Install Request: Update Electrical and Electronic Eng COMSOL to V6.1 [IN06125518] [IN06134254]

[balston]

This is effectively a repeat of:

https://github.com/UCL-RITS/rcps-buildscripts/issues/515

but for Electrical and Electronic Eng whose reserved application group is legcomsl

We should still have to installer but if not, we can get it via the RF ticket.

[balston]

/shared/ucl/apps/comsol/

is the location for EEE COMSOL installations. The COMSOL 6.1 installer is in:

/shared/ucl/apps/pkg-store/ COMSOL61_lnx.zip

on both Myriad and Kathleen.

[balston]

We have a build script for 6.1 but this is for the Chem Eng installation. Will need to copy and modify for EEE.

[balston]

Myriad install progressing running:

 ./comsol-6.1_EEE_install 2>&1 | tee ~/Software/COMSOL/comsol-6.1_EEE_install.log

from the ccspapp account. It is quite slow and will be even slower on Katrhleen.

[balston]

It took about 30 minutes for the install to complete. Looks Ok:

    ==========================
    =    Post Build Info     =
    ==========================

    Package label:            comsol/6.1
    Build took place in:      /dev/shm/comsol-build.akqQtLR83X
    Modules were put in:      /shared/ucl/apps/comsol/6.1/.uclrc_modules
    Package was installed to: /shared/ucl/apps/comsol/6.1
    Package size:             8.1GB

    -- First execs (max 10) --
/shared/ucl/apps/comsol/6.1/license/glnxa64/lmcomsol.service
/shared/ucl/apps/comsol/6.1/license/glnxa64/LMCOMSOL
/shared/ucl/apps/comsol/6.1/license/glnxa64/lmutil
/shared/ucl/apps/comsol/6.1/license/glnxa64/lmgrd
/shared/ucl/apps/comsol/6.1/bin/setuplibpath
/shared/ucl/apps/comsol/6.1/bin/servers/webbridge/conf/Catalina/localhost/ROOT.xml
/shared/ucl/apps/comsol/6.1/bin/servers/webbridge/conf/Catalina/localhost/webbridge.xml
/shared/ucl/apps/comsol/6.1/bin/servers/webbridge/conf/server.xml
/shared/ucl/apps/comsol/6.1/bin/servers/webbridge/webapps/ROOT/WEB-INF/web.xml
/shared/ucl/apps/comsol/6.1/bin/servers/webbridge/webapps/ROOT/error.html

    ==========================
Note that module files will need altering to handle setting I_MPI_FABRICS per-cluster. This is not currently automated.

Next task create a module file. Should be straightforward as the current 6.1 Chem Eng one can be used as a template.

[balston]

Module file done. Now need to test if it works against the EEE License Manager.

[balston]

I can't use my account for testing as I'm not in the correct group (I'm in the Chem Eng one) so I will use ccspapp

[balston]

Test job submitted:

job-ID  prior   name       user         state submit/start at     queue                          slots ja-task-ID
-----------------------------------------------------------------------------------------------------------------
9999883 0.00000 Comsol_par ccspapp      qw    08/22/2023 18:11:35                                    8

[balston]

The first test job failed:

-          Current Progress:  11 % - Assembling matrices
Memory: 5501/7111 12255/14824

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   RANK 0 PID 61514 RUNNING AT node-b00a-013
=   KILLED BY SIGNAL: 9 (Killed)
===================================================================================
Finished.

This was with 1GB memory per core. I've resubmitted it with 4GB per core and it works:

---------- Current Progress: 100 % - 
Solution time: 320 s. (5 minutes, 20 seconds)
Physical memory: 5.08 GB
Virtual memory: 12.62 GB
Ended at Aug 23, 2023, 11:34:57 AM.
----- Stationary Solver 2 in Study 1/Solution 1 (sol1) ------------------------>
Run time: 820 s.
Saving model: /lustre/scratch/scratch/ccspapp/COMSOL_Examples/6.1/Comsol_parallel_1_4177/micromixer_batch.mph_batch_output_4177.mph
Save time: 1 s.
Total time: 835 s.
---------- Current Progress: 100 % - Done
Memory: 4738/8580 11515/15963
Finished.

The 1GB job worked with the Chem Eng COMSOL 6.1 version back in May so it looks like some jobs need more memory to run that they did.

[balston]

I've asked Electrical and Electronic Eng to check their LM logs to make sure licenses were issued from the correct LM!

[balston]

Unfortunately I had forgotten to save the updated module file before uploading it to Myriad so it still have the Chem Eng LM in there. I've now fixed it so I need to re-submit the test job.

[balston]

Test job fails with:

Model to run is micromixer_batch.mph
(node-b00a-011:0)

ERROR: A start error occurred on node 0: License_error_-15_Cannot_connect_to_license_server_system
Finished.

Investigating ...

[balston]

The problem is with the EEE firewall. An email has been sent asking for this to be updated.

[balston]

EEE have made a firewall change which appears to have worked. Just need to confirm from the EEE LM logs.

[balston]

Yay we have:

18:03:33 (LMCOMSOL) OUT: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:03:33 (LMCOMSOL) IN: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:03:33 (LMCOMSOL) OUT: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:03:33 (LMCOMSOL) IN: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:03:33 (LMCOMSOL) OUT: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:03:33 (LMCOMSOL) OUT: "CLUSTERNODE" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:03:33 (LMCOMSOL) OUT: "COMSOLUSER" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:03:47 (LMCOMSOL) OUT: "COMSOL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:04:33 (LMCOMSOL) IN: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:04:33 (LMCOMSOL) OUT: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:14:26 (LMCOMSOL) IN: "COMSOL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:14:26 (LMCOMSOL) IN: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:14:26 (LMCOMSOL) OUT: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:14:26 (LMCOMSOL) IN: "COMSOLUSER" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:14:26 (LMCOMSOL) IN: "CLUSTERNODE" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>
18:14:27 (LMCOMSOL) IN: "SERIAL" [ccspapp@node-b00a-005.myriad.ucl.ac.uk](mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk)<mailto:ccspapp@node-b00a-005.myriad.ucl.ac.uk>

in the EEE LM logs. It works!

[balston]

Done on Myriad and requesters informed.

Will install on Kathleen next.

[balston]

Installing on Kathleen now.

[balston]

The Kathleen installation is taking a very long time in its final stage. I started it just after lunch.

[balston]

It's moved from running the chgrp command to the chmod command which is them last major step in the install script.

[balston]

The install has finally finished.

Submitting an 80 core test job now.

[balston]

My test job on Kathleen worked.

User informed.