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Commit cf46944f authored by Michael Blaschek's avatar Michael Blaschek :bicyclist:
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Update VSC.md, TeachingHub.md, SRVX2.md, SRVX1.md files

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SRVX1.md
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......@@ -51,7 +51,7 @@ These software libraries are usually handled by environment modules.
## Currently installed modules
```
```bash
$ module av
-------------------------------- /home/opt/spack/share/spack/modules/linux-centos6-sandybridge --------------------------------
anaconda3/2020.07-gcc-5.3.0 gcc/5.3.0-gcc-5.3.0 netcdf-c/4.7.4-gcc-5.3.0 zlib/1.2.11-gcc-5.3.0
......
SRVX2.md
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......@@ -34,7 +34,7 @@ These software libraries are usually handled by environment modules.
![](https://upload.wikimedia.org/wikipedia/en/thumb/0/0a/Environment_Modules_logo.svg/320px-Environment_Modules_logo.svg.png)
## Currently installed modules
```
```bash
$ module av
------------------------------ /home/spack-root/share/spack/modules/linux-centos8-skylake_avx512 ------------------------------
anaconda3/2020.07-gcc-8.3.1 intel-parallel-studio/composer.2020.2-intel-20.0.2 netcdf-fortran/4.5.3-gcc-8.3.1
......@@ -45,6 +45,7 @@ eccodes/2.21.0-intel-20.0.2 ncl/6.6.2-gcc-8.3.1
hdf5/1.10.7-gcc-8.3.1 netcdf-c/4.7.4-gcc-8.3.1 openmpi/3.1.6-gcc-8.3.1
hdf5/1.10.7-intel-20.0.2 netcdf-c/4.7.4-intel-20.0.2 openmpi/3.1.6-intel-20.0.2
```
on how to use environment modules go to [Using Environment Modules](Misc/Environment-Modules.md)
TeachingHub.md
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......@@ -36,7 +36,7 @@ Account expires: 2021-08-30
...
```
Use these to login to the server and change the password to something better and still something that is safe:
```
```bash
$ ssh [user]@srvx1.img.univie.ac.at
----------------------------------------------
_
......
VSC.md
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......@@ -9,9 +9,9 @@ We have the privilege to be part of the VSC and have private nodes at VSC-4 (sin
Access is primarily via SSH:
```
ssh user@vsc4.vsc.ac.at
ssh user@vsc3.vsc.ac.at
```bash
$ ssh user@vsc4.vsc.ac.at
$ ssh user@vsc3.vsc.ac.at
```
Please follow some connection instruction on the [wiki](https://wiki.vsc.ac.at) which is similar to all other servers (e.g. [SRVX1](SRVX1.md)).
......@@ -27,6 +27,15 @@ CPU model: Intel(R) Xeon(R) Platinum 8174 CPU @ 3.10GHz
378 GB Memory
```
We have access to 5 private Nodes of that kind. Check with
```bash
$ sqos
qos_name total used free walltime priority partitions
=========================================================================
p71386_0384 5 1 4 10-00:00:00 100000 mem_0384
```
## Storage on VSC-4
All quotas are shared between users:
......@@ -37,13 +46,13 @@ All quotas are shared between users:
- `$BINFS` (up to 2GB, SSD fast)
Check quotas:
```
mmlsquota --block-size auto -j data_fs71386 data
```bash
$ mmlsquota --block-size auto -j data_fs71386 data
Block Limits | File Limits
Filesystem type blocks quota limit in_doubt grace | files quota limit in_doubt grace Remarks
data FILESET 4.027T 9.766T 9.766T 482.4M none | 176664 1000000 1000000 65 none vsc-storage.vsc4.opa
mmlsquota --block-size auto -j home_fs71386 home
$ mmlsquota --block-size auto -j home_fs71386 home
Block Limits | File Limits
Filesystem type blocks quota limit in_doubt grace | files quota limit in_doubt grace Remarks
home FILESET 62.17G 100G 100G 207.8M none | 631852 1000000 1000000 287 none vsc-storage.vsc4.opa
......@@ -68,8 +77,8 @@ All quotas are shared between users:
- `$BINFS` (up to 2 GB, SSD fast)
Check quotas:
```
beegfs-ctl --getquota --cfgFile=/etc/beegfs/global3.d/beegfs-client.conf --gid 70653
```bash
$ beegfs-ctl --getquota --cfgFile=/etc/beegfs/global3.d/beegfs-client.conf --gid 70653
user/group || size || chunk files
name | id || used | hard || used | hard
--------------|------||------------|------------||---------|---------
......@@ -82,8 +91,8 @@ beegfs-ctl --getquota --cfgFile=/etc/beegfs/global3.d/beegfs-client.conf --gid 7
On VSC-3 we have a max runtime of 10 days for the private Queue. The normal queues have 3 days. the devel only 10 min (for testing)
```
sacctmgr show qos format=name%20s,priority,grpnodes,maxwall,description%40s
```bash
$ sacctmgr show qos format=name%20s,priority,grpnodes,maxwall,description%40s
Name Priority GrpNodes MaxWall Descr
-------------------- ---------- -------- ----------- ----------------------------------------
......@@ -96,8 +105,8 @@ sacctmgr show qos format=name%20s,priority,grpnodes,maxwall,description%40s
```
on VSC-4 accordingly.
```
sacctmgr show qos format=name%20s,priority,grpnodes,maxwall,description%40s
```bash
$ sacctmgr show qos format=name%20s,priority,grpnodes,maxwall,description%40s
Name Priority GrpNodes MaxWall Descr
-------------------- ---------- -------- ----------- ----------------------------------------
......@@ -113,7 +122,7 @@ sacctmgr show qos format=name%20s,priority,grpnodes,maxwall,description%40s
```
SLURM allows for setting a run time limit below the default QOS's run time limit. After the specified time is elapsed, the job is killed:
```
```bash
#SBATCH --time=<time>
```
Acceptable time formats include `minutes`, `minutes:seconds`, `hours:minutes:seconds`, `days-hours`, `days-hours:minutes` and `days-hours:minutes:seconds`.
......@@ -134,8 +143,8 @@ We have 16 CPUs per Node. In order to fill:
The core hours will be charged to the specified account. If not specified, the default account will be used.
on VSC-3 our account is called:
```
sacctmgr show user `id -u` withassoc format=user,defaultaccount,account,qos%40s,defaultqos%20s
```bash
$ sacctmgr show user `id -u` withassoc format=user,defaultaccount,account,qos%40s,defaultqos%20s
User Def Acct Account QOS Def QOS
---------- ---------- ---------- ---------------------------------------- --------------------
......@@ -145,7 +154,7 @@ sacctmgr show user `id -u` withassoc format=user,defaultaccount,account,qos%40s,
Put this in the Job file:
```
```bash
#!/bin/bash
#
#SBATCH -J TEST_JOB
......@@ -175,10 +184,10 @@ Put this in the Job file:
* **--mail-type** sends an email at specific events. The SLURM doku lists the following valid mail-type values: *"BEGIN, END, FAIL, REQUEUE, ALL (equivalent to BEGIN, END, FAIL and REQUEUE), TIME_LIMIT, TIME_LIMIT_90 (reached 90 percent of time limit), TIME_LIMIT_80 (reached 80 percent of time limit), and TIME_LIMIT_50 (reached 50 percent of time limit). Multiple type values may be specified in a comma separated list."* [cited from the SLURM doku](http://slurm.schedmd.com)
* **--mail-user** sends an email to this address
```
[username@l31 ~]$ sbatch check.slrm # to submit the job
[username@l31 ~]$ squeue -u `whoami` # to check the status of own jobs
[username@l31 ~]$ scancel JOBID # for premature removal, where JOBID
```bash
$ sbatch check.slrm # to submit the job
$ squeue -u `whoami` # to check the status of own jobs
$ scancel JOBID # for premature removal, where JOBID
# is obtained from the previous command
```
......@@ -191,8 +200,8 @@ We have 48 CPUs per Node. In order to fill:
The core hours will be charged to the specified account. If not specified, the default account will be used.
on VSC-4 our account is called:
```
sacctmgr show user `id -u` withassoc format=user,defaultaccount,account,qos%40s,defaultqos%20s
```bash
$ sacctmgr show user `id -u` withassoc format=user,defaultaccount,account,qos%40s,defaultqos%20s
User Def Acct Account QOS Def QOS
---------- ---------- ---------- ---------------------------------------- --------------------
......@@ -201,7 +210,7 @@ sacctmgr show user `id -u` withassoc format=user,defaultaccount,account,qos%40s,
```
Put this in the Job file:
```
```bash
#!/bin/bash
#
#SBATCH -J TEST_JOB
......@@ -223,10 +232,10 @@ Put this in the Job file:
submit the job
```
[username@l31 ~]$ sbatch check.slrm # to submit the job
[username@l31 ~]$ squeue -u `whoami` # to check the status of own jobs
[username@l31 ~]$ scancel JOBID # for premature removal, where JOBID
```bash
$ sbatch check.slrm # to submit the job
$ squeue -u `whoami` # to check the status of own jobs
$ scancel JOBID # for premature removal, where JOBID
# is obtained from the previous command
```
......@@ -238,12 +247,12 @@ The VSC use the same software system as Jet and have environmental modules avail
- VSC-3 has an `anaconda3` module
- VSC-4 has `miniconda3` modules for GNU and INTEL ;)
```
[username@l34 ~]$ module avail # lists the **available** Application-Software,
# Compilers, Parallel-Environment, and Libraries
[username@l34 ~]$ module list # shows currently loaded package of your session
[username@l34 ~]$ module unload <xyz> # unload a particular package <xyz> from your session
[username@l34 ~]$ module load <xyz> # load a particular package <xyz> into your session
```bash
$ module avail # lists the **available** Application-Software,
# Compilers, Parallel-Environment, and Libraries
$ module list # shows currently loaded package of your session
$ module unload <xyz> # unload a particular package <xyz> from your session
$ module load <xyz> # load a particular package <xyz> into your session
```
will load the intel compiler suite and add variables to your environment.
......@@ -257,12 +266,12 @@ Currently (6.2021) there is no development queue on VSC-4 and the support sugges
```bash
# Request resources from slurm (-N 1, a full Node)
salloc -N 1 -p mem_0384 --qos p71386_0384 --no-shell
$ salloc -N 1 -p mem_0384 --qos p71386_0384 --no-shell
# Once the node is assigned / job is running
# Check with
squeue -u $USER
$ squeue -u $USER
# connect to the Node with ssh
ssh [Node]
$ ssh [Node]
# test and debug the model there.
```
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