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cluster:214 [2022/07/26 14:28] hmeij07 [Amber22] |
cluster:214 [2023/08/18 16:19] (current) hmeij07 [Upgrading] |
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==== 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 | ||
+ | * OneAPI similar conflicts? (/opt/intel and / | ||
+ | * slurm complications? | ||
+ | * **Upgrade Openhpc, OneAPI should be on new head node** | ||
+ | * test compatibility compilers | ||
+ | * slurm clients | ||
< | < | ||
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yum upgrade " | yum upgrade " | ||
yum upgrade " | yum upgrade " | ||
+ | |||
+ | or | ||
+ | |||
+ | yum update --disablerepo=* --enablerepo=[oneAPI, | ||
</ | </ | ||
+ | **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 ==== | ||
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Amber cmake download fails with READLINE error ... package readline-devel needs to be installed to get past that which pulls in | Amber cmake download fails with READLINE error ... package readline-devel needs to be installed to get past that which pulls in | ||
- | ** Example script run.rocky for cpu or gpu run** (not for queues | + | ** Example script run.rocky for cpu or gpu run** (for queues |
< | < | ||
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</ | </ | ||
- | ** Example script run.centos for cpui or gpu run** (queues mwgpu, exx96) | + | ** Example script run.centos for cpus or gpu run** (queues mwgpu, exx96) |
< | < | ||
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==== Amber22 ==== | ==== Amber22 ==== | ||
- | First establish a successfull | + | Amber22 is somehow incompatible with CentOS/ |
+ | |||
+ | https:// | ||
+ | " | ||
+ | |||
+ | < | ||
+ | |||
+ | [hmeij@n79 src]$ echo $AMBERHOME | ||
+ | / | ||
+ | |||
+ | [hmeij@n79 src]$ which mpirun mpicc | ||
+ | / | ||
+ | / | ||
+ | |||
+ | </ | ||
+ | |||
+ | First establish a successful | ||
< | < | ||
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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 |
module --ignore_cache avail | module --ignore_cache avail | ||
Line 658: | Line 691: | ||
</ | </ | ||
- | Amber22 is somehow incompatible | + | First establish a success full run with the **run.centos** script for Amber20 |
+ | |||
+ | Then edit the | ||
+ | |||
+ | < | ||
+ | |||
+ | # comment out the 2 export lines pointing to openmpi | ||
+ | ##export PATH=/ | ||
+ | ##export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | # additional gcc 6.5.0 | ||
+ | export | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | |||
+ | # edit or add correct | ||
+ | ###source / | ||
+ | ###source / | ||
+ | source / | ||
+ | which nvcc mpirun python | ||
+ | ldd `which pmemd.cuda_SPFP` | ||
+ | |||
+ | </ | ||
\\ | \\ |