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cluster:214 [2022/08/02 14:40] hmeij07 [Amber22] |
cluster:214 [2022/08/03 14:05] hmeij07 |
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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 |
< | < | ||
Line 531: | Line 531: | ||
</ | </ | ||
- | ** Example script run.centos for cpui or gpu run** (queues mwgpu, exx96) | + | ** Example script run.centos for cpus or gpu run** (queues mwgpu, exx96) |
< | < | ||
Line 642: | Line 642: | ||
==== 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 | ||
< | < | ||
Line 648: | Line 664: | ||
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- | # treat your cache as out of date | + | # treat your module |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 674: | ||
</ | </ | ||
- | Amber22 is somehow incompatible | + | First establish a success full run with the **run.centos** |
- | https:// | + | Then edit the script and apply these edits. We had to use a specific compatible '' |
- | " | + | |
< | < | ||
- | [hmeij@n79 src]$ echo $AMBERHOME | + | # comment out the 2 export lines pointing to openmpi |
- | / | + | ##export PATH=/ |
- | [hmeij@n79 src]$ which mpirun mpicc | + | ##export LD_LIBRARY_PATH=/ |
- | / | + | |
- | / | + | |
- | </code> | + | # additional gcc 6.5.0 |
+ | export PATH=/share/ | ||
+ | export LD_LIBRARY_PATH=/ | ||
+ | # edit or add correct source line, which and ldd lines just for debugging | ||
+ | ###source / | ||
+ | ###source / | ||
+ | source / | ||
+ | which nvcc mpirun python | ||
+ | ldd `which pmemd.cuda_SPFP` | ||
+ | </ | ||
\\ | \\ |