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Merge pull request #530 from boegel/fix_default_cluster
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correct default cluster (doduo, not victini)
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@itkovian
itkovian authored Jun 27, 2023
2 parents acd2c93 + ffac6aa commit 92491a1
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10 changes: 5 additions & 5 deletions mkdocs/docs/HPC/MATLAB.md
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Expand Up @@ -29,10 +29,10 @@ To access the MATLAB compiler, the `MATLAB` module should be loaded
first. Make sure you are using the same `MATLAB` version to compile and
to run the compiled MATLAB program.

<pre><code>$ <b>module avail MATLAB</b>
----------------------/apps/gent/victini/modules/all----------------------
MATLAB/2016b MATLAB/2017b MATLAB/2018a (D)
$ <b>module load MATLAB/2018a</b>
<pre><code>$ <b>module avail MATLAB/</b>
----------------------/apps/gent/RHEL8/zen2-ib/modules/all----------------------
MATLAB/2021b MATLAB/2022b-r5 (D)
$ <b>module load MATLAB/2021b</b>
</code></pre>

After loading the `MATLAB` module, the `mcc` command can be used. To get
Expand All @@ -52,7 +52,7 @@ To compile a MATLAB program, use `mcc -mv`:

<pre><code><b>mcc -mv example.m</b>
Opening log file: {{homedir}}/java.log.34090
Compiler version: 6.6 (R2018a)
Compiler version: 8.3 (R2021b)
Dependency analysis by REQUIREMENTS.
Parsing file "{{homedir}}/example.m"
(Referenced from: "Compiler Command Line").
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48 changes: 25 additions & 23 deletions mkdocs/docs/HPC/running_batch_jobs.md
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Expand Up @@ -318,9 +318,11 @@ It's also possible to get detailed information about a specific module:
{% if site == gent %}
You will need to load all module(s) on any one of the lines below before the "example/1.2.3" module is available to load.

cluster/accelgor
cluster/doduo
cluster/donphan
cluster/gallade
cluster/joltik
cluster/kirlia
cluster/skitty
cluster/swalot
cluster/victini
Expand Down Expand Up @@ -482,21 +484,21 @@ filled with jobs, completely filled with jobs, ....
You can also get this information in text form (per cluster separately)
with the `pbsmon` command:

<pre><code><b>$ module swap cluster /kirlia</b>
<pre><code><b>$ module swap cluster/donphan</b>
<b>$ pbsmon</b>
3401 3402 3403 3404 3405 3406 3407
J j j J J j J
4001 4002 4003 4004 4005 4006 4007
_ j j j _ _ .

3408 3409 3410 3411 3412 3413 3414
J J J J J J J
4008 4009 4010 4011 4012 4013 4014
_ _ . _ _ _ _

3415 3416
J J
4015 4016
_ _

_ free : 0 | X down : 0 |
_ free : 11 | X down : 0 |
j partial : 3 | x down_on_error : 0 |
J full : 13 | m maintenance : 0 |
| . offline : 0 |
J full : 0 | m maintenance : 0 |
| . offline : 2 |
| o other (R, *, ...) : 0 |

Node type:
Expand Down Expand Up @@ -761,33 +763,33 @@ To use other clusters, you can swap the `cluster` module. This is a
special module that change what modules are available for you, and what
cluster your jobs will be queued in.

By default you are working on {{ defaultcluster }}. To switch to, e.g., {{ othercluster }} you need to redefine
the environment so you get access to all modules installed on the {{ othercluster }}
cluster, and to be able to submit jobs to the {{ othercluster }} scheduler so your jobs
will start on {{ othercluster }} instead of the default {{ defaultcluster }} cluster.
By default you are working on `{{ defaultcluster }}`. To switch to, e.g., `{{ othercluster }}` you need to redefine
the environment so you get access to all modules installed on the `{{ othercluster }}`
cluster, and to be able to submit jobs to the `{{ othercluster }}` scheduler so your jobs
will start on `{{ othercluster }}` instead of the default `{{ defaultcluster }}` cluster.

<pre><code><b>$ module swap cluster/{{ othercluster }}</b>
</code></pre>

Note: the {{ othercluster }} modules may not work directly on the login nodes, because the
login nodes do not have the same architecture as the {{ othercluster }} cluster, they have
the same architecture as the {{ defaultcluster }} cluster however, so this is why by default
Note: the `{{ othercluster }}` modules may not work directly on the login nodes, because the
login nodes do not have the same architecture as the `{{ othercluster }}` cluster, they have
the same architecture as the `{{ defaultcluster }}` cluster however, so this is why by default
software works on the login nodes. See [the section on Running software that is incompatible with host](../intro-HPC/troubleshooting/#running-software-that-is-incompatible-with-host) for why this is and how to fix
this.

To list the available cluster modules, you can use the
`module avail cluster/` command:

<pre><code><b>$ module avail cluster/</b>
------------------------------------------------------------------------------------
/etc/modulefiles/vsc
------------------------------------------------------------------------------------
cluster/doduo (S) cluster/joltik (S) cluster/kirlia (S)
cluster/skitty (S) cluster/swalot (S) cluster/victini (S,L)
--------------------------------------- /etc/modulefiles/vsc ----------------------------------------
cluster/accelgor (S) cluster/donphan (S) cluster/skitty (S)
cluster/default cluster/gallade (S) cluster/swalot (S)
cluster/doduo (S,D,) cluster/joltik (S) cluster/victini (S)

Where:
S: Module is Sticky, requires --force to unload or purge
L: Module is loaded
D: Default Module

If you need software that is not listed,
request it via <a href="https://www.ugent.be/hpc/en/support/software-installation-request">https://www.ugent.be/hpc/en/support/software-installation-request</a>
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35 changes: 17 additions & 18 deletions mkdocs/docs/HPC/troubleshooting.md
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Expand Up @@ -427,25 +427,20 @@ The correct command is `module swap cluster/{{othercluster}}`. See also [Specify
When running software provided through modules (see [Modules](../running_batch_jobs/#modules)), you may run into
errors like:

<pre><code>$ <b>module swap cluster/kirlia</b>
The following have been reloaded with a version change:
1) cluster/victini => cluster/kirlia
<pre><code>$ <b>module swap cluster/donphan</b>
The following have been reloaded with a version change:
1) cluster/doduo => cluster/donphan 3) env/software/doduo => env/software/donphan
2) env/slurm/doduo => env/slurm/donphan 4) env/vsc/doduo => env/vsc/donphan

$ <b>module load Python/2.7.14-intel-2018a</b>
$ <b>module load Python/3.10.8-GCCcore-12.2.0</b>
$ <b>python</b>

Please verify that both the operating system and the processor support
Intel(R) MOVBE, F16C, FMA, BMI, LZCNT and AVX2 instructions.
</code></pre>

or errors like:

<pre><code>$ <b>module swap cluster/doduo</b>

The following have been reloaded with a version change:
1) cluster/victini => cluster/doduo

$ <b>module load Python/2.7.14-foss-2018a</b>
<pre><code>
$ <b>python</b>
Illegal instruction
</code></pre>
Expand All @@ -464,17 +459,21 @@ all our modules will get reloaded. This means that all current modules
will be unloaded and then loaded again, so they'll work on the newly
loaded cluster. Here's an example of how that would look like:

<pre><code>$ <b>module load Python/2.7.14-intel-2018a</b>
$ <b>module swap cluster/swalot</b>
<pre><code>$ <b>module load Python/3.10.8-GCCcore-12.2.0</b>
$ <b>module swap cluster/donphan</b>

Due to MODULEPATH changes, the following have been reloaded:
1) GCCcore/6.4.0 5) Tcl/8.6.8-GCCcore-6.4.0 9) iccifort/2018.1.163-GCC-6.4.0-2.28 13) impi/2018.1.163-iccifort-2018.1.163-GCC-6.4.0-2.28 17) ncurses/6.0-GCCcore-6.4.0
2) GMP/6.1.2-GCCcore-6.4.0 6) binutils/2.28-GCCcore-6.4.0 10) ifort/2018.1.163-GCC-6.4.0-2.28 14) intel/2018a 18) zlib/1.2.11-GCCcore-6.4.0
3) Python/2.7.14-intel-2018a 7) bzip2/1.0.6-GCCcore-6.4.0 11) iimpi/2018a 15) libffi/3.2.1-GCCcore-6.4.0
4) SQLite/3.21.0-GCCcore-6.4.0 8) icc/2018.1.163-GCC-6.4.0-2.28 12) imkl/2018.1.163-iimpi-2018a 16) libreadline/7.0-GCCcore-6.4.0
1) GCCcore/12.2.0 8) binutils/2.39-GCCcore-12.2.0
2) GMP/6.2.1-GCCcore-12.2.0 9) bzip2/1.0.8-GCCcore-12.2.0
3) OpenSSL/1.1 10) libffi/3.4.4-GCCcore-12.2.0
4) Python/3.10.8-GCCcore-12.2.0 11) libreadline/8.2-GCCcore-12.2.0
5) SQLite/3.39.4-GCCcore-12.2.0 12) ncurses/6.3-GCCcore-12.2.0
6) Tcl/8.6.12-GCCcore-12.2.0 13) zlib/1.2.12-GCCcore-12.2.0
7) XZ/5.2.7-GCCcore-12.2.0

The following have been reloaded with a version change:
1) cluster/victini => cluster/swalot
1) cluster/doduo => cluster/donphan 3) env/software/doduo => env/software/donphan
2) env/slurm/doduo => env/slurm/donphan 4) env/vsc/doduo => env/vsc/donphan
</code></pre>

This might result in the same problems as mentioned above. When swapping
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8 changes: 4 additions & 4 deletions mkdocs/extra/gent.yml
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Expand Up @@ -67,10 +67,10 @@ homedir: /user/home/gent/vsc400/vsc40000
datadir: /user/data/gent/vsc400/vsc40000
scratchdir: /user/scratch/gent/vsc400/vsc40000
jobid: 123456
computenode: node3200.victini.gent.vsc
computenodeshort: node3200
defaultcluster: victini
othercluster: skitty
computenode: node3501.doduo.gent.vsc
computenodeshort: node3501
defaultcluster: doduo
othercluster: donphan
# Support
hpcinfo: hpc@ugent.be
hpcusersml: hpc-users@lists.ugent.be
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