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cluster:214 [2022/08/02 18:25] – [Amber22] hmeij07cluster:214 [2023/08/18 16:19] (current) – [Upgrading] hmeij07
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>
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 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 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>
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 ==== 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> <code>
  
-module load amber/22+[hmeij@n79 src]$ echo $AMBERHOME 
 +/share/apps/CENTOS7/amber/amber22
  
-# if the module does not show up in the output of+[hmeij@n79 src]$ which mpirun mpicc 
 +/share/apps/CENTOS7/amber/amber22/bin/mpirun 
 +/share/apps/CENTOS7/amber/amber22/bin/mpicc
  
-module avail+</code>
  
-# treat your cache as out of date+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)
  
-module --ignore_cache avail+<code>
  
-</code>+module load amber/22
  
-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...)+# if the module does not show up in the output of your console
  
-https://ambermd.org/InstCentOS.php\\ +module avail
-"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>+# treat your module cache as out of date
  
-[hmeij@n79 src]$ echo $AMBERHOME +module --ignore_cache avail
-/share/apps/CENTOS7/amber/amber22 +
-[hmeij@n79 src]$ which mpirun mpicc +
-/share/apps/CENTOS7/amber/amber22/bin/mpirun +
-/share/apps/CENTOS7/amber/amber22/bin/mpicc+
  
 </code> </code>
  
-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, for cpus or gpus on queues mwgpu and exx96).  
 + 
 +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.
  
 <code> <code>
  
 # 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
  
 +# 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
  
-<code>+# 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/214.1659464717.txt.gz · Last modified: by hmeij07