From: Amit Paliwal (paliwal_at_jhu.edu)
Date: Fri Sep 03 2004 - 12:11:51 CDT
Hi,
I am running into some compilation errors while installing NAMD on P4
cluster at Ohio Supercomputing center. Precompiled binaries crash after
running for 2000 steps, this is reproducible.
Charm++ compiles successfully with mpi-linux-icc option but I can not
compile namd2. Any ideas ? Also validation programs like
samplearrayhello could not be run and ./charmrun +p4 ./hello returns :
Can't find MPIRUN machine file for machine vapi and architecture Linux.
( NO device specified)
Here is what charmrun in simplearrayhello is also attached.
If anyone has compiled NAMD on OSC cluster , do let me know of any
special tasks involved in compiling NAMD there.
-Amit.
#!/bin/sh
#
# Conv-host for MPI:
# Translates +pN-style conv-host options into
# mpirun -npN options.
args=""
pes=1
while [ $# -gt 0 ]
do
case $1 in
+ppn)
args=$args" +ppn "$2
shift
;;
+ppn*)
args=$args" "$1
;;
+p)
pes=$2
shift
;;
+p*)
pes=`echo $1 | awk '{print substr($1,3)}'`
;;
*)
args=$args" "$1
;;
esac
shift
done
echo "Running on $pes processors: $args"
mpirun -np $pes $args
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