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= Using your own license = | = Using your own license = | ||
Abaqus is available on Compute Canada clusters, but you must provide your own license. | Abaqus is available on Compute Canada clusters, but you must provide your own license. To configure your cluster account, create a file named <tt>$HOME/.licenses/abaqus.lic</tt> corresponding to the module version you want to use (otherwise abaqus jobs will fail). This must be done on each cluster where you plan to run abaqus as follows:<br><br> | ||
Module Version 2020 | |||
{{File | |||
|name=abaqus.lic | |||
|contents= | |||
prepend_path("ABAQUSLM_LICENSE_FILE","port@server") | |||
}} | |||
Module Version 6.14.1 | |||
{{File | {{File | ||
|name=abaqus.lic | |name=abaqus.lic | ||
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}} | }} | ||
Replace <code>port@server</code> with the port number and name of your Abaqus license server. Your license server must be reachable by our compute nodes, so your firewall will need to be configured appropriately. This usually requires our technical team to get in touch with the technical people managing your license software. Please contact our [[Technical support|technical support]] and we will provide a list of IP addresses used by our clusters and obtain the information we need on the port and IP address of your server. | |||
Your license server must be reachable by our compute nodes, so your firewall will need to be configured appropriately. This usually requires our technical team to get in touch with the technical people managing your license software. Please contact our [[Technical support|technical support]] and we will provide a list of IP addresses used by our clusters and obtain the information we need on the port and IP address of your server. | |||
= Cluster batch job submission = | = Cluster batch job submission = | ||
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{{File|contents= | {{File|contents= | ||
#!/bin/bash | #!/bin/bash | ||
#SBATCH --account=def-account # | #SBATCH --account=def-account # some account | ||
#SBATCH --time=00-06:00 # days-hours:minutes | #SBATCH --time=00-06:00 # days-hours:minutes | ||
#SBATCH --mem= | #SBATCH --mem=2G # memory on node | ||
#SBATCH --cpus-per-task=4 # | #SBATCH --cpus-per-task=4 # number of cores | ||
module load abaqus/6.14.1 | module load abaqus/6.14.1 (or abaqus/2020) | ||
unset SLURM_GTIDS | unset SLURM_GTIDS | ||
export MPI_IC_ORDER='tcp' | export MPI_IC_ORDER='tcp' | ||
abaqus job= | abaqus job=Test input=Sample.inp scratch=$SCRATCH cpus=$SLURM_CPUS_ON_NODE interactive | ||
}} | }} | ||
For a list of available Abaqus' command line options, load an abaqus module and run command: <code>abaqus -help | less</code> | |||
= Site specific usage = | = Site specific usage = | ||
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=== License server file === | === License server file === | ||
The configuration of your cluster account abaqus license file depends on the abaqus module version:<br> | |||
Module Version 2020 | |||
<source lang="bash"> | |||
[gra-login1:~] cat ~/.licenses/abaqus.lic | |||
prepend_path("ABAQUSLM_LICENSE_FILE","27050@license3.sharcnet.ca") | |||
</source> | |||
Module Version 6.14.1 | |||
<source lang="bash"> | <source lang="bash"> | ||
[gra-login1:~] cat ~/.licenses/abaqus.lic | [gra-login1:~] cat ~/.licenses/abaqus.lic | ||
prepend_path("LM_LICENSE_FILE","27050@license3.sharcnet.ca") | prepend_path("LM_LICENSE_FILE","27050@license3.sharcnet.ca") | ||
</source> | </source> | ||
If your abaqus jobs fail with error message [*** ABAQUS/eliT_CheckLicense rank 0 terminated by signal 11 (Segmentation fault)] in the slurm output file verify your <code>abaqus.lic</code> file contains ABAQUSLM_LICENSE_FILE to use abaqus/2020. If your abaqus jobs fail with error message starting [License server machine is down or not responding etc] in the output file verify your <code>abaqus.lic</code> file contains LM_LICENSE_FILE to use abaqus/6.14.1 as shown. | |||
=== Check license server === | === Check license server === | ||
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</source> | </source> | ||
=== Core | When <i>abaqus licensing lmstat</i> shows your job is "queued" this means it has entered the "R"unning state from the squeue command perspective but is waiting for a license (not started) and therefore idle. This will have the same impact on your account priority as if the job were consuming cputime and thus should be avoided. When <i>abaqus licensing lmstat</i> indicates the job is in the "start" state then it has acquired the required abaqus tokens from the license and consuming cputime ... | ||
=== Check cpu utilization === | |||
To determine the total cpu utilization of a running (and started) job execute the follow command. The real time %CPU will be shown in the third column. If the value is less then 90% perform scaling tests to determine the optimal number of cpu's for the slurm script and re-submit the job. | |||
<source lang="bash"> | |||
srun --jobid=JobNumber ps ux | grep "CPU\|std" | |||
</source> | |||
Other misc information about a running job can be shown with <code>scontrol show job JobNumber</code>. To determine the percent cpu utilization of a completed abaqus job use <code>seff JobNumber</code>. | |||
=== Core token mapping === | |||
<pre> | <pre> | ||
CORES 1 | TOKENS 5 6 7 8 10 12 14 16 19 21 25 28 34 38 | ||
CORES 1 2 3 4 6 8 12 16 24 32 48 64 96 128 | |||
</pre> | </pre> | ||
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=== Remote visualization === | === Remote visualization === | ||
A) First install the TigerVNC client on your desktop as described in [[VNC]]. Once logged in, | A) First install the TigerVNC client on your desktop as described in [[VNC]]. Once logged in, start abaqus as follows: | ||
# Connect to gra-vdi.computecanada.ca with TigerVNC | # Connect to gra-vdi.computecanada.ca with TigerVNC | ||
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# module load SnEnv | # module load SnEnv | ||
# module load abaqus | # module load abaqus | ||
# export ABAQUSLM_LICENSE_FILE= | # export ABAQUSLM_LICENSE_FILE="port@server" | ||
# abaqus cae | # abaqus cae | ||
You must first request your "port@server" be setup by submitting a ticket before jobs can be run on graham. | |||
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== Western license == | |||
<!--T:72--> | |||
The Western site license may only be used by Western researchers with hardware located on Western's campus such as the Dusky legacy cluster. Graham and gra-vdi are excluded since they are located at Waterloo (use the Sharcnet License for these systems as described above). Contact the Western abaqus license server administrator (located in Robarts) to make arrangements before attempting to use the Western abaqus license. Submit a ticket to Compute Canada support to request the admins contact information if necessary. You will need to provide your Compute Canada username and likely make arrangements to purchase tokens. If you are granted access request the port and server values and enter them into your abaqus.lic file as shown in 1) near the top of this wiki which will in turn be used by the Compute Canada module on dusky when it loads. | The Western site license may only be used by Western researchers with hardware located on Western's campus such as the Dusky legacy cluster. Graham and gra-vdi are excluded since they are located at Waterloo (use the Sharcnet License for these systems as described above). Contact the Western abaqus license server administrator (located in Robarts) to make arrangements before attempting to use the Western abaqus license. Submit a ticket to Compute Canada support to request the admins contact information if necessary. You will need to provide your Compute Canada username and likely make arrangements to purchase tokens. If you are granted access request the port and server values and enter them into your abaqus.lic file as shown in 1) near the top of this wiki which will in turn be used by the Compute Canada module on dusky when it loads. | ||