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| software:abaqus:farber [2018-10-09 19:50] – anita | software:abaqus:farber [2021-04-27 16:21] (current) – external edit 127.0.0.1 |
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| ==== Serial ==== | ==== Serial ==== |
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| Below is a queue submission script example for Abaqus copied and modified from the serial template found in ''/opt/templates/gridengine/serial.qs''. It is important to read the comments and make the necessary changes for the example to work. Specifically, you must change ''port@lm.udel.edu'' to your Abaqus license server information. Please refer to your account sponsor on the cluster to determine if you have access to Abaqus. | Below is a queue submission script example for Abaqus copied and modified from the serial template found in ''/opt/shared/templates/gridengine/serial.qs''. It is important to read the comments and make the necessary changes for the example to work. Specifically, you must change ''port@lm.udel.edu'' to your Abaqus license server information. Please refer to your account sponsor on the cluster to determine if you have access to Abaqus. |
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| <code - abaqus-serial.qs> | <code - abaqus-serial.qs> |
| It is necessary to decide which parallel environment you want to use for your Abaqus job. Based on the number of licenses required and the number of cores per node, it is likely that Abaqus will not parallelize well beyond 8-12 core. The OpenMP parallel environment, threads, works best using multiple cores (cpus) on a single node. Keep in mind that a license is needed for each cpu (core per node) in addition to the 5 licenses. | It is necessary to decide which parallel environment you want to use for your Abaqus job. Based on the number of licenses required and the number of cores per node, it is likely that Abaqus will not parallelize well beyond 8-12 core. The OpenMP parallel environment, threads, works best using multiple cores (cpus) on a single node. Keep in mind that a license is needed for each cpu (core per node) in addition to the 5 licenses. |
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| Below is a queue submission script example for Abaqus copied and modified from the OpenMP template found in ''/opt/templates/gridengine/openmp/openmp.qs'' to change ''NPROC'' to 8. It is important to read the comments and make the necessary changes for the example to work. Specifically, you must change ''port@lm.udel.edu'' to your Abaqus license server information. Please refer to your account sponsor on the cluster to determine if you have access to Abaqus. | Below is a queue submission script example for Abaqus copied and modified from the OpenMP template found in ''/opt/shared/templates/gridengine/openmp/openmp.qs'' to change ''NPROC'' to 8. It is important to read the comments and make the necessary changes for the example to work. Specifically, you must change ''port@lm.udel.edu'' to your Abaqus license server information. Please refer to your account sponsor on the cluster to determine if you have access to Abaqus. |
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| <code - abaqus-openmp.qs> | <code - abaqus-openmp.qs> |
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| Below is a queue submission script example for Abaqus copied and modified from the generic MPI template found in ''/opt/templates/gridengine/generic-mpi/generic-mpi.qs'' where ''NPROC'' was changed to 48. Keep in mind that this job will be assigned to as many node(s) needed for 48 cores. This may be 1 node with 48 cores or multiple nodes with less cores available. However, you are not guaranteed that all licenses will be available, so you should only be specifying the number of cores relative to the number of licenses available for your research group. Keep in mind using more than 8-12 cores on a single node has NOT shown to provide significant speedup. | Below is a queue submission script example for Abaqus copied and modified from the generic MPI template found in ''/opt/shared/templates/gridengine/generic-mpi/generic-mpi.qs'' where ''NPROC'' was changed to 48. Keep in mind that this job will be assigned to as many node(s) needed for 48 cores. This may be 1 node with 48 cores or multiple nodes with less cores available. However, you are not guaranteed that all licenses will be available, so you should only be specifying the number of cores relative to the number of licenses available for your research group. Keep in mind using more than 8-12 cores on a single node has NOT shown to provide significant speedup. |
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| <code - abaqus-mpi.qs> | <code - abaqus-mpi.qs> |
| </code> | </code> |
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| Equally as important is to specify the [[:abstract:farber:runjobs:schedule_jobs#resource-management-options-on-farber|memory resource requirements]] using ''mem_free'' and ''ram_free'' in your job script. This prevents your job from being assigned to a node unless it has enough memory available on the node before it starts and it reserves this amount of memory during the run to prevent another job from being assigned to it. If we are specifying multiple cpus in a parallel environment such threads or MPI, then we divide the amount of memory needed by the number of cpus. For example, if we need 48GB using 8 cpus, then we would specify | Equally as important is to specify the [[:abstract:farber:runjobs:schedule_jobs#resource-management-options-on-farber|memory resource requirements]] using ''mem_free'' and ''m_mem_free'' in your job script. This prevents your job from being assigned to a node unless it has enough memory available on the node before it starts and it reserves this amount of memory during the run to prevent another job from being assigned to it. If we are specifying multiple cpus in a parallel environment such threads or MPI, then we divide the amount of memory needed by the number of cpus. For example, if we need 48GB using 8 cpus, then we would specify |
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| <code> | <code> |
| #$ -l pe threads 8 | #$ -l pe threads 8 |
| #$ -l mem_free=6G | #$ -l mem_free=6G |
| #$ -l ram_free=6G | #$ -l m_mem_free=6G |
| </code> | </code> |
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| Last login: Tue Nov 27 14:13:55 2012 from farber.farber.hpc.udel.edu | Last login: Tue Nov 27 14:13:55 2012 from farber.farber.hpc.udel.edu |
| [traine@n016 ABAQUS]$ pwd | [traine@n016 ABAQUS]$ pwd |
| /lustre/work/it_css/traine/ABAQUS | /home/work/it_css/traine/ABAQUS |
| [traine@n016 ABAQUS]$ vpkg_require abaqus | [traine@n016 ABAQUS]$ vpkg_require abaqus |
| Adding dependency `x11/RHEL6.1` to your environment | Adding dependency `x11/RHEL6.1` to your environment |