Re: FEP/λ-REMD Simulation error

From: Ropón-Palacios G. (biodano.geo_at_gmail.com)
Date: Mon Nov 09 2020 - 14:30:01 CST

You are running charmm++ as stand alone?, this run good into other jobs?

  El 9/11/20 a las 14:00, Alao, John-Paul escribió:
> 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 <mailto: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 <mailto: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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