From 5d0d47af510632295190cc72337f81dbd4614a64 Mon Sep 17 00:00:00 2001 From: comeani Date: Mon, 11 Dec 2023 14:31:39 -0500 Subject: [PATCH] content transfer for COMSOL --- docs/applications/licensed-software/comsol.md | 339 +++++++++++++++++- 1 file changed, 338 insertions(+), 1 deletion(-) diff --git a/docs/applications/licensed-software/comsol.md b/docs/applications/licensed-software/comsol.md index 566a78a..c3a800e 100644 --- a/docs/applications/licensed-software/comsol.md +++ b/docs/applications/licensed-software/comsol.md @@ -1 +1,338 @@ -# COMSOL Multiphysics \ No newline at end of file +# COMSOL Multiphysics + +This page contains info aimed at first time users of COMSOL on CRC, but may also be useful to more experienced users. + +##Available Modules + +COMSOL Multiphysics is a suite of engineering and scientific simulation tools. The current version available on the +cluster is COMSOL 6.1. Please be aware that newer COMSOL files are not backward compatible with older versions. Below +is a list of specialized add-ons that the CRC is licensed to use: + +### Electromagnetics: + +AC/DC, RF, and Semiconductor + +### Structural Mechanics & Acoustics: + +Acoustic, MEMS, Structural Mechanics + +### Multipurpose Products + +Particle Tracing + +### Fluid Flow & Heat Transfer Modules + +CFD, Heat Transfer, Porous Media Flow + +### Chemical Engineering Modules + +Battery Design, Chemical Reaction Engineering, Corrosion, Electrodeposition, Electrochemistry, Fuel Cell & Electrolyzer + +### Interfacing Products + +CAD Import Module, Design Module, Matlab/Simulink + +## Access modalities for COMSOL + +### 1- Using graphic user interface (VIZ) + + Please read the documentation on crc.pitt.edu/viz on how to access VIZ and then watch the video below: + + + +### 2- Using command line interface + + + + + +!!! note + + If you are using the same Slurm job submission script for your own simulation, all you have to do is to change + the name of your input file and the number of nodes, cores, etc. + +!!! note + + If you want to run a COMSOL simulation on the `mpi` cluster, look at this template: + `/ihome/crc/how_to_run/comsol/micromixer` + +!!! note + + If you are using COMSOL for teaching purposes (for a course), you need to load the teaching module: + + ```commandline + [shs159@login0 bed_reactor]$ module load comsol/5.6-teaching + [shs159@login0 bed_reactor]$ ml + + Currently Loaded Modules: + 1) comsol/5.6-teaching + + [shs159@login0 bed_reactor]$ + ``` + +## Sample script + +```shell +#!/bin/bash -l + +#SBATCH --job-name=comsol_micromix +#SBATCH --nodes=1 +#SBATCH --ntasks-per-node=4 +#SBATCH --time=0-01:00:00 # Syntax is DD-HH:MM:SS +#SBATCH --cluster=smp # Run crc-sinfo.py to get the cluster and partition details +#SBATCH --partition=smp + +# Load Modules +module load comsol/5.6 + +# define input +inp=packed_bed_reactor_3d # First input argument: Name of input without extention +ext=mph # We use the same naming scheme as the software default extention + +########################## +#DO NOT TOUCH THE FOLLOWING +########################## +# define directories +submitdir=${SLURM_SUBMIT_DIR} + +# run Comsol +comsol batch -nn ${SLURM_NNODES}\ + -np ${SLURM_NTASKS_PER_NODE}\ + -inputfile ${inp}.${ext}\ + -outputfile ${inp}_out.${ext}\ + -batch \ + -mlroot /ihome/crc/install/matlab/R2021a/\ + -batchlog logfile.log +``` + +You may now have submitted your first COMSOL job. + +Good luck with your (MULTI)physics! + + +## Checking the License Status + +The CRC is licensed to use COMSOL, but the number of licenses is not particularly high for certain tools. + +The licenses also operate on a per-node basis, meaning two jobs by the same user submitted to different compute nodes +will use up a license until those jobs are completed. Please be considerate of other users when submitting long jobs. +Also, if you use VIZ to access COMSOL with a GUI, please make sure your session is ended properly when you are done so +that others may use it. + +When you load the COMSOL module, truncated version of the license output will appear. + +```commandline +[nlc60@login0b ~]#module load comsol + +CURRENT LICENSE AVAILABILITY OF COMSOL GUI: +Users of COMSOLGUI: (Total of 5 licenses issued; Total of 2 licenses in use) + "COMSOLGUI" v6.0, vendor: LMCOMSOL, expiry: 1-oct-2022 +[nlc60@login0b comsol] : module list + +Currently Loaded Modules: + 1) comsol/5.6 +``` + +This shows the availability of COMSOL GUI for users attempting to open COMSOL on VIZ. + +You may see an error like this if all the GUI licenses are in use: + +![](https://crc.pitt.edu/sites/default/files/pictures/COMSOL%20License%20Issues.png) + +For the full license information output, open +[the SSOE license server](https://ssoe-vlic-09.engr.pitt.edu/details.php?listing=0&server=9) +(which is behind the Pitt firewall just as the cluster) + +```commandline +CURRENT LICENSE AVAILIBILITY FOR COMSOL: +lmutil - Copyright (c) 1989-2021 Flexera. All Rights Reserved. +Flexible License Manager status on Thu 2/10/2022 17:21 + +License server status: 4800@ssoe-vlic-07.engr.pitt.edu + License file(s) on ssoe-vlic-07.engr.pitt.edu: C:\Program Files\COMSOL\COMSOL60\Multiphysics\license\license.dat: + +ssoe-vlic-07.engr.pitt.edu: license server UP (MASTER) v11.18.1 + +Vendor daemon status (on ssoe-vlic-07.engr.pitt.edu): + + LMCOMSOL: UP v11.18.1 +Feature usage info: + +Users of PERMANENT: (Uncounted, node-locked) + +Users of SERIAL: (Uncounted, node-locked) + + "SERIAL" v6.0, vendor: LMCOMSOL, expiry: 1-oct-2022 + vendor_string: Y,57F1198202190D83 + uncounted nodelocked license locked to NOTHING (hostid=ANY) + + bam184 viz-n1.crc.pitt.edu /dev/pts/22 (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 1408), start Mon 2/7 11:59 + jre31 smp-n162.crc.pitt.edu /dev/tty (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 688), start Thu 2/10 15:05 + +Users of ACDC: (Total of 5 licenses issued; Total of 0 licenses in use) + +Users of ACDCBATCH: (Total of 5 licenses issued; Total of 0 licenses in use) + +Users of ACOUSTICS: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of ACOUSTICSBATCH: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of BATTERYDESIGN: (Total of 1 license issued; Total of 0 licenses in use) + +Users of BATTERYDESIGNBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of CADIMPORT: (Total of 4 licenses issued; Total of 0 licenses in use) + +Users of CADIMPORTBATCH: (Total of 4 licenses issued; Total of 0 licenses in use) + +Users of CFD: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of CFDBATCH: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of CHEM: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of CHEMBATCH: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of COMSOL: (Total of 5 licenses issued; Total of 2 licenses in use) + + "COMSOL" v6.0, vendor: LMCOMSOL, expiry: 1-oct-2022 + floating license + + bam184 viz-n1.crc.pitt.edu /dev/pts/22 (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 943), start Mon 2/7 11:59 + jre31 smp-n162.crc.pitt.edu /dev/tty (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 353), start Thu 2/10 15:05 + +Users of COMSOLBATCH: (Total of 5 licenses issued; Total of 0 licenses in use) + +Users of CORROSION: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of CORROSIONBATCH: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of DESIGN: (Total of 1 license issued; Total of 0 licenses in use) + +Users of DESIGNBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of ELECTROCHEMISTRY: (Total of 1 license issued; Total of 0 licenses in use) + +Users of ELECTROCHEMISTRYBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of ELECTRODEPOSITION: (Total of 1 license issued; Total of 0 licenses in use) + +Users of ELECTRODEPOSITIONBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of FUELCELLANDELECTROLYZER: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of FUELCELLANDELECTROLYZERBATCH: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of HEATTRANSFER: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of HEATTRANSFERBATCH: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of LLMATLAB: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of LLMATLABBATCH: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of MEMS: (Total of 1 license issued; Total of 0 licenses in use) + +Users of MEMSBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of PARTICLETRACING: (Total of 1 license issued; Total of 0 licenses in use) + +Users of PARTICLETRACINGBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of POROUSMEDIAFLOW: (Total of 1 license issued; Total of 0 licenses in use) + +Users of POROUSMEDIAFLOWBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of RF: (Total of 1 license issued; Total of 0 licenses in use) + +Users of RFBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of SEMICONDUCTOR: (Total of 2 licenses issued; Total of 2 licenses in use) + + "SEMICONDUCTOR" v6.0, vendor: LMCOMSOL, expiry: 1-oct-2022 + floating license + + bam184 viz-n1.crc.pitt.edu /dev/pts/22 (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 1515), start Wed 2/9 10:18 + jre31 smp-n162.crc.pitt.edu /dev/tty (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 2321), start Thu 2/10 15:05 + +Users of SEMICONDUCTORBATCH: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of STRUCTURALMECHANICS: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of STRUCTURALMECHANICSBATCH: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of COMSOLGUI: (Total of 5 licenses issued; Total of 1 license in use) + + "COMSOLGUI" v6.0, vendor: LMCOMSOL, expiry: 1-oct-2022 + floating license + + bam184 viz-n1.crc.pitt.edu /dev/pts/22 (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 213), start Mon 2/7 11:59 + +Users of CLIENTSERVER: (Total of 5 licenses issued; Total of 0 licenses in use) + +Users of CLUSTERNODE: (Total of 5 licenses issued; Total of 1 license in use) + + "CLUSTERNODE" v6.0, vendor: LMCOMSOL, expiry: 1-oct-2022 + floating license + + jre31 smp-n162.crc.pitt.edu /dev/tty (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 1228), start Thu 2/10 15:05 + +Users of COMSOLUSER: (Total of 5 licenses issued; Total of 2 licenses in use) + + "COMSOLUSER" v6.0, vendor: LMCOMSOL, expiry: 1-oct-2022 + floating license + + bam184 viz-n1.crc.pitt.edu /dev/pts/22 (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 115), start Mon 2/7 11:59 + jre31 smp-n162.crc.pitt.edu /dev/tty (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 1334), start Thu 2/10 15:05 + +Users of MODELMANAGER: (Total of 5 licenses issued; Total of 0 licenses in use) + +Users of MODELMANAGERBATCH: (Total of 5 licenses issued; Total of 0 licenses in use) + +Users of MODELMANAGERSERVER: (Total of 5 licenses issued; Total of 0 licenses in use) + +Users of MODELMANAGERSERVERBATCH: (Total of 5 licenses issued; Total of 0 licenses in use) + +Users of CADREADER: (Total of 4 licenses issued; Total of 0 licenses in use) + +Users of CADREADERBATCH: (Total of 4 licenses issued; Total of 0 licenses in use) + +Users of CADIMPORTUSER: (Total of 4 licenses issued; Total of 0 licenses in use) + +Users of BATTERIESANDFUELCELLS: (Total of 1 license issued; Total of 0 licenses in use) + +Users of BATTERIESANDFUELCELLSBATCH: (Total of 1 license issued; Total of 0 licenses in use) + +Users of ACO: (Total of 2 licenses issued; Total of 0 licenses in use) + +Users of HT: (Total of 3 licenses issued; Total of 0 licenses in use) + +Users of SME: (Total of 3 licenses issued; Total of 0 licenses in use) +``` + +If you know the name of the functionality you want to use, you can pipe the output to grep for a more concise output. + +If the particular tool you want to use does not have available licenses for you to use, you will need to wait until +another user's jobs finish. + + +With a username from the license file, you can check the remaining time on their jobs with squeue. For example, let's +look at the user jre31 from the license server output above: + +```commandline +​ jre31 smp-n162.crc.pitt.edu /dev/tty (v5.6) (ssoe-vlic-07.engr.pitt.edu/4800 1334), start Thu 2/10 15:05 +``` + +Their username is `jre31`, and their job is running on a compute node in the `smp` cluster (smp-n162). + +```commandline +squeue -M smp -u jre31 -o "%.18i %.9P %.8j %.8u %.2t %.10M %.6D %.20R %L" +``` + +will show their jobs on that cluster, and providing the `%L` argument to the format of the output of that function +shows the `TIME_LEFT (D-HH:MM:SS)` given how long the job has been running and the QOS they defined for the job.