td><p>OMEGADIFF</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Calculate Omega and Dps/Dt from continuity
equation for diagnostic purposes and include it in file OMEGAyymmddhh</p></td>
@@ -732,7 +732,7 @@ equation for diagnostic purposes and include it in file OMEGAyymmddhh</p></td>
</tr>
<tr class="row-even"><td><p>ETA</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to read ETADOT precalculated by ECMWF and multiply it with DPDETA to be compatible with ETADOT calculated from continuity equation.
ETADOT calculation from continuity equation on either Gaussian or lat/lon grid is disabled unless ETADIFF is set to 1 as well.</p></td>
@@ -740,14 +740,14 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
</tr>
<tr class="row-odd"><td><p>ETADIFF</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to calculate etadot and Dps/Dt from continuity equation for diagnostic purposes and include it in file ETAyymmddhh. Expensive option, only for debugging purposes.</p></td>
<td><p></p></td>
</tr>
<tr class="row-even"><td><p>DPDETA</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>1</p></td>
<td><p>Switch to multiply etadot with dpdeta – this is the default. In some future version this may change.</p></td>
<td><p></p></td>
@@ -767,12 +767,12 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
<table class="docutils align-default" id="id9">
<caption><span class="caption-text">Additional data parameters in CONTROL file</span><a class="headerlink" href="#id9" title="Permalink to this table">¶</a></caption>
<colgroup>
-<col style="width: 17%" />
+<col style="width: 16%" />
<col style="width: 9%" />
-<col style="width: 13%" />
+<col style="width: 12%" />
<col style="width: 11%" />
-<col style="width: 15%" />
-<col style="width: 35%" />
+<col style="width: 14%" />
+<col style="width: 36%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>PARAMETER</p></th>
@@ -786,14 +786,14 @@ ETADOT calculation from continuity equation on either Gaussian or lat/lon grid i
<tbody>
<tr class="row-even"><td><p>CWC</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to retrieve cloud water content (sum of cloud liquid water and cloud ice) (1) or not (0).</p></td>
<td><p></p></td>
</tr>
<tr class="row-odd"><td><p>DOUBLEELDA</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Switch to select the calculation of extra ensemble members for the ELDA stream. It doubles the amount of retrieved ensemble members.</p></td>
<td><p>Each ensemble member is used to create a new synthesized ensemble member by subtracting 2 * ( current time step value - last time step value ) from the current time step value</p></td>
diff --git a/Documentation/html/Documentation/Input/ecmwf_env.html b/Documentation/html/Documentation/Input/ecmwf_env.html
index db8373ad33148261261dbaa38b2c4dde05708f11..46a37c70d0aee8a29c20216a0b7ba48768f286c2 100644
--- a/Documentation/html/Documentation/Input/ecmwf_env.html
+++ b/Documentation/html/Documentation/Input/ecmwf_env.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ECMWF user credential file ECMWF_ENV — flex_extract 7.1.1 documentation</title>
+ <title>ECMWF user credential file ECMWF_ENV — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/examples.html b/Documentation/html/Documentation/Input/examples.html
index d9f5d60ab08865efe8492cb8d64391ba3002977c..c87a5e850b37a868099a5b60abb6073079d35779 100644
--- a/Documentation/html/Documentation/Input/examples.html
+++ b/Documentation/html/Documentation/Input/examples.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>CONTROL file examples — flex_extract 7.1.1 documentation</title>
+ <title>CONTROL file examples — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -223,9 +223,9 @@ CONTROL_OD.OPER.FC.twicedaily.1hourly
CONTROL_OD.OPER.FC.twicedaily.3hourly
</pre></div>
</div>
-<div class="admonition-todo admonition" id="id1">
-<p class="admonition-title">Todo</p>
-<p>#PS some information to be added.</p>
+<div class="admonition note">
+<p class="admonition-title">Note</p>
+<p>Further information will follow.</p>
</div>
<div class="toctree-wrapper compound">
</div>
diff --git a/Documentation/html/Documentation/Input/fortran_makefile.html b/Documentation/html/Documentation/Input/fortran_makefile.html
index 3d331fb0669afd72efcbd429af47a545b5aac8c9..aca972bb6e89c572a1b815d0bf4da0148a3ec48a 100644
--- a/Documentation/html/Documentation/Input/fortran_makefile.html
+++ b/Documentation/html/Documentation/Input/fortran_makefile.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The Fortran makefile for calc_etadot — flex_extract 7.1.1 documentation</title>
+ <title>The Fortran makefile for calc_etadot — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Input/jobscript.html b/Documentation/html/Documentation/Input/jobscript.html
index 058dd5e7a47fa43b7342d2c049decdd0c530fe94..57ea5ab4f23341dd7713786503fa07ad1b1ff2a5 100644
--- a/Documentation/html/Documentation/Input/jobscript.html
+++ b/Documentation/html/Documentation/Input/jobscript.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The job script job.ksh — flex_extract 7.1.1 documentation</title>
+ <title>The job script job.ksh — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -101,7 +101,7 @@
<li class="toctree-l3"><a class="reference internal" href="run.html">The executable script - <code class="docutils literal notranslate"><span class="pre">run.sh</span></code></a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a><ul>
<li class="toctree-l4"><a class="reference internal" href="#what-does-the-job-script-do">What does the job script do?</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#example-jobscript-ksh">Example <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code></a></li>
+<li class="toctree-l4"><a class="reference internal" href="#example-job-ksh">Example <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code></a></li>
</ul>
</li>
<li class="toctree-l3"><a class="reference internal" href="control.html">The CONTROL file</a></li>
@@ -195,11 +195,11 @@
<div class="section" id="the-job-script-job-ksh">
<h1>The job script <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code><a class="headerlink" href="#the-job-script-job-ksh" title="Permalink to this headline">¶</a></h1>
<p>The job script is a Korn-shell script which will be created at runtime for each <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> execution in the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
-<p>It is based on the <code class="docutils literal notranslate"><span class="pre">job.temp</span></code> template file stored in the <code class="docutils literal notranslate"><span class="pre">Templates</span></code> directory.
-This template is generated in the installation process from a <code class="docutils literal notranslate"><span class="pre">job.template</span></code> template file.</p>
+<p>It is based on the <code class="docutils literal notranslate"><span class="pre">submitscript.template</span></code> template file stored in the <code class="docutils literal notranslate"><span class="pre">Templates</span></code> directory.
+This template is generated in the installation process from a <code class="docutils literal notranslate"><span class="pre">jobscript.template</span></code> template file.</p>
<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> uses the Python package <a class="reference external" href="https://genshi.edgewall.org/">genshi</a> to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by <code class="docutils literal notranslate"><span class="pre">$$</span></code> in <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>.</p>
+These individual parameters are marked by <code class="docutils literal notranslate"><span class="pre">$$</span></code> in <code class="docutils literal notranslate"><span class="pre">jobscript.template</span></code>.</p>
<p>The job script has a number of settings for the batch system which are fixed, and differentiates between the <em>ecgate</em> and the <em>cca/ccb</em>
server system to load the necessary modules for the environment when submitted to the batch queue.</p>
<p>The submission is done by the <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> tool from within <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the command <code class="docutils literal notranslate"><span class="pre">ecaccess-job-submit</span></code>.</p>
@@ -211,14 +211,14 @@ server system to load the necessary modules for the environment when submitted t
<li><p>It prepares the job environment at the ECMWF servers by loading the necessary library modules.</p></li>
<li><p>It sets some environment variables for the single session.</p></li>
<li><p>It creates the directory structure in the user’s <code class="docutils literal notranslate"><span class="pre">$SCRATCH</span></code> file system.</p></li>
-<li><p>It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code>. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> as an environment variable.</p></li>
+<li><p>It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code>. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> as an environment variable.</p></li>
<li><p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is started from within the <code class="docutils literal notranslate"><span class="pre">work</span></code> directory of the new directory structure by calling the <code class="docutils literal notranslate"><span class="pre">submit.py</span></code> script. It sets new paths for input and output directories and the recently generated <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p></li>
<li><p>At the end, it checks whether the script has returned an error or not, and emails the log file to the user.</p></li>
</ol>
</div></blockquote>
</div>
-<div class="section" id="example-jobscript-ksh">
-<h2>Example <code class="docutils literal notranslate"><span class="pre">jobscript.ksh</span></code><a class="headerlink" href="#example-jobscript-ksh" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="example-job-ksh">
+<h2>Example <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code><a class="headerlink" href="#example-job-ksh" title="Permalink to this headline">¶</a></h2>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
<span class="c1"># ON ECGB:</span>
@@ -249,20 +249,17 @@ server system to load the necessary modules for the environment when submitted t
<span class="k">case</span> <span class="si">${</span><span class="nv">HOST</span><span class="si">}</span> in
*ecg*<span class="o">)</span>
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="si">${</span><span class="nv">PATH</span><span class="si">}</span>:<span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v7.1/Source/Python
<span class="p">;;</span>
*cca*<span class="o">)</span>
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
<span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span><span class="si">${</span><span class="nv">TMPDIR</span><span class="si">}</span>
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="si">${</span><span class="nv">PATH</span><span class="si">}</span>:<span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v7.1/Source/Python
<span class="p">;;</span>
@@ -288,7 +285,7 @@ cat ><span class="si">${</span><span class="nv">CONTROL</span><span class="si
<span class="s">dataset None</span>
<span class="s">date_chunk 3</span>
<span class="s">debug 1</span>
-<span class="s">destination annep@genericSftp</span>
+<span class="s">destination <specificname>@genericSftp</span>
<span class="s">doubleelda 0</span>
<span class="s">dpdeta 1</span>
<span class="s">dtime 3</span>
@@ -309,7 +306,7 @@ cat ><span class="si">${</span><span class="nv">CONTROL</span><span class="si
<span class="s">gaussian</span>
<span class="s">grib2flexpart 0</span>
<span class="s">grid 1.0/1.0</span>
-<span class="s">inputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace</span>
+<span class="s">inputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace</span>
<span class="s">install_target None</span>
<span class="s">job_chunk 1</span>
<span class="s">job_template job.temp</span>
@@ -326,7 +323,7 @@ cat ><span class="si">${</span><span class="nv">CONTROL</span><span class="si
<span class="s">omega 0</span>
<span class="s">omegadiff 0</span>
<span class="s">oper 0</span>
-<span class="s">outputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace</span>
+<span class="s">outputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace</span>
<span class="s">prefix CE</span>
<span class="s">public 0</span>
<span class="s">purefc 0</span>
diff --git a/Documentation/html/Documentation/Input/run.html b/Documentation/html/Documentation/Input/run.html
index 6aa4c5719f9faddb052be0dc2267347db9586526..90abff872bfbbe5c0a6d7f7d7fe51d3fa9c512a7 100644
--- a/Documentation/html/Documentation/Input/run.html
+++ b/Documentation/html/Documentation/Input/run.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The executable script - run.sh — flex_extract 7.1.1 documentation</title>
+ <title>The executable script - run.sh — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -205,16 +205,16 @@ the command line parameters, and the so-called <code class="docutils literal not
<table class="docutils align-default" id="id1">
<caption><span class="caption-text">Parameters for submission</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
<colgroup>
-<col style="width: 12%" />
-<col style="width: 9%" />
-<col style="width: 9%" />
-<col style="width: 9%" />
-<col style="width: 27%" />
-<col style="width: 33%" />
+<col style="width: 13%" />
+<col style="width: 13%" />
+<col style="width: 8%" />
+<col style="width: 8%" />
+<col style="width: 26%" />
+<col style="width: 32%" />
</colgroup>
<thead>
<tr class="row-odd"><th class="head"><p>PARAMETER</p></th>
-<th class="head"><p>Datatype</p></th>
+<th class="head"><p>Format</p></th>
<th class="head"><p>Possible values</p></th>
<th class="head"><p>Default</p></th>
<th class="head"><p>Description</p></th>
@@ -223,14 +223,14 @@ the command line parameters, and the so-called <code class="docutils literal not
</thead>
<tbody>
<tr class="row-even"><td><p>START_DATE</p></td>
-<td><p>String YYYYMMDD</p></td>
+<td><p>String (YYYYMMDD)</p></td>
<td><p>depends on dataset</p></td>
<td><p>None</p></td>
<td><p>The first day of the retrieval period.</p></td>
-<td><p>If END_DATE is set, START_DATE must be greater than END_DATE.</p></td>
+<td><p>If END_DATE is set, START_DATE must be earlier or equal than END_DATE.</p></td>
</tr>
<tr class="row-odd"><td><p>END_DATE</p></td>
-<td><p>String YYYYMMDD</p></td>
+<td><p>String (YYYYMMDD)</p></td>
<td><p>depends on dataset</p></td>
<td><p>None</p></td>
<td><p>The last day of the retrieval period. For a one day retrieval it has to be the same date as START_DATE. If not set, it is automatically equal to START_DATE. </p></td>
@@ -259,63 +259,66 @@ the command line parameters, and the so-called <code class="docutils literal not
</tr>
<tr class="row-odd"><td><p>BASETIME</p></td>
<td><p>Integer</p></td>
-<td><p>[0; 12]</p></td>
+<td><p>0; 12</p></td>
<td><p>None</p></td>
<td><p>This parameter is intended for half-day retrievals. Only half a day will be retrieved starting from BASETIME going back 12 hours. E.g. 20180510 with a BASETIME = 00 would lead to a data retrieval of 20180509 12h until 20180510 00h.</p></td>
<td><p>Can be set to 00 or 12 only.</p></td>
</tr>
<tr class="row-even"><td><p>STEP</p></td>
-<td><p>list of String [xx xx … xx] or as String [x/to/x]</p></td>
-<td><p>[00 - max available STEP in data set]</p></td>
+<td><p>blank seperated list of Integers (ii ii … ii) or as String (start/to/end)</p></td>
+<td><p>00 - max available STEP in data set</p></td>
<td><p>None</p></td>
<td><p>This is the forecast time step in hours for each corresponding field type (TYPE). Counting of the steps starts from the forecast times. E.g. In Era-Interim, for forecasts at 3, 6, 9 UTC the STEPS 3,6 and 9 are used and the forecast TIME 00 UTC. </p></td>
<td><p>Has to have the same amount of values as in TYPE and TIME! For analysis (AN) fields the STEP has to be 00 always! It is more easily set in the CONTROL file. For pure forecast modes it might be set here as e.g. 0/to/36</p></td>
</tr>
<tr class="row-odd"><td><p>LEVELIST</p></td>
-<td><p>String [start/to/end]</p></td>
+<td><p>String (start/to/end)</p></td>
<td><p>1/to/137; depends on dataset</p></td>
<td><p>None</p></td>
<td><p>List of vertical levels for MARS request. It can be a subset of levels but it has to include the maximum level (end).</p></td>
<td><p>If full list of levels is needed and parameter LEVEL is set, the LEVELIST parameter is not needed. “end” has to be the maximum number of possible levels and has to be the same as in LEVEL, if specified.</p></td>
</tr>
<tr class="row-even"><td><p>AREA</p></td>
-<td><p>Double [f/f/f/f]</p></td>
+<td><p>Double (f/f/f/f)</p></td>
<td><p>any float within lat and lon boundaries</p></td>
-<td><p>‘’</p></td>
+<td><p>None</p></td>
<td><p>Area defined as north/west/south/east</p></td>
<td><p></p></td>
</tr>
<tr class="row-odd"><td><p>DEBUG</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Debug mode - leave temporary files intact</p></td>
<td><p>Usually only the final FLEXPART inputfiles are saved.</p></td>
</tr>
<tr class="row-even"><td><p>OPER</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Operational mode - prepares dates with environment variables</p></td>
<td><p></p></td>
</tr>
<tr class="row-odd"><td><p>REQUEST</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1,2]</p></td>
+<td><p>0;1;2</p></td>
<td><p>0</p></td>
-<td><p>List all mars requests with its specifc values in file mars_requests.dat</p></td>
+<td><p>List all mars requests with its specifc values in file mars_requests.dat
+0 – no file
+1 – only mars_requests.csv
+2 – file and extraction</p></td>
<td><p>Very useful for documentation or debugging reasons.</p></td>
</tr>
<tr class="row-even"><td><p>PUBLIC</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Public mode - retrieves the public datasets</p></td>
<td><p>IMPORTANT: This is necessary to select for each PUBLIC user!</p></td>
</tr>
<tr class="row-odd"><td><p>RRINT</p></td>
<td><p>Integer</p></td>
-<td><p>[0,1]</p></td>
+<td><p>0;1</p></td>
<td><p>0</p></td>
<td><p>Selection of old or new precipitation interpolation ;
0 - old method;
@@ -345,8 +348,8 @@ the command line parameters, and the so-called <code class="docutils literal not
</tr>
<tr class="row-odd"><td><p>JOB_TEMPLATE</p></td>
<td><p>String</p></td>
-<td><p>job.temp</p></td>
-<td><p>job.temp</p></td>
+<td><p>jobscript.template</p></td>
+<td><p>jobscript.template</p></td>
<td><p>The job template file which are adapted to be submitted to the batch system on ECMWF server.</p></td>
<td><p></p></td>
</tr>
diff --git a/Documentation/html/Documentation/Input/setup.html b/Documentation/html/Documentation/Input/setup.html
index 425b45cce682fb9df8a4e6b3d6791b17c29651b3..9cdd15428c8cb3925b91551b2ee2d63a8ebab1fd 100644
--- a/Documentation/html/Documentation/Input/setup.html
+++ b/Documentation/html/Documentation/Input/setup.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>The installation script - setup.sh — flex_extract 7.1.1 documentation</title>
+ <title>The installation script - setup.sh — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -234,15 +234,15 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<tbody>
<tr class="row-even"><td><p>TARGET</p></td>
<td><p>String</p></td>
-<td><p>local, ecgate, cca</p></td>
+<td><p>local, ecgate, cca, ccb</p></td>
<td><p>None</p></td>
-<td><p>Defines the flex_extract application mode to be used. Local = local mode; egate = Remote or Gateway mode, cca = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here.</p></td>
+<td><p>Defines the flex_extract application mode to be used. Local = local mode; ecgate = Remote or Gateway mode, cca or ccb = Remote or Gateway mode (HPC). Whether the local mode is for public or member state users doesn’t matter here.</p></td>
</tr>
<tr class="row-odd"><td><p>MAKEFILE</p></td>
<td><p>String</p></td>
<td><p>any makefile present in the Fortran source directory</p></td>
<td><p>None</p></td>
-<td><p>Name of the makefile in source/fortran directory to be used for compiling the Fortran program. </p></td>
+<td><p>Name of the makefile in Source/Fortran directory to be used for compiling the Fortran program. </p></td>
</tr>
<tr class="row-even"><td><p>ECUID</p></td>
<td><p>String</p></td>
@@ -272,12 +272,12 @@ It calls the top-level Python script <code class="docutils literal notranslate">
<td><p>String</p></td>
<td><p>a full path </p></td>
<td><p>$HOME on ECMWF server and current flex_extract root path on local machine</p></td>
-<td><p>Root path where flex_extract should be installed. If it is not set, it will be $HOME on ECMWF servers and to the current flex_extract root path on local servers. </p></td>
+<td><p>Root path where flex_extract should be installed. It will always be $HOME on ECMWF servers and if not set for the local mode, it will be the current flex_extract root path on local servers. </p></td>
</tr>
<tr class="row-odd"><td><p>JOB_TEMPLATE</p></td>
<td><p>String</p></td>
-<td><p>job.template</p></td>
-<td><p>job.template</p></td>
+<td><p>installscript.template</p></td>
+<td><p>installscript.template</p></td>
<td><p>The rudimentary template file to create a batch job template for submission to ECMWF servers. Should not be changed because it is already optimised for ECMWF servers. (Remote and Gateway mode)</p></td>
</tr>
<tr class="row-even"><td><p>CONTROLFILE</p></td>
diff --git a/Documentation/html/Documentation/Input/templates.html b/Documentation/html/Documentation/Input/templates.html
index 72a9af33b4c41baea3ce2efc50dac6ad41ea8c7a..cf6f3916cbf9f1e73cebcb798c73e073f39236c5 100644
--- a/Documentation/html/Documentation/Input/templates.html
+++ b/Documentation/html/Documentation/Input/templates.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Templates — flex_extract 7.1.1 documentation</title>
+ <title>Templates — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -106,11 +106,11 @@
<li class="toctree-l3"><a class="reference internal" href="changes.html">CONTROL file changes</a></li>
<li class="toctree-l3"><a class="reference internal" href="ecmwf_env.html">ECMWF user credential file <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code></a></li>
<li class="toctree-l3 current"><a class="current reference internal" href="#">Templates</a><ul>
-<li class="toctree-l4"><a class="reference internal" href="#convert-nl">convert.nl</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#ecmwf-env-template">ecmwf_env.template</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#compilejob-template">compilejob.template</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#job-temp">job.temp</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#job-template">job.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#calc-etadot-nml-template">calc_etadot_nml.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#ecmwf-env-template">ECMWF_ENV.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#installscript-template">installscript.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#submitscript-template">submitscript.template</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#jobscript-template">jobscript.template</a></li>
</ul>
</li>
</ul>
@@ -202,10 +202,10 @@
<p class="admonition-title">Note</p>
<p>Do not change anything in these files unless you understand the effects!</p>
</div>
-<p>Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading <code class="docutils literal notranslate"><span class="pre">$</span></code> sign. In case of the Kornshell job scripts, where (environment) variables are used, the <code class="docutils literal notranslate"><span class="pre">$</span></code> sign needs to be doubled for <cite>escaping</cite>.</p>
+<p>Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading <code class="docutils literal notranslate"><span class="pre">$</span></code> sign. In case of the Korn shell job scripts, where (environment) variables are used, the <code class="docutils literal notranslate"><span class="pre">$</span></code> sign needs to be doubled for <cite>escaping</cite>.</p>
<p>The following templates are used; they can be found in the directory <code class="docutils literal notranslate"><span class="pre">flex_extract_vX.X/Templates</span></code>:</p>
-<div class="section" id="convert-nl">
-<h2>convert.nl<a class="headerlink" href="#convert-nl" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="calc-etadot-nml-template">
+<h2>calc_etadot_nml.template<a class="headerlink" href="#calc-etadot-nml-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This is the template for a Fortran namelist file called <code class="docutils literal notranslate"><span class="pre">fort.4</span></code> read by <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code>.
It contains all the parameters <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> needs.</p>
@@ -233,7 +233,7 @@ It contains all the parameters <code class="docutils literal notranslate"><span
</div></blockquote>
</div>
<div class="section" id="ecmwf-env-template">
-<h2>ecmwf_env.template<a class="headerlink" href="#ecmwf-env-template" title="Permalink to this headline">¶</a></h2>
+<h2>ECMWF_ENV.template<a class="headerlink" href="#ecmwf-env-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This template is used to create the <code class="docutils literal notranslate"><span class="pre">ECMWF_ENV</span></code> file in the application modes <strong>gateway</strong> and <strong>remote</strong>. It contains the user credentials and gateway server settings for the file transfers.</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>ECUID <span class="nv">$user_name</span>
@@ -244,8 +244,8 @@ DESTINATION <span class="nv">$destination_name</span>
</div>
</div></blockquote>
</div>
-<div class="section" id="compilejob-template">
-<h2>compilejob.template<a class="headerlink" href="#compilejob-template" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="installscript-template">
+<h2>installscript.template<a class="headerlink" href="#installscript-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This template is used to create the job script file called <code class="docutils literal notranslate"><span class="pre">compilejob.ksh</span></code> during the installation process for the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
<p>At the beginning, some directives for the batch system are set.
@@ -283,21 +283,18 @@ For the high-performance computers <strong>cca</strong> and <strong>ccb</strong>
<span class="k">case</span> <span class="nv">$$</span><span class="o">{</span>HOST<span class="o">}</span> in
*ecg*<span class="o">)</span>
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
<span class="nb">export</span> <span class="nv">FLEXPART_ROOT_SCRIPTS</span><span class="o">=</span><span class="nv">$fp_root_scripts</span>
<span class="nb">export</span> <span class="nv">MAKEFILE</span><span class="o">=</span><span class="nv">$makefile</span>
<span class="p">;;</span>
*cca*<span class="o">)</span>
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
<span class="nb">echo</span> <span class="nv">$$</span><span class="o">{</span>GROUP<span class="o">}</span>
<span class="nb">echo</span> <span class="nv">$$</span><span class="o">{</span>HOME<span class="o">}</span>
<span class="nb">echo</span> <span class="nv">$$</span><span class="o">{</span>HOME<span class="o">}</span> <span class="p">|</span> awk -F / <span class="s1">'{print $1, $2, $3, $4}'</span>
@@ -328,8 +325,8 @@ ls -l <span class="nv">$fortran_program</span> >>flexcompile
</div>
</div></blockquote>
</div>
-<div class="section" id="job-temp">
-<h2>job.temp<a class="headerlink" href="#job-temp" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="submitscript-template">
+<h2>submitscript.template<a class="headerlink" href="#submitscript-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
<div><p>This template is used to create the actual job script file called <code class="docutils literal notranslate"><span class="pre">job.ksh</span></code> for the execution of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the application modes <strong>remote</strong> and <strong>gateway</strong>.</p>
<p>At the beginning, some directives for the batch system are set.
@@ -367,23 +364,20 @@ for details see <a class="reference external" href="https://confluence.ecmwf.int
<span class="nb">export</span> <span class="nv">VERSION</span><span class="o">=</span><span class="m">7</span>.1
<span class="k">case</span> <span class="nv">$$</span><span class="o">{</span>HOST<span class="o">}</span> in
*ecg*<span class="o">)</span>
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
- <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$$</span><span class="o">{</span>PATH<span class="o">}</span>:<span class="nv">$$</span><span class="o">{</span>HOME<span class="o">}</span>/flex_extract_v7.1/Source/Python
- <span class="p">;;</span>
- *cca*<span class="o">)</span>
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
- <span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span><span class="nv">$$</span><span class="o">{</span>TMPDIR<span class="o">}</span>
- <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$$</span><span class="o">{</span>PATH<span class="o">}</span>:<span class="nv">$$</span><span class="o">{</span>HOME<span class="o">}</span>/flex_extract_v7.1/Source/Python
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="si">${</span><span class="nv">PATH</span><span class="si">}</span>:<span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v7.1/Source/Python
+ <span class="p">;;</span>
+ *cca*<span class="o">)</span>
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ <span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span><span class="si">${</span><span class="nv">TMPDIR</span><span class="si">}</span>
+ <span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="si">${</span><span class="nv">PATH</span><span class="si">}</span>:<span class="si">${</span><span class="nv">HOME</span><span class="si">}</span>/flex_extract_v7.1/Source/Python
<span class="p">;;</span>
<span class="k">esac</span>
@@ -421,10 +415,10 @@ submit.py --controlfile<span class="o">=</span><span class="nv">$$</span><span c
</div>
</div></blockquote>
</div>
-<div class="section" id="job-template">
-<h2>job.template<a class="headerlink" href="#job-template" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="jobscript-template">
+<h2>jobscript.template<a class="headerlink" href="#jobscript-template" title="Permalink to this headline">¶</a></h2>
<blockquote>
-<div><p>This template is used to create the template for the execution job script <code class="docutils literal notranslate"><span class="pre">job.temp</span></code> for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the installation process. A description of the file can be found under <code class="docutils literal notranslate"><span class="pre">job.temp</span></code>. Several parameters are set in this process, such as the user credentials and the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version number.</p>
+<div><p>This template is used to create the template for the execution job script <code class="docutils literal notranslate"><span class="pre">submitscript.template</span></code> for <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> in the installation process. A description of the file can be found under <code class="docutils literal notranslate"><span class="pre">submitscript.template</span></code>. Several parameters are set in this process, such as the user credentials and the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> version number.</p>
<div class="highlight-ksh notranslate"><div class="highlight"><pre><span></span><span class="ch">#!/bin/ksh</span>
<span class="c1"># ON ECGB:</span>
@@ -454,21 +448,18 @@ submit.py --controlfile<span class="o">=</span><span class="nv">$$</span><span c
<span class="nb">export</span> <span class="nv">VERSION</span><span class="o">=</span><span class="nv">$version_number</span>
<span class="k">case</span> <span class="nv">$$$$</span><span class="o">{</span>HOST<span class="o">}</span> in
*ecg*<span class="o">)</span>
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$$$$</span><span class="o">{</span>PATH<span class="o">}</span>:<span class="nv">$fp_root_path</span>
<span class="p">;;</span>
*cca*<span class="o">)</span>
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
<span class="nb">export</span> <span class="nv">SCRATCH</span><span class="o">=</span><span class="nv">$$$$</span><span class="o">{</span>TMPDIR<span class="o">}</span>
<span class="nb">export</span> <span class="nv">PATH</span><span class="o">=</span><span class="nv">$$$$</span><span class="o">{</span>PATH<span class="o">}</span>:<span class="nv">$fp_root_path</span>
<span class="p">;;</span>
diff --git a/Documentation/html/Documentation/Overview/app_modes.html b/Documentation/html/Documentation/Overview/app_modes.html
index e29f2fadb1369148bd7375e66c3161912c27994d..462af6b4ed9742458cd40d35a33f072b73e3adbd 100644
--- a/Documentation/html/Documentation/Overview/app_modes.html
+++ b/Documentation/html/Documentation/Overview/app_modes.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Application modes — flex_extract 7.1.1 documentation</title>
+ <title>Application modes — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/Overview/prog_flow.html b/Documentation/html/Documentation/Overview/prog_flow.html
index 42570c48e7d38172bcb0b55a1aa9bb8ceb29f34f..046be30c451fdad452fd3d3b43c41f9b2e1b6496 100644
--- a/Documentation/html/Documentation/Overview/prog_flow.html
+++ b/Documentation/html/Documentation/Overview/prog_flow.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Program flow — flex_extract 7.1.1 documentation</title>
+ <title>Program flow — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/api.html b/Documentation/html/Documentation/api.html
index fbe7fb5aa23fa7999ae48ceb1c4ce472d401e38c..392d3c1533643fc06ef0b9d1701803378fb6a550 100644
--- a/Documentation/html/Documentation/api.html
+++ b/Documentation/html/Documentation/api.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Auto-generated documentation — flex_extract 7.1.1 documentation</title>
+ <title>Auto-generated documentation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/disagg.html b/Documentation/html/Documentation/disagg.html
index 3ad73396e27d34faf7a9eac3ae41731c7d00bea0..25951259523379066c28190f877f45ee736dcc67 100644
--- a/Documentation/html/Documentation/disagg.html
+++ b/Documentation/html/Documentation/disagg.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Disaggregation of flux data — flex_extract 7.1.1 documentation</title>
+ <title>Disaggregation of flux data — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -200,39 +200,39 @@ pre-processing has to be applied.</p>
<tr class="row-odd"><th class="head"><p>Short Name</p></th>
<th class="head"><p>Name</p></th>
<th class="head"><p>Units</p></th>
-<th class="head"><p>Interpolation Type</p></th>
+<th class="head"><p>Disaggregation</p></th>
</tr>
</thead>
<tbody>
<tr class="row-even"><td><p>LSP</p></td>
<td><p>large-scale precipitation</p></td>
<td><p>m</p></td>
-<td><p>modified linear interpolation</p></td>
+<td><p>precipitation</p></td>
</tr>
<tr class="row-odd"><td><p>CP</p></td>
<td><p>convective precipitation</p></td>
<td><p>m</p></td>
-<td><p>modified linear interpolation</p></td>
+<td><p>precipitation</p></td>
</tr>
<tr class="row-even"><td><p>SSHF</p></td>
<td><p>surface sensible heat flux</p></td>
-<td><p>J m:math:<cite>^{-2}</cite></p></td>
-<td><p>bicubic interpolation</p></td>
+<td><p>J m <span class="math notranslate nohighlight">\(^{-2}\)</span></p></td>
+<td><p>flux</p></td>
</tr>
<tr class="row-odd"><td><p>EWSS</p></td>
<td><p>eastward turbulent surface stress</p></td>
-<td><p>N m:math:<cite>^{-2}</cite> s</p></td>
-<td><p>bicubic interpolation</p></td>
+<td><p>N m <span class="math notranslate nohighlight">\(^{-2}\)</span> s</p></td>
+<td><p>flux</p></td>
</tr>
<tr class="row-even"><td><p>NSSS</p></td>
<td><p>northward turbulent surface stress</p></td>
-<td><p>N m:math:<cite>^{-2}</cite> s</p></td>
-<td><p>bicubic interpolation</p></td>
+<td><p>N m <span class="math notranslate nohighlight">\(^{-2}\)</span> s</p></td>
+<td><p>flux</p></td>
</tr>
<tr class="row-odd"><td><p>SSR</p></td>
<td><p>surface net solar radiation</p></td>
-<td><p>J m:math:<cite>^{-2}</cite></p></td>
-<td><p>bicubic interpolation</p></td>
+<td><p>J m <span class="math notranslate nohighlight">\(^{-2}\)</span></p></td>
+<td><p>flux</p></td>
</tr>
</tbody>
</table>
@@ -249,7 +249,7 @@ They are retrieved automatically. Thus, data for flux computation will be reques
<h2>Disaggregation for precipitation in older versions<a class="headerlink" href="#disaggregation-for-precipitation-in-older-versions" title="Permalink to this headline">¶</a></h2>
<p>In <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> up to version 5, the disaggregation was done with a Fortran program (FLXACC2). In version 6, this part was recoded in Python.</p>
<p>In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> for all variables.
-This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
+This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6).
The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
It is even possible to produce non-zero precipitation in dry intervals bordering a precipitation period as shown in Fig. 1.
@@ -311,16 +311,11 @@ The height is thereby determined by the condition of conservation of the integra
<div class="section" id="disaggregation-for-the-other-flux-fields">
<h2>Disaggregation for the other flux fields<a class="headerlink" href="#disaggregation-for-the-other-flux-fields" title="Permalink to this headline">¶</a></h2>
<p>The accumulated values for the other variables are first divided by the number of hours and
-then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for four adjacent time intervals (<span class="math notranslate nohighlight">\(p_a, p_b, p_c, p_d\)</span>) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.</p>
+then disaggregates to the exact times and conserves the integrals of the fluxes within each timespan.
+Disaggregation is done for four adjacent time intervals (<span class="math notranslate nohighlight">\(F_0, F_1, F_2, F_3\)</span>) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+This new point <span class="math notranslate nohighlight">\(F\)</span> is used for linear interpolation of the complete timeseries afterwards.</p>
<div class="math notranslate nohighlight">
-\[\begin{split}p_a &= (a_3 - a_0 + 3. * (a_1 - a_2)) / 6. \\
-p_b &= (a_2 + a_0) / 2. - a_1 - 9. * p_a / 2. \\
-p_c &= a_1 - a_0 - 7. * p_a / 2. - 2. * p_b \\
-p_d &= a_0 - p_a / 4. - p_b / 3. - p_c / 2.\end{split}\]</div>
-<p>This new point <span class="math notranslate nohighlight">\(p\)</span> is used for linear interpolation of the complete timeseries afterwards.</p>
-<div class="math notranslate nohighlight">
-\[p = 8. * p_a + 4. * p_b + 2. * p_c + p_d\]</div>
+\[F = -\frac{1}{12}F_0 + \frac{7}{12}F_1 + \frac{7}{12}F_2 -\frac{1}{12}F_3\]</div>
<div class="toctree-wrapper compound">
</div>
</div>
diff --git a/Documentation/html/Documentation/input.html b/Documentation/html/Documentation/input.html
index b799afb6ae2a2183e729d8f5334c206955177e4c..790bb28b005e5363df2be813ff967fd317ae0feb 100644
--- a/Documentation/html/Documentation/input.html
+++ b/Documentation/html/Documentation/input.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Control & input data — flex_extract 7.1.1 documentation</title>
+ <title>Control & input data — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -218,10 +218,7 @@ python3 Source/Python/install.py --help
python3 Source/Python/submit.py --help
</pre></div>
</div>
-<dl class="simple">
-<dt>With version 7.1, we provide also wrapper shell scripts <a class="reference external" href="Input/setup.html">setup</a> and <a class="reference external" href="Input/run.html">run</a> which set the command-line parameters, do some checks, and execute the corresponing Python scripts <code class="docutils literal notranslate"><span class="pre">install.py</span></code> and <code class="docutils literal notranslate"><span class="pre">submit.py</span></code>, respectively.</dt><dd><p>It might be faster and easier for beginners if they are used. See <a class="reference internal" href="../quick_start.html"><span class="doc">Usage</span></a> for information on how to use them.</p>
-</dd>
-</dl>
+<p>With version 7.1, we provide also wrapper shell scripts <a class="reference external" href="Input/setup.html">setup</a> and <a class="reference external" href="Input/run.html">run</a> which set the command-line parameters, do some checks, and execute the corresponing Python scripts <code class="docutils literal notranslate"><span class="pre">install.py</span></code> and <code class="docutils literal notranslate"><span class="pre">submit.py</span></code>, respectively. It might be faster and easier for beginners if they are used. See <a class="reference internal" href="../quick_start.html"><span class="doc">Usage</span></a> for information on how to use them.</p>
<p><code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> also creates the Korn shell scripts <a class="reference internal" href="Input/compilejob.html"><span class="doc">The compilation job script compilejob.ksh</span></a> and <a class="reference internal" href="Input/jobscript.html"><span class="doc">The job script job.ksh</span></a> which will be sent to the ECMWF servers in the <strong>remote mode</strong> and the <strong>gateway mode</strong> for starting batch jobs.</p>
<p>The Fortran program is compiled during the installation process using the <a class="reference internal" href="Input/fortran_makefile.html"><span class="doc">The Fortran makefile for calc_etadot</span></a>.</p>
<p>To sum up, the following scripts control <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>:</p>
diff --git a/Documentation/html/Documentation/output.html b/Documentation/html/Documentation/output.html
index 463712a3c8ed189bab0fac677ea06d7ef0317557..623e9135f237aa2bb6d95d5f438a744cc778919e 100644
--- a/Documentation/html/Documentation/output.html
+++ b/Documentation/html/Documentation/output.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Output data — flex_extract 7.1.1 documentation</title>
+ <title>Output data — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -98,7 +98,7 @@
<li class="toctree-l2 current"><a class="current reference internal" href="#">Output data</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#flexpart-input-files"><code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> input files</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#standard-output-files">Standard output files</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#output-files-for-pure-forecast">Output files for pure forecast</a></li>
+<li class="toctree-l4"><a class="reference internal" href="#output-files-for-long-forecast">Output files for long forecast</a></li>
<li class="toctree-l4"><a class="reference internal" href="#output-files-for-ensemble-predictions">Output files for ensemble predictions</a></li>
<li class="toctree-l4"><a class="reference internal" href="#additional-fields-with-new-precipitation-disaggregation">Additional fields with new precipitation disaggregation</a></li>
</ul>
@@ -106,7 +106,6 @@
<li class="toctree-l3"><a class="reference internal" href="#temporary-files">Temporary files</a><ul>
<li class="toctree-l4"><a class="reference internal" href="#mars-grib-files">MARS grib files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#mars-request-file">MARS request file</a></li>
-<li class="toctree-l4"><a class="reference internal" href="#vertical-ec">VERTICAL.EC</a></li>
<li class="toctree-l4"><a class="reference internal" href="#index-file">Index file</a></li>
<li class="toctree-l4"><a class="reference internal" href="#flux-files">Flux files</a></li>
<li class="toctree-l4"><a class="reference internal" href="#fort-files">fort files</a></li>
@@ -277,9 +276,9 @@ edition centre date dataType gridType stepRange ty
</pre></div>
</div>
</div>
-<div class="section" id="output-files-for-pure-forecast">
-<h3>Output files for pure forecast<a class="headerlink" href="#output-files-for-pure-forecast" title="Permalink to this headline">¶</a></h3>
-<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:</p>
+<div class="section" id="output-files-for-long-forecast">
+<h3>Output files for long forecast<a class="headerlink" href="#output-files-for-long-forecast" title="Permalink to this headline">¶</a></h3>
+<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in long forecast mode is introduced:</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><prefix>YYMMDD.HH.<FORECAST_STEP>
</pre></div>
</div>
@@ -370,18 +369,9 @@ request_number, accuracy, area, dataset, date, expver, gaussian, grid, levelist,
</pre></div>
</div>
</div>
-<div class="section" id="vertical-ec">
-<h3>VERTICAL.EC<a class="headerlink" href="#vertical-ec" title="Permalink to this headline">¶</a></h3>
-<p>This file contains information describing the vertical discretisation (model levels)
-in form of the <code class="docutils literal notranslate"><span class="pre">A</span></code> and <code class="docutils literal notranslate"><span class="pre">B</span></code> parameters which allow to calculate the actual pressure of a model level from the surface pressure.</p>
-</div>
<div class="section" id="index-file">
<h3>Index file<a class="headerlink" href="#index-file" title="Permalink to this headline">¶</a></h3>
<p>This file is called <code class="docutils literal notranslate"><span class="pre">date_time_stepRange.idx</span></code>. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.</p>
-<div class="admonition-todo admonition" id="id1">
-<p class="admonition-title">Todo</p>
-<p>#PS NEEDS MORE DESCRIPTION</p>
-</div>
</div>
<div class="section" id="flux-files">
<h3>Flux files<a class="headerlink" href="#flux-files" title="Permalink to this headline">¶</a></h3>
@@ -404,8 +394,8 @@ in form of the <code class="docutils literal notranslate"><span class="pre">A</s
<p>where <code class="docutils literal notranslate"><span class="pre">xx</span></code> is a number which defines the meteorological fields stored in these files.
They are generated by the Python code in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> by splitting the meteorological fields for a unique time stamp from the <code class="docutils literal notranslate"><span class="pre">*.grb</span></code> files, storing them under the names <code class="docutils literal notranslate"><span class="pre">fort.<XX></span></code> where <XX> represents some number.
The following table defines the numbers and the corresponding content:</p>
-<table class="colwidths-given docutils align-default" id="id2">
-<caption><span class="caption-text">Content of fort - files</span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
+<table class="colwidths-given docutils align-default" id="id1">
+<caption><span class="caption-text">Content of fort - files</span><a class="headerlink" href="#id1" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
@@ -450,8 +440,8 @@ The following table defines the numbers and the corresponding content:</p>
</table>
<p>Some of the fields are solely retrieved with specific settings, e. g., the eta-coordinate vertical velocity is not available in ERA-Interim datasets, and the total cloud-water content is an optional field which is useful for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span> <span class="pre">v10</span></code> and newer.</p>
<p>The <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> program saves its results in file <code class="docutils literal notranslate"><span class="pre">fort.15</span></code> which typically contains:</p>
-<table class="colwidths-given docutils align-default" id="id3">
-<caption><span class="caption-text">Output file of the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></span><a class="headerlink" href="#id3" title="Permalink to this table">¶</a></caption>
+<table class="colwidths-given docutils align-default" id="id2">
+<caption><span class="caption-text">Output file of the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code></span><a class="headerlink" href="#id2" title="Permalink to this table">¶</a></caption>
<colgroup>
<col style="width: 20%" />
<col style="width: 80%" />
diff --git a/Documentation/html/Documentation/overview.html b/Documentation/html/Documentation/overview.html
index 7ed14471d7c2ca4cbb87e2078793ed91d4aa27a4..868bc6158064e72c733ad8627b702faac876aecc 100644
--- a/Documentation/html/Documentation/overview.html
+++ b/Documentation/html/Documentation/overview.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Overview — flex_extract 7.1.1 documentation</title>
+ <title>Overview — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Documentation/vertco.html b/Documentation/html/Documentation/vertco.html
index 369a39311d71b41b1b79e14a9d8b5da15b170e71..35cf305036f643fcb85d2be9e87fd1912cc52422 100644
--- a/Documentation/html/Documentation/vertco.html
+++ b/Documentation/html/Documentation/vertco.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Vertical wind — flex_extract 7.1.1 documentation</title>
+ <title>Vertical wind — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -184,13 +184,11 @@
<h1>Vertical wind<a class="headerlink" href="#vertical-wind" title="Permalink to this headline">¶</a></h1>
<div class="section" id="calculation-of-vertical-velocity-and-preparation-of-output-files">
<h2>Calculation of vertical velocity and preparation of output files<a class="headerlink" href="#calculation-of-vertical-velocity-and-preparation-of-output-files" title="Permalink to this headline">¶</a></h2>
-<dl class="simple">
-<dt>Two methods are provided in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> for the calculation of the vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>:</dt><dd><ol class="lowerroman simple">
+<p>Two methods are provided in <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> for the calculation of the vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXTRA</span></code>/<code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code>:</p>
+<ol class="lowerroman simple">
<li><p>from the horizontal wind field,</p></li>
<li><p>from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets <strong>ERA5</strong> and <strong>CERA-20C</strong>, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.</p></li>
</ol>
-</dd>
-</dl>
<p>Especially for high resolution data, use of the <code class="docutils literal notranslate"><span class="pre">MARS</span></code> parameter 77 is recommended,
since the computational cost (measured in ECMWF HPC units) is reduced by 90-95% at
T799. The extraction time, which depends heavily also on the performance of <code class="docutils literal notranslate"><span class="pre">MARS</span></code>, is
@@ -207,18 +205,18 @@ V40_update_protocol.pdf. The computational demand and accuracy of <code class="d
dependent on the specification of parameters <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> and <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code>. The
following guidance can be given for choosing the right parameters:</p>
<blockquote>
-<div><ul class="simple">
+<div><ul>
<li><p>For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (<code class="docutils literal notranslate"><span class="pre">RESOL=799</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=0</span></code>). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on <em>ecgate</em>, the computation of the vertical velocity is feasible only on the lat/lon grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.</p></li>
-<li><dl class="simple">
-<dt>For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:</dt><dd><ul>
+<li><p>For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:</p>
+<blockquote>
+<div><ul class="simple">
<li><p>For 1.0 degree grids: <code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL=255</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=179</span></code></p></li>
<li><p>For 0.5 degree grids: <code class="docutils literal notranslate"><span class="pre">GAUSS=1</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL=399</span></code>, <code class="docutils literal notranslate"><span class="pre">SMOOTH=359</span></code></p></li>
<li><p>Calculation on the lat/lon grid is not recommended for less than the operational (T1279) resolution.</p></li>
<li><p>If <code class="docutils literal notranslate"><span class="pre">GAUSS</span></code> is set to 1, only the following choices are possible for <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> on <em>ecgate</em>: 159,255,319,399,511,799, (on the HPC also 1279; 2047 in future model versions). This choice is restricted because a reduced Gaussian grid is defined in the ECMWF EMOSLIB only for these spectral resolutions. For <code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>, <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> can be any value below the operational resolution.</p></li>
<li><p>For <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code>, any resolution lower than <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> is possible. If no smoothing is desired, <code class="docutils literal notranslate"><span class="pre">SMOOTH=0</span></code> should be chosen. <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> has no effect if the vertical velocity is calculated on a lat/lon grid (<code class="docutils literal notranslate"><span class="pre">GAUSS=0</span></code>).</p></li>
</ul>
-</dd>
-</dl>
+</div></blockquote>
</li>
<li><p>The on-demand scripts send an error message for settings where <code class="docutils literal notranslate"><span class="pre">SMOOTH</span></code> (if set) and <code class="docutils literal notranslate"><span class="pre">RESOL</span></code> are larger than 360./<code class="docutils literal notranslate"><span class="pre">GRID</span></code>/2, since in this case, the output grid cannot resolve the highest wave numbers. The scripts continue operations, however.</p></li>
<li><p>Regional grids are not cyclic in zonal directions, but global grids are. The software assumes a cyclic grid if <code class="docutils literal notranslate"><span class="pre">RIGHT</span></code>-<code class="docutils literal notranslate"><span class="pre">LEFT</span></code> is equal to <code class="docutils literal notranslate"><span class="pre">GRID</span></code> or is equal to <code class="docutils literal notranslate"><span class="pre">GRID</span></code>-360.</p></li>
diff --git a/Documentation/html/Ecmwf/access.html b/Documentation/html/Ecmwf/access.html
index 055965d74b530b46ddf562e77f00f0073e57f8f6..381c89f71b9fe2100c1549f6c5b53002c31c7676 100644
--- a/Documentation/html/Ecmwf/access.html
+++ b/Documentation/html/Ecmwf/access.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Access modes — flex_extract 7.1.1 documentation</title>
+ <title>Access modes — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Ecmwf/ec-links.html b/Documentation/html/Ecmwf/ec-links.html
index 322312f9a163ee383e4bc3811a24500462bef4c7..da9852793cf86d6145d41c2190c090d70e3bab79 100644
--- a/Documentation/html/Ecmwf/ec-links.html
+++ b/Documentation/html/Ecmwf/ec-links.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Link collection — flex_extract 7.1.1 documentation</title>
+ <title>Link collection — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Ecmwf/hintsecmwf.html b/Documentation/html/Ecmwf/hintsecmwf.html
index d749c68b0f8da030d67fe3bef5fb7c96c00ad8f5..c83ec47e6c99e5d0c222ec0ba803fef96125fed2 100644
--- a/Documentation/html/Ecmwf/hintsecmwf.html
+++ b/Documentation/html/Ecmwf/hintsecmwf.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Hints for data set selection — flex_extract 7.1.1 documentation</title>
+ <title>Hints for data set selection — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Ecmwf/msdata.html b/Documentation/html/Ecmwf/msdata.html
index 52096894ebb8243a7f851848ad1a63522ab5a86a..00ceeb220a1bde3e61466137547f1464128c8d5b 100644
--- a/Documentation/html/Ecmwf/msdata.html
+++ b/Documentation/html/Ecmwf/msdata.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Available data sets for member-state users — flex_extract 7.1.1 documentation</title>
+ <title>Available data sets for member-state users — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Ecmwf/pubdata.html b/Documentation/html/Ecmwf/pubdata.html
index 46b69a4cf29da88bf6b76f82a48788fa22d98061..834de86211b5622ec73a9757f33980e24820d792 100644
--- a/Documentation/html/Ecmwf/pubdata.html
+++ b/Documentation/html/Ecmwf/pubdata.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Available data sets for public users — flex_extract 7.1.1 documentation</title>
+ <title>Available data sets for public users — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Evaluation/metrics.html b/Documentation/html/Evaluation/metrics.html
index 2986296500dbb09bb421c95ace71c42257a768f3..f821f64df6dca7faae95936037280b19716cba03 100644
--- a/Documentation/html/Evaluation/metrics.html
+++ b/Documentation/html/Evaluation/metrics.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Metrics — flex_extract 7.1.1 documentation</title>
+ <title>Metrics — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Evaluation/staticcode.html b/Documentation/html/Evaluation/staticcode.html
index 9d2673e736dc86d204b7b19236944ff1e365b3b2..9a3983c02594ad2aee9aee69fd9154ce4ba5310b 100644
--- a/Documentation/html/Evaluation/staticcode.html
+++ b/Documentation/html/Evaluation/staticcode.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Static code analysis — flex_extract 7.1.1 documentation</title>
+ <title>Static code analysis — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Evaluation/testcases.html b/Documentation/html/Evaluation/testcases.html
index 14246cb2e5ae3d78562046ebd48236ab5e83d036..30bdf0bc607f4a46a70421f0362414fbd4a5dcb5 100644
--- a/Documentation/html/Evaluation/testcases.html
+++ b/Documentation/html/Evaluation/testcases.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Test cases — flex_extract 7.1.1 documentation</title>
+ <title>Test cases — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Installation/gateway.html b/Documentation/html/Installation/gateway.html
index ec5611476c245e2e28521e2b55efd0754e4deceb..fefd970414249f8b6aff5c377142a448ac326bef 100644
--- a/Documentation/html/Installation/gateway.html
+++ b/Documentation/html/Installation/gateway.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Gateway mode installation — flex_extract 7.1.1 documentation</title>
+ <title>Gateway mode installation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -255,7 +255,7 @@ The job script, send to the job queue via the ECaccess software, loads the requi
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'<gatewayname>'</span>
<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'<assoc_name>@genericSftp'</span>
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'installscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
@@ -274,7 +274,7 @@ The job script, send to the job queue via the ECaccess software, loads the requi
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'<gatewayname>'</span>
<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'<assoc_name>@genericSftp'</span>
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'installscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
diff --git a/Documentation/html/Installation/local.html b/Documentation/html/Installation/local.html
index 650175a28f5e86b12cf8c5597dd7e61438bdf87a..0008fb61e6be01ab5a111a42df1beb0d82049b4c 100644
--- a/Documentation/html/Installation/local.html
+++ b/Documentation/html/Installation/local.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Local mode installation — flex_extract 7.1.1 documentation</title>
+ <title>Local mode installation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -207,7 +207,7 @@ and libraries, since the preparation of the extraction and the post-processing i
<li><p><a class="reference external" href="https://www.python.org/">Python3</a></p></li>
<li><p><a class="reference external" href="http://www.numpy.org/">numpy</a></p></li>
<li><p><a class="reference external" href="https://genshi.edgewall.org/">genshi</a></p></li>
-<li><p><a class="reference external" href="https://pypi.org/project/eccodes-python/">eccodes for python</a></p></li>
+<li><p><a class="reference external" href="https://pypi.org/project/eccodes/">eccodes for python</a></p></li>
<li><p><a class="reference external" href="https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home">ecmwf-api-client</a> (everything except ERA5)</p></li>
<li><p><a class="reference external" href="https://cds.climate.copernicus.eu/api-how-to">cdsapi</a> (just for ERA5 and member user)</p></li>
</ul>
@@ -273,16 +273,15 @@ and then install the <code class="docutils literal notranslate"><span class="pre
</div>
<div class="section" id="testing-the-local-environment">
<span id="ref-test-local"></span><h2>Testing the local environment<a class="headerlink" href="#testing-the-local-environment" title="Permalink to this headline">¶</a></h2>
-<p>Check the availability of the python packages by typing <code class="docutils literal notranslate"><span class="pre">python3</span></code> in a terminal window and run the <code class="docutils literal notranslate"><span class="pre">import</span></code> commands in the python shell:
-.. code-block:: python</p>
-<blockquote>
-<div><p># check in python3 console
-import eccodes
-import genshi
-import numpy
-import cdsapi
-import ecmwfapi</p>
-</div></blockquote>
+<p>Check the availability of the python packages by typing <code class="docutils literal notranslate"><span class="pre">python3</span></code> in a terminal window and run the <code class="docutils literal notranslate"><span class="pre">import</span></code> commands in the python shell:</p>
+<div class="highlight-python notranslate"><div class="highlight"><pre><span></span><span class="c1"># check in python3 console</span>
+<span class="kn">import</span> <span class="nn">eccodes</span>
+<span class="kn">import</span> <span class="nn">genshi</span>
+<span class="kn">import</span> <span class="nn">numpy</span>
+<span class="kn">import</span> <span class="nn">cdsapi</span>
+<span class="kn">import</span> <span class="nn">ecmwfapi</span>
+</pre></div>
+</div>
<p>If there are no error messages, you succeeded in setting up the environment.</p>
<div class="section" id="testing-the-web-apis">
<h3>Testing the Web APIs<a class="headerlink" href="#testing-the-web-apis" title="Permalink to this headline">¶</a></h3>
@@ -410,12 +409,13 @@ with an editor and adapt the installation parameters in the section labelled wit
<span class="c1"># THE USER HAS TO SPECIFY THESE PARAMETER</span>
<span class="c1">#</span>
<span class="nv">TARGET</span><span class="o">=</span><span class="s1">'local'</span>
+<span class="nv">MAKEFILE</span><span class="o">=</span><name_of_your_makefile>
<span class="nv">ECUID</span><span class="o">=</span>None
<span class="nv">ECGID</span><span class="o">=</span>None
<span class="nv">GATEWAY</span><span class="o">=</span>None
<span class="nv">DESTINATION</span><span class="o">=</span>None
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">''</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
diff --git a/Documentation/html/Installation/remote.html b/Documentation/html/Installation/remote.html
index 33e73245a12c114b6505438394759ae3e207b1d9..baf068eb4f687f5310bba4f6aa2ab070003fafba 100644
--- a/Documentation/html/Installation/remote.html
+++ b/Documentation/html/Installation/remote.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Remote mode installation — flex_extract 7.1.1 documentation</title>
+ <title>Remote mode installation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -286,7 +286,7 @@ described in <a class="reference internal" href="../Documentation/Input/setup.ht
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'<gatewayname>'</span>
<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'<username>@genericSftp'</span>
<span class="nv">INSTALLDIR</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'installscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
@@ -305,7 +305,7 @@ described in <a class="reference internal" href="../Documentation/Input/setup.ht
<span class="nv">GATEWAY</span><span class="o">=</span><span class="s1">'<gatewayname>'</span>
<span class="nv">DESTINATION</span><span class="o">=</span><span class="s1">'<username>@genericSftp'</span>
<span class="nv">INSTALLDIR</span><span class="o">=</span><span class="s1">''</span>
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.template'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'installscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_EA5'</span>
...
</pre></div>
@@ -321,8 +321,7 @@ with your own ones (look at any of your files with ``ls -l’’ to see uid and
<p>If a local gateway server is available, files can be transferred with <code class="docutils literal notranslate"><span class="pre">ECaccess</span></code> commands. In that case, a valid <em>GATEWAY</em> and <em>DESTINATION</em> have to be present in the <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code> file (even if not used, the lines must not be deleted).</p>
</div>
<p>Afterwards, type:</p>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>module load python3
-./setup.sh
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>./setup.sh
</pre></div>
</div>
<p>to start the installation. You should see the following on standard output.</p>
diff --git a/Documentation/html/Support/faq.html b/Documentation/html/Support/faq.html
index 6a0de9105c9099ca27fb2716565d7763b2ac6980..4d5123589b5ccadb394f8b9d6ac4ef642e2acd63 100644
--- a/Documentation/html/Support/faq.html
+++ b/Documentation/html/Support/faq.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>FAQ - Frequently asked questions — flex_extract 7.1.1 documentation</title>
+ <title>FAQ - Frequently asked questions — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/Support/known_bugs_issues.html b/Documentation/html/Support/known_bugs_issues.html
index 8f166fda369b1fb2df578838afc89cde9aac0500..1bd969f8ea2a16fcf6ccf45e6e520adb0a3564c6 100644
--- a/Documentation/html/Support/known_bugs_issues.html
+++ b/Documentation/html/Support/known_bugs_issues.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Known Bugs and Issues — flex_extract 7.1.1 documentation</title>
+ <title>Known Bugs and Issues — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/ControlFile.html b/Documentation/html/_modules/ControlFile.html
index 8fad03ccf8b6a726ca764fdf42660ccea2225f9e..91d39a8c447140f2bef357509cddcb8d4d194efc 100644
--- a/Documentation/html/_modules/ControlFile.html
+++ b/Documentation/html/_modules/ControlFile.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ControlFile — flex_extract 7.1.1 documentation</title>
+ <title>ControlFile — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/EcFlexpart.html b/Documentation/html/_modules/EcFlexpart.html
index 789f353a48216ba5402403544d9c725d5b466c73..a0b36add3577dbfbd67f621242c3a1432f4e28bd 100644
--- a/Documentation/html/_modules/EcFlexpart.html
+++ b/Documentation/html/_modules/EcFlexpart.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>EcFlexpart — flex_extract 7.1.1 documentation</title>
+ <title>EcFlexpart — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/GribUtil.html b/Documentation/html/_modules/GribUtil.html
index 3506e58f3bf2e961864a4c1adf172fcf02fd25bc..a6b59b2139981870387478bb9df3aeef9028dd11 100644
--- a/Documentation/html/_modules/GribUtil.html
+++ b/Documentation/html/_modules/GribUtil.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>GribUtil — flex_extract 7.1.1 documentation</title>
+ <title>GribUtil — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/MarsRetrieval.html b/Documentation/html/_modules/MarsRetrieval.html
index d61076ca8867272cf0292feb0b9c52094fed1a46..365955295652928a7f959de4ba8a857800bb4481 100644
--- a/Documentation/html/_modules/MarsRetrieval.html
+++ b/Documentation/html/_modules/MarsRetrieval.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>MarsRetrieval — flex_extract 7.1.1 documentation</title>
+ <title>MarsRetrieval — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/UioFiles.html b/Documentation/html/_modules/UioFiles.html
index 3c25272e83fcacc6c10cfefbea05314d8473f08f..9b059c21b8205c97e0119a4da252413340d5345c 100644
--- a/Documentation/html/_modules/UioFiles.html
+++ b/Documentation/html/_modules/UioFiles.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>UioFiles — flex_extract 7.1.1 documentation</title>
+ <title>UioFiles — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/checks.html b/Documentation/html/_modules/checks.html
index 2bcab08e2bb2d54d5d1af4cbc31ce1b426b00126..d592b9a9ab6aa5e9f831419a9cd6d1dd384903c0 100644
--- a/Documentation/html/_modules/checks.html
+++ b/Documentation/html/_modules/checks.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>checks — flex_extract 7.1.1 documentation</title>
+ <title>checks — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/disaggregation.html b/Documentation/html/_modules/disaggregation.html
index 001f47aacabcec56831c14f60e9eab2b62eb0e6b..9cbef22aa11fff7273561b16b987461eb51a6850 100644
--- a/Documentation/html/_modules/disaggregation.html
+++ b/Documentation/html/_modules/disaggregation.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>disaggregation — flex_extract 7.1.1 documentation</title>
+ <title>disaggregation — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/get_mars_data.html b/Documentation/html/_modules/get_mars_data.html
index d7abc19a5659becca92ae751ea59856d133f0bf5..c33539161c59598bdc1a8401c4b4c1bb44252b9b 100644
--- a/Documentation/html/_modules/get_mars_data.html
+++ b/Documentation/html/_modules/get_mars_data.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>get_mars_data — flex_extract 7.1.1 documentation</title>
+ <title>get_mars_data — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/index.html b/Documentation/html/_modules/index.html
index e094c3724f69c7a29010bcbfd9702d16217bc603..743fb3784dd4772533562ad01f90040f0ecb6c93 100644
--- a/Documentation/html/_modules/index.html
+++ b/Documentation/html/_modules/index.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Overview: module code — flex_extract 7.1.1 documentation</title>
+ <title>Overview: module code — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/install.html b/Documentation/html/_modules/install.html
index 31f7762898d39233dd685506e2b0c73533bb858b..bfe349c10cb6c39098afdfb47293662a731ec803 100644
--- a/Documentation/html/_modules/install.html
+++ b/Documentation/html/_modules/install.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>install — flex_extract 7.1.1 documentation</title>
+ <title>install — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/prepare_flexpart.html b/Documentation/html/_modules/prepare_flexpart.html
index 86971b289363c5aa01d0a7c33440ca0583cb9a36..f032ab554dbade028bdc21d99ed152e25f3c809c 100644
--- a/Documentation/html/_modules/prepare_flexpart.html
+++ b/Documentation/html/_modules/prepare_flexpart.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>prepare_flexpart — flex_extract 7.1.1 documentation</title>
+ <title>prepare_flexpart — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/submit.html b/Documentation/html/_modules/submit.html
index f61eb0a3c730450ae8cf57a6659c68d658aa22e3..1db3ca87ed0032582422f5b1d952f47ccfdf6262 100644
--- a/Documentation/html/_modules/submit.html
+++ b/Documentation/html/_modules/submit.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>submit — flex_extract 7.1.1 documentation</title>
+ <title>submit — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_modules/tools.html b/Documentation/html/_modules/tools.html
index 0222c7c23d5ed083d5f254cab1c4905c03caae93..4d028f07e072d287f41ef66aa3dbd1c422aeb77a 100644
--- a/Documentation/html/_modules/tools.html
+++ b/Documentation/html/_modules/tools.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>tools — flex_extract 7.1.1 documentation</title>
+ <title>tools — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt b/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
index 7eac32c0626ae8e63276c2a80f30eb6dc12eaed3..214a0965e69bd22b7d63858d1b3b7f5fd84ba26d 100644
--- a/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/compilejob.rst.txt
@@ -1,14 +1,14 @@
-*********************************************
+*************************************************
The compilation job script ``compilejob.ksh``
-*********************************************
+*************************************************
-The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.
+The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``installscript.template`` in the template directory.
``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by a doubled ``$`` sign in ``job.temp``.
+These individual parameters are marked by a doubled ``$`` sign in ``installscript.template``.
-The job script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
+The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
The submission is done by the ``ECaccess`` tool from within ``flex_extract`` with the command ``ecaccess-job-submit``.
@@ -23,7 +23,7 @@ What does the compilation script do?
#. It sets some environment variables for the single session
#. It creates the ``flex_extract`` root directory in the ``$HOME`` path of the user
#. It untars the tarball into the root directory.
- #. It compiles the Fortran program using ``Makefile``.
+ #. It compiles the Fortran program using ``makefile``.
#. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
@@ -66,21 +66,18 @@ Example ``compilejob.ksh``
case ${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export FLEXPART_ROOT_SCRIPTS=${HOME}
export MAKEFILE=makefile_ecgate
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
echo ${GROUP}
echo ${HOME}
echo ${HOME} | awk -F / '{print $1, $2, $3, $4}'
diff --git a/Documentation/html/_sources/Documentation/Input/examples.rst.txt b/Documentation/html/_sources/Documentation/Input/examples.rst.txt
index f69fd02641edbf9e42e102092decaf1b8286a96a..8ed3c767048545c50d6be66b536a1476282ecfa8 100644
--- a/Documentation/html/_sources/Documentation/Input/examples.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/examples.rst.txt
@@ -35,9 +35,9 @@ CONTROL.documentation
CONTROL_OD.OPER.FC.twicedaily.1hourly
CONTROL_OD.OPER.FC.twicedaily.3hourly
-.. todo::
+.. note::
- #PS some information to be added.
+ Further information will follow.
.. toctree::
:hidden:
diff --git a/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt b/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
index 6a8b7600ea32b442140b22d465e7c93e907dd1bf..a1f43b258cb17a867825d5a97241870e67e75193 100644
--- a/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/jobscript.rst.txt
@@ -4,12 +4,12 @@ The job script ``job.ksh``
The job script is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
-It is based on the ``job.temp`` template file stored in the ``Templates`` directory.
-This template is generated in the installation process from a ``job.template`` template file.
+It is based on the ``submitscript.template`` template file stored in the ``Templates`` directory.
+This template is generated in the installation process from a ``jobscript.template`` template file.
``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by ``$$`` in ``job.temp``.
+These individual parameters are marked by ``$$`` in ``jobscript.template``.
The job script has a number of settings for the batch system which are fixed, and differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
@@ -25,14 +25,14 @@ What does the job script do?
#. It prepares the job environment at the ECMWF servers by loading the necessary library modules.
#. It sets some environment variables for the single session.
#. It creates the directory structure in the user's ``$SCRATCH`` file system.
- #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``jobscript.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
+ #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``job.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
#. ``Flex_extract`` is started from within the ``work`` directory of the new directory structure by calling the ``submit.py`` script. It sets new paths for input and output directories and the recently generated ``CONTROL`` file.
#. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
-Example ``jobscript.ksh``
+Example ``job.ksh``
-------------------------
.. code-block:: bash
@@ -67,20 +67,17 @@ Example ``jobscript.ksh``
case ${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
export SCRATCH=${TMPDIR}
export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
@@ -106,7 +103,7 @@ Example ``jobscript.ksh``
dataset None
date_chunk 3
debug 1
- destination annep@genericSftp
+ destination <specificname>@genericSftp
doubleelda 0
dpdeta 1
dtime 3
@@ -127,7 +124,7 @@ Example ``jobscript.ksh``
gaussian
grib2flexpart 0
grid 1.0/1.0
- inputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+ inputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
install_target None
job_chunk 1
job_template job.temp
@@ -144,7 +141,7 @@ Example ``jobscript.ksh``
omega 0
omegadiff 0
oper 0
- outputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+ outputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
prefix CE
public 0
purefc 0
diff --git a/Documentation/html/_sources/Documentation/Input/run.rst.txt b/Documentation/html/_sources/Documentation/Input/run.rst.txt
index 1e3ad685d5b5d23c1adea0e66b36a64a5f65aab1..21b1ddb3369ce1238e3a28b9e7c075994d6557e7 100644
--- a/Documentation/html/_sources/Documentation/Input/run.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/run.rst.txt
@@ -30,8 +30,7 @@ Content of ``run.sh``
.. literalinclude:: ../../../../../Run/run.sh
:language: bash
- :caption: run.sh
-
+ :caption: run.sh
diff --git a/Documentation/html/_sources/Documentation/Input/templates.rst.txt b/Documentation/html/_sources/Documentation/Input/templates.rst.txt
index 786679efaf40d9bb6eaced866ba44a1cb59800e3..4a26a545f83fe834b14e2298fedd2f5c705c636e 100644
--- a/Documentation/html/_sources/Documentation/Input/templates.rst.txt
+++ b/Documentation/html/_sources/Documentation/Input/templates.rst.txt
@@ -7,12 +7,12 @@ In ``flex_extract``, the Python package `genshi <https://genshi.edgewall.org/>`_
.. note::
Do not change anything in these files unless you understand the effects!
-Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Kornshell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
+Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Korn shell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
The following templates are used; they can be found in the directory ``flex_extract_vX.X/Templates``:
-convert.nl
-----------
+calc_etadot_nml.template
+-------------------------
This is the template for a Fortran namelist file called ``fort.4`` read by ``calc_etadot``.
It contains all the parameters ``calc_etadot`` needs.
@@ -39,7 +39,7 @@ convert.nl
mdpdeta = $mdpdeta
/
-ecmwf_env.template
+ECMWF_ENV.template
------------------
This template is used to create the ``ECMWF_ENV`` file in the application modes **gateway** and **remote**. It contains the user credentials and gateway server settings for the file transfers.
@@ -51,8 +51,8 @@ ecmwf_env.template
GATEWAY $gateway_name
DESTINATION $destination_name
-compilejob.template
--------------------
+installscript.template
+----------------------
This template is used to create the job script file called ``compilejob.ksh`` during the installation process for the application modes **remote** and **gateway**.
@@ -96,21 +96,18 @@ compilejob.template
case $${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
export MAKEFILE=$makefile
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
echo $${GROUP}
echo $${HOME}
echo $${HOME} | awk -F / '{print $1, $2, $3, $4}'
@@ -139,8 +136,8 @@ compilejob.template
fi
-job.temp
---------
+submitscript.template
+---------------------
This template is used to create the actual job script file called ``job.ksh`` for the execution of ``flex_extract`` in the application modes **remote** and **gateway**.
@@ -184,23 +181,20 @@ job.temp
export VERSION=7.1
case $${HOST} in
*ecg*)
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
- export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
- ;;
- *cca*)
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
- export SCRATCH=$${TMPDIR}
- export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
+ ;;
+ *cca*)
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ export SCRATCH=${TMPDIR}
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
esac
@@ -236,10 +230,10 @@ job.temp
fi
-job.template
-------------
+jobscript.template
+------------------
- This template is used to create the template for the execution job script ``job.temp`` for ``flex_extract`` in the installation process. A description of the file can be found under ``job.temp``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
+ This template is used to create the template for the execution job script ``submitscript.template`` for ``flex_extract`` in the installation process. A description of the file can be found under ``submitscript.template``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
.. code-block:: ksh
@@ -272,21 +266,18 @@ job.template
export VERSION=$version_number
case $$$${HOST} in
*ecg*)
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
export PATH=$$$${PATH}:$fp_root_path
;;
*cca*)
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
export SCRATCH=$$$${TMPDIR}
export PATH=$$$${PATH}:$fp_root_path
;;
diff --git a/Documentation/html/_sources/Documentation/disagg.rst.txt b/Documentation/html/_sources/Documentation/disagg.rst.txt
index 64a3e3de5ad8e75ec093c6745af8152b52ec69ec..9a51e6be2b3385e289f1794bdcb0ec0c8d3dcc07 100644
--- a/Documentation/html/_sources/Documentation/disagg.rst.txt
+++ b/Documentation/html/_sources/Documentation/disagg.rst.txt
@@ -12,16 +12,16 @@ pre-processing has to be applied.
.. _ref-table-fluxpar:
.. csv-table:: Flux fields
- :header: "Short Name", "Name", "Units", "Interpolation Type"
+ :header: "Short Name", "Name", "Units", "Disaggregation"
:align: center
:widths: 5,15,5,10
- LSP, "large-scale precipitation", "m", "modified linear interpolation"
- CP, "convective precipitation", "m", "modified linear interpolation"
- SSHF, "surface sensible heat flux", "J m:math:`^{-2}`", "bicubic interpolation"
- EWSS, "eastward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
- NSSS, "northward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
- SSR, "surface net solar radiation", "J m:math:`^{-2}`", "bicubic interpolation"
+ LSP, "large-scale precipitation", "m", "precipitation "
+ CP, "convective precipitation", "m", "precipitation"
+ SSHF, "surface sensible heat flux", "J m :math:`^{-2}`", "flux"
+ EWSS, "eastward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
+ NSSS, "northward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
+ SSR, "surface net solar radiation", "J m :math:`^{-2}`", "flux "
The first step is to *de-accumulate* the fields in time so that each value represents non-overlapping integrals in x-, y-, and t-space.
@@ -42,7 +42,7 @@ Disaggregation for precipitation in older versions
In ``flex_extract`` up to version 5, the disaggregation was done with a Fortran program (FLXACC2). In version 6, this part was recoded in Python.
In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in ``FLEXPART`` for all variables.
-This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
+This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6).
The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
It is even possible to produce non-zero precipitation in dry intervals bordering a precipitation period as shown in Fig. 1.
@@ -160,21 +160,14 @@ Disaggregation for the other flux fields
----------------------------------------------
The accumulated values for the other variables are first divided by the number of hours and
-then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for four adjacent time intervals (:math:`p_a, p_b, p_c, p_d`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+then disaggregates to the exact times and conserves the integrals of the fluxes within each timespan.
+Disaggregation is done for four adjacent time intervals (:math:`F_0, F_1, F_2, F_3`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+This new point :math:`F` is used for linear interpolation of the complete timeseries afterwards.
.. math::
-
- p_a &= (a_3 - a_0 + 3. * (a_1 - a_2)) / 6. \\
- p_b &= (a_2 + a_0) / 2. - a_1 - 9. * p_a / 2. \\
- p_c &= a_1 - a_0 - 7. * p_a / 2. - 2. * p_b \\
- p_d &= a_0 - p_a / 4. - p_b / 3. - p_c / 2.
-
-This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards.
-.. math::
- p = 8. * p_a + 4. * p_b + 2. * p_c + p_d
+ F = -\frac{1}{12}F_0 + \frac{7}{12}F_1 + \frac{7}{12}F_2 -\frac{1}{12}F_3
diff --git a/Documentation/html/_sources/Documentation/input.rst.txt b/Documentation/html/_sources/Documentation/input.rst.txt
index 0a0e11d66cd7bdffa7762fdb86eaafe2c59302de..64f33664d5560b05f990ed4e15ac6b68ff14ba23 100644
--- a/Documentation/html/_sources/Documentation/input.rst.txt
+++ b/Documentation/html/_sources/Documentation/input.rst.txt
@@ -35,8 +35,8 @@ Controlling
python3 Source/Python/install.py --help
python3 Source/Python/submit.py --help
- With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively.
- It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
+
+ With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively. It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
``flex_extract`` also creates the Korn shell scripts :doc:`Input/compilejob` and :doc:`Input/jobscript` which will be sent to the ECMWF servers in the **remote mode** and the **gateway mode** for starting batch jobs.
diff --git a/Documentation/html/_sources/Documentation/output.rst.txt b/Documentation/html/_sources/Documentation/output.rst.txt
index 8a25f252022e118e62de2570426b24f7619e6899..4f6aebf29647f4d80251448a9799367e8c5c9b6d 100644
--- a/Documentation/html/_sources/Documentation/output.rst.txt
+++ b/Documentation/html/_sources/Documentation/output.rst.txt
@@ -80,10 +80,10 @@ Here is an example output which lists the meteorological fields in a single file
35 of 35 messages in CE00010800
-Output files for pure forecast
+Output files for long forecast
------------------------------
-``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:
+``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in long forecast mode is introduced:
.. code-block:: bash
@@ -193,22 +193,12 @@ Example output of a one-day retrieval of CERA-20C data:
4, 24, 40.0/-5.0/30.0/5.0, None, 20000108/to/20000108, 1, , 1.0/1.0, 1, SFC, EP, 000, 141.128/151.128/164.128/165.128/166.128/167.128/168.128/129.128/172.128/027.128/028.128/186.128/187.128/188.128/235.128/139.128/039.128/173.128, , 159, 00, ENDA, /mnt/nas/Anne/Interpolation/flexextract/flex_extract_v7.1/run/./workspace/CERA_testgrid_local_cds/ANOG__SL.20000108.23903.23904.grb, 00/03/06/09/12/15/18/21, AN
-VERTICAL.EC
------------
-
-This file contains information describing the vertical discretisation (model levels)
-in form of the ``A`` and ``B`` parameters which allow to calculate the actual pressure of a model level from the surface pressure.
-
Index file
----------
This file is called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
-.. todo::
-
- #PS NEEDS MORE DESCRIPTION
-
Flux files
----------
diff --git a/Documentation/html/_sources/Documentation/vertco.rst.txt b/Documentation/html/_sources/Documentation/vertco.rst.txt
index fcc1d14faabe35e602a735b786c52f96c711c4d5..2196482626ea6e55fc6fa88f85375bff802d5ae2 100644
--- a/Documentation/html/_sources/Documentation/vertco.rst.txt
+++ b/Documentation/html/_sources/Documentation/vertco.rst.txt
@@ -6,8 +6,9 @@ Calculation of vertical velocity and preparation of output files
================================================================
Two methods are provided in ``flex_extract`` for the calculation of the vertical velocity for ``FLEXTRA``/``FLEXPART``:
- (i) from the horizontal wind field,
- (ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
+
+(i) from the horizontal wind field,
+(ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
Especially for high resolution data, use of the ``MARS`` parameter 77 is recommended,
since the computational cost (measured in ECMWF HPC units) is reduced by 90-95% at
@@ -30,6 +31,7 @@ following guidance can be given for choosing the right parameters:
* For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (``RESOL=799``, ``SMOOTH=0``). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (``GAUSS=1``) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on *ecgate*, the computation of the vertical velocity is feasible only on the lat/lon grid (``GAUSS=0``), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.
* For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:
+
- For 1.0 degree grids: ``GAUSS=1``, ``RESOL=255``, ``SMOOTH=179``
- For 0.5 degree grids: ``GAUSS=1``, ``RESOL=399``, ``SMOOTH=359``
- Calculation on the lat/lon grid is not recommended for less than the operational (T1279) resolution.
diff --git a/Documentation/html/_sources/Installation/gateway.rst.txt b/Documentation/html/_sources/Installation/gateway.rst.txt
index 34764c8fe0bc88e8352d77daa5dd4fb57bda945a..06f50a949babcea30cdd67ff8318ac4003f64b7e 100644
--- a/Documentation/html/_sources/Installation/gateway.rst.txt
+++ b/Documentation/html/_sources/Installation/gateway.rst.txt
@@ -128,7 +128,7 @@ Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values:
| GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' |
| DESTINATION='<assoc_name>@genericSftp' | DESTINATION='<assoc_name>@genericSftp' |
| INSTALLDIR=None | INSTALLDIR=None |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| JOB_TEMPLATE='installscript.template' | JOB_TEMPLATE='installscript.template' |
| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
| ... | ... |
+----------------------------------------------+----------------------------------------------+
diff --git a/Documentation/html/_sources/Installation/local.rst.txt b/Documentation/html/_sources/Installation/local.rst.txt
index 5e20d27a5564d8b317b247d021d39c9a9ebe06a7..9f9c012b9299f66d5ce9b7c9315f4c5481c569ce 100644
--- a/Documentation/html/_sources/Installation/local.rst.txt
+++ b/Documentation/html/_sources/Installation/local.rst.txt
@@ -16,8 +16,8 @@ Local mode installation
.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
.. _genshi: https://genshi.edgewall.org/
-.. _eccodes for python: https://pypi.org/project/eccodes-python/
-.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _eccodes for python: https://pypi.org/project/eccodes/
+.. _eccodes for conda: https://anaconda.org/conda-forge/python-eccodes
.. _gfortran: https://gcc.gnu.org/wiki/GFortran
.. _fftw3: http://www.fftw.org
.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
@@ -119,6 +119,7 @@ Testing the local environment
=============================
Check the availability of the python packages by typing ``python3`` in a terminal window and run the ``import`` commands in the python shell:
+
.. code-block:: python
# check in python3 console
@@ -286,12 +287,13 @@ with an editor and adapt the installation parameters in the section labelled wit
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='local'
+ MAKEFILE=<name_of_your_makefile>
ECUID=None
ECGID=None
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
- JOB_TEMPLATE='job.template'
+ JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
diff --git a/Documentation/html/_sources/Installation/remote.rst.txt b/Documentation/html/_sources/Installation/remote.rst.txt
index 95f0c63eb8dde3542ad1fdc0eaf44f7341cf24e7..127e2b76b8a9142827ef35ac710a7024957425ad 100644
--- a/Documentation/html/_sources/Installation/remote.rst.txt
+++ b/Documentation/html/_sources/Installation/remote.rst.txt
@@ -137,7 +137,7 @@ Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values:
| GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' |
| DESTINATION='<username>@genericSftp' | DESTINATION='<username>@genericSftp' |
| INSTALLDIR=None | INSTALLDIR='' |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| JOB_TEMPLATE='installscript.template' | JOB_TEMPLATE='installscript.template' |
| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
| ... | ... |
+----------------------------------------------+----------------------------------------------+
@@ -152,8 +152,7 @@ with your own ones (look at any of your files with ``ls -l'' to see uid and gid)
Afterwards, type:
.. code-block:: bash
-
- module load python3
+
./setup.sh
to start the installation. You should see the following on standard output.
diff --git a/Documentation/html/_sources/authors.rst.txt b/Documentation/html/_sources/authors.rst.txt
index 3992e33b734ee403c6a50ce04457212659bafd1d..5636f8db342d26f1ea7338730b59405b0a0e0321 100644
--- a/Documentation/html/_sources/authors.rst.txt
+++ b/Documentation/html/_sources/authors.rst.txt
@@ -8,18 +8,24 @@ Developer Team
| University of Vienna
| Althanstraße 14 / UZA II
| 1090 Vienna, Austria
-| mail: anne.philipp [at] univie.ac.at
+| e-mail: anne.philipp [at] univie.ac.at
-
| Leopold Haimberger
| Department of Meteorology and Geophysics
| University of Vienna
| Althanstraße 14 / UZA II
| 1090 Vienna, Austria
-| mail: leopold.haimberger [at] univie.ac.at
+| e-mail: leopold.haimberger [at] univie.ac.at
-
+
+| Petra Seibert
+| Institute of Meteorology (BOKU-Met)
+| University of Natural Resources & Life Sciences (BOKU)
+| Gregor-Mendel-Str. 33
+| 1180 Wien, Austria
+| e-mail: petra.seibert ./at/. boku.ac.at
+
.. toctree::
:hidden:
:maxdepth: 2
diff --git a/Documentation/html/_sources/changelog.rst.txt b/Documentation/html/_sources/changelog.rst.txt
index b3f98e0544b60c1c70d0fc0804f71c9a1c80e60b..ed72fc18dfd338fbf6a73aad5bc1f5e11540545a 100644
--- a/Documentation/html/_sources/changelog.rst.txt
+++ b/Documentation/html/_sources/changelog.rst.txt
@@ -10,6 +10,25 @@ Changelog
.. _new algorithm: https://www.geosci-model-dev.net/11/2503/2018/
+.. _ref-v712:
+
+Release v7.1.2
+--------------
+
+Changes
+#########
+ * changed naming of template files
+ * separate loading of Python3 module in remote mode is no longer necessary
+ * updated module versions for ECMWF servers
+ * changed names of working directories on ECMWF servers
+ * select makefile automatically regarding application mode if it was not set in ``setup.sh``
+ * updated online documentation
+ * converted most important Fortran code documentation from German to English
+ * deactivate writing of VERTICAL.EC file by Fortran code
+ * adapt and improve Fortran regression test scripts
+ * remove jasper lib from Fortran makefiles
+
+
.. _ref-v711:
Release v7.1.1
diff --git a/Documentation/html/_sources/installation.rst.txt b/Documentation/html/_sources/installation.rst.txt
index 6a0c8a56649245a1ead5dc7f1e77771c84875207..97c5cb873c8d97a2fbe859b8759f2e3e27c8d76a 100644
--- a/Documentation/html/_sources/installation.rst.txt
+++ b/Documentation/html/_sources/installation.rst.txt
@@ -139,7 +139,7 @@ The software required to run ``flex_extract`` depends on the :doc:`Documentation
Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries.
We tested ``flex_extract`` with the Python3 package from the the GNU/Linux distribution and Anaconda Python. The required Python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).
-Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system)``rpm -q <package_name>``. For example:
+Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system) ``rpm -q <package_name>``. For example:
.. code-block:: sh
@@ -197,14 +197,14 @@ Fortran program test
To check whether the Fortran program ``calc_etadot`` has been compiled and runs properly, it can be applied to a prepared minimal dataset.
-For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Convert/`` directory and execute the Fortran program.
+For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Calc_etadot/`` directory and execute the Fortran program.
.. note::
Remember that you might have to log in at the ECMWF server if you used the installation for the **remote** or **gateway** mode. There you find the ``flex_extract`` root directory in your ``$HOME`` directory.
.. code-block:: bash
- cd Testing/Installation/Convert
+ cd Testing/Installation/Calc_etadot
# execute the Fortran progam without arguments
../../../Source/Fortran/calc_etadot
diff --git a/Documentation/html/_sources/quick_start.rst.txt b/Documentation/html/_sources/quick_start.rst.txt
index baa36ca5f5c0014af22356a02c4807ad43796d02..381644220d5b9771b1e5ca93e463283a5816a7e0 100644
--- a/Documentation/html/_sources/quick_start.rst.txt
+++ b/Documentation/html/_sources/quick_start.rst.txt
@@ -64,7 +64,6 @@ Remote mode
.. code-block:: bash
# On ECMWF server
- [<ecuid>@ecgb11 ~]$ module load python3
[<ecuid>@ecgb11 ~]$ cd flex_extract_vX.X/Run
@@ -103,7 +102,7 @@ Therefore open the ``run.sh`` file and modify the parameter block marked in the
INPUTDIR=None
OUTPUTDIR=None
PP_ID=None
- JOB_TEMPLATE='job.temp'
+ JOB_TEMPLATE='jobscript.template'
CONTROLFILE='CONTROL_CERA'
DEBUG=0
REQUEST=2
@@ -137,12 +136,12 @@ In case the job fails you will receive an email with the subject ``ERROR!`` and
cd $SCRATCH
ls -rthl
-The last command lists the most recent logs and temporary retrieval directories (usually ``pythonXXXXX``, where XXXXX is the process id). Under ``pythonXXXXX`` a copy of the ``CONTROL`` file is stored under the name ``CONTROL``, the protocol is stored in the file ``prot`` and the temporary files as well as the resulting files are stored in a directory ``work``. The original name of the ``CONTROL`` file is stored in this new file under parameter ``controlfile``.
+The last command lists the most recent logs and temporary retrieval directories (usually ``extractXXXXX``, where XXXXX is the process id). Under ``extractXXXXX`` a copy of the ``CONTROL`` file is stored under the name ``CONTROL``, the protocol is stored in the file ``prot`` and the temporary files as well as the resulting files are stored in a directory ``work``. The original name of the ``CONTROL`` file is stored in this new file under parameter ``controlfile``.
.. code-block:: bash
:caption: "Example structure of ``flex_extract`` output directory on ECMWF servers."
- pythonXXXXX
+ extractXXXXX
├── CONTROL
├── prot
├── work
@@ -357,8 +356,8 @@ These files defines the minimum number of parameters necessary to retrieve a dai
Please see `Information about MARS retrievement <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency>`_ for hints about retrieval efficiency and troubleshooting.
-Pure forecast
- It is possible to retrieve pure forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
+Long forecast
+ It is possible to retrieve long forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
The *CV* field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the *CF* type since this is available from 1992 (3-hourly) on up to today (1-hourly). *CV* and *CF* field types belong to the *Ensemble prediction system (ENFO)* which currently works with 50 ensemble members.
Please be aware that in this case it is necessary to set the type for flux fields explicitly, otherwise a default value might be selected, different from what you expect!
@@ -417,10 +416,6 @@ Field type and time
The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be ``0``.
The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of ``TYPE``, ``TIME`` and ``STEP`` because the temporal (hourly) resolution with the ``DTIME`` parameter will select the correct combinations.
- .. todo::
-
- #PS needs to be rephrased
-
.. code-block:: bash
:caption: Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.
@@ -450,9 +445,6 @@ Grid resolution and domain
The grid and domain parameters depends on each other. ``grid`` refers to the grid resolution. It can be given as decimal values (e.g., ``1.`` meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., ``1000`` means also 1°). The code applies common sense to determine what format is to be assumed.
After selecting grid, the ``domain`` has to be defined. The extension in longitude or latitude direction must be an integer multiple of ``grid``.
- .. todo::
-
- #PS shouldn't we explain how to define a domain??
The horizontal resolution for spectral fields is set by the parameter ``RESOL``. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found `in this entry of the ECMWF on-line documentation <https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol>`_ and `this table (also ECMWF documentation) <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation>`_.
@@ -469,12 +461,8 @@ Grid resolution and domain
Flux data
- Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.
-
- .. todo::
-
- #PS for which application would this be typical?
-
+ Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP. These values will be set automatically if not provided in a ``CONTROL`` file.
+
.. code-block:: bash
:caption: Example setting for the definition of flux fields.
diff --git a/Documentation/html/_static/documentation_options.js b/Documentation/html/_static/documentation_options.js
index 3efa03045fc5699f2715a41c7a8cd3b34e2d1067..bc92269577c481f42a9dd7312efad46de1fd4a5e 100644
--- a/Documentation/html/_static/documentation_options.js
+++ b/Documentation/html/_static/documentation_options.js
@@ -1,6 +1,6 @@
var DOCUMENTATION_OPTIONS = {
URL_ROOT: document.getElementById("documentation_options").getAttribute('data-url_root'),
- VERSION: '7.1.1',
+ VERSION: '7.1.2',
LANGUAGE: 'None',
COLLAPSE_INDEX: false,
BUILDER: 'html',
diff --git a/Documentation/html/authors.html b/Documentation/html/authors.html
index 1ca2cbcde86876163d115d141767b9e72a0dcc08..08ad4e844605f2108e3542716b40e1a63fdc3f42 100644
--- a/Documentation/html/authors.html
+++ b/Documentation/html/authors.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Developer Team — flex_extract 7.1.1 documentation</title>
+ <title>Developer Team — flex_extract 7.1.2 documentation</title>
@@ -62,7 +62,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -173,7 +173,7 @@
<div class="line">University of Vienna</div>
<div class="line">Althanstraße 14 / UZA II</div>
<div class="line">1090 Vienna, Austria</div>
-<div class="line">mail: anne.philipp [at] univie.ac.at</div>
+<div class="line">e-mail: anne.philipp [at] univie.ac.at</div>
</div>
<div class="line-block">
<div class="line">Leopold Haimberger</div>
@@ -181,7 +181,15 @@
<div class="line">University of Vienna</div>
<div class="line">Althanstraße 14 / UZA II</div>
<div class="line">1090 Vienna, Austria</div>
-<div class="line">mail: leopold.haimberger [at] univie.ac.at</div>
+<div class="line">e-mail: leopold.haimberger [at] univie.ac.at</div>
+</div>
+<div class="line-block">
+<div class="line">Petra Seibert</div>
+<div class="line">Institute of Meteorology (BOKU-Met)</div>
+<div class="line">University of Natural Resources & Life Sciences (BOKU)</div>
+<div class="line">Gregor-Mendel-Str. 33</div>
+<div class="line">1180 Wien, Austria</div>
+<div class="line">e-mail: petra.seibert ./at/. boku.ac.at</div>
</div>
<div class="toctree-wrapper compound">
</div>
diff --git a/Documentation/html/changelog.html b/Documentation/html/changelog.html
index a0eab663a6fff2a36e86305fa55ad280e35ffc20..0f4763300bb9980e2fbf541cd97a27e36cb5c308 100644
--- a/Documentation/html/changelog.html
+++ b/Documentation/html/changelog.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Changelog — flex_extract 7.1.1 documentation</title>
+ <title>Changelog — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -96,27 +96,31 @@
<li class="toctree-l1"><a class="reference internal" href="evaluation.html">Evaluation</a></li>
<li class="toctree-l1"><a class="reference internal" href="dev_guide.html">Developer Guide</a></li>
<li class="toctree-l1 current"><a class="current reference internal" href="#">Changelog</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="#release-v7-1-2">Release v7.1.2</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="#changes">Changes</a></li>
+</ul>
+</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-1-1">Release v7.1.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#bug-fixes">Bug fixes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-1">Release v7.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="#new-features">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#changes">Changes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id1">Changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-0-4">Release v7.0.4</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id1">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id2">Bug fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id2">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id3">Bug fixes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-0-3">Release v7.0.3</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id3">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id4">New Features</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v7-0-2">Release v7.0.2</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="#id4">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="#id5">Changes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id5">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="#id6">Changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="#release-v0-1-v6-0">Release v0.1 - v6.0</a></li>
@@ -193,6 +197,26 @@
<h1>Changelog<a class="headerlink" href="#changelog" title="Permalink to this headline">¶</a></h1>
<div class="toctree-wrapper compound">
</div>
+<div class="section" id="release-v7-1-2">
+<span id="ref-v712"></span><h2>Release v7.1.2<a class="headerlink" href="#release-v7-1-2" title="Permalink to this headline">¶</a></h2>
+<div class="section" id="changes">
+<h3>Changes<a class="headerlink" href="#changes" title="Permalink to this headline">¶</a></h3>
+<blockquote>
+<div><ul class="simple">
+<li><p>changed naming of template files</p></li>
+<li><p>separate loading of Python3 module in remote mode is no longer necessary</p></li>
+<li><p>updated module versions for ECMWF servers</p></li>
+<li><p>changed names of working directories on ECMWF servers</p></li>
+<li><p>select makefile automatically regarding application mode if it was not set in <code class="docutils literal notranslate"><span class="pre">setup.sh</span></code></p></li>
+<li><p>updated online documentation</p></li>
+<li><p>converted most important Fortran code documentation from German to English</p></li>
+<li><p>deactivate writing of VERTICAL.EC file by Fortran code</p></li>
+<li><p>adapt and improve Fortran regression test scripts</p></li>
+<li><p>remove jasper lib from Fortran makefiles</p></li>
+</ul>
+</div></blockquote>
+</div>
+</div>
<div class="section" id="release-v7-1-1">
<span id="ref-v711"></span><h2>Release v7.1.1<a class="headerlink" href="#release-v7-1-1" title="Permalink to this headline">¶</a></h2>
<div class="section" id="bug-fixes">
@@ -221,8 +245,8 @@
</ul>
</div></blockquote>
</div>
-<div class="section" id="changes">
-<h3>Changes<a class="headerlink" href="#changes" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id1">
+<h3>Changes<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>upgraded to Python3</p></li>
@@ -239,16 +263,16 @@
</div>
<div class="section" id="release-v7-0-4">
<span id="ref-v704"></span><h2>Release v7.0.4<a class="headerlink" href="#release-v7-0-4" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="id1">
-<h3>New Features<a class="headerlink" href="#id1" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id2">
+<h3>New Features<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>Ensemble retrieval for ENFO and ELDA stream (ZAMG specific with extra synthesized ensembles for ELDA stream)</p></li>
</ul>
</div></blockquote>
</div>
-<div class="section" id="id2">
-<h3>Bug fixes<a class="headerlink" href="#id2" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id3">
+<h3>Bug fixes<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>various problems with ERA 5 retrieval</p></li>
@@ -263,8 +287,8 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span
</div>
<div class="section" id="release-v7-0-3">
<span id="ref-v703"></span><h2>Release v7.0.3<a class="headerlink" href="#release-v7-0-3" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="id3">
-<h3>New Features<a class="headerlink" href="#id3" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id4">
+<h3>New Features<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>output of MARS requests to an extra file (debugging and documentation)</p></li>
@@ -278,16 +302,16 @@ with <code class="docutils literal notranslate"><span class="pre">field=0.</span
</div>
<div class="section" id="release-v7-0-2">
<span id="ref-v702"></span><h2>Release v7.0.2<a class="headerlink" href="#release-v7-0-2" title="Permalink to this headline">¶</a></h2>
-<div class="section" id="id4">
-<h3>New Features<a class="headerlink" href="#id4" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id5">
+<h3>New Features<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>Python-based version</p></li>
</ul>
</div></blockquote>
</div>
-<div class="section" id="id5">
-<h3>Changes<a class="headerlink" href="#id5" title="Permalink to this headline">¶</a></h3>
+<div class="section" id="id6">
+<h3>Changes<a class="headerlink" href="#id6" title="Permalink to this headline">¶</a></h3>
<blockquote>
<div><ul class="simple">
<li><p>korn shell scripts substituted by Python scripts</p></li>
diff --git a/Documentation/html/dev_guide.html b/Documentation/html/dev_guide.html
index 0c8112ccbc23fa2940243cceac347efbcee2e12b..56d7d212d3e9180be56b087a10217b1ac098135e 100644
--- a/Documentation/html/dev_guide.html
+++ b/Documentation/html/dev_guide.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Developer Guide — flex_extract 7.1.1 documentation</title>
+ <title>Developer Guide — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/documentation.html b/Documentation/html/documentation.html
index 9d1a864e5b8603cba03da701c309026e87ef88ff..3fc7d93604d1b6ddf6f089df9ea36bb2e5cb072c 100644
--- a/Documentation/html/documentation.html
+++ b/Documentation/html/documentation.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Code-Level Documentation — flex_extract 7.1.1 documentation</title>
+ <title>Code-Level Documentation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/ecmwf_data.html b/Documentation/html/ecmwf_data.html
index b5ca88a13e09f99ca4461dbe3071ccab95a6e2bc..2f8f1fcb65153c9593b92c6e3e9172d814b67124 100644
--- a/Documentation/html/ecmwf_data.html
+++ b/Documentation/html/ecmwf_data.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ECMWF Data — flex_extract 7.1.1 documentation</title>
+ <title>ECMWF Data — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/evaluation.html b/Documentation/html/evaluation.html
index 5e5e02020d9d4f323f6db68df07c1611e1be3a09..b3771fcee62c68ae5f42665e9da3aa4195513c3c 100644
--- a/Documentation/html/evaluation.html
+++ b/Documentation/html/evaluation.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Evaluation — flex_extract 7.1.1 documentation</title>
+ <title>Evaluation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/genindex.html b/Documentation/html/genindex.html
index 7aa6b98ab0fb896e8769c39e3c975c2651a2f686..2bea1d441d6e30dc3c8b273b465485ba1c05b34d 100644
--- a/Documentation/html/genindex.html
+++ b/Documentation/html/genindex.html
@@ -9,7 +9,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Index — flex_extract 7.1.1 documentation</title>
+ <title>Index — flex_extract 7.1.2 documentation</title>
@@ -62,7 +62,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/index.html b/Documentation/html/index.html
index 97ce63ad3b749e82defad64dfa41edff329be7ad..452dcf1a0e30b0ad7379f21613715e560eb4b2d8 100644
--- a/Documentation/html/index.html
+++ b/Documentation/html/index.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Welcome to the flex_extract Documentation! — flex_extract 7.1.1 documentation</title>
+ <title>Welcome to the flex_extract Documentation! — flex_extract 7.1.2 documentation</title>
@@ -62,7 +62,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -318,27 +318,31 @@ Creative Commons, PO Box 1866, Mountain View, CA 94042, USA.</p>
<li class="toctree-l1"><a class="reference internal" href="evaluation.html">Evaluation</a></li>
<li class="toctree-l1"><a class="reference internal" href="dev_guide.html">Developer Guide</a></li>
<li class="toctree-l1"><a class="reference internal" href="changelog.html">Changelog</a><ul>
+<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-1-2">Release v7.1.2</a><ul>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#changes">Changes</a></li>
+</ul>
+</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-1-1">Release v7.1.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#bug-fixes">Bug fixes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-1">Release v7.1</a><ul>
<li class="toctree-l3"><a class="reference internal" href="changelog.html#new-features">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#changes">Changes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id1">Changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-0-4">Release v7.0.4</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id1">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id2">Bug fixes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id2">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id3">Bug fixes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-0-3">Release v7.0.3</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id3">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id4">New Features</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v7-0-2">Release v7.0.2</a><ul>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id4">New Features</a></li>
-<li class="toctree-l3"><a class="reference internal" href="changelog.html#id5">Changes</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id5">New Features</a></li>
+<li class="toctree-l3"><a class="reference internal" href="changelog.html#id6">Changes</a></li>
</ul>
</li>
<li class="toctree-l2"><a class="reference internal" href="changelog.html#release-v0-1-v6-0">Release v0.1 - v6.0</a></li>
diff --git a/Documentation/html/installation.html b/Documentation/html/installation.html
index 1985aa7f79de9ba91dee9d7377fedb1ed5889193..84574bf1ec305621c81f022fc55df639c5384db6 100644
--- a/Documentation/html/installation.html
+++ b/Documentation/html/installation.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Installation — flex_extract 7.1.1 documentation</title>
+ <title>Installation — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -285,7 +285,7 @@
<p>The software required to run <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> depends on the <a class="reference internal" href="Documentation/Overview/app_modes.html"><span class="doc">Application modes</span></a> and therefore is described in the respective specific installation sections.</p>
<p>Generally speaking, <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> requires <a class="reference external" href="https://docs.python.org/3/">Python 3</a> and Fortran together with certain modules / libraries.
We tested <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> with the Python3 package from the the GNU/Linux distribution and Anaconda Python. The required Python3 modules should prefarably be installed as distribution packages, or alternatively using Python’s own package manager <code class="docutils literal notranslate"><span class="pre">pip</span></code> (this may mess up some aspects of your python installation, especially if you use <code class="docutils literal notranslate"><span class="pre">pip</span></code> as root. Think about using virtual environments.).</p>
-<p>Before installing the system packages check the availability with (Debian-based system) <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or (Redhat-based system)``rpm -q <package_name>``. For example:</p>
+<p>Before installing the system packages check the availability with (Debian-based system) <code class="docutils literal notranslate"><span class="pre">dpkg</span> <span class="pre">-s</span> <span class="pre"><package-name></span> <span class="pre">|</span>  <span class="pre">grep</span> <span class="pre">Status</span></code> or (Redhat-based system) <code class="docutils literal notranslate"><span class="pre">rpm</span> <span class="pre">-q</span> <span class="pre"><package_name></span></code>. For example:</p>
<div class="highlight-sh notranslate"><div class="highlight"><pre><span></span>$ dpkg -s libeccodes-dev <span class="p">|</span> grep Status
<span class="c1"># or</span>
$ rpm -q libeccodes-dev
@@ -317,12 +317,12 @@ installation has to be done. At the users local side not all software has to be
<div class="section" id="fortran-program-test">
<h3>Fortran program test<a class="headerlink" href="#fortran-program-test" title="Permalink to this headline">¶</a></h3>
<p>To check whether the Fortran program <code class="docutils literal notranslate"><span class="pre">calc_etadot</span></code> has been compiled and runs properly, it can be applied to a prepared minimal dataset.</p>
-<p>For this, go from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory to the <code class="docutils literal notranslate"><span class="pre">Testing/Installation/Convert/</span></code> directory and execute the Fortran program.</p>
+<p>For this, go from the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory to the <code class="docutils literal notranslate"><span class="pre">Testing/Installation/Calc_etadot/</span></code> directory and execute the Fortran program.</p>
<div class="admonition note">
<p class="admonition-title">Note</p>
<p>Remember that you might have to log in at the ECMWF server if you used the installation for the <strong>remote</strong> or <strong>gateway</strong> mode. There you find the <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> root directory in your <code class="docutils literal notranslate"><span class="pre">$HOME</span></code> directory.</p>
</div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> Testing/Installation/Convert
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="nb">cd</span> Testing/Installation/Calc_etadot
<span class="c1"># execute the Fortran progam without arguments</span>
../../../Source/Fortran/calc_etadot
</pre></div>
diff --git a/Documentation/html/objects.inv b/Documentation/html/objects.inv
index bbc9b03bab4eeae44caefa9ad02af7af4a3c06d0..b03f28865e5d03c538c593f1e7abfda3267c9e31 100644
Binary files a/Documentation/html/objects.inv and b/Documentation/html/objects.inv differ
diff --git a/Documentation/html/py-modindex.html b/Documentation/html/py-modindex.html
index c1f0bff6130880322ddd546f0729c3cf47d7fc8a..b68f278a6be4fbb7a95a055deaa8bc03876d8441 100644
--- a/Documentation/html/py-modindex.html
+++ b/Documentation/html/py-modindex.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Python Module Index — flex_extract 7.1.1 documentation</title>
+ <title>Python Module Index — flex_extract 7.1.2 documentation</title>
@@ -68,7 +68,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/quick_start.html b/Documentation/html/quick_start.html
index 1addb3583556f59d3e346367b65054c69c658cce..651f61aef2695b87c00bc2f946dea8b67d7f5452 100644
--- a/Documentation/html/quick_start.html
+++ b/Documentation/html/quick_start.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Usage — flex_extract 7.1.1 documentation</title>
+ <title>Usage — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
@@ -226,7 +226,6 @@ ssh -X <ecuid>@ecaccess.ecmwf.int
</pre></div>
</div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span><span class="c1"># On ECMWF server</span>
-<span class="o">[</span><ecuid>@ecgb11 ~<span class="o">]</span>$ module load python3
<span class="o">[</span><ecuid>@ecgb11 ~<span class="o">]</span>$ <span class="nb">cd</span> flex_extract_vX.X/Run
</pre></div>
</div>
@@ -259,7 +258,7 @@ ssh <user>@<gatewayserver>
<span class="nv">INPUTDIR</span><span class="o">=</span>None
<span class="nv">OUTPUTDIR</span><span class="o">=</span>None
<span class="nv">PP_ID</span><span class="o">=</span>None
-<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'job.temp'</span>
+<span class="nv">JOB_TEMPLATE</span><span class="o">=</span><span class="s1">'jobscript.template'</span>
<span class="nv">CONTROLFILE</span><span class="o">=</span><span class="s1">'CONTROL_CERA'</span>
<span class="nv">DEBUG</span><span class="o">=</span><span class="m">0</span>
<span class="nv">REQUEST</span><span class="o">=</span><span class="m">2</span>
@@ -284,10 +283,10 @@ FLEX_EXTRACT JOB SCRIPT IS SUBMITED!
ls -rthl
</pre></div>
</div>
-<p>The last command lists the most recent logs and temporary retrieval directories (usually <code class="docutils literal notranslate"><span class="pre">pythonXXXXX</span></code>, where XXXXX is the process id). Under <code class="docutils literal notranslate"><span class="pre">pythonXXXXX</span></code> a copy of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored under the name <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code>, the protocol is stored in the file <code class="docutils literal notranslate"><span class="pre">prot</span></code> and the temporary files as well as the resulting files are stored in a directory <code class="docutils literal notranslate"><span class="pre">work</span></code>. The original name of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored in this new file under parameter <code class="docutils literal notranslate"><span class="pre">controlfile</span></code>.</p>
-<div class="literal-block-wrapper docutils container" id="id5">
-<div class="code-block-caption"><span class="caption-text">“Example structure of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> output directory on ECMWF servers.”</span><a class="headerlink" href="#id5" title="Permalink to this code">¶</a></div>
-<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>pythonXXXXX
+<p>The last command lists the most recent logs and temporary retrieval directories (usually <code class="docutils literal notranslate"><span class="pre">extractXXXXX</span></code>, where XXXXX is the process id). Under <code class="docutils literal notranslate"><span class="pre">extractXXXXX</span></code> a copy of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored under the name <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code>, the protocol is stored in the file <code class="docutils literal notranslate"><span class="pre">prot</span></code> and the temporary files as well as the resulting files are stored in a directory <code class="docutils literal notranslate"><span class="pre">work</span></code>. The original name of the <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file is stored in this new file under parameter <code class="docutils literal notranslate"><span class="pre">controlfile</span></code>.</p>
+<div class="literal-block-wrapper docutils container" id="id2">
+<div class="code-block-caption"><span class="caption-text">“Example structure of <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code> output directory on ECMWF servers.”</span><a class="headerlink" href="#id2" title="Permalink to this code">¶</a></div>
+<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>extractXXXXX
├── CONTROL
├── prot
├── work
@@ -398,8 +397,8 @@ ls -rthl
<p>Additionally, you can find a lot of helpful links to dataset documentations, direct links to specific dataset web catalogues or further general information at the <a class="reference external" href="Ecmwf/ec-links.html">link collection</a> in the ECMWF data section.</p>
<p><code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> is specialised to retrieve a limited number of datasets, namely <em>ERA-Interim</em>, <em>CERA-20C</em>, <em>ERA5</em> and <em>HRES (operational data)</em> as well as the <em>ENS (operational data, 15-day forecast)</em>. The limitation relates mainly to the dataset itself, the stream (what kind of forecast or what subset of dataset) and the experiment number. Mostly, the experiment number is equal to <code class="docutils literal notranslate"><span class="pre">1</span></code> to signal that the actual version should be used.</p>
<p>The next level of differentiation would be the field type, level type and time period. <code class="docutils literal notranslate"><span class="pre">Flex_extract</span></code> currently only supports the main streams for the re-analysis datasets and provides extraction of different streams for the operational dataset. The possibilities of compositions of dataset and stream selection are represented by the current list of example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files. You can see this in the naming of the example files:</p>
-<div class="literal-block-wrapper docutils container" id="id6">
-<div class="code-block-caption"><span class="caption-text">“Current example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files distributed with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. “</span><a class="headerlink" href="#id6" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id3">
+<div class="code-block-caption"><span class="caption-text">“Current example <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> files distributed with <code class="docutils literal notranslate"><span class="pre">flex_extract</span></code>. “</span><a class="headerlink" href="#id3" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_CERA
CONTROL_CERA.global
CONTROL_CERA.public
@@ -489,7 +488,7 @@ CONTROL_OD.OPER.FC.gauss.highres
<p>Please see <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency">Information about MARS retrievement</a> for hints about retrieval efficiency and troubleshooting.</p>
</div>
<dl>
-<dt>Pure forecast</dt><dd><p>It is possible to retrieve pure forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of <em>Forecast (FC)</em>, <em>Control forecast (CF)</em> and <em>Calibration/Validation forecast (CV)</em>.
+<dt>Long forecast</dt><dd><p>It is possible to retrieve long forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of <em>Forecast (FC)</em>, <em>Control forecast (CF)</em> and <em>Calibration/Validation forecast (CV)</em>.
The <em>CV</em> field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the <em>CF</em> type since this is available from 1992 (3-hourly) on up to today (1-hourly). <em>CV</em> and <em>CF</em> field types belong to the <em>Ensemble prediction system (ENFO)</em> which currently works with 50 ensemble members.
Please be aware that in this case it is necessary to set the type for flux fields explicitly, otherwise a default value might be selected, different from what you expect!</p>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>CONTROL_OD.ENFO.CF.36hours
@@ -540,12 +539,8 @@ CONTROL_OD.ENFO.PF.ens
<dt>Field type and time</dt><dd><p>This combination is very important. It defines the temporal resolution and which field type is extracted on each time step.
The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be <code class="docutils literal notranslate"><span class="pre">0</span></code>.
The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of <code class="docutils literal notranslate"><span class="pre">TYPE</span></code>, <code class="docutils literal notranslate"><span class="pre">TIME</span></code> and <code class="docutils literal notranslate"><span class="pre">STEP</span></code> because the temporal (hourly) resolution with the <code class="docutils literal notranslate"><span class="pre">DTIME</span></code> parameter will select the correct combinations.</p>
-<div class="admonition-todo admonition" id="id2">
-<p class="admonition-title">Todo</p>
-<p>#PS needs to be rephrased</p>
-</div>
-<div class="literal-block-wrapper docutils container" id="id7">
-<div class="code-block-caption"><span class="caption-text">Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.</span><a class="headerlink" href="#id7" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id4">
+<div class="code-block-caption"><span class="caption-text">Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.</span><a class="headerlink" href="#id4" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> DTIME <span class="m">3</span>
TYPE AN FC FC FC AN FC FC FC
TIME <span class="m">00</span> <span class="m">00</span> <span class="m">00</span> <span class="m">00</span> <span class="m">12</span> <span class="m">12</span> <span class="m">12</span> <span class="m">12</span>
@@ -557,8 +552,8 @@ The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of
<dt>Vertical velocity</dt><dd><p>The vertical velocity for <code class="docutils literal notranslate"><span class="pre">FLEXPART</span></code> is not directly available from MARS and has to be calculated.
There are several options for this, and the following parameters are responsible for the selection. See <a class="reference internal" href="Documentation/vertco.html"><span class="doc">Vertical wind</span></a> for a detailed explanation. Using <code class="docutils literal notranslate"><span class="pre">ETADIFF</span> <span class="pre">1</span></code>, <code class="docutils literal notranslate"><span class="pre">OMEGA</span> <span class="pre">1</span></code> and <code class="docutils literal notranslate"><span class="pre">OMEGADIFF</span> <span class="pre">1</span></code> is recommended for debugging and testing only.
Usually, one has to decide between <code class="docutils literal notranslate"><span class="pre">GAUSS</span> <span class="pre">1</span></code> and <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code>. <code class="docutils literal notranslate"><span class="pre">GAUSS</span> <span class="pre">1</span></code> means that spectral fields of the horizontal wind fields and the divergence are retrieved and that the vertical velocity is calculate using the continuity equation. <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code> means that horizontal wind fields etadot are retrieved on a regular lat-lon grid. It is recommended to use <code class="docutils literal notranslate"><span class="pre">ETA</span> <span class="pre">1</span></code> where possible, as there is a substantial computational overhead for solving the continuity equation.</p>
-<div class="literal-block-wrapper docutils container" id="id8">
-<div class="code-block-caption"><span class="caption-text">Example setting for the vertical coordinate retrieval (recommended if etadot fields are available).</span><a class="headerlink" href="#id8" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id5">
+<div class="code-block-caption"><span class="caption-text">Example setting for the vertical coordinate retrieval (recommended if etadot fields are available).</span><a class="headerlink" href="#id5" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>GAUSS <span class="m">0</span>
ETA <span class="m">1</span>
ETADIFF <span class="m">0</span>
@@ -571,15 +566,9 @@ OMEGADIFF <span class="m">0</span>
</dd>
<dt>Grid resolution and domain</dt><dd><p>The grid and domain parameters depends on each other. <code class="docutils literal notranslate"><span class="pre">grid</span></code> refers to the grid resolution. It can be given as decimal values (e.g., <code class="docutils literal notranslate"><span class="pre">1.</span></code> meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., <code class="docutils literal notranslate"><span class="pre">1000</span></code> means also 1°). The code applies common sense to determine what format is to be assumed.
After selecting grid, the <code class="docutils literal notranslate"><span class="pre">domain</span></code> has to be defined. The extension in longitude or latitude direction must be an integer multiple of <code class="docutils literal notranslate"><span class="pre">grid</span></code>.</p>
-<blockquote>
-<div><div class="admonition-todo admonition" id="id3">
-<p class="admonition-title">Todo</p>
-<p>#PS shouldn’t we explain how to define a domain??</p>
-</div>
-</div></blockquote>
<p>The horizontal resolution for spectral fields is set by the parameter <code class="docutils literal notranslate"><span class="pre">RESOL</span></code>. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol">in this entry of the ECMWF on-line documentation</a> and <a class="reference external" href="https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation">this table (also ECMWF documentation)</a>.</p>
-<div class="literal-block-wrapper docutils container" id="id9">
-<div class="code-block-caption"><span class="caption-text">Example setting for a domain covering the northern hemisphere domain with a grid resolution of <code class="docutils literal notranslate"><span class="pre">0.25°</span></code>.</span><a class="headerlink" href="#id9" title="Permalink to this code">¶</a></div>
+<div class="literal-block-wrapper docutils container" id="id6">
+<div class="code-block-caption"><span class="caption-text">Example setting for a domain covering the northern hemisphere domain with a grid resolution of <code class="docutils literal notranslate"><span class="pre">0.25°</span></code>.</span><a class="headerlink" href="#id6" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span>GRID <span class="m">0</span>.25
RESOL <span class="m">799</span>
SMOOTH <span class="m">0</span>
@@ -591,15 +580,9 @@ RIGHT <span class="m">180</span>.
</div>
</div>
</dd>
-<dt>Flux data</dt><dd><p>Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. <code class="docutils literal notranslate"><span class="pre">ACCTYPE</span></code> is the field type (must be a type of forecast), <code class="docutils literal notranslate"><span class="pre">ACCTIME</span></code> the forecast starting time, and <code class="docutils literal notranslate"><span class="pre">ACCMAXSTEP</span></code> the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.</p>
-<blockquote>
-<div><div class="admonition-todo admonition" id="id4">
-<p class="admonition-title">Todo</p>
-<p>#PS for which application would this be typical?</p>
-</div>
-</div></blockquote>
-<div class="literal-block-wrapper docutils container" id="id10">
-<div class="code-block-caption"><span class="caption-text">Example setting for the definition of flux fields.</span><a class="headerlink" href="#id10" title="Permalink to this code">¶</a></div>
+<dt>Flux data</dt><dd><p>Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields. <code class="docutils literal notranslate"><span class="pre">ACCTYPE</span></code> is the field type (must be a type of forecast), <code class="docutils literal notranslate"><span class="pre">ACCTIME</span></code> the forecast starting time, and <code class="docutils literal notranslate"><span class="pre">ACCMAXSTEP</span></code> the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP. These values will be set automatically if not provided in a <code class="docutils literal notranslate"><span class="pre">CONTROL</span></code> file.</p>
+<div class="literal-block-wrapper docutils container" id="id7">
+<div class="code-block-caption"><span class="caption-text">Example setting for the definition of flux fields.</span><a class="headerlink" href="#id7" title="Permalink to this code">¶</a></div>
<div class="highlight-bash notranslate"><div class="highlight"><pre><span></span> DTIME <span class="m">3</span>
ACCTYPE FC
ACCTIME <span class="m">00</span>/12
diff --git a/Documentation/html/search.html b/Documentation/html/search.html
index 9a1d20485d1dd70854c781aa2f278bb3eabc5ed0..533e75521f9a80d9daffba4038e02e7d31319be0 100644
--- a/Documentation/html/search.html
+++ b/Documentation/html/search.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Search — flex_extract 7.1.1 documentation</title>
+ <title>Search — flex_extract 7.1.2 documentation</title>
@@ -62,7 +62,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/searchindex.js b/Documentation/html/searchindex.js
index a19a783f517eea90310756bff022fb35b87391e4..f73bd59c99edbcfa182032425f1b2c5667585fd7 100644
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the documentation","Auto-generated documentation for the Fortran programme","Auto-generated documentation for the Python scripts","CONTROL file changes","The compilation job script <code class=\"docutils literal notranslate\"><span class=\"pre\">compilejob.ksh</span></code>","The CONTROL file","The CONTROL parameters","ECMWF user credential file <code class=\"docutils literal notranslate\"><span class=\"pre\">ECMWF_ENV</span></code>","CONTROL file examples","The Fortran makefile for <code class=\"docutils literal notranslate\"><span class=\"pre\">calc_etadot</span></code>","The job script <code class=\"docutils literal notranslate\"><span class=\"pre\">job.ksh</span></code>","The executable script - <code class=\"docutils literal notranslate\"><span class=\"pre\">run.sh</span></code>","The installation script - <code class=\"docutils literal notranslate\"><span class=\"pre\">setup.sh</span></code>","Templates","Application modes","Program flow","Auto-generated documentation","Disaggregation of flux data","Control & input data","Output data","Overview","Vertical wind","Access modes","Link collection","Hints for data set selection","Available data sets for member-state users","Available data sets for public users","Metrics","Static code analysis","Test cases","Gateway mode installation","Local mode installation","Remote mode installation","FAQ - Frequently asked questions","Known Bugs and Issues","Developer Team","Changelog","Developer Guide","Code-Level Documentation","ECMWF Data","Evaluation","Welcome to the <code class=\"docutils literal notranslate\"><span class=\"pre\">flex_extract</span></code> Documentation!","Installation","Usage","Support","ToDos"],titleterms:{"case":29,"class":2,"long":19,"new":[19,36],"public":[26,42,43],"static":28,CDS:[31,34],The:[4,5,6,9,10,11,12],accept:42,access:22,addit:[0,6,19],adjust:43,agreement:[],analysi:28,api:[31,34],applic:[14,15],ask:33,auto:[1,2,16],avail:[24,25,26],block:0,bug:[34,36,44],calc_etadot:[9,19,34],calc_etadot_nml:13,calcul:21,can:[24,33],cera:43,certain:43,chang:[3,36],changelog:36,check:2,code:[28,34,38],collect:23,combin:[42,43],comparison:29,compil:4,compilejob:4,content:[7,11,12,19],continu:21,control:[3,5,6,8,18,43],controlfil:2,convert:[],coordin:[],credenti:7,data:[6,17,18,19,24,25,26,34,39,43],dataset:[42,43],definit:43,depend:[30,31,32,42],destin:34,develop:[35,37],diagramm:0,differ:15,disaggreg:[2,17,19],distribut:33,document:[0,1,2,16,38,41],doe:[4,10],domain:6,download:42,eccod:34,ecflexpart:2,ecmwf:[7,31,39,42],ecmwf_env:[7,13],ensembl:19,environ:[30,31,32],equat:21,era5:34,era:43,error:34,evalu:40,exampl:[4,5,8,10,15],execut:11,faq:[33,44],featur:[36,43],field:[6,17,19],file:[3,5,6,7,8,19,21,29,43],find:24,finder:[],fix:36,flex_extract:[41,42],flexpart:[19,42],flow:15,flux:[6,17,19],forecast:19,format:5,fort:19,fortran:[1,9,19,34,42],frequent:33,from:[21,33],full:42,gatewai:[30,34,43],gener:[1,2,6,15,16],get_mars_data:2,grib:[19,29],gributil:2,guid:37,hint:[24,43],horizont:21,how:24,index:19,input:[18,19],instal:[2,12,30,31,32,33,34,42],installscript:13,interim:43,issu:[34,44],job:[4,10,43],jobscript:13,known:[34,44],ksh:[4,10],level:[25,38],librari:33,licenc:42,line:0,link:23,list:44,local:[15,31,43],mail:44,makefil:9,mar:[19,21,29],marsretriev:2,member:[15,25],metric:27,mode:[14,15,22,30,31,32,43],model:25,modul:2,older:17,onlin:[],oper:43,option:[11,12],other:17,out:24,output:[19,21],overview:20,packag:33,paramet:[6,11,12,21,34,43],parti:33,pre:21,precipit:[17,19],predict:19,prepar:[21,30,31,32,43],prepare_flexpart:2,problem:34,program:[2,15,19,34,42],programm:1,proper:43,pure:[],python:2,question:33,quick:[],registr:42,releas:[34,36],remot:[32,43],report:44,request:[19,29],rest:[],retriev:[],run:11,script:[2,4,10,11,12],section:6,select:[24,43],sequenc:0,set:[15,24,25,26],setup:12,softwar:0,some:[],specif:43,specifi:[],sphinx:0,standard:19,start:[],state:25,submiss:11,submit:[2,11],submitscript:13,support:44,surfac:25,system:44,team:35,temp:[],templat:13,temporari:19,test:[29,30,31,42],testcas:[],third:33,ticket:44,time:6,todo:45,tool:2,uiofil:2,updat:0,usag:[11,12,43],user:[6,7,15,25,26],using:21,veloc:21,version:17,vertic:[6,21],web:31,welcom:41,what:[4,10,24,33],wind:[6,21],workflow:15}})
\ No newline at end of file
diff --git a/Documentation/html/support.html b/Documentation/html/support.html
index 666510cc539e41800a8f0f965d099dcc0626ac7b..aca09f45d95798f1a2ded5f152cc98dcb0ef21f9 100644
--- a/Documentation/html/support.html
+++ b/Documentation/html/support.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>Support — flex_extract 7.1.1 documentation</title>
+ <title>Support — flex_extract 7.1.2 documentation</title>
@@ -63,7 +63,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/Documentation/html/todo.html b/Documentation/html/todo.html
index 4d320bfc849688b6664e4e2695cf3f35c94bcdff..4a64edee8e209630b4d32425d96ff673d19b0ffa 100644
--- a/Documentation/html/todo.html
+++ b/Documentation/html/todo.html
@@ -8,7 +8,7 @@
<meta name="viewport" content="width=device-width, initial-scale=1.0">
- <title>ToDos — flex_extract 7.1.1 documentation</title>
+ <title>ToDos — flex_extract 7.1.2 documentation</title>
@@ -61,7 +61,7 @@
<div class="version">
- 7.1.1
+ 7.1.2
</div>
diff --git a/For_developers/CONTROLparameter.xls b/For_developers/CONTROLparameter.xls
index 04e5442c4edb776e63342df2de398d85348f1c11..c6cfbc81cf8d5d1ac0a383b12e2a440a82322937 100644
Binary files a/For_developers/CONTROLparameter.xls and b/For_developers/CONTROLparameter.xls differ
diff --git a/For_developers/InstallationParameter.xls b/For_developers/InstallationParameter.xls
index 5e897bc13c277bfdd7683703dfa7ea816d3c154b..5a7ab0dd2d436c1fe93ee25269ed51865f8e6f8a 100644
Binary files a/For_developers/InstallationParameter.xls and b/For_developers/InstallationParameter.xls differ
diff --git a/For_developers/Sphinx/Source/Documentation/Input/compilejob.rst b/For_developers/Sphinx/Source/Documentation/Input/compilejob.rst
index 7eac32c0626ae8e63276c2a80f30eb6dc12eaed3..214a0965e69bd22b7d63858d1b3b7f5fd84ba26d 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/compilejob.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/compilejob.rst
@@ -1,14 +1,14 @@
-*********************************************
+*************************************************
The compilation job script ``compilejob.ksh``
-*********************************************
+*************************************************
-The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``compilejob.template`` in the template directory.
+The compile job is a Korn-shell script which will be created during the installation process for the application modes **remote** and **gateway** from a template called ``installscript.template`` in the template directory.
``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by a doubled ``$`` sign in ``job.temp``.
+These individual parameters are marked by a doubled ``$`` sign in ``installscript.template``.
-The job script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
+The compilation script has a number of settings for the batch system which are fixed, and it differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
The submission is done by the ``ECaccess`` tool from within ``flex_extract`` with the command ``ecaccess-job-submit``.
@@ -23,7 +23,7 @@ What does the compilation script do?
#. It sets some environment variables for the single session
#. It creates the ``flex_extract`` root directory in the ``$HOME`` path of the user
#. It untars the tarball into the root directory.
- #. It compiles the Fortran program using ``Makefile``.
+ #. It compiles the Fortran program using ``makefile``.
#. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
@@ -66,21 +66,18 @@ Example ``compilejob.ksh``
case ${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export FLEXPART_ROOT_SCRIPTS=${HOME}
export MAKEFILE=makefile_ecgate
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
echo ${GROUP}
echo ${HOME}
echo ${HOME} | awk -F / '{print $1, $2, $3, $4}'
diff --git a/For_developers/Sphinx/Source/Documentation/Input/examples.rst b/For_developers/Sphinx/Source/Documentation/Input/examples.rst
index f69fd02641edbf9e42e102092decaf1b8286a96a..8ed3c767048545c50d6be66b536a1476282ecfa8 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/examples.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/examples.rst
@@ -35,9 +35,9 @@ CONTROL.documentation
CONTROL_OD.OPER.FC.twicedaily.1hourly
CONTROL_OD.OPER.FC.twicedaily.3hourly
-.. todo::
+.. note::
- #PS some information to be added.
+ Further information will follow.
.. toctree::
:hidden:
diff --git a/For_developers/Sphinx/Source/Documentation/Input/jobscript.rst b/For_developers/Sphinx/Source/Documentation/Input/jobscript.rst
index 6a8b7600ea32b442140b22d465e7c93e907dd1bf..a1f43b258cb17a867825d5a97241870e67e75193 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/jobscript.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/jobscript.rst
@@ -4,12 +4,12 @@ The job script ``job.ksh``
The job script is a Korn-shell script which will be created at runtime for each ``flex_extract`` execution in the application modes **remote** and **gateway**.
-It is based on the ``job.temp`` template file stored in the ``Templates`` directory.
-This template is generated in the installation process from a ``job.template`` template file.
+It is based on the ``submitscript.template`` template file stored in the ``Templates`` directory.
+This template is generated in the installation process from a ``jobscript.template`` template file.
``Flex_extract`` uses the Python package `genshi <https://genshi.edgewall.org/>`_ to generate
the Korn-shell script from the template files by substituting the individual parameters.
-These individual parameters are marked by ``$$`` in ``job.temp``.
+These individual parameters are marked by ``$$`` in ``jobscript.template``.
The job script has a number of settings for the batch system which are fixed, and differentiates between the *ecgate* and the *cca/ccb*
server system to load the necessary modules for the environment when submitted to the batch queue.
@@ -25,14 +25,14 @@ What does the job script do?
#. It prepares the job environment at the ECMWF servers by loading the necessary library modules.
#. It sets some environment variables for the single session.
#. It creates the directory structure in the user's ``$SCRATCH`` file system.
- #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``jobscript.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
+ #. It creates a CONTROL file on the ECMWF servers whith the parameters set before creating the ``job.ksh``. ``Flex_extract`` has a set of parameters which are passed to the job script with their default or the user-defined values. It also sets ``CONTROL`` as an environment variable.
#. ``Flex_extract`` is started from within the ``work`` directory of the new directory structure by calling the ``submit.py`` script. It sets new paths for input and output directories and the recently generated ``CONTROL`` file.
#. At the end, it checks whether the script has returned an error or not, and emails the log file to the user.
-Example ``jobscript.ksh``
+Example ``job.ksh``
-------------------------
.. code-block:: bash
@@ -67,20 +67,17 @@ Example ``jobscript.ksh``
case ${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
export SCRATCH=${TMPDIR}
export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
@@ -106,7 +103,7 @@ Example ``jobscript.ksh``
dataset None
date_chunk 3
debug 1
- destination annep@genericSftp
+ destination <specificname>@genericSftp
doubleelda 0
dpdeta 1
dtime 3
@@ -127,7 +124,7 @@ Example ``jobscript.ksh``
gaussian
grib2flexpart 0
grid 1.0/1.0
- inputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+ inputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
install_target None
job_chunk 1
job_template job.temp
@@ -144,7 +141,7 @@ Example ``jobscript.ksh``
omega 0
omegadiff 0
oper 0
- outputdir /raid60/nas/tmc/Anne/Interpolation/flexextract/flex_extract_v7.1/run/workspace
+ outputdir <path-to-flex_extract>/flex_extract_v7.1/run/workspace
prefix CE
public 0
purefc 0
diff --git a/For_developers/Sphinx/Source/Documentation/Input/run.rst b/For_developers/Sphinx/Source/Documentation/Input/run.rst
index 1e3ad685d5b5d23c1adea0e66b36a64a5f65aab1..21b1ddb3369ce1238e3a28b9e7c075994d6557e7 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/run.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/run.rst
@@ -30,8 +30,7 @@ Content of ``run.sh``
.. literalinclude:: ../../../../../Run/run.sh
:language: bash
- :caption: run.sh
-
+ :caption: run.sh
diff --git a/For_developers/Sphinx/Source/Documentation/Input/templates.rst b/For_developers/Sphinx/Source/Documentation/Input/templates.rst
index 786679efaf40d9bb6eaced866ba44a1cb59800e3..4a26a545f83fe834b14e2298fedd2f5c705c636e 100644
--- a/For_developers/Sphinx/Source/Documentation/Input/templates.rst
+++ b/For_developers/Sphinx/Source/Documentation/Input/templates.rst
@@ -7,12 +7,12 @@ In ``flex_extract``, the Python package `genshi <https://genshi.edgewall.org/>`_
.. note::
Do not change anything in these files unless you understand the effects!
-Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Kornshell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
+Each template file has its content framework and keeps so-called placeholder variables in the positions where the values need to be substituted at run time. These placeholders are marked by a leading ``$`` sign. In case of the Korn shell job scripts, where (environment) variables are used, the ``$`` sign needs to be doubled for `escaping`.
The following templates are used; they can be found in the directory ``flex_extract_vX.X/Templates``:
-convert.nl
-----------
+calc_etadot_nml.template
+-------------------------
This is the template for a Fortran namelist file called ``fort.4`` read by ``calc_etadot``.
It contains all the parameters ``calc_etadot`` needs.
@@ -39,7 +39,7 @@ convert.nl
mdpdeta = $mdpdeta
/
-ecmwf_env.template
+ECMWF_ENV.template
------------------
This template is used to create the ``ECMWF_ENV`` file in the application modes **gateway** and **remote**. It contains the user credentials and gateway server settings for the file transfers.
@@ -51,8 +51,8 @@ ecmwf_env.template
GATEWAY $gateway_name
DESTINATION $destination_name
-compilejob.template
--------------------
+installscript.template
+----------------------
This template is used to create the job script file called ``compilejob.ksh`` during the installation process for the application modes **remote** and **gateway**.
@@ -96,21 +96,18 @@ compilejob.template
case $${HOST} in
*ecg*)
module unload grib_api
- module unload eccodes
- module unload python
module unload emos
module load python3
- module load eccodes/2.12.0
+ module load eccodes
module load emos/455-r64
export FLEXPART_ROOT_SCRIPTS=$fp_root_scripts
export MAKEFILE=$makefile
;;
*cca*)
- module unload python
module switch PrgEnv-cray PrgEnv-intel
module load python3
- module load eccodes/2.12.0
- module load emos
+ module load eccodes
+ module load emos/455-r64
echo $${GROUP}
echo $${HOME}
echo $${HOME} | awk -F / '{print $1, $2, $3, $4}'
@@ -139,8 +136,8 @@ compilejob.template
fi
-job.temp
---------
+submitscript.template
+---------------------
This template is used to create the actual job script file called ``job.ksh`` for the execution of ``flex_extract`` in the application modes **remote** and **gateway**.
@@ -184,23 +181,20 @@ job.temp
export VERSION=7.1
case $${HOST} in
*ecg*)
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
- export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
- ;;
- *cca*)
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
- export SCRATCH=$${TMPDIR}
- export PATH=$${PATH}:$${HOME}/flex_extract_v7.1/Source/Python
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
+ ;;
+ *cca*)
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
+ export SCRATCH=${TMPDIR}
+ export PATH=${PATH}:${HOME}/flex_extract_v7.1/Source/Python
;;
esac
@@ -236,10 +230,10 @@ job.temp
fi
-job.template
-------------
+jobscript.template
+------------------
- This template is used to create the template for the execution job script ``job.temp`` for ``flex_extract`` in the installation process. A description of the file can be found under ``job.temp``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
+ This template is used to create the template for the execution job script ``submitscript.template`` for ``flex_extract`` in the installation process. A description of the file can be found under ``submitscript.template``. Several parameters are set in this process, such as the user credentials and the ``flex_extract`` version number.
.. code-block:: ksh
@@ -272,21 +266,18 @@ job.template
export VERSION=$version_number
case $$$${HOST} in
*ecg*)
- module unload grib_api
- module unload eccodes
- module unload python
- module unload emos
- module load python3
- module load eccodes/2.12.0
- module load emos/455-r64
+ module unload grib_api
+ module unload emos
+ module load python3
+ module load eccodes
+ module load emos/455-r64
export PATH=$$$${PATH}:$fp_root_path
;;
*cca*)
- module unload python
- module switch PrgEnv-cray PrgEnv-intel
- module load python3
- module load eccodes/2.12.0
- module load emos
+ module switch PrgEnv-cray PrgEnv-intel
+ module load python3
+ module load eccodes
+ module load emos/455-r64
export SCRATCH=$$$${TMPDIR}
export PATH=$$$${PATH}:$fp_root_path
;;
diff --git a/For_developers/Sphinx/Source/Documentation/disagg.rst b/For_developers/Sphinx/Source/Documentation/disagg.rst
index 64a3e3de5ad8e75ec093c6745af8152b52ec69ec..9a51e6be2b3385e289f1794bdcb0ec0c8d3dcc07 100644
--- a/For_developers/Sphinx/Source/Documentation/disagg.rst
+++ b/For_developers/Sphinx/Source/Documentation/disagg.rst
@@ -12,16 +12,16 @@ pre-processing has to be applied.
.. _ref-table-fluxpar:
.. csv-table:: Flux fields
- :header: "Short Name", "Name", "Units", "Interpolation Type"
+ :header: "Short Name", "Name", "Units", "Disaggregation"
:align: center
:widths: 5,15,5,10
- LSP, "large-scale precipitation", "m", "modified linear interpolation"
- CP, "convective precipitation", "m", "modified linear interpolation"
- SSHF, "surface sensible heat flux", "J m:math:`^{-2}`", "bicubic interpolation"
- EWSS, "eastward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
- NSSS, "northward turbulent surface stress", "N m:math:`^{-2}` s", "bicubic interpolation"
- SSR, "surface net solar radiation", "J m:math:`^{-2}`", "bicubic interpolation"
+ LSP, "large-scale precipitation", "m", "precipitation "
+ CP, "convective precipitation", "m", "precipitation"
+ SSHF, "surface sensible heat flux", "J m :math:`^{-2}`", "flux"
+ EWSS, "eastward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
+ NSSS, "northward turbulent surface stress", "N m :math:`^{-2}` s", "flux "
+ SSR, "surface net solar radiation", "J m :math:`^{-2}`", "flux "
The first step is to *de-accumulate* the fields in time so that each value represents non-overlapping integrals in x-, y-, and t-space.
@@ -42,7 +42,7 @@ Disaggregation for precipitation in older versions
In ``flex_extract`` up to version 5, the disaggregation was done with a Fortran program (FLXACC2). In version 6, this part was recoded in Python.
In the old versions (below 7.1), a relatively simple method processes the precipitation fields in a way that is consistent with the linear interpolation between times where input fields are available that is applied in ``FLEXPART`` for all variables.
-This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6). ???
+This scheme (from Paul James) at first divides the accumulated values by the number of hours (i.e., 3 or 6).
The best option for disaggregation, which was realised, is conservation within the interval under consideration plus the two adjacent ones.
Unfortunately, this leads to undesired temporal smoothing of the precipitation time series – maxima are damped and minima are raised.
It is even possible to produce non-zero precipitation in dry intervals bordering a precipitation period as shown in Fig. 1.
@@ -160,21 +160,14 @@ Disaggregation for the other flux fields
----------------------------------------------
The accumulated values for the other variables are first divided by the number of hours and
-then interpolated to the exact times using a bicubic interpolation which conserves the integrals of the fluxes within each timespan.
-Disaggregation is done for four adjacent time intervals (:math:`p_a, p_b, p_c, p_d`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+then disaggregates to the exact times and conserves the integrals of the fluxes within each timespan.
+Disaggregation is done for four adjacent time intervals (:math:`F_0, F_1, F_2, F_3`) which produces a new, disaggregated value that is the output at the central point of the four adjacent time intervals.
+This new point :math:`F` is used for linear interpolation of the complete timeseries afterwards.
.. math::
-
- p_a &= (a_3 - a_0 + 3. * (a_1 - a_2)) / 6. \\
- p_b &= (a_2 + a_0) / 2. - a_1 - 9. * p_a / 2. \\
- p_c &= a_1 - a_0 - 7. * p_a / 2. - 2. * p_b \\
- p_d &= a_0 - p_a / 4. - p_b / 3. - p_c / 2.
-
-This new point :math:`p` is used for linear interpolation of the complete timeseries afterwards.
-.. math::
- p = 8. * p_a + 4. * p_b + 2. * p_c + p_d
+ F = -\frac{1}{12}F_0 + \frac{7}{12}F_1 + \frac{7}{12}F_2 -\frac{1}{12}F_3
diff --git a/For_developers/Sphinx/Source/Documentation/input.rst b/For_developers/Sphinx/Source/Documentation/input.rst
index 0a0e11d66cd7bdffa7762fdb86eaafe2c59302de..64f33664d5560b05f990ed4e15ac6b68ff14ba23 100644
--- a/For_developers/Sphinx/Source/Documentation/input.rst
+++ b/For_developers/Sphinx/Source/Documentation/input.rst
@@ -35,8 +35,8 @@ Controlling
python3 Source/Python/install.py --help
python3 Source/Python/submit.py --help
- With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively.
- It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
+
+ With version 7.1, we provide also wrapper shell scripts setup_ and run_ which set the command-line parameters, do some checks, and execute the corresponing Python scripts ``install.py`` and ``submit.py``, respectively. It might be faster and easier for beginners if they are used. See :doc:`../quick_start` for information on how to use them.
``flex_extract`` also creates the Korn shell scripts :doc:`Input/compilejob` and :doc:`Input/jobscript` which will be sent to the ECMWF servers in the **remote mode** and the **gateway mode** for starting batch jobs.
diff --git a/For_developers/Sphinx/Source/Documentation/output.rst b/For_developers/Sphinx/Source/Documentation/output.rst
index 8a25f252022e118e62de2570426b24f7619e6899..4f6aebf29647f4d80251448a9799367e8c5c9b6d 100644
--- a/For_developers/Sphinx/Source/Documentation/output.rst
+++ b/For_developers/Sphinx/Source/Documentation/output.rst
@@ -80,10 +80,10 @@ Here is an example output which lists the meteorological fields in a single file
35 of 35 messages in CE00010800
-Output files for pure forecast
+Output files for long forecast
------------------------------
-``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in pure forecast mode is introduced:
+``Flex_extract`` is able to retrieve forecasts with a lead time of more than 23 hours. In order to avoid collisions of time steps names, a new scheme for filenames in long forecast mode is introduced:
.. code-block:: bash
@@ -193,22 +193,12 @@ Example output of a one-day retrieval of CERA-20C data:
4, 24, 40.0/-5.0/30.0/5.0, None, 20000108/to/20000108, 1, , 1.0/1.0, 1, SFC, EP, 000, 141.128/151.128/164.128/165.128/166.128/167.128/168.128/129.128/172.128/027.128/028.128/186.128/187.128/188.128/235.128/139.128/039.128/173.128, , 159, 00, ENDA, /mnt/nas/Anne/Interpolation/flexextract/flex_extract_v7.1/run/./workspace/CERA_testgrid_local_cds/ANOG__SL.20000108.23903.23904.grb, 00/03/06/09/12/15/18/21, AN
-VERTICAL.EC
------------
-
-This file contains information describing the vertical discretisation (model levels)
-in form of the ``A`` and ``B`` parameters which allow to calculate the actual pressure of a model level from the surface pressure.
-
Index file
----------
This file is called ``date_time_stepRange.idx``. It contains indices pointing to specific grib messages from one or more grib files. The messages are selected with a composition of grib message keywords.
-.. todo::
-
- #PS NEEDS MORE DESCRIPTION
-
Flux files
----------
diff --git a/For_developers/Sphinx/Source/Documentation/vertco.rst b/For_developers/Sphinx/Source/Documentation/vertco.rst
index fcc1d14faabe35e602a735b786c52f96c711c4d5..2196482626ea6e55fc6fa88f85375bff802d5ae2 100644
--- a/For_developers/Sphinx/Source/Documentation/vertco.rst
+++ b/For_developers/Sphinx/Source/Documentation/vertco.rst
@@ -6,8 +6,9 @@ Calculation of vertical velocity and preparation of output files
================================================================
Two methods are provided in ``flex_extract`` for the calculation of the vertical velocity for ``FLEXTRA``/``FLEXPART``:
- (i) from the horizontal wind field,
- (ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
+
+(i) from the horizontal wind field,
+(ii) from the MARS parameter 77, which is available for operational forecasts and analyses since September 2008 and for reanalysis datasets **ERA5** and **CERA-20C**, which contains the vertical velocity directly in the eta coordinate system of the ECMWF model.
Especially for high resolution data, use of the ``MARS`` parameter 77 is recommended,
since the computational cost (measured in ECMWF HPC units) is reduced by 90-95% at
@@ -30,6 +31,7 @@ following guidance can be given for choosing the right parameters:
* For very fine output grids (0.25 degree or finer), the full resolution T799 or even T1279 of the operational model is required (``RESOL=799``, ``SMOOTH=0``). The highest available resolution (and the calculation of vertical velocity on the Gaussian grid (``GAUSS=1``) is, however, rather demanding and feasible only for resolutions up to T799. Higher resolutions are achievable on the HPC. If data retrieval at T1279 needs to be performed on *ecgate*, the computation of the vertical velocity is feasible only on the lat/lon grid (``GAUSS=0``), which also yields very good results. Please read document v20_update_protocol.pdf-v60_update_protocol.pdf to see if the errors incurred are acceptable for the planned application.
* For lower resolution (often global) output grids, calculation of vertical velocities with lower than operational spectral resolution is recommended. For global grids the following settings appear optimal:
+
- For 1.0 degree grids: ``GAUSS=1``, ``RESOL=255``, ``SMOOTH=179``
- For 0.5 degree grids: ``GAUSS=1``, ``RESOL=399``, ``SMOOTH=359``
- Calculation on the lat/lon grid is not recommended for less than the operational (T1279) resolution.
diff --git a/For_developers/Sphinx/Source/Installation/gateway.rst b/For_developers/Sphinx/Source/Installation/gateway.rst
index 34764c8fe0bc88e8352d77daa5dd4fb57bda945a..06f50a949babcea30cdd67ff8318ac4003f64b7e 100644
--- a/For_developers/Sphinx/Source/Installation/gateway.rst
+++ b/For_developers/Sphinx/Source/Installation/gateway.rst
@@ -128,7 +128,7 @@ Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values:
| GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' |
| DESTINATION='<assoc_name>@genericSftp' | DESTINATION='<assoc_name>@genericSftp' |
| INSTALLDIR=None | INSTALLDIR=None |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| JOB_TEMPLATE='installscript.template' | JOB_TEMPLATE='installscript.template' |
| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
| ... | ... |
+----------------------------------------------+----------------------------------------------+
diff --git a/For_developers/Sphinx/Source/Installation/local.rst b/For_developers/Sphinx/Source/Installation/local.rst
index 5e20d27a5564d8b317b247d021d39c9a9ebe06a7..9f9c012b9299f66d5ce9b7c9315f4c5481c569ce 100644
--- a/For_developers/Sphinx/Source/Installation/local.rst
+++ b/For_developers/Sphinx/Source/Installation/local.rst
@@ -16,8 +16,8 @@ Local mode installation
.. _ecmwf-api-client: https://confluence.ecmwf.int/display/WEBAPI/ECMWF+Web+API+Home
.. _cdsapi: https://cds.climate.copernicus.eu/api-how-to
.. _genshi: https://genshi.edgewall.org/
-.. _eccodes for python: https://pypi.org/project/eccodes-python/
-.. _eccodes for conda: https://anaconda.org/conda-forge/eccodes
+.. _eccodes for python: https://pypi.org/project/eccodes/
+.. _eccodes for conda: https://anaconda.org/conda-forge/python-eccodes
.. _gfortran: https://gcc.gnu.org/wiki/GFortran
.. _fftw3: http://www.fftw.org
.. _eccodes: https://software.ecmwf.int/wiki/display/ECC
@@ -119,6 +119,7 @@ Testing the local environment
=============================
Check the availability of the python packages by typing ``python3`` in a terminal window and run the ``import`` commands in the python shell:
+
.. code-block:: python
# check in python3 console
@@ -286,12 +287,13 @@ with an editor and adapt the installation parameters in the section labelled wit
# THE USER HAS TO SPECIFY THESE PARAMETER
#
TARGET='local'
+ MAKEFILE=<name_of_your_makefile>
ECUID=None
ECGID=None
GATEWAY=None
DESTINATION=None
INSTALLDIR=None
- JOB_TEMPLATE='job.template'
+ JOB_TEMPLATE=''
CONTROLFILE='CONTROL_EA5'
...
diff --git a/For_developers/Sphinx/Source/Installation/remote.rst b/For_developers/Sphinx/Source/Installation/remote.rst
index 95f0c63eb8dde3542ad1fdc0eaf44f7341cf24e7..127e2b76b8a9142827ef35ac710a7024957425ad 100644
--- a/For_developers/Sphinx/Source/Installation/remote.rst
+++ b/For_developers/Sphinx/Source/Installation/remote.rst
@@ -137,7 +137,7 @@ Open ``setup.sh`` with your preferred editor (e.g., nano) and adapt the values:
| GATEWAY='<gatewayname>' | GATEWAY='<gatewayname>' |
| DESTINATION='<username>@genericSftp' | DESTINATION='<username>@genericSftp' |
| INSTALLDIR=None | INSTALLDIR='' |
-| JOB_TEMPLATE='job.template' | JOB_TEMPLATE='job.template' |
+| JOB_TEMPLATE='installscript.template' | JOB_TEMPLATE='installscript.template' |
| CONTROLFILE='CONTROL_EA5' | CONTROLFILE='CONTROL_EA5' |
| ... | ... |
+----------------------------------------------+----------------------------------------------+
@@ -152,8 +152,7 @@ with your own ones (look at any of your files with ``ls -l'' to see uid and gid)
Afterwards, type:
.. code-block:: bash
-
- module load python3
+
./setup.sh
to start the installation. You should see the following on standard output.
diff --git a/For_developers/Sphinx/Source/authors.rst b/For_developers/Sphinx/Source/authors.rst
index 3992e33b734ee403c6a50ce04457212659bafd1d..5636f8db342d26f1ea7338730b59405b0a0e0321 100644
--- a/For_developers/Sphinx/Source/authors.rst
+++ b/For_developers/Sphinx/Source/authors.rst
@@ -8,18 +8,24 @@ Developer Team
| University of Vienna
| Althanstraße 14 / UZA II
| 1090 Vienna, Austria
-| mail: anne.philipp [at] univie.ac.at
+| e-mail: anne.philipp [at] univie.ac.at
-
| Leopold Haimberger
| Department of Meteorology and Geophysics
| University of Vienna
| Althanstraße 14 / UZA II
| 1090 Vienna, Austria
-| mail: leopold.haimberger [at] univie.ac.at
+| e-mail: leopold.haimberger [at] univie.ac.at
-
+
+| Petra Seibert
+| Institute of Meteorology (BOKU-Met)
+| University of Natural Resources & Life Sciences (BOKU)
+| Gregor-Mendel-Str. 33
+| 1180 Wien, Austria
+| e-mail: petra.seibert ./at/. boku.ac.at
+
.. toctree::
:hidden:
:maxdepth: 2
diff --git a/For_developers/Sphinx/Source/changelog.rst b/For_developers/Sphinx/Source/changelog.rst
index b3f98e0544b60c1c70d0fc0804f71c9a1c80e60b..ed72fc18dfd338fbf6a73aad5bc1f5e11540545a 100644
--- a/For_developers/Sphinx/Source/changelog.rst
+++ b/For_developers/Sphinx/Source/changelog.rst
@@ -10,6 +10,25 @@ Changelog
.. _new algorithm: https://www.geosci-model-dev.net/11/2503/2018/
+.. _ref-v712:
+
+Release v7.1.2
+--------------
+
+Changes
+#########
+ * changed naming of template files
+ * separate loading of Python3 module in remote mode is no longer necessary
+ * updated module versions for ECMWF servers
+ * changed names of working directories on ECMWF servers
+ * select makefile automatically regarding application mode if it was not set in ``setup.sh``
+ * updated online documentation
+ * converted most important Fortran code documentation from German to English
+ * deactivate writing of VERTICAL.EC file by Fortran code
+ * adapt and improve Fortran regression test scripts
+ * remove jasper lib from Fortran makefiles
+
+
.. _ref-v711:
Release v7.1.1
diff --git a/For_developers/Sphinx/Source/conf.py b/For_developers/Sphinx/Source/conf.py
index 2a077966650a7fd3eb51d737442a437e62a66a4c..7110349c3558443e754ed5685156f93e85480624 100644
--- a/For_developers/Sphinx/Source/conf.py
+++ b/For_developers/Sphinx/Source/conf.py
@@ -31,9 +31,9 @@ copyright = u'2020, Anne Philipp, Leopold Haimberger and Petra Seibert'
author = u'Anne Philipp, Leopold Haimberger and Petra Seibert'
# The short X.Y version
-version = u'7.1.1'
+version = u'7.1.2'
# The full version, including alpha/beta/rc tags
-release = u'7.1.1'
+release = u'7.1.2'
# -- General configuration ---------------------------------------------------
diff --git a/For_developers/Sphinx/Source/installation.rst b/For_developers/Sphinx/Source/installation.rst
index 6a0c8a56649245a1ead5dc7f1e77771c84875207..97c5cb873c8d97a2fbe859b8759f2e3e27c8d76a 100644
--- a/For_developers/Sphinx/Source/installation.rst
+++ b/For_developers/Sphinx/Source/installation.rst
@@ -139,7 +139,7 @@ The software required to run ``flex_extract`` depends on the :doc:`Documentation
Generally speaking, ``flex_extract`` requires `Python 3`_ and Fortran together with certain modules / libraries.
We tested ``flex_extract`` with the Python3 package from the the GNU/Linux distribution and Anaconda Python. The required Python3 modules should prefarably be installed as distribution packages, or alternatively using Python's own package manager ``pip`` (this may mess up some aspects of your python installation, especially if you use ``pip`` as root. Think about using virtual environments.).
-Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system)``rpm -q <package_name>``. For example:
+Before installing the system packages check the availability with (Debian-based system) ``dpkg -s <package-name> | grep Status`` or (Redhat-based system) ``rpm -q <package_name>``. For example:
.. code-block:: sh
@@ -197,14 +197,14 @@ Fortran program test
To check whether the Fortran program ``calc_etadot`` has been compiled and runs properly, it can be applied to a prepared minimal dataset.
-For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Convert/`` directory and execute the Fortran program.
+For this, go from the ``flex_extract`` root directory to the ``Testing/Installation/Calc_etadot/`` directory and execute the Fortran program.
.. note::
Remember that you might have to log in at the ECMWF server if you used the installation for the **remote** or **gateway** mode. There you find the ``flex_extract`` root directory in your ``$HOME`` directory.
.. code-block:: bash
- cd Testing/Installation/Convert
+ cd Testing/Installation/Calc_etadot
# execute the Fortran progam without arguments
../../../Source/Fortran/calc_etadot
diff --git a/For_developers/Sphinx/Source/quick_start.rst b/For_developers/Sphinx/Source/quick_start.rst
index baa36ca5f5c0014af22356a02c4807ad43796d02..381644220d5b9771b1e5ca93e463283a5816a7e0 100644
--- a/For_developers/Sphinx/Source/quick_start.rst
+++ b/For_developers/Sphinx/Source/quick_start.rst
@@ -64,7 +64,6 @@ Remote mode
.. code-block:: bash
# On ECMWF server
- [<ecuid>@ecgb11 ~]$ module load python3
[<ecuid>@ecgb11 ~]$ cd flex_extract_vX.X/Run
@@ -103,7 +102,7 @@ Therefore open the ``run.sh`` file and modify the parameter block marked in the
INPUTDIR=None
OUTPUTDIR=None
PP_ID=None
- JOB_TEMPLATE='job.temp'
+ JOB_TEMPLATE='jobscript.template'
CONTROLFILE='CONTROL_CERA'
DEBUG=0
REQUEST=2
@@ -137,12 +136,12 @@ In case the job fails you will receive an email with the subject ``ERROR!`` and
cd $SCRATCH
ls -rthl
-The last command lists the most recent logs and temporary retrieval directories (usually ``pythonXXXXX``, where XXXXX is the process id). Under ``pythonXXXXX`` a copy of the ``CONTROL`` file is stored under the name ``CONTROL``, the protocol is stored in the file ``prot`` and the temporary files as well as the resulting files are stored in a directory ``work``. The original name of the ``CONTROL`` file is stored in this new file under parameter ``controlfile``.
+The last command lists the most recent logs and temporary retrieval directories (usually ``extractXXXXX``, where XXXXX is the process id). Under ``extractXXXXX`` a copy of the ``CONTROL`` file is stored under the name ``CONTROL``, the protocol is stored in the file ``prot`` and the temporary files as well as the resulting files are stored in a directory ``work``. The original name of the ``CONTROL`` file is stored in this new file under parameter ``controlfile``.
.. code-block:: bash
:caption: "Example structure of ``flex_extract`` output directory on ECMWF servers."
- pythonXXXXX
+ extractXXXXX
├── CONTROL
├── prot
├── work
@@ -357,8 +356,8 @@ These files defines the minimum number of parameters necessary to retrieve a dai
Please see `Information about MARS retrievement <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Retrievalefficiency>`_ for hints about retrieval efficiency and troubleshooting.
-Pure forecast
- It is possible to retrieve pure forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
+Long forecast
+ It is possible to retrieve long forecasts exceeding one day. The forecast period available depends on the date and forecast field type. Please use MARS catalogue to check the availability. Below are some examples for 36 hour forecasts of *Forecast (FC)*, *Control forecast (CF)* and *Calibration/Validation forecast (CV)*.
The *CV* field type was only available 3-hourly from 2006 up to 2016. It is recommended to use the *CF* type since this is available from 1992 (3-hourly) on up to today (1-hourly). *CV* and *CF* field types belong to the *Ensemble prediction system (ENFO)* which currently works with 50 ensemble members.
Please be aware that in this case it is necessary to set the type for flux fields explicitly, otherwise a default value might be selected, different from what you expect!
@@ -417,10 +416,6 @@ Field type and time
The time declaration for analysis (AN) fields uses the times of the specific analysis while the (forecast time) step has to be ``0``.
The forecast field types (e.g. FC, CF, CV, PF) need to declare a combination of (forescast start) time and the (forecast) step. Together they define the actual time. It is important to know the forecast starting times for the dataset to be retrieved, since they are different. In general, it is sufficient to give information for the exact time steps, but it is also possible to have more time step combinations of ``TYPE``, ``TIME`` and ``STEP`` because the temporal (hourly) resolution with the ``DTIME`` parameter will select the correct combinations.
- .. todo::
-
- #PS needs to be rephrased
-
.. code-block:: bash
:caption: Example of a setting for the field types and temporal resolution. It will retrieve 3-hourly fields, with analyses at 00 and 12 UTC and the corresponding forecasts inbetween.
@@ -450,9 +445,6 @@ Grid resolution and domain
The grid and domain parameters depends on each other. ``grid`` refers to the grid resolution. It can be given as decimal values (e.g., ``1.`` meaning 1.0°), or as in previous versions of flex_extract, as integer values refering to 1/1000 degrees (e.g., ``1000`` means also 1°). The code applies common sense to determine what format is to be assumed.
After selecting grid, the ``domain`` has to be defined. The extension in longitude or latitude direction must be an integer multiple of ``grid``.
- .. todo::
-
- #PS shouldn't we explain how to define a domain??
The horizontal resolution for spectral fields is set by the parameter ``RESOL``. For information about how to select an appropriate value please read the explanation of the MARS keyword RESOL as found `in this entry of the ECMWF on-line documentation <https://confluence.ecmwf.int/display/UDOC/Post-processing+keywords#Post-processingkeywords-resol>`_ and `this table (also ECMWF documentation) <https://confluence.ecmwf.int/display/UDOC/Retrieve#Retrieve-Truncationbeforeinterpolation>`_.
@@ -469,12 +461,8 @@ Grid resolution and domain
Flux data
- Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields, if provided. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP.
-
- .. todo::
-
- #PS for which application would this be typical?
-
+ Flux fields are always forecast fields and contain values of the fluxes accumulated since the start of the respective forecast. As certain re-analysis dataset cover all time steps with analysis fields, it was necessary to define a new parameter set for the definition of the flux fields. The following parameters are used specifically for flux fields. ``ACCTYPE`` is the field type (must be a type of forecast), ``ACCTIME`` the forecast starting time, and ``ACCMAXSTEP`` the maximum forecast step;``DTIME`` the temporal resolution. ACCTYPE is assumed to be the same during the whole period given by ACCTIME and ACCMAXSTEP. These values will be set automatically if not provided in a ``CONTROL`` file.
+
.. code-block:: bash
:caption: Example setting for the definition of flux fields.
diff --git a/For_developers/SubmitParameters.xls b/For_developers/SubmitParameters.xls
index cdabd624d54618daf8c8608e24864cfd4352f33f..f73e63b16b4570d110ef24a30c508a27d8666fd0 100644
Binary files a/For_developers/SubmitParameters.xls and b/For_developers/SubmitParameters.xls differ