User Tools

Site Tools


cluster:214

Warning: Undefined array key -1 in /usr/share/dokuwiki/inc/html.php on line 1458

Differences

This shows you the differences between two versions of the page.

Link to this comparison view

Both sides previous revision Previous revision
Next revision
Previous revision
cluster:214 [2022/08/03 09:10]
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 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 641: Line 658:
  
 ==== Amber22 ==== ==== Amber22 ====
- 
-First establish a successful run with the **run.rocky** script for Amber20 (listed above). Then change the module in your script. 
- 
-<code> 
- 
-module load amber/22 
- 
-# if the module does not show up in the output of your console 
- 
-module avail 
- 
-# treat your module cache as out of date 
- 
-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...) 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...)
Line 674: Line 675:
 </code> </code>
  
-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.+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> 
 + 
 +module load amber/22 
 + 
 +# if the module does not show up in the output of your console 
 + 
 +module avail 
 + 
 +# treat your module cache as out of date 
 + 
 +module --ignore_cache avail 
 + 
 +</code> 
 + 
 +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>
Line 686: Line 705:
 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 711:
 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/214.1659532252.txt.gz · Last modified: 2022/08/03 09:10 by hmeij07