compiling NAMD on OSC P4 cluster

From: Amit Paliwal (
Date: Fri Sep 03 2004 - 12:11:51 CDT

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.


# Conv-host for MPI:
# Translates +pN-style conv-host options into
# mpirun -npN options.


while [ $# -gt 0 ]
        case $1 in
                args=$args" +ppn "$2
                args=$args" "$1
                pes=`echo $1 | awk '{print substr($1,3)}'`
                args=$args" "$1

echo "Running on $pes processors: $args"

mpirun -np $pes $args

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