Re: Couldn't open DCD file

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Wed Oct 31 2018 - 15:33:06 CDT

You are trying to launch the single-process "multicore" binary with
mpiexec. If you look at the simple runbatch script that ships with the
multicore binaries you will see that it does not understand ++mpiexec, so
it is just running "mpiexec -n 80 ..." and therefore you are getting 80
independent copies of "namd2 +p80", which are stepping on top of each
other all trying to write the same dcd file.

Jim

On Wed, 31 Oct 2018, Hazard, E. Starr wrote:

> I'm not able to get this BPTI example to execute
>
> https://www.ks.uiuc.edu/Research/namd/2.13b2/ug/node17.html
>
> The first error is that the program cannot open a file that does exist
>
> ls -ltr *dcd*
> -rw-r--r-- 1 hazards hazards 13512 Oct 31 15:11 bpti.dcd
> -rw-r--r-- 1 hazards hazards 39984 Oct 31 15:11 bpti.dcd.BAK
>
> If this is a permissions issue how can set permissions in a submit script?
>
> ------------- Processor 0 Exiting: Called CmiAbort ------------
> Reason: FATAL ERROR: Couldn't open DCD file output/bpti.dcd: File exists
>
>
> Here's my namd conf file
>
> cat bpti.namd
> # NAMD configuration file for BPTI
> # molecular system
> structure output/bpti.psf
> # force field
> paratypecharmm on
> parameters toppar/par_all36m_prot.prm
> parameters toppar/toppar_water_ions.str
> parameters toppar/par_all36_lipid.prm
> parameters toppar/par_all36_carb.prm
> parameters toppar/par_all36_cgenff.prm
> parameters toppar/par_all36_na.prm
> exclude scaled1-4
> 1-4scaling 1.0
> # approximations
> switching on
> switchdist 8
> cutoff 12
> pairlistdist 13.5
> margin 0
> stepspercycle 20
> #integrator
> timestep 1.0
> #output
> outputenergies 10
> outputtiming 100
> binaryoutput no
> # molecular system
> coordinates output/bpti.pdb
> #output
> outputname output/bpti
> dcdfreq 1000
> #protocol
> temperature 0
> reassignFreq 1000
> reassignTemp 25
> reassignIncr 25
> reassignHold 300
> #script
> minimize 1000
> run 20000
>
> here's my LSF submission script
>
> #!/bin/bash
> #BSUB -J NAMD2018
> #BSUB -o NAMD2018_OUT%J
> #BSUB -e NAMDERR.e%J
> #BSUB -n 80
> #BSUB -u hazards_at_musc.edu
> export MPICH_HOME=/shared/app/mpich2-1.41pl_intel_12_install
> export HYDRA_HOST_FILE=/home/hazards/machines
> export PWD=/home/hazards/NAMD/:$PWD
> export PATH=/home/hazards/NAMD/toppar:$PATH
> date
> /shared/app/NAMD_Linux-x86_64-multicore/charmrun ++mpiexec $MPICH_HOME/bin/mpiexec -launcher ssh -f /home/hazards/machines -n 80 \
> /shared/app/NAMD_Linux-x86_64-multicore/namd2 +p80 /home/hazards/NAMD/bpti.namd > \
> /home/hazards/NAMD/bpti_mpiexec.out
>
>
> Thanks
>
> Starr
>
>
>
>
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