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cluster:214 [2022/08/02 14:25] hmeij07 [Amber22] |
cluster:214 [2022/08/03 09:10] hmeij07 [Amber22] |
==== Amber22 ==== | ==== Amber22 ==== |
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First establish a successfull run with the **run.rocky** script for Amber20 (listed above). Then change the module in your script. | First establish a successful run with the **run.rocky** script for Amber20 (listed above). Then change the module in your script. |
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<code> | <code> |
module load amber/22 | module load amber/22 |
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# if the module does not show up in the output of | # if the module does not show up in the output of your console |
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module avail | module avail |
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# treat your cache as out of date | # treat your module cache as out of date |
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module --ignore_cache avail | module --ignore_cache avail |
</code> | </code> |
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Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just sure to source amber.sh in your script. (compile instructions below for me...) | Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just be sure to source amber.sh in your script. (compile instructions below for me...) |
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https://ambermd.org/InstCentOS.php\\ | https://ambermd.org/InstCentOS.php\\ |
"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME | "download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME)" |
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<code> | <code> |
[hmeij@n79 src]$ echo $AMBERHOME | [hmeij@n79 src]$ echo $AMBERHOME |
/share/apps/CENTOS7/amber/amber22 | /share/apps/CENTOS7/amber/amber22 |
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[hmeij@n79 src]$ which mpirun mpicc | [hmeij@n79 src]$ which mpirun mpicc |
/share/apps/CENTOS7/amber/amber22/bin/mpirun | /share/apps/CENTOS7/amber/amber22/bin/mpirun |
</code> | </code> |
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First establish a successfull run with the **run.centos7** script for Amber20 (listed above). Then change the script like so. | First establish a success full run with the **run.centos** script for Amber20 (listed above). Then edit the script and apply these edits. We had to use a specific compatible ''gcc/g++'' version to make this work. Hardware is getting too old. |
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<code> | <code> |
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# comment out the 2 export lines pointing to openmpi | # comment out the 2 export lines pointing to openmpi |
# mpi is setup by sourcing the amber.sh file | ##export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH |
| ##export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH |
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| # additional gcc 6.5.0 |
| export PATH=/share/apps/CENTOS7/gcc/6.5.0/bin:$PATH |
| export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$LD_LIBRARY_PATH |
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| ###source /usr/local/amber16/amber.sh # works on mwgpu |
| ###source /usr/local/amber20/amber.sh # works on exx96 |
| source /share/apps/CENTOS7/amber/amber22/amber.sh # works on mwgpu and exx96 |
| which nvcc mpirun python |
| ldd `which pmemd.cuda_SPFP` |
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| # which and ldd just for debugging |
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</code> | </code> |