From: Jeffery Klauda (jbklauda_at_umd.edu)
Date: Wed Jul 16 2014 - 13:28:27 CDT
I would like to run NAMD optimized for MIC and CUDA on Stampede. I have
been able to use the provided scripts in the following directory:
/home1/00288/tg455591/NAMD_scripts
For example, runbatch_latest_mic runs fine. The issue is I would like
to use my own queue submission script and have not been able to get it
to work. I have tried scripts in CSH and BASH with no luck. I am
confused why runbatch_latest_mic works but when I run the script below
it outputs the following error:
TACC: Starting up job 3694819
TACC: Setting up parallel environment for MVAPICH2+mpispawn.
TACC: Starting parallel tasks...
Charmrun: Bad initnode data length. Aborting
Charmrun> IBVERBS version of charmrun
**Submission Script**
#!/bin/csh
#SBATCH -J emre16 # Job name
#SBATCH -o emre.o%j # output and error file name (%j expands to
jobID)
#SBATCH -N 1 # total number of nodes
#SBATCH -n 16 # total number of mpi tasks requested
#SBATCH -p normal-mic # queue (partition) -- normal, development, etc.
#SBATCH -t 02:00:00 # run time (hh:mm:ss)
module load fftw3
# Set variables per Schulten Lab /home1/00288/tg455591/NAMD_scripts
set BINDIR =
/work/00288/tg455591/NAMD_build.latest/NAMD_2.9_Linux-x86_64-ibverbs-smp-Stampede-MIC
set SCRIPTDIR = /home1/00288/tg455591/NAMD_scripts
@ REALNUMPROCS = 1 * 15
@ NUMTASKS = 1
echo Running on host `hostname`
echo Time is `date`
echo Directory is `pwd`
# Execution of the script
$BINDIR/charmrun +p$REALNUMPROCS ++ppn 15 ++mpiexec ++remote-shell
$SCRIPTDIR/mpiexec $BINDIR/namd2 +commap 0 +pemap 1-15 +devices 0
dyn.inp >& dyn2.out
Jeff
-- ***************************************************** Jeffery B. Klauda Associate Professor Department of Chemical and Biomolecular Engineering 2113 Building 90 University of Maryland College Park, MD 20742 Phone: (301) 405-1320 Fax: (301) 314-9126 Office: 1227A Chemical & Nuclear Engineering Bldg. Web: terpconnect.umd.edu/~jbklauda *****************************************************
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