Installing NAMD in Ethernet (1Gbps) cluster

From: Yasser Bruno Ruiz Blanco (
Date: Fri Apr 16 2021 - 04:15:08 CDT

Dear all,

I am trying to set up NAMD in a small dedicated cluster (20 nodes with AMD
EPYC 7402 processors) connected via Ethernet 1Gbps (no
high-performance network such as Infiniband or Omni path).

I have tried to run directly the prebuild version:
"NAMD_2.14_Linux-x86_64-netlrts". However, it produces errors related to
lack of authorization for accessing the nodes

I then tried to compile the code using MPI libraries but the jobs hang
without output.

I would be grateful to receive advice about the use of the prebuild version
in a cluster with the characteristics mentioned above. Or, some additional
guidelines for the compilation.

Also, could you comment on the expected scaling in such a cluster?

Kind regards. Stay healthy,

Dr. Yasser B. Ruiz-Blanco
Postdoctoral Researcher
Computational Biochemistry
Faculty of Biology
University of Duisburg-Essen

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