compiling NAMD on OSC P4 cluster

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

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:18:22 CST