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cluster:214 [2022/08/02 14:40] hmeij07 [Amber22] |
cluster:214 [2022/08/03 13:59] hmeij07 [Amber22] |
Amber cmake download fails with READLINE error ... package readline-devel needs to be installed to get past that which pulls in ncurses-c++-libs-6.1-9.20180224.el8.x86_64 ncurses-devel-6.1-9.20180224.el8.x86_64 readline-devel-7.0-10.el8.x86_64 | Amber cmake download fails with READLINE error ... package readline-devel needs to be installed to get past that which pulls in ncurses-c++-libs-6.1-9.20180224.el8.x86_64 ncurses-devel-6.1-9.20180224.el8.x86_64 readline-devel-7.0-10.el8.x86_64 |
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** Example script run.rocky for cpu or gpu run** (not for queues mwgpu, exx96) | ** Example script run.rocky for cpu or gpu run** (for queues amber128 [n78] and test [n100-n101] for gpus and mw128 and tinymem for cpus) |
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<code> | <code> |
==== 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. | Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just be sure to source amber.sh in your script. (compile instructions below for me...) |
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| https://ambermd.org/InstCentOS.php\\ |
| "download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME)" |
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| <code> |
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| [hmeij@n79 src]$ echo $AMBERHOME |
| /share/apps/CENTOS7/amber/amber22 |
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| [hmeij@n79 src]$ which mpirun mpicc |
| /share/apps/CENTOS7/amber/amber22/bin/mpirun |
| /share/apps/CENTOS7/amber/amber22/bin/mpicc |
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| </code> |
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| 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 $AMBERHOME. No need to set PATHs, just sure to source amber.sh in your script. (compile instructions below for me...) | First establish a success full run with the **run.centos** script for Amber20 (listed above). Then edit the script and apply these edits. We had to use a specific compatible ''gcc/g++'' version to make this work. Hardware is getting too old. |
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https://ambermd.org/InstCentOS.php\\ | |
"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME | |
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<code> | <code> |
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[hmeij@n79 src]$ echo $AMBERHOME | # comment out the 2 export lines pointing to openmpi |
/share/apps/CENTOS7/amber/amber22 | ##export PATH=/share/apps/CENTOS7/openmpi/4.0.4/bin:$PATH |
[hmeij@n79 src]$ which mpirun mpicc | ##export LD_LIBRARY_PATH=/share/apps/CENTOS7/openmpi/4.0.4/lib:$LD_LIBRARY_PATH |
/share/apps/CENTOS7/amber/amber22/bin/mpirun | |
/share/apps/CENTOS7/amber/amber22/bin/mpicc | |
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</code> | # additional gcc 6.5.0 |
| export PATH=/share/apps/CENTOS7/gcc/6.5.0/bin:$PATH |
| export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$LD_LIBRARY_PATH |
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| # edit or add correct source line, which and ldd lines just for debugging |
| ###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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| </code> |
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\\ | \\ |