Setting up / Running NAMD on HPC

From: Gerald Keller (
Date: Mon May 25 2020 - 03:56:34 CDT

Hi all,

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?

Best regards,


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