Re: running NAMD with Slurm on cluster

From: Victor Kwan (vkwan8_at_uwo.ca)
Date: Wed Jan 09 2019 - 12:05:07 CST

The Linux-x86_64-multicore (64-bit Intel/AMD single node) binary does
not have support for multiple nodes. Contact your admin (or use
`module spyder namd`) to find what version of namd that support
multiple nodes is available.

Victor

On Wed, Jan 9, 2019 at 10:09 AM Seibold, Steve Allan <stevesei_at_ku.edu> wrote:
>
> I using a Slurm script for running NAMD across several machines (or attempting to that is). When I run 2 nodes with each having 15 cores, the Slurm output says, I am running "2 nodes" each with "15 cores". A total of 30 cores; however, my namd output (log file) says that I am running on 15 cores...
>
>
> Below is my command line information...I know I don't use "+p ", but I have tried "mpirun" , "charmrun", and "mpiexe" placement in the below command line and I get "no such file or directory"...
>
>
> I am using the NAMD_2.13 binary obtained from NAMD site...Do I need to build/compile it instead with mpi..?
>
>
>
> ~/NAMD2/NAMD_2.13_Linux-x86_64/namd2 md6_3BP.namd
>
>
> Thanks, Steve

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