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cluster:214 [2022/08/03 09:10]
hmeij07 [Amber22] 		cluster:214 [2022/08/03 09:59]
hmeij07 [Amber22]
Line 641: Line 641:
  
 ==== Amber22 ==== ==== Amber22 ====
 +
 +Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just be sure to source amber.sh in your script. (compile instructions below for me...)
 +
 +https://ambermd.org/InstCentOS.php\\
 +"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME)"
 +
 +<code>
 +
 +[hmeij@n79 src]$ echo $AMBERHOME
 +/share/apps/CENTOS7/amber/amber22
 +
 +[hmeij@n79 src]$ which mpirun mpicc
 +/share/apps/CENTOS7/amber/amber22/bin/mpirun
 +/share/apps/CENTOS7/amber/amber22/bin/mpicc
 +
 +</code>
  
 First establish a successful 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.
Line 655: Line 671:
  
 module --ignore_cache avail module --ignore_cache avail
- 
-</code> 
- 
-Amber22 is somehow incompatible with CentOS/Rocky openmpi (yum install). Hence the latest version of openmpi was compiled and installed into $AMBERHOME. No need to set PATHs, just be sure to source amber.sh in your script. (compile instructions below for me...) 
- 
-https://ambermd.org/InstCentOS.php\\ 
-"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME)" 
- 
-<code> 
- 
-[hmeij@n79 src]$ echo $AMBERHOME 
-/share/apps/CENTOS7/amber/amber22 
- 
-[hmeij@n79 src]$ which mpirun mpicc 
-/share/apps/CENTOS7/amber/amber22/bin/mpirun 
-/share/apps/CENTOS7/amber/amber22/bin/mpicc 
  
 </code> </code>
Line 686: Line 686:
 export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$LD_LIBRARY_PATH export LD_LIBRARY_PATH=/share/apps/CENTOS7/gcc/6.5.0/lib64:$LD_LIBRARY_PATH
  
 +# 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/amber16/amber.sh # works on mwgpu
 ###source /usr/local/amber20/amber.sh # works on exx96 ###source /usr/local/amber20/amber.sh # works on exx96
Line 691: Line 692:
 which nvcc mpirun python which nvcc mpirun python
 ldd `which pmemd.cuda_SPFP` ldd `which pmemd.cuda_SPFP`
- 
-# which and ldd just for debugging 
  
 </code> </code>
cluster/214.txt ยท Last modified: 2023/08/18 12:19 by hmeij07

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