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cluster:214 [2022/08/02 10:40]
hmeij07 [Amber22] 		cluster:214 [2023/08/18 12:19] (current)
hmeij07 [Upgrading]
Line 397: Line 397:
 ==== Upgrading ==== ==== Upgrading ====
  
-Figure out an upgrade process before going production (don't forget any chroot images and rebuild images).+Figure out an upgrade process before going production. 
 + 
 +  * **Do you actually want to upgrade OpenHPC?** 
 +    * v2.6 deploys ww4.x (maybe not want this, containers) 
 +    * chroot images and rebuild images running rocky 8 
 +    * OneAPI similar conflicts? (/opt/intel and /opt/ohpc/pub) 
 +    * slurm complications? 
 +  * **Upgrade Openhpc, OneAPI should be on new head node** 
 +    * test compatibility compilers 
 +    * slurm clients
  
 <code> <code>
Line 403: Line 412:
 yum upgrade "*-ohpc" yum upgrade "*-ohpc"
 yum upgrade "ohpc-base" yum upgrade "ohpc-base"
 +
 +or
 +
 +yum update --disablerepo=* --enablerepo=[oneAPI,OpenHPC]
  
 </code> </code>
  
 +**Upgrade history**
  
 +  * OS only, 30 Jun 2022 (90+ days up) - no ohpc, oneapi (/opt)
 +  * OS only, 18 Aug 2023 (440+ days up) - no ohpc, oneapi (/opt)
 +  * 
 ==== example modules ==== ==== example modules ====
  
Line 460: Line 477:
 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  
  
-** 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)
  
 <code> <code>
Line 531: Line 548:
 </code> </code>
  
-** Example script run.centos for cpui or gpu run** (queues mwgpu, exx96)+** Example script run.centos for cpus or gpu run** (queues mwgpu, exx96)
  
 <code> <code>
Line 642: Line 659:
 ==== Amber22 ==== ==== Amber22 ====
  
-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 $AMBERHOME. No need to set PATHs, just be sure to source amber.sh in your script. (compile instructions below for me...) 
 + 
 +https://ambermd.org/InstCentOS.php\\ 
 +"download a recent version of OpenMPI at open-mpi.org, untar the distribution in amber22_src/AmberTools/src, and execute in that directory the configure_openmpi script. (Do this after you have done a serial install, and have sourced the amber.sh script in the installation folder to create an AMBERHOME)" 
 + 
 +<code> 
 + 
 +[hmeij@n79 src]$ 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. (for queues amber128 [n78] and test [n100-n101] for gpus and mw128 and tinymem for cpus)
  
 <code> <code>
Line 648: Line 681:
 module load amber/22 module load amber/22
  
-# if the module does not show up in the output of+# if the module does not show up in the output of your console
  
 module avail module avail
  
-# treat your cache as out of date+# treat your module cache as out of date
  
 module --ignore_cache avail module --ignore_cache avail
Line 658: Line 691:
 </code> </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 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, for cpus or gpus on queues mwgpu and exx96). 
  
-https://ambermd.org/InstCentOS.php\\ +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.
-"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> <code>
  
-[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+
  
-</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
  
 +# 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`
  
 +</code>
  
 \\ \\
cluster/214.1659451257.txt.gz · Last modified: 2022/08/02 10:40 by hmeij07

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