From: Gerald Keller (gerald.keller_at_uni-wuerzburg.de)
Date: Mon May 25 2020 - 03:56:34 CDT
I'm usually running NAMD on local single nodes in our working group. Since we are at the limit of our resources I'd like to run NAMD simulations on a HPC.
On the desired HPC, NAMD is not preinstalled / can't be loaded as a module, SLURM and infiniband are available. I'm not using GPUs.
Now I'm not really sure how to get started.
I downloaded the precompiled version of ibverbs and ibverbs-smp of NAMD 2.13, respectively and tried to do a test run.
Then I only observe errors:
Assertion "num_devices > 0" failed in file machine-ibverbs.c line 482 and that the tasks have segmentation fault.
I have run the test simulation with:
srun -N 1 -n 3 -p partition_name namd2 conffile
Could anybody point me into the right direction? Do I have to compile NAMD for the HPC on my own? Am I running completely wrong parameters regarding to srun?
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