diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e19c3efcab5c80a82c473c8a56c22efd12253d8a..30570213afb7dcfc318f9e65944416b1f82cd367 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -2,7 +2,7 @@ stages:
- build
- test
- compare
- # - container
+ - container
default:
image:
@@ -189,6 +189,36 @@ documentation:
- cd ./documentation && mkdocs build -c --verbose
- sshpass -p "$WOLKE_PASSWORD" rsync -autv --delete -e "ssh -o StrictHostKeyChecking=no" /tmp/cr-site/* "$WOLKE_USER@wolke.img.univie.ac.at:/var/www/flexpart/docs"
-# base:
-# stage: container
-# image:
\ No newline at end of file
+base:
+ stage: container
+ image: quay.io/podman/stable
+ when: manual
+ script:
+ - podman build -t "harbor.wolke.img.univie.ac.at/flexpart/rockylinux9:latest" -f ./tests/Dockerfile
+ - podman push "harbor.wolke.img.univie.ac.at/flexpart/rockylinux9:latest"
+
+post:
+ stage: container
+ image: quay.io/podman/stable
+ when: manual
+ script:
+ - podman build -t "harbor.wolke.img.univie.ac.at/flexpart/postprocessing:py39" -f ./tests/Dockerfile.python
+ - podman push "harbor.wolke.img.univie.ac.at/flexpart/postprocessing:py39"
+
+flexpart:
+ stage: container
+ image: quay.io/podman/stable
+ when: manual
+ script:
+ - podman build -t "harbor.wolke.img.univie.ac.at/flexpart/flexpartv11-${CI_COMMIT_REF_NAME}:${CI_COMMIT_SHA:0:8}" --build-arg COMMIT=${CI_COMMIT_SHA:0:8} -f ./containers/Dockerfile ../
+ - podman push "harbor.wolke.img.univie.ac.at/flexpart/flexpartv11-${CI_COMMIT_REF_NAME}:${CI_COMMIT_SHA:0:8}"
+
+flexpartv10:
+ stage: container
+ image: quay.io/podman/stable
+ when: manual
+ script:
+ - podman build -t "harbor.wolke.img.univie.ac.at/flexpart/flexpartv10.4:latest" -f ./containers/Dockerfile.v10.4 ../
+ - podman push "harbor.wolke.img.univie.ac.at/flexpart/flexpartv10.4:latest"
+
+# add a build for apptainer ?
\ No newline at end of file
diff --git a/AVAILABLE b/AVAILABLE
index 17640db9723700f0ab006629ff15ac0fe752f0ab..d237605c916b106b4c7dd9c670680efebeb1647b 100644
--- a/AVAILABLE
+++ b/AVAILABLE
@@ -1,27 +1,5 @@
XXXXXX EMPTY LINES XXXXXXXXX
XXXXXX EMPTY LINES XXXXXXXX
YYYYMMDD HHMMSS name of the file(up to 80 characters)
-20120101 000000 EA12010100 ON DISK
-20120101 010000 EA12010101 ON DISK
-20120101 020000 EA12010102 ON DISK
-20120101 030000 EA12010103 ON DISK
-20120101 040000 EA12010104 ON DISK
-20120101 050000 EA12010105 ON DISK
-20120101 060000 EA12010106 ON DISK
-20120101 070000 EA12010107 ON DISK
-20120101 080000 EA12010108 ON DISK
-20120101 090000 EA12010109 ON DISK
-20120101 100000 EA12010110 ON DISK
-20120101 110000 EA12010111 ON DISK
-20120101 120000 EA12010112 ON DISK
-20120101 130000 EA12010113 ON DISK
-20120101 140000 EA12010114 ON DISK
-20120101 150000 EA12010115 ON DISK
-20120101 160000 EA12010116 ON DISK
-20120101 170000 EA12010117 ON DISK
-20120101 180000 EA12010118 ON DISK
-20120101 190000 EA12010119 ON DISK
-20120101 200000 EA12010120 ON DISK
-20120101 210000 EA12010121 ON DISK
-20120101 220000 EA12010122 ON DISK
-20120101 230000 EA12010123 ON DISK
+20090101 000000 EC2009010100 ON DISK
+20090101 060000 EC2009010106 ON DISK
diff --git a/Dockerfile_flexpart b/Dockerfile_flexpart
deleted file mode 100644
index b21156010cdb6a06faa2557fcb59f0c27afcfa87..0000000000000000000000000000000000000000
--- a/Dockerfile_flexpart
+++ /dev/null
@@ -1,37 +0,0 @@
-#
-# Dockerfile for CI and Flexpart container images
-# Options:
-# - COMMIT = ... (use git log --pretty=format:'%h %D (%s %at)' -n 1)
-# with this option Flexpart is build inside the container
-# Build Examples:
-# - podman build -t harbor.wolke.img.univie.ac.at/flexpart/flexpartv11:$(git rev-parse --abbrev-ref HEAD) -f Dockerfile_flexpart --build-arg COMMIT="$(git log --pretty=format:'%h %D %ad' -n 1)"
-#
-#
-# Build image with Flexpart inside
-#
-#FROM harbor.wolke.img.univie.ac.at/flexpart/almalinux8:latest
-FROM harbor.wolke.img.univie.ac.at/flexpart/rockylinux9:latest
-ARG COMMIT=0
-ENV COMMIT=$COMMIT
-COPY ./src /src
-COPY ./tests/default_options /options
-
-# since the new data set is larger, we download the data for the container
-RUN wget -P /inputs "https://webdata.wolke.img.univie.ac.at/flexpart/*"
-# COPY ./tests/default_winds /inputs
-
-COPY ./entrypoint.sh /entrypoint.sh
-WORKDIR /src
-#
-# compile using a standardized
-# need to fix march to x86_64_v3 , remove mtune
-# here generic means core_avx2
-RUN make -f makefile_gfortran eta=no arch=generic \
- && make -f makefile_gfortran arch=generic \
- && mkdir -p /output \
- && echo -e "/options/\n/output/\n/inputs/\n/inputs/AVAILABLE" > /pathnames
-# In the Dockerfile, the ENTRYPOINT command defines the executable,
-# while CMD sets the default parameter.
-# so here our entrypoint run script and default FLEXPART_ETA or FLEXPART
-ENTRYPOINT ["/entrypoint.sh"]
-CMD ["FLEXPART_ETA"]
diff --git a/Dockerfile_jasper b/Dockerfile_jasper
deleted file mode 100644
index 46396ba4d6007076b547ad57add0fd50ea92bcb8..0000000000000000000000000000000000000000
--- a/Dockerfile_jasper
+++ /dev/null
@@ -1,30 +0,0 @@
-#
-# Dockerfile for CI and Flexpart container images
-# Build Examples:
-# - podman build -t harbor.wolke.img.univie.ac.at/flexpart/almalinux8:jasper -f Dockerfile
-#
-FROM almalinux:8-minimal
-#
-# Build development image (with/without jasper)
-# jasper was used in FP 10.4 (eccodes, emoslib)
-#
-RUN microdnf install -y epel-release && \
- microdnf install -y --enablerepo=powertools make netcdf-fortran-devel.x86_64 netcdf.x86_64 cmake tar gcc-c++ perl jasper-libs.x86_64 && \
- microdnf clean all -y
-
-#
-# Download ECCODES Version
-# note 2.30.0 has an issue!!!
-#
-RUN curl https://confluence.ecmwf.int/download/attachments/45757960/eccodes-2.31.0-Source.tar.gz | tar xz
-RUN mkdir build && \
- cd build && \
- cmake -DENABLE_ECCODES_OMP_THREADS=ON ../eccodes-*/ && \
- make -j8 && \
- make install
-#
-# set environment variables
-#
-ENV FC=gfortran
-ENV LIBRARY_PATH=/usr/lib64:/usr/local/lib64
-ENV CPATH=/usr/include:/usr/local/include:/usr/lib64/gfortran/modules
diff --git a/README.md b/README.md
index 6c26f5d235c9e4a81c750c018ca6cff69e591062..a50b282f2c0aba1e41cf64259fcafe7a2fc55aa5 100644
--- a/README.md
+++ b/README.md
@@ -12,409 +12,23 @@ Other references:
* This repository contains versions of the Lagrangian model FLEXPART
* Development versions
-* Issues on the FLEXPART model
+* Issues on the FLEXPART model, [tickets](./-/issues)/[mail](mailto:flexpart-support.img-wien@univie.ac.at)
* Feature requests for future versions
## Getting started with Flexpart
-The model is written in Fortran. It needs to be compiled for the architecture that runs it.
-
-
-### 1.Configuration
-
- The Makefiles e.g. `src/makefile_gfortran` can use environmental variables:
- - `CPATH` for include directories
- - `LIBRARY_PATH` for libraries
-
- This is commonly used on HPC systems. e.g. JET and VSC. These paths will be added via `rpath` so statically linked.
- Otherwise edit the makefile with the paths to libraries and include files.
-
-**Required Dependencies:**
-
- * [ecCodes](https://confluence.ecmwf.int/display/ECC) from ECMWF (Jasper is not a requirement).
- * [NetCDF](https://www.unidata.ucar.edu/software/netcdf/) (optional) from UCAR
- * Fortran Compiler with [Fortran 2008](https://fortranwiki.org/fortran/show/Fortran+2008+status) standard, e.g. GCC compiler `8+` or INTEL `19+` or INTEL-ONEAPI
- * make utils
-
-### 2.Compilation
-
-Clone the git repository or download one of the [releases](https://gitlab.phaidra.org/flexpart/flexpart/-/releases)
-
-```bash
-# clone the repository to your directory or download one of our releases
-git clone https://gitlab.phaidra.org/flexpart/flexpart.git
-# change to the SRC directory
-cd flexpart/src
-# Remember to configure your libraries in the makefile or environmental variables
-# use for example the GCC makefile
-make -f makefile_gfortran
-# this will create the FLEXPART executable
-file ./FLEXPART
-# Check its dependencies:
-ldd ./FLEXPART
-```
-Now you are almost ready to run.
-
-### 3.Deployment instructions
-
- FLEXPART is a standalone executable
- The necessary ECMWF wind fields can be obtained testing flex_ecmwf
- The AVAILABLE file works with the default ERA 5 retrieved winds
- In the winds are available in flex_ecmwf/work it should suffice to execute
- `./src/FLEXPART` in the main directory
-
-### Container version
-
-since version 11, FLEXPART is also available as a container. There is a Dockerfile and some instructions on how to build the container from scratch or you can download the container from our [registry](https://harbor.wolke.img.univie.ac.at) using for example podman/docker or singularity/apptainer:
-
-Specifications:
-- compiled using `march=core-avx2`, compatible with CPUs above AVX2 (since Haswell or Zen)
-- ecCodes
-
-
-```sh
-# registry download, replace podman to docker or vice versa
-podman pull harbor.wolke.img.univie.ac.at/flexpart/flexpartv11:master
-# using singularity/apptainer for running FLEXPART
-# there might be some warnings about EPERM (can be ignored)
-apptainer pull flexpart.sif docker://harbor.wolke.img.univie.ac.at/flexpart/flexpartv11:master
-```
-
-running it using podman/docker or singularity/apptainer:
-
-```sh
-# simple run the container with default settings
-podman run harbor.wolke.img.univie.ac.at/flexpart/flexpartv11:master
-# running the container requires a writable output directory
-# mounting the local directory to /output inside the container
-apptainer run -B .:/output flexpart.sif
-```
-
-
-
-<details>
-<summary>podman/docker flexpart run log</summary>
-<pre><code class="shell">
-Welcome, running FLEXPART
-Using defaults (/pathnames)
-/options/
-/output/
-/inputs/
-/inputs/AVAILABLE
-Mount volumes to change inputs
-Git: c5bdd94 HEAD -> master, origin/master, origin/HEAD Tue Nov 21 16:15:27 2023 +0100
-EXECUTING FLEXPART
-trying to execute: /src/FLEXPART_ETA
-Executing: /src/FLEXPART_ETA
- Welcome to FLEXPART Version 11
- Git: undefined
- FLEXPART is free software released under the GNU General Public License.
- FLEXPART is running with ETA coordinates.
- ----------------
- INFORMATION: SUBGRIDSCALE TERRAIN EFFECT IS
- NOT PARAMETERIZED DURING THIS SIMULATION.
- ----------------
-
- *********** WARNING **********************************
- * FLEXPART running in parallel mode *
- * Number of uncertainty classes in *
- * set to number of threads: 1 *
- * All other computations are done with 8 threads. *
- *******************************************************
-
- FLEXPART WARNING: TIME DIFFERENCE BETWEEN TWO
- WIND FIELDS IS BIG. THIS MAY CAUSE A DEGRADATION
- OF SIMULATION QUALITY.
- ECMWF metdata detected
- NXSHIFT is set to 0
- grid dim: 181 91 92 92 91 92
- Vertical levels in ECMWF data: 92 92
-
- Mother domain:
- Longitude range: -178.00000 to 182.00000 Grid distance: 2.00000
- Latitude range : -90.00000 to 90.00000 Grid distance: 2.00000
-
- Number of receptors: 2
- Releasepoints : 1
- reading SPECIES 24
- Particle shape SPHERE for particle 24
-
- SPECIES: 24 AIRTRACER (GAS)
- Wet removal for gases is turned: OFF
- Dry deposition for gases is turned: OFF
- Below-cloud scavenging: OFF
- In-cloud scavenging: OFF
- Particles released (numpartmax): 10000
- Total mass released: 1.0000000E+00
- Allocating fields for global output (x,y): 85 65
- Concentrations are calculated using kernel
- WARNING: turbulence switched off.
- Simulated 0.0 hours ( 0 s), 0 particles
- Time: 0 seconds. Total spawned: 0 alive: 0 terminated: 0
- Allocating 10000 particles 0 0 0
- Finished allocation
- Time: 900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 1800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 2700 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 3600 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- 3600 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
- Time: 4500 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 5400 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 6300 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 7200 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- 7200 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
- Time: 8100 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 9000 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 9900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 10800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- 10800 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
- Read wind fields: 0.609375000 seconds
- Timemanager: 1.17187500 seconds,first timestep: 1.09375000 seconds
- Write particle files: 4.68750000E-02 seconds
- Total running time: 1.81250000 seconds
- tps,io,tot: 1.95312500E-02 0.131249994 1.81250000
- CONGRATULATIONS: YOU HAVE SUCCESSFULLY COMPLETED A FLEXPART MODEL RUN!
-FINISHED
-</code></pre>
-</details>
-
-
-<details>
-<summary>singularity/apptainer flexpart run log</summary>
-<pre>
-<code class="language-shell">
-INFO: gocryptfs not found, will not be able to use gocryptfs
-Welcome, running FLEXPART
-Using defaults (/pathnames)
-/options/
-/output/
-/inputs/
-/inputs/AVAILABLE
-Mount volumes to change inputs
-Git: c5bdd94 HEAD -> master, origin/master, origin/HEAD Tue Nov 21 16:15:27 2023 +0100
-EXECUTING FLEXPART
-trying to execute: /src/FLEXPART_ETA
-Executing: /src/FLEXPART_ETA
- Welcome to FLEXPART Version 11
- Git: undefined
- FLEXPART is free software released under the GNU General Public License.
- FLEXPART is running with ETA coordinates.
- ----------------
- INFORMATION: SUBGRIDSCALE TERRAIN EFFECT IS
- NOT PARAMETERIZED DURING THIS SIMULATION.
- ----------------
-
- *********** WARNING **********************************
- * FLEXPART running in parallel mode *
- * Number of uncertainty classes in *
- * set to number of threads: 1 *
- * All other computations are done with 8 threads. *
- *******************************************************
-
- FLEXPART WARNING: TIME DIFFERENCE BETWEEN TWO
- WIND FIELDS IS BIG. THIS MAY CAUSE A DEGRADATION
- OF SIMULATION QUALITY.
- ECMWF metdata detected
- NXSHIFT is set to 0
- grid dim: 181 91 92 92 91 92
- Vertical levels in ECMWF data: 92 92
-
- Mother domain:
- Longitude range: -178.00000 to 182.00000 Grid distance: 2.00000
- Latitude range : -90.00000 to 90.00000 Grid distance: 2.00000
-
- Number of receptors: 2
- Releasepoints : 1
- reading SPECIES 24
- Particle shape SPHERE for particle 24
-
- SPECIES: 24 AIRTRACER (GAS)
- Wet removal for gases is turned: OFF
- Dry deposition for gases is turned: OFF
- Below-cloud scavenging: OFF
- In-cloud scavenging: OFF
- Particles released (numpartmax): 10000
- Total mass released: 1.0000000E+00
- Allocating fields for global output (x,y): 85 65
- Concentrations are calculated using kernel
- WARNING: turbulence switched off.
- Simulated 0.0 hours ( 0 s), 0 particles
- Time: 0 seconds. Total spawned: 0 alive: 0 terminated: 0
- Allocating 10000 particles 0 0 0
- Finished allocation
- Time: 900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 1800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 2700 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 3600 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- 3600 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
- Time: 4500 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 5400 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 6300 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 7200 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- 7200 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
- Time: 8100 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 9000 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 9900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- Time: 10800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
- 10800 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
- Read wind fields: 0.703125000 seconds
- Timemanager: 1.25000000 seconds,first timestep: 1.15625000 seconds
- Write particle files: 1.56250000E-02 seconds
- Total running time: 2.00000000 seconds
- tps,io,tot: 2.34375000E-02 0.143749997 2.00000000
- CONGRATULATIONS: YOU HAVE SUCCESSFULLY COMPLETED A FLEXPART MODEL RUN!
-FINISHED
-</code></pre>
-</details>
-
-<details>
-<summary>ncdump of default run output</summary>
-<pre><code class="language-shell">
-# check the output
-ncdump -h grid_conc_20090101000000.nc
-netcdf grid_conc_20090101000000 {
-dimensions:
- time = UNLIMITED ; // (3 currently)
- longitude = 85 ;
- latitude = 65 ;
- height = 4 ;
- numspec = 1 ;
- pointspec = 1 ;
- nageclass = 1 ;
- nchar = 45 ;
- ncharrec = 16 ;
- numpoint = 1 ;
- receptor = UNLIMITED ; // (2 currently)
-variables:
- int time(time) ;
- time:units = "seconds since 2009-01-01 00:00" ;
- time:calendar = "proleptic_gregorian" ;
- float longitude(longitude) ;
- longitude:long_name = "longitude in degree east" ;
- longitude:axis = "Lon" ;
- longitude:units = "degrees_east" ;
- longitude:standard_name = "grid_longitude" ;
- longitude:description = "grid cell centers" ;
- float latitude(latitude) ;
- latitude:long_name = "latitude in degree north" ;
- latitude:axis = "Lat" ;
- latitude:units = "degrees_north" ;
- latitude:standard_name = "grid_latitude" ;
- latitude:description = "grid cell centers" ;
- float height(height) ;
- height:units = "meters" ;
- height:positive = "up" ;
- height:standard_name = "height" ;
- height:long_name = "height above ground" ;
- char RELCOM(numpoint, nchar) ;
- RELCOM:long_name = "release point name" ;
- float RELLNG1(numpoint) ;
- RELLNG1:units = "degrees_east" ;
- RELLNG1:long_name = "release longitude lower left corner" ;
- float RELLNG2(numpoint) ;
- RELLNG2:units = "degrees_east" ;
- RELLNG2:long_name = "release longitude upper right corner" ;
- float RELLAT1(numpoint) ;
- RELLAT1:units = "degrees_north" ;
- RELLAT1:long_name = "release latitude lower left corner" ;
- float RELLAT2(numpoint) ;
- RELLAT2:units = "degrees_north" ;
- RELLAT2:long_name = "release latitude upper right corner" ;
- float RELZZ1(numpoint) ;
- RELZZ1:units = "meters" ;
- RELZZ1:long_name = "release height bottom" ;
- float RELZZ2(numpoint) ;
- RELZZ2:units = "meters" ;
- RELZZ2:long_name = "release height top" ;
- int RELKINDZ(numpoint) ;
- RELKINDZ:long_name = "release kind" ;
- int RELSTART(numpoint) ;
- RELSTART:units = "seconds" ;
- RELSTART:long_name = "release start relative to simulation start" ;
- int RELEND(numpoint) ;
- RELEND:units = "seconds" ;
- RELEND:long_name = "release end relative to simulation start" ;
- int RELPART(numpoint) ;
- RELPART:long_name = "number of release particles" ;
- float RELXMASS(numspec, numpoint) ;
- RELXMASS:long_name = "total release particle mass" ;
- int LAGE(nageclass) ;
- LAGE:units = "seconds" ;
- LAGE:long_name = "age class" ;
- int ORO(latitude, longitude) ;
- ORO:standard_name = "surface altitude" ;
- ORO:long_name = "outgrid surface altitude" ;
- ORO:units = "m" ;
- char receptor(receptor, ncharrec) ;
- receptor:long_name = "receptor name" ;
- float spec001_mr(nageclass, pointspec, time, height, latitude, longitude) ;
- spec001_mr:units = "ng m-3" ;
- spec001_mr:long_name = "AIRTRACER" ;
- spec001_mr:decay = -0.07001485f ;
- spec001_mr:weightmolar = 29.f ;
- spec001_mr:ohcconst = -9.e-10f ;
- spec001_mr:ohdconst = -9.9f ;
- spec001_mr:vsetaver = 0.f ;
- float receptor_conc001(receptor, time) ;
- receptor_conc001:units = "ng m-3" ;
- receptor_conc001:_FillValue = -1.f ;
- receptor_conc001:positive = "up" ;
- receptor_conc001:standard_name = "receptor_conc" ;
- receptor_conc001:long_name = "receptor_concentration" ;
-
-// global attributes:
- :Conventions = "CF-1.6" ;
- :title = "FLEXPART model output" ;
- :git = "undefined" ;
- :source = "Version 11 model output" ;
- :history = "2023-11-21 16:22 +0100 created by mblaschek on NB513" ;
- :references = "Stohl et al., Atmos. Chem. Phys., 2005, doi:10.5194/acp-5-2461-200" ;
- :outlon0 = -25.f ;
- :outlat0 = 10.f ;
- :dxout = 1.f ;
- :dyout = 1.f ;
- :ldirect = 1 ;
- :ibdate = "20090101" ;
- :ibtime = "000000" ;
- :iedate = "20090101" ;
- :ietime = "030000" ;
- :loutstep = 3600 ;
- :loutaver = 3600 ;
- :loutsample = 900 ;
- :loutrestart = -1 ;
- :lsynctime = 900 ;
- :ctl = -0.2f ;
- :ifine = 1 ;
- :iout = 1 ;
- :ipout = 0 ;
- :lsubgrid = 0 ;
- :lconvection = 0 ;
- :lagespectra = 0 ;
- :ipin = 0 ;
- :ioutputforeachrelease = 0 ;
- :iflux = 0 ;
- :mdomainfill = 0 ;
- :ind_source = 1 ;
- :ind_receptor = 1 ;
- :mquasilag = 0 ;
- :nested_output = 0 ;
- :sfc_only = 0 ;
- :linit_cond = 0 ;
-}
-</code>
-</pre>
-</details>
+The model is written in Fortran. It needs to be compiled for the architecture that runs it. Please have a look at the instructions on building FLEXPART available [here](./documentation/docs/building.md) or [online](https://flexpart.img.univie.ac.at/docs). There is also a containerized version of FLEXPART available.
### Contribution guidelines
* The version contributed should compile on a reference version of the system and compiler.
- - `FLEXPART 10.4` used as reference gfortran 5.4 on Ubuntu 16.04
- - `FLEXPART 11` uses as reference gfortran 8.5.0 on AlmaLinux 8/RockyLinux 8 or gfortran 11.4.1 on RockyLinux 9
+ - `FLEXPART 10.4` used as a reference gfortran 5.4 on Ubuntu 16.04
+ - `FLEXPART 11` uses as a reference gfortran 8.5.0 on AlmaLinux 8/RockyLinux 8 or gfortran 11.4.1 on RockyLinux 9
* Code contribution including new features and bug fixes should be complemented with appropriate tests
An essential test consists of a set of input files and directories that allow FLEXPART to run.
A test can be accompanied by output files for verification
* Code review
* report issues via mail to [support](mailto:flexpart-support.img-wien@univie.ac.at)
-* become an active developer and request a user account.
\ No newline at end of file
+* become an active developer and request a user account on gitlab.
\ No newline at end of file
diff --git a/containers/Dockerfile b/containers/Dockerfile
new file mode 100644
index 0000000000000000000000000000000000000000..0d9a164f53370a47555732d4becc90164c43653b
--- /dev/null
+++ b/containers/Dockerfile
@@ -0,0 +1,48 @@
+FROM rockylinux:9-minimal
+RUN microdnf install -y epel-release && \
+ microdnf install -y --enablerepo=crb make netcdf-fortran-devel.x86_64 netcdf.x86_64 eccodes eccodes-devel cmake tar gcc-c++ perl git wget && \
+ microdnf clean all -y && \
+ rm -rf /var/cache/yum
+#
+# Download ECCODES Version
+# note 2.30.0 has an issue!!!
+# ENV ECCODES=2.31.0
+# RUN curl https://confluence.ecmwf.int/download/attachments/45757960/eccodes-${ECCODES}-Source.tar.gz | tar xz
+# RUN mkdir build && \
+# cd build && \
+# cmake -DENABLE_ECCODES_OMP_THREADS=ON ../eccodes-*/ && \
+# make -j8 && \
+# make install
+#
+# set environment variables
+#
+ENV FC=gfortran
+ENV LIBRARY_PATH=/usr/lib64:/usr/local/lib64
+ENV CPATH=/usr/include:/usr/local/include:/usr/lib64/gfortran/modules
+# cmd Arguments for COMMIT ID/tag
+ARG COMMIT=0
+ENV COMMIT=$COMMIT
+COPY ./src /src
+# since the new data set is larger, we download the data for the container
+# EC 2009 01 01 00 - 06
+RUN wget -r -np -nd -A 'EC*' -P /inputs "https://webdata.wolke.img.univie.ac.at/flexpart/"
+WORKDIR /src
+#
+# compile using a standardized
+# need to fix march to x86_64_v3 , remove mtune
+# here generic means core_avx2
+RUN make -f makefile_gfortran eta=no arch=generic \
+ && make -f makefile_gfortran arch=generic \
+ && mkdir -p /output \
+ && echo -e "/options/\n/output/\n/inputs/\n/inputs/AVAILABLE" > /pathnames
+
+COPY ./AVAILABLE /inputs/AVAILABLE
+# Entrypoint script (user tips)
+COPY ./containers/entrypoint.sh /entrypoint.sh
+COPY ./tests/default_options /options
+# In the Dockerfile, the ENTRYPOINT command defines the executable,
+# while CMD sets the default parameter.
+# so here our entrypoint run script and default FLEXPART_ETA or FLEXPART
+ENTRYPOINT ["/entrypoint.sh"]
+# Could be FLEXPART_ETA pathnames_custom
+CMD ["FLEXPART_ETA"]
diff --git a/containers/Dockerfile.v10.4 b/containers/Dockerfile.v10.4
new file mode 100644
index 0000000000000000000000000000000000000000..b9eb95aa8e345da1a6883914198326bfe5ed631c
--- /dev/null
+++ b/containers/Dockerfile.v10.4
@@ -0,0 +1,59 @@
+#
+# Dockerfile for CI and Flexpart container images
+# Build Examples:
+# - podman build -t harbor.wolke.img.univie.ac.at/flexpart/almalinux8:jasper -f Dockerfile
+#
+FROM almalinux:8-minimal
+#
+# Build development image (with/without jasper)
+# jasper was used in FP 10.4 (eccodes, emoslib)
+#
+RUN microdnf install -y epel-release && \
+ microdnf install -y --enablerepo=powertools make netcdf-fortran-devel.x86_64 netcdf.x86_64 cmake tar gcc-c++ perl jasper-libs.x86_64 && \
+ microdnf clean all -y
+
+#
+# Download ECCODES Version
+# note 2.30.0 has an issue!!!
+#
+RUN curl https://confluence.ecmwf.int/download/attachments/45757960/eccodes-2.31.0-Source.tar.gz | tar xz
+RUN mkdir build && \
+ cd build && \
+ cmake -DENABLE_ECCODES_OMP_THREADS=ON ../eccodes-*/ && \
+ make -j8 && \
+ make install
+#
+# set environment variables
+#
+ENV FC=gfortran
+ENV LIBRARY_PATH=/usr/lib64:/usr/local/lib64
+ENV CPATH=/usr/include:/usr/local/include:/usr/lib64/gfortran/modules
+
+WORKDIR /
+# clone just that version for FLEXPART v10.4 + small fixes
+RUN git clone --branch v10.4.1 --single-branch https://gitlab.phaidra.org/flexpart/flexpart.git \
+ && cp -r flexpart/src /src
+
+ENV COMMIT=v10.4
+COPY ./tests/default_options /options
+
+# since the new data set is larger, we download the data for the container
+RUN wget -r --no-parent -A 'EC*' -P /inputs "https://webdata.wolke.img.univie.ac.at/flexpart/"
+COPY ./AVAILABLE /inputs/
+# Entrypoint script (user tips)
+COPY ./entrypoint.sh /entrypoint.sh
+WORKDIR /src
+#
+# compile using a subset of microarch
+# need to fix march to x86_64_v3 , remove mtune
+# here generic means core_avx2
+RUN make -f makefile_gfortran eta=no arch=generic \
+ && make -f makefile_gfortran arch=generic \
+ && mkdir -p /output \
+ && echo -e "/options/\n/output/\n/inputs/\n/inputs/AVAILABLE" > /pathnames
+# In the Dockerfile, the ENTRYPOINT command defines the executable,
+# while CMD sets the default parameter.
+# so here our entrypoint run script and default FLEXPART_ETA or FLEXPART
+ENTRYPOINT ["/entrypoint.sh"]
+# Could be FLEXPART_ETA pathnames_custom
+CMD ["FLEXPART"]
diff --git a/containers/Singularity b/containers/Singularity
new file mode 100644
index 0000000000000000000000000000000000000000..2fa369908bbb2de1c384adcde5c011a877b87d02
--- /dev/null
+++ b/containers/Singularity
@@ -0,0 +1,70 @@
+Bootstrap: docker
+From: rockylinux:9-minimal
+Stage: spython-base
+
+%files
+../src /src
+../AVAILABLE /inputs/AVAILABLE
+./entrypoint.sh /entrypoint.sh
+../tests/default_options /options
+
+%post
+microdnf install -y epel-release && \
+microdnf install -y --enablerepo=crb make netcdf-fortran-devel.x86_64 netcdf.x86_64 eccodes eccodes-devel cmake tar gcc-c++ perl git wget && \
+microdnf clean all -y && \
+rm -rf /var/cache/yum
+#
+# Download ECCODES Version
+# note 2.30.0 has an issue!!!
+# ENV ECCODES=2.31.0
+# RUN curl https://confluence.ecmwf.int/download/attachments/45757960/eccodes-${ECCODES}-Source.tar.gz | tar xz
+# RUN mkdir build && \
+# cd build && \
+# cmake -DENABLE_ECCODES_OMP_THREADS=ON ../eccodes-*/ && \
+# make -j8 && \
+# make install
+#
+# set environment variables
+#
+FC=gfortran
+LIBRARY_PATH=/usr/lib64:/usr/local/lib64
+CPATH=/usr/include:/usr/local/include:/usr/lib64/gfortran/modules
+# cmd Arguments for COMMIT ID/tag
+COMMIT=0
+COMMIT=$COMMIT
+# since the new data set is larger, we download the data for the container
+# EC 2009 01 01 00 - 06
+wget -r -np -nd -A 'EC*' -P /inputs "https://webdata.wolke.img.univie.ac.at/flexpart/"
+mkdir -p /src
+cd /src
+export FC=gfortran
+export LIBRARY_PATH=/usr/lib64:/usr/local/lib64
+export CPATH=/usr/include:/usr/local/include:/usr/lib64/gfortran/modules
+#
+# compile using a standardized
+# need to fix march to x86_64_v3 , remove mtune
+# here generic means core_avx2
+make -f makefile_gfortran eta=no arch=generic \
+&& make -f makefile_gfortran arch=generic \
+&& mkdir -p /output \
+&& echo -e "/options/\n/output/\n/inputs/\n/inputs/AVAILABLE" > /pathnames
+
+# Entrypoint script (user tips)
+# In the Dockerfile, the ENTRYPOINT command defines the executable,
+# while CMD sets the default parameter.
+# so here our entrypoint run script and default FLEXPART_ETA or FLEXPART
+# Could be FLEXPART_ETA pathnames_custom
+%environment
+export FC=gfortran
+export LIBRARY_PATH=/usr/lib64:/usr/local/lib64
+export CPATH=/usr/include:/usr/local/include:/usr/lib64/gfortran/modules
+export COMMIT=$COMMIT
+
+# add a check if output is writeable?
+%runscript
+cd /src
+exec /entrypoint.sh FLEXPART_ETA "$@"
+
+%startscript
+cd /src
+exec /entrypoint.sh FLEXPART_ETA "$@"
diff --git a/containers/build.sh b/containers/build.sh
new file mode 100755
index 0000000000000000000000000000000000000000..39aeeeb948faa3b5baf5428235e08a5876cdf0ad
--- /dev/null
+++ b/containers/build.sh
@@ -0,0 +1,22 @@
+#!/bin/bash
+# By MB
+# Build a FLEXPART container
+CPATH=$(dirname $0)
+#
+# using podman to build containers
+#
+BRANCH=$(git rev-parse --abbrev-ref HEAD)
+COMMIT=$(git log --pretty=format:'%h' -n 1)
+echo "Building flexpart v11 branch: $BRANCH : $COMMIT"
+read -n1 -rsp $'Press any key to continue or Ctrl+C to exit...\n'
+
+cd $CPATH
+
+if [ "$1" != "apptainer" ]; then
+ # build with subdirectory as root
+ podman build -f Dockerfile -t flexpartv11-${BRANCH}:${COMMIT} --build-arg COMMIT=$COMMIT ../
+ # registry
+ # podman build -t harbor.wolke.img.univie.ac.at/flexpart/flexpartv11-${BRANCH}:$COMMIT --build-arg COMMIT=$COMMIT ..
+else
+ apptainer build flexpartv11-${BRANCH}-${COMMIT}.sif Singularity
+fi
\ No newline at end of file
diff --git a/containers/entrypoint.sh b/containers/entrypoint.sh
new file mode 100755
index 0000000000000000000000000000000000000000..5bd2387c8c622971aee4aec40f1520739f0ca06c
--- /dev/null
+++ b/containers/entrypoint.sh
@@ -0,0 +1,50 @@
+#!/bin/bash
+# By MB
+# run FLEXPART, but provide a bit of information
+
+RED='\033[0;31m'
+GREEN='\033[0;32m'
+YELLOW='\033[1;33m'
+NC='\033[0m'
+report() {
+ if [ $? -eq 0 ]; then
+ printf "%-68s[$GREEN%10s$NC]\n" "$@" "OK"
+ return 0
+ else
+ printf "%-68s[$RED%10s$NC]\n" "$@" "FAILED"
+ return 1
+ fi
+}
+
+echo "Welcome, running FLEXPART "
+test -e /pathnames
+report "Using defaults (/pathnames)"
+cat /pathnames
+echo "Mount volumes to change inputs"
+echo "Git: $COMMIT"
+echo "EXECUTING FLEXPART"
+if [ $# -eq 1 ]; then
+ test -e /src/"$1"
+ report "Executing: /src/$1"
+ if [ $? -eq 0 ]; then
+ /src/"$1" /pathnames
+ else
+ test -e "$1"
+ report "Executing: $1"
+ if [ $? -eq 0 ]; then
+ exec "$1"
+ fi
+ fi
+
+elif [ $# -eq 2 ]; then
+ test -e /src/"$1"
+ report "Executing: /src/$1 $2"
+ if [ $? -eq 0 ]; then
+ /src/"$1" "$2"
+ fi
+else
+ test -e /src/FLEXPART_ETA
+ report "Executing: /src/FLEXPART_ETA"
+ /src/FLEXPART_ETA /pathnames
+fi
+echo "FINISHED"
diff --git a/create_tarball.sh b/create_tarball.sh
deleted file mode 100755
index eebe81a3df49d89cab657cab955d7e5a453d5a81..0000000000000000000000000000000000000000
--- a/create_tarball.sh
+++ /dev/null
@@ -1,242 +0,0 @@
-#!/bin/bash
-# Ignacio Pisso, May 2017
-# Changes 2018-2019
-
-echo CREATE A NEW FLEXPART DISTRIBUTION
-
-# get current commit hash
-githash=$(git rev-parse --short --verify HEAD)
-echo githash $githash
-#define version number with hash
-version=10.4_$githash
-echo version $version
-
-# define tarball name
-targetdir=../flexpart_distribution/
-echo targetdir $targetdir
-
-# name distribution version
-distribution_name=flexpart_v$version
-
-# name distribution temporary dir
-tarball_tmp=${targetdir}flexpart_v$version
-echo tarball_tmp $tarball_tmp
-
-# name distribution tarball file
-#tarball=${targetdir}flexpart_v$version.tar
-tarball=${tarball_tmp}.tar
-echo tarball $tarball
-
-# if needed clean old package
-if [ -d $tarball_tmp ]; then
- echo
- echo clean old tarball
- hora=$(date +"%Y-%m-%d_%H%M%S")
- tarball_tmp_bk=$tarball_tmp$tarball_tmp_$hora
- echo tarball_tmp=$tarball_tmp exists: move to tarball_tmp_bk=$tarball_tmp_bk #and exit
- mkdir $tarball_tmp_bk
- mv $tarball_tmp $tarball_tmp_bk/
- mv $tarball $tarball_tmp_bk/
- #exit
- echo old files moved to tarball_tmp_bk=$tarball_tmp_bk
- echo
-fi
-
-# start packing
-## needs in addition to the git repo ANCILLARY git repos
-# VERIFY THESE RESOURCES EXIST BEFORE PACKING DISTRIBUTION
-#1 OH file OH_variables.bin || OH_variables=../flexin/OH_FIELDS/OH_variables.bin
-#2 flex_extract || flex_extract=../flex_extract_v7.0.4/
-#3 flex_read_fortran from ../flex_read_matlab/export_basic TODO: add functions to ../flex_read_matlab/export/
-# flex_read_matlab_src=../flex_read_matlab/export_basic
-#4 tests/examples ../flex_tests_examples/examples/*
-
-
-
-
-# mkdir container
-echo ---------------------------------------------------------
-echo ')' create basis dir $tarball_tmp
-mkdir $tarball_tmp
-echo ---------------------------------------------------------
-
-echo
-
-# patnames
-echo ---------------------------------------------------------
-echo ')' copy pathnames
-cp pathnames $tarball_tmp/pathnames
-echo ---------------------------------------------------------
-
-echo
-
-# fortran source files
-echo ---------------------------------------------------------
-echo ')' copy src/
-mkdir $tarball_tmp/src
-cp src/*.f90 $tarball_tmp/src
-cp -r src/gributils $tarball_tmp/src
-cp src/makefile $tarball_tmp/src
-echo ---------------------------------------------------------
-
-cp LICENSE $tarball_tmp/LICENSE_GPLv3
-cp src/flexpart_license.txt $tarball_tmp/src
-
-echo
-
-# options dir
-echo ---------------------------------------------------------
-echo ')' copy options/
-echo ---------------------------------------------------------
-mkdir $tarball_tmp/options
-user_input_files="AGECLASSES COMMAND IGBP_int1.dat OUTGRID OUTGRID_NEST RECEPTORS RELEASES surfdata.t surfdepo.t"
-for i in $user_input_files
-do
- echo $i
- cp -r options/$i $tarball_tmp/options
-done
-mkdir $tarball_tmp/options/SPECIES
-cp options/SPECIES/SPECIES* $tarball_tmp/options/SPECIES/
-cp options/SPECIES/specoverview.f90 $tarball_tmp/options/SPECIES/
-echo copy options/SPECIES/ to $tarball_tmp/options/SPECIES/
-echo ---------------------------------------------------------
-
-echo
-
-# OH file
-echo ---------------------------------------------------------
-echo ')' copy OH_variables.bin to flexin
-mkdir $tarball_tmp/flexin
-OH_variables=../flexin/OH_FIELDS/OH_variables.bin
-cp $OH_variables $tarball_tmp/flexin/
-echo ---------------------------------------------------------
-
-echo
-
-# AVAILABLE
-echo ---------------------------------------------------------
-echo ')' copy AVAILABLE
-cp AVAILABLE $tarball_tmp/AVAILABLE
-echo ---------------------------------------------------------
-
-echo
-
-# output
-echo ---------------------------------------------------------
-echo ')' create output/ # mkdir $tarball_tmp/output
-mkdir $tarball_tmp/output
-echo ---------------------------------------------------------
-echo output reference?
-echo ---------------------------------------------------------
-
-echo
-
-# preprocess
-echo ---------------------------------------------------------
-echo ')' preprocess/
-mkdir $tarball_tmp/preprocess
-echo -----------------flex_extract-------------------
-mkdir $tarball_tmp/preprocess/flex_extract
-flex_extract=../flex_extract_v7.0.4/
-echo include flex_extract v7.0.4 b7c1c04a204c91e53759ef590504bf52dfaece64
-echo from $flex_extract [use git modules?] IP 3/2018
-cp $flex_extract/README.md $tarball_tmp/preprocess/flex_extract
-cp -r $flex_extract/docs $tarball_tmp/preprocess/flex_extract
-cp -r $flex_extract/grib_templates $tarball_tmp/preprocess/flex_extract
-cp -r $flex_extract/python $tarball_tmp/preprocess/flex_extract
-cp -r $flex_extract/src $tarball_tmp/preprocess/flex_extract
-echo flex_extract copied
-echo ---------------------------------------------------------
-echo AVAILABLE generation scripts?
-echo ---------------------------------------------------------
-
-echo
-
-# postprocess
-echo ---------------------------------------------------------
-echo ')' postprocess/
-
-postprocess=postprocess
-mkdir $tarball_tmp/$postprocess
-echo -----------------flex_read_fortran-------------------
-flex_read_fortran_src=$postprocess/flex_read_fortran/
-mkdir $tarball_tmp/$postprocess/flex_read_fortran
-cp $postprocess/flex_read_fortran/*.f $tarball_tmp/$postprocess/flex_read_fortran
-cp $postprocess/flex_read_fortran/*.f90 $tarball_tmp/$postprocess/flex_read_fortran
-cp $postprocess/flex_read_fortran/makefile $tarball_tmp/$postprocess/flex_read_fortran
-echo flex_read_fortran copied from $flex_read_fortran_src
-
-echo -----------------flex_read_matlab-------------------
-flex_read_matlab_src=../flex_read_matlab/export_basic
-mkdir $tarball_tmp/$postprocess/flex_read_matlab
-cp -r $flex_read_matlab_src/* $tarball_tmp/$postprocess/flex_read_matlab
-echo flex_read_fortran from $flex_read_matlab_src # NOT copied
-echo ---------------------------------------------------------
-
-echo
-
-echo ---------------------------------------------------------
-echo ')' tests/
-#echo '13) tests'
-mkdir $tarball_tmp/tests
-echo ----------------- examples -------------------
-
-mkdir $tarball_tmp/tests/examples
-cp -r ../flex_tests_examples/examples/* $tarball_tmp/tests/examples/
-
-echo ----------------- examples_reference -------------------
-cp -r ./tests/examples_reference $tarball_tmp/tests/
-
-echo -----------------read examples-------------------
-
-mkdir $tarball_tmp/tests/read_examples
-
-cp tests/read_examples/declare_examples $tarball_tmp/tests/read_examples/
-cp tests/read_examples/display_examples.sh $tarball_tmp/tests/read_examples/
-cp tests/read_examples/examples_output.txt $tarball_tmp/tests/read_examples/
-cp tests/read_examples/read_examples.sh $tarball_tmp/tests/read_examples/
-cp tests/read_examples/read_grids.sh $tarball_tmp/tests/read_examples/
-cp tests/read_examples/read_parts.sh $tarball_tmp/tests/read_examples/
-cp tests/read_examples/set_examples_all $tarball_tmp/tests/read_examples/
-cp tests/read_examples/set_examples_3.sh $tarball_tmp/tests/read_examples/
-cp tests/read_examples/read_headers.sh $tarball_tmp/tests/read_examples/
-cp tests/read_examples/read_examples_output.txt $tarball_tmp/tests/ #read_examples/
-
-echo ------------compare examples-------------------
-mkdir $tarball_tmp/tests/compare_examples
-
-
-cp tests/compare_examples/*.sh $tarball_tmp/tests/compare_examples
-cp tests/compare_examples/compare_grids_output.txt $tarball_tmp/tests/ #compare_examples
-
-echo
-
-echo ---------------------------------------------------------
-echo create tarball
-
-cd $targetdir
-tar cf $distribution_name.tar $distribution_name
-
-pwd
-
-echo tarball $tarball complete
-echo exported untarred files in $tarball_tmp
-
-echo verify:
-echo cp -r preprocess/flex_extract/work $tarball_tmp/preprocess/flex_extract/
-echo cd $tarball_tmp/src
-echo $HOME/repos/flexpart/src/make_in_laptop.sh
-echo cd .. ';' ./src/FLEXPART
-echo cd postprocess/flex_read_fortran
-echo make test
-echo e.g.: max: 0.115784094 mean: 4.70877676E-05
-echo cd ../../tests/examples ';' make run
-echo cd ../read_examples
-echo ./read_examples.sh
-echo ./read_examples.sh '>' ../read_examples_output.txt
-echo cd ../compare_examples
-echo ./compare_grids.sh
-echo ./compare_grids.sh '>' ../compare_grids_output.txt
-
-echo e.g. tar --append --file=$tarball_tmp/ ../compare_grids_output.txt ../read_examples_output.txt
-
diff --git a/documentation/docs/containers.md b/documentation/docs/containers.md
new file mode 100644
index 0000000000000000000000000000000000000000..e15288a8e1f368ebec61e1ac3720a81f76ea8eab
--- /dev/null
+++ b/documentation/docs/containers.md
@@ -0,0 +1,399 @@
+# Containers
+
+There are two most commonly used container formats available:
+
+1. Docker/Podman
+2. Singularity/Apptainer
+
+with FLEXPART and recipes can be found in containers folder.
+
+Since version 11, FLEXPART is also available as a container. There is a Dockerfile and some instructions on how to build the container from scratch using for example podman/docker or singularity/apptainer:
+
+Specifications:
+- compiled using `march=core-avx2`, compatible with CPUs above AVX2 (since Haswell or Zen)
+- ecCodes
+
+
+```sh
+# build container using podman (adjust for docker)
+$ ./containers/build.sh
+
+Building flexpart v11 branch: master : 2464aef
+Press any key to continue or Ctrl+C to exit...
+STEP 1/16: FROM rockylinux:9-minimal
+...
+STEP 16/16: CMD ["FLEXPART_ETA"]
+--> Using cache 200844128a6919007417f3fa905221c8dbdea4bb285895ef80e89d3df80274b6
+COMMIT flexpartv11-master:2464aef
+--> 200844128a69
+Successfully tagged localhost/flexpartv11-master:2464aef
+200844128a6919007417f3fa905221c8dbdea4bb285895ef80e89d3df80274b6
+# finished
+
+# using singularity/apptainer for running FLEXPART
+# there might be some warnings about EPERM (can be ignored)
+$ ./containers/build.sh apptainer
+
+Building flexpart v11 branch: master : 2464aef
+Press any key to continue or Ctrl+C to exit...
+INFO: Starting build...
+INFO: Adding environment to container
+INFO: Adding startscript
+INFO: Adding runscript
+INFO: Creating SIF file...
+INFO: Build complete: flexpartv11-master-2464aef.sif
+# finished
+```
+
+running it using podman/docker or singularity/apptainer:
+
+```sh
+# simple run the container with default settings
+podman run localhost/flexpartv11-master:2464aef
+# running the container requires a writable output directory
+# mounting the local directory to /output inside the container
+apptainer run -B .:/output flexpartv11-master-2464aef.sif
+```
+
+
+
+<details>
+<summary>podman/docker flexpart run log</summary>
+<pre><code class="shell">
+Welcome, running FLEXPART
+Using defaults (/pathnames)
+/options/
+/output/
+/inputs/
+/inputs/AVAILABLE
+Mount volumes to change inputs
+Git: c5bdd94 HEAD -> master, origin/master, origin/HEAD Tue Nov 21 16:15:27 2023 +0100
+EXECUTING FLEXPART
+trying to execute: /src/FLEXPART_ETA
+Executing: /src/FLEXPART_ETA
+ Welcome to FLEXPART Version 11
+ Git: undefined
+ FLEXPART is free software released under the GNU General Public License.
+ FLEXPART is running with ETA coordinates.
+ ----------------
+ INFORMATION: SUBGRIDSCALE TERRAIN EFFECT IS
+ NOT PARAMETERIZED DURING THIS SIMULATION.
+ ----------------
+
+ *********** WARNING **********************************
+ * FLEXPART running in parallel mode *
+ * Number of uncertainty classes in *
+ * set to number of threads: 1 *
+ * All other computations are done with 8 threads. *
+ *******************************************************
+
+ FLEXPART WARNING: TIME DIFFERENCE BETWEEN TWO
+ WIND FIELDS IS BIG. THIS MAY CAUSE A DEGRADATION
+ OF SIMULATION QUALITY.
+ ECMWF metdata detected
+ NXSHIFT is set to 0
+ grid dim: 181 91 92 92 91 92
+ Vertical levels in ECMWF data: 92 92
+
+ Mother domain:
+ Longitude range: -178.00000 to 182.00000 Grid distance: 2.00000
+ Latitude range : -90.00000 to 90.00000 Grid distance: 2.00000
+
+ Number of receptors: 2
+ Releasepoints : 1
+ reading SPECIES 24
+ Particle shape SPHERE for particle 24
+
+ SPECIES: 24 AIRTRACER (GAS)
+ Wet removal for gases is turned: OFF
+ Dry deposition for gases is turned: OFF
+ Below-cloud scavenging: OFF
+ In-cloud scavenging: OFF
+ Particles released (numpartmax): 10000
+ Total mass released: 1.0000000E+00
+ Allocating fields for global output (x,y): 85 65
+ Concentrations are calculated using kernel
+ WARNING: turbulence switched off.
+ Simulated 0.0 hours ( 0 s), 0 particles
+ Time: 0 seconds. Total spawned: 0 alive: 0 terminated: 0
+ Allocating 10000 particles 0 0 0
+ Finished allocation
+ Time: 900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 1800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 2700 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 3600 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ 3600 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
+ Time: 4500 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 5400 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 6300 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 7200 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ 7200 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
+ Time: 8100 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 9000 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 9900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 10800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ 10800 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
+ Read wind fields: 0.609375000 seconds
+ Timemanager: 1.17187500 seconds,first timestep: 1.09375000 seconds
+ Write particle files: 4.68750000E-02 seconds
+ Total running time: 1.81250000 seconds
+ tps,io,tot: 1.95312500E-02 0.131249994 1.81250000
+ CONGRATULATIONS: YOU HAVE SUCCESSFULLY COMPLETED A FLEXPART MODEL RUN!
+FINISHED
+</code></pre>
+</details>
+
+
+<details>
+<summary>singularity/apptainer flexpart run log</summary>
+<pre>
+<code class="language-shell">
+INFO: gocryptfs not found, will not be able to use gocryptfs
+Welcome, running FLEXPART
+Using defaults (/pathnames)
+/options/
+/output/
+/inputs/
+/inputs/AVAILABLE
+Mount volumes to change inputs
+Git: c5bdd94 HEAD -> master, origin/master, origin/HEAD Tue Nov 21 16:15:27 2023 +0100
+EXECUTING FLEXPART
+trying to execute: /src/FLEXPART_ETA
+Executing: /src/FLEXPART_ETA
+ Welcome to FLEXPART Version 11
+ Git: undefined
+ FLEXPART is free software released under the GNU General Public License.
+ FLEXPART is running with ETA coordinates.
+ ----------------
+ INFORMATION: SUBGRIDSCALE TERRAIN EFFECT IS
+ NOT PARAMETERIZED DURING THIS SIMULATION.
+ ----------------
+
+ *********** WARNING **********************************
+ * FLEXPART running in parallel mode *
+ * Number of uncertainty classes in *
+ * set to number of threads: 1 *
+ * All other computations are done with 8 threads. *
+ *******************************************************
+
+ FLEXPART WARNING: TIME DIFFERENCE BETWEEN TWO
+ WIND FIELDS IS BIG. THIS MAY CAUSE A DEGRADATION
+ OF SIMULATION QUALITY.
+ ECMWF metdata detected
+ NXSHIFT is set to 0
+ grid dim: 181 91 92 92 91 92
+ Vertical levels in ECMWF data: 92 92
+
+ Mother domain:
+ Longitude range: -178.00000 to 182.00000 Grid distance: 2.00000
+ Latitude range : -90.00000 to 90.00000 Grid distance: 2.00000
+
+ Number of receptors: 2
+ Releasepoints : 1
+ reading SPECIES 24
+ Particle shape SPHERE for particle 24
+
+ SPECIES: 24 AIRTRACER (GAS)
+ Wet removal for gases is turned: OFF
+ Dry deposition for gases is turned: OFF
+ Below-cloud scavenging: OFF
+ In-cloud scavenging: OFF
+ Particles released (numpartmax): 10000
+ Total mass released: 1.0000000E+00
+ Allocating fields for global output (x,y): 85 65
+ Concentrations are calculated using kernel
+ WARNING: turbulence switched off.
+ Simulated 0.0 hours ( 0 s), 0 particles
+ Time: 0 seconds. Total spawned: 0 alive: 0 terminated: 0
+ Allocating 10000 particles 0 0 0
+ Finished allocation
+ Time: 900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 1800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 2700 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 3600 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ 3600 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
+ Time: 4500 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 5400 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 6300 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 7200 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ 7200 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
+ Time: 8100 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 9000 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 9900 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ Time: 10800 seconds. Total spawned: 10000 alive: 10000 terminated: 0
+ 10800 Seconds simulated: 10000 Particles: Uncertainty: 0.000 0.000 0.000
+ Read wind fields: 0.703125000 seconds
+ Timemanager: 1.25000000 seconds,first timestep: 1.15625000 seconds
+ Write particle files: 1.56250000E-02 seconds
+ Total running time: 2.00000000 seconds
+ tps,io,tot: 2.34375000E-02 0.143749997 2.00000000
+ CONGRATULATIONS: YOU HAVE SUCCESSFULLY COMPLETED A FLEXPART MODEL RUN!
+FINISHED
+</code></pre>
+</details>
+
+<details>
+<summary>ncdump of default run output</summary>
+<pre><code class="language-shell">
+# check the output
+ncdump -h grid_conc_20090101000000.nc
+netcdf grid_conc_20090101000000 {
+dimensions:
+ time = UNLIMITED ; // (3 currently)
+ longitude = 85 ;
+ latitude = 65 ;
+ height = 4 ;
+ numspec = 1 ;
+ pointspec = 1 ;
+ nageclass = 1 ;
+ nchar = 45 ;
+ ncharrec = 16 ;
+ numpoint = 1 ;
+ receptor = UNLIMITED ; // (2 currently)
+variables:
+ int time(time) ;
+ time:units = "seconds since 2009-01-01 00:00" ;
+ time:calendar = "proleptic_gregorian" ;
+ float longitude(longitude) ;
+ longitude:long_name = "longitude in degree east" ;
+ longitude:axis = "Lon" ;
+ longitude:units = "degrees_east" ;
+ longitude:standard_name = "grid_longitude" ;
+ longitude:description = "grid cell centers" ;
+ float latitude(latitude) ;
+ latitude:long_name = "latitude in degree north" ;
+ latitude:axis = "Lat" ;
+ latitude:units = "degrees_north" ;
+ latitude:standard_name = "grid_latitude" ;
+ latitude:description = "grid cell centers" ;
+ float height(height) ;
+ height:units = "meters" ;
+ height:positive = "up" ;
+ height:standard_name = "height" ;
+ height:long_name = "height above ground" ;
+ char RELCOM(numpoint, nchar) ;
+ RELCOM:long_name = "release point name" ;
+ float RELLNG1(numpoint) ;
+ RELLNG1:units = "degrees_east" ;
+ RELLNG1:long_name = "release longitude lower left corner" ;
+ float RELLNG2(numpoint) ;
+ RELLNG2:units = "degrees_east" ;
+ RELLNG2:long_name = "release longitude upper right corner" ;
+ float RELLAT1(numpoint) ;
+ RELLAT1:units = "degrees_north" ;
+ RELLAT1:long_name = "release latitude lower left corner" ;
+ float RELLAT2(numpoint) ;
+ RELLAT2:units = "degrees_north" ;
+ RELLAT2:long_name = "release latitude upper right corner" ;
+ float RELZZ1(numpoint) ;
+ RELZZ1:units = "meters" ;
+ RELZZ1:long_name = "release height bottom" ;
+ float RELZZ2(numpoint) ;
+ RELZZ2:units = "meters" ;
+ RELZZ2:long_name = "release height top" ;
+ int RELKINDZ(numpoint) ;
+ RELKINDZ:long_name = "release kind" ;
+ int RELSTART(numpoint) ;
+ RELSTART:units = "seconds" ;
+ RELSTART:long_name = "release start relative to simulation start" ;
+ int RELEND(numpoint) ;
+ RELEND:units = "seconds" ;
+ RELEND:long_name = "release end relative to simulation start" ;
+ int RELPART(numpoint) ;
+ RELPART:long_name = "number of release particles" ;
+ float RELXMASS(numspec, numpoint) ;
+ RELXMASS:long_name = "total release particle mass" ;
+ int LAGE(nageclass) ;
+ LAGE:units = "seconds" ;
+ LAGE:long_name = "age class" ;
+ int ORO(latitude, longitude) ;
+ ORO:standard_name = "surface altitude" ;
+ ORO:long_name = "outgrid surface altitude" ;
+ ORO:units = "m" ;
+ char receptor(receptor, ncharrec) ;
+ receptor:long_name = "receptor name" ;
+ float spec001_mr(nageclass, pointspec, time, height, latitude, longitude) ;
+ spec001_mr:units = "ng m-3" ;
+ spec001_mr:long_name = "AIRTRACER" ;
+ spec001_mr:decay = -0.07001485f ;
+ spec001_mr:weightmolar = 29.f ;
+ spec001_mr:ohcconst = -9.e-10f ;
+ spec001_mr:ohdconst = -9.9f ;
+ spec001_mr:vsetaver = 0.f ;
+ float receptor_conc001(receptor, time) ;
+ receptor_conc001:units = "ng m-3" ;
+ receptor_conc001:_FillValue = -1.f ;
+ receptor_conc001:positive = "up" ;
+ receptor_conc001:standard_name = "receptor_conc" ;
+ receptor_conc001:long_name = "receptor_concentration" ;
+
+// global attributes:
+ :Conventions = "CF-1.6" ;
+ :title = "FLEXPART model output" ;
+ :git = "undefined" ;
+ :source = "Version 11 model output" ;
+ :history = "2023-11-21 16:22 +0100 created by mblaschek on NB513" ;
+ :references = "Stohl et al., Atmos. Chem. Phys., 2005, doi:10.5194/acp-5-2461-200" ;
+ :outlon0 = -25.f ;
+ :outlat0 = 10.f ;
+ :dxout = 1.f ;
+ :dyout = 1.f ;
+ :ldirect = 1 ;
+ :ibdate = "20090101" ;
+ :ibtime = "000000" ;
+ :iedate = "20090101" ;
+ :ietime = "030000" ;
+ :loutstep = 3600 ;
+ :loutaver = 3600 ;
+ :loutsample = 900 ;
+ :loutrestart = -1 ;
+ :lsynctime = 900 ;
+ :ctl = -0.2f ;
+ :ifine = 1 ;
+ :iout = 1 ;
+ :ipout = 0 ;
+ :lsubgrid = 0 ;
+ :lconvection = 0 ;
+ :lagespectra = 0 ;
+ :ipin = 0 ;
+ :ioutputforeachrelease = 0 ;
+ :iflux = 0 ;
+ :mdomainfill = 0 ;
+ :ind_source = 1 ;
+ :ind_receptor = 1 ;
+ :mquasilag = 0 ;
+ :nested_output = 0 ;
+ :sfc_only = 0 ;
+ :linit_cond = 0 ;
+}
+</code>
+</pre>
+</details>
+
+Interactive shells can be launched into containers, to have a look at configurations and to better understand what might go wrong. Podman/Docker allows to alter files inside of the container and save these changes. Singularity/Apptainer containers are not writeable, but acts like a normal executable with access to host files.
+
+
+```sh
+# using podman
+$ podman run -it localhost/flexpartv11-master:2464aef /bin/bash
+Welcome, running FLEXPART
+Using defaults (/pathnames) [ OK]
+/options/
+/output/
+/inputs/
+/inputs/AVAILABLE
+Mount volumes to change inputs
+Git: 2464aef
+EXECUTING FLEXPART
+Executing: /src//bin/bash [ FAILED]
+Executing: /bin/bash [ OK]
+bash-5.1#
+# now you are inside the container
+bash-5.1# pwd
+/src
+# important directories are /input, /output, /src, /options
+
+#
+# using singularity/apptainer
+$ apptainer run
+```
\ No newline at end of file
diff --git a/documentation/mkdocs.yml b/documentation/mkdocs.yml
index 9cddeee8112c79a762643c00a6defddf2b4b5e05..e0e0f01772ce74dc5c15494726147c2eb40053f6 100644
--- a/documentation/mkdocs.yml
+++ b/documentation/mkdocs.yml
@@ -38,5 +38,6 @@ nav:
- 'transport.md'
- 'evolution.md'
- 'examples.md'
+ - 'containers.md'
- 'troubleshooting.md'
diff --git a/entrypoint.sh b/entrypoint.sh
deleted file mode 100755
index 5fb5f2902975e561208044db36913791b4b62f1f..0000000000000000000000000000000000000000
--- a/entrypoint.sh
+++ /dev/null
@@ -1,23 +0,0 @@
-#!/bin/bash
-# By MB
-# run FLEXPART, but provide a bit of information
-echo "Welcome, running FLEXPART "
-echo "Using defaults (/pathnames)"
-cat /pathnames
-echo "Mount volumes to change inputs"
-echo "Git: $COMMIT"
-echo "EXECUTING FLEXPART"
-if [ $# -eq 1 ]; then
- echo "trying to execute: /src/$1"
- if [ -e /src/"$1" ]; then
- echo "Executing: /src/$1"
- /src/"$1" /pathnames
- else
- echo "Falling back to default, executing: /src/FLEXPART_ETA"
- /src/FLEXPART_ETA /pathnames
- fi
-else
- echo "Executing: /src/FLEXPART_ETA"
- /src/FLEXPART_ETA /pathnames
-fi
-echo "FINISHED"
diff --git a/pathnames b/pathnames
index 6571a6256ae107e4817e6adb3f13b2650640cef6..2f9a3548c3054ce02f88b5480ffc4c6fb9f9aa8c 100644
--- a/pathnames
+++ b/pathnames
@@ -1,4 +1,4 @@
./options/
./output/
-./preprocess/flex_extract/work/
+./inputs
./AVAILABLE
diff --git a/pathnames_ECMWF_OPER b/pathnames_ECMWF_OPER
deleted file mode 100644
index c464acb3c5e8761746d0a540cfa52a93d0a096a0..0000000000000000000000000000000000000000
--- a/pathnames_ECMWF_OPER
+++ /dev/null
@@ -1,6 +0,0 @@
-./options/
-./output/
-/
-/xnilu_wrk/flex_wrk/WIND_FIELDS/AVAILABLE_ECMWF_OPER_fields_global
-============================================
-
diff --git a/Dockerfile b/tests/Dockerfile
similarity index 56%
rename from Dockerfile
rename to tests/Dockerfile
index 9aea002457f59bab4759a78b4b2dc8572c45e347..5fea829dd09526b1fdee6763565e06d984355a3b 100644
--- a/Dockerfile
+++ b/tests/Dockerfile
@@ -1,27 +1,13 @@
-#
-# Dockerfile for CI and Flexpart container images
-# Build Examples:
-# - podman build -t harbor.wolke.img.univie.ac.at/flexpart/almalinux8 -f Dockerfile
-# - podman build -t harbor.wolke.img.univie.ac.at/flexpart/rockylinux9 -f Dockerfile
-#
-# FROM rockylinux:8-minimal
FROM rockylinux:9-minimal
-#
-# Build development image (with/without jasper)
-# jasper was used in FP 10.4 (eccodes, emoslib)
-#
-# 8: --enablerepo=powertools
-# since 9, there is 2.31 eccodes in epel
RUN microdnf install -y epel-release && \
- microdnf install -y --enablerepo=crb make netcdf-fortran-devel.x86_64 netcdf.x86_64 eccodes eccodes-devel cmake tar gcc-c++ perl git && \
+ microdnf install -y --enablerepo=crb make netcdf-fortran-devel.x86_64 netcdf.x86_64 eccodes eccodes-devel cmake tar gcc-c++ perl git wget && \
microdnf clean all -y && \
rm -rf /var/cache/yum
-
#
# Download ECCODES Version
# note 2.30.0 has an issue!!!
-#
-# RUN curl https://confluence.ecmwf.int/download/attachments/45757960/eccodes-2.31.0-Source.tar.gz | tar xz
+# ENV ECCODES=2.31.0
+# RUN curl https://confluence.ecmwf.int/download/attachments/45757960/eccodes-${ECCODES}-Source.tar.gz | tar xz
# RUN mkdir build && \
# cd build && \
# cmake -DENABLE_ECCODES_OMP_THREADS=ON ../eccodes-*/ && \
@@ -32,4 +18,4 @@ RUN microdnf install -y epel-release && \
#
ENV FC=gfortran
ENV LIBRARY_PATH=/usr/lib64:/usr/local/lib64
-ENV CPATH=/usr/include:/usr/local/include:/usr/lib64/gfortran/modules
+ENV CPATH=/usr/include:/usr/local/include:/usr/lib64/gfortran/modules
\ No newline at end of file