VMD-L Mailing List
From: Rachel (comeonsos_at_googlemail.com)
Date: Wed Jul 25 2007 - 11:11:34 CDT
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Dear all,
I have VMD installed on IBM cluster, and I need to run some scripts with VMD
which takes long time to finish when ran interactively, therefore I am
wondering if I submit to queueing system it may be much faster, here is the
script I used to submit the job:
-------------------------------------------------------------------------------------------------------------------------------------------------
#@ shell = /bin/bash
#
#@ job_name = model_VMD
#
#@ job_type = parallel
#@ cpus = 16
#@ node_usage = not_shared
#
#@ bulkxfer = yes
#
#@ wall_clock_limit = 06:00:00
#@ account_no = a129
#
#@ output = $(job_name).$(schedd_host).$(jobid).out
#@ error = $(job_name).$(schedd_host).$(jobid).err
#@ notification = never
#
#
#@ queue
# suggested environment settings:
export MP_EAGER_LIMIT=65536
export MP_SHARED_MEMORY=yes
export MEMORY_AFFINITY=MCM
export MP_TASK_AFFINITY=MCM
vmd mol new model.prmtop
vmd mol addfile model_md1to5.mdcrd type crdbox waitfor all
vmd source myscript.tcl
vmd myscript
--------------------------------------------------------------------------------------------------------------------------------------------------
And the following are the output and error messages:
Info) VMD for AIX5_64, version 1.8.6 (April 6, 2007)
Info) http://www.ks.uiuc.edu/Research/vmd/
Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
Info) Please include this reference in published work using VMD:
Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1 , 33-38.
Info) -------------------------------------------------------------
Info) Multithreading available, 16 CPUs detected.
Info) Free system memory: 0MB (-9223372036854775808%)
Info) VMD for AIX5_64, version 1.8.6 (April 6, 2007)
Info) Exiting normally.
/var/loadl/execute/l1f402.211658.0/run_VMD: mol: command not found
/var/loadl/execute/l1f402.211658.0/run_VMD: mol: command not found
/var/loadl/execute/l1f402.211658.0/run_VMD: proc: command not found
/var/loadl/execute/l1f402.211658.0/run_VMD: puts: command not found
/var/loadl/execute/l1f402.211658.0/run_VMD: myscript.tcl: line 7: syntax
error near unexpected token `i'
---------------------------------------------------------------------------------------------------------------------------------------------------
I haven't used VMD in this way before, therefore not sure whether it is the
right way to do so. What I really need is a way to use VMD for analysis that
takes long time that I can logoff without killing the process.
Thank you in advance for any advice.
Kind regards,
Rachel
- Next message: Axel Kohlmeyer: "Re: how to run VMD on IBM machines"
- Previous message: Rachel : "how to wrap trajectory into truncated octahedral box"
- Next in thread: Axel Kohlmeyer: "Re: how to run VMD on IBM machines"
- Reply: Axel Kohlmeyer: "Re: how to run VMD on IBM machines"
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