From: Alao, John-Paul (alaooj_at_miamioh.edu)
Date: Mon Nov 09 2020 - 13:00:39 CST
Yes, I do. I'm running it on a cluster, and I requested 24 procs to run the
job.
On Mon, Nov 9, 2020 at 1:51 PM "ROPÓN-PALACIOS G." <biodano.geo_at_gmail.com>
wrote:
> This approach need that you runs this On 24 cores, you have 24 cores into
> your machine?
>
> Enviado desde mi iPhone
>
> El 9 nov. 2020, a la(s) 12:03 p. m., Alao, John-Paul <alaooj_at_miamioh.edu>
> escribió:
>
>
> Dear mailing list,
>
> I generated the configuration files to run absolute protein-ligand binding
> free energy using Charmm-GUI. However, this part of the code crashes.
>
> # FEP/λ-REMD Simulation, Runing 4 ns (200 ps x 20)
> cnt=0
> cntmax=20
>
> while [ ${cnt} -le ${cntmax} ]
> do
> if [ ${cnt} -eq 0 ]
> then
> charmrun /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2
> +p24 +replicas 24 fep_${system}.conf --source FEP_remd_softcore.namd
> +stdout output_${system}/%d/job${cnt}.%d.log
> else
> charmrun /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2
> +p24 +replicas 24 restart_${cnt}.conf --source FEP_remd_softcore.namd
> +stdout output_${system}/%d/job${cnt}.%d.log
> fi
> cnt=$[$cnt+1]
> done
>
> *The error message is:*
>
> Running command: /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2
> +p24 +replicas 24 fep_solv.conf --source FEP_remd_softcore.namd +stdout
> output_solv/%d/job0.%d.log
>
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in Multicore mode: 24 threads
> ./fep.sh: line 40: 106230 Segmentation fault (core dumped) charmrun
> /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2 +p24 +replicas 24
> fep_${system}.conf --source FEP_remd_softcore.namd +stdout
> output_${system}/%d/job${cnt}.%d.log
> Running command: /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2
> +p24 +replicas 24 restart_1.conf --source FEP_remd_softcore.namd +stdout
> output_solv/%d/job1.%d.log
>
> Charm++: standalone mode (not using charmrun)
> Charm++> Running in Multicore mode: 24 threads
> ./fep.sh: line 40: 106232 Segmentation fault (core dumped) charmrun
> /software/NAMD/NAMD_2.13_Linux-x86_64-multicore/namd2 +p24 +replicas 24
> restart_${cnt}.conf --source FEP_remd_softcore.namd +stdout
> output_${system}/%d/job${cnt}.%d.log
>
> Please can anyone assist with information on how to get around this?
> Thanks a lot.
>
>
>
>
>
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