http://www.ks.uiuc.edu/Research/namd/
2.13
--- src/arch/mpi/charmrun.org 2018-11-26 16:02:00.000000000 +0900
+++ src/arch/mpi/charmrun 2018-11-26 16:04:16.000000000 +0900
@@ -37,11 +37,11 @@
+p[0-9]*)
pes=`echo $1 | awk '{print substr($1,3)}'`
;;
- -machinefile)
- machinefile=$2
- args=" "$1" "$2" "$args
- shift
- ;;
+# -machinefile)
+# machinefile=$2
+# args=" "$1" "$2" "$args
+# shift
+# ;;
++quiet)
QUIET=1
args=$args" "$1
@@ -88,7 +88,7 @@
mpirun -np $pes $args
# mpdallexit
else # normal case
- test -z "$machinefile" && args=-machinefile" "$PBS_NODEFILE" "$args
+ #test -z "$machinefile" && args=-machinefile" "$PBS_NODEFILE" "$args
test $QUIET -eq 0 && echo mpirun -np $pes $args
mpirun -np $pes $args
fi
#!/bin/sh
VERSION=2.13
CHARM_VERSION=6.8.2
WORKDIR=/work/users/${USER}
SOURCEDIR=/home/users/${USER}/Software/NAMD/${VERSION}
NAME=NAMD_${VERSION}_Source
TARBALL=${SOURCEDIR}/${NAME}.tar.gzLIBURL=http://www.ks.uiuc.edu/Research/namd/libraries
TCL=tcl8.5.9-linux-x86_64
TCL_URL=${LIBURL}/${TCL}.tar.gz
TCL_THREADED=tcl8.5.9-linux-x86_64-threaded
TCL_THREADED_URL=${LIBURL}/${TCL_THREADED}.tar.gzPATCH0=${SOURCEDIR}/charmrun.patch
PARALLEL=12
#------------------------------------------------------------------
umask 0022export LANG=""
export LC_ALL=Cmodule purge
module load intel/18.0.5
module load mpi/openmpi/3.1.0/intel
module load mkl/2018.0.4cd ${WORKDIR}
if [ -d ${NAME} ]; then
mv ${NAME} namd_erase
rm -rf namd_erase &
fitar zxf ${TARBALL}
cd ${NAME}
tar xf charm-${CHARM_VERSION}.tarcd charm-${CHARM_VERSION}
patch -p0 < ${PATCH0}
sed -i -e "s/_OPTIMIZE/_OPTIMIZE -xHost/" src/scripts/charmcexport CC=icc
export CXX=icpc
export F90=ifort
export F77=ifort
export MPICXX=mpicxx
export MPICC=mpicc
export MPIF90=mpif90
export MPIF77=mpif90./build charm++ mpi-linux-x86_64-iccstatic \
--no-build-shared --with-production -j${PARALLEL}
cd mpi-linux-x86_64-iccstatic/tests/charm++/megatest
make pgm
mpirun -np ${PARALLEL} ./pgm
cd ../../../../
cd ../wget ${FFTW_URL}
tar zxf ${FFTW}.tar.gz
mv linux-x86_64 fftw
wget ${TCL_URL}
tar zxf ${TCL}.tar.gz
mv ${TCL} tcl
wget ${TCL_THREADED_URL}
tar zxf ${TCL_THREADED}.tar.gz
mv ${TCL_THREADED} tcl-threadedNEWOPTS="-xHost -static-intel -O3 -ip -fp-model fast=2 -DNAMD_DISABLE_SSE"
./config Linux-x86_64-icc \
--charm-arch mpi-linux-x86_64-iccstatic \
--with-mkl \
--with-python \
--cxx-opts "$NEWOPTS" \
--cxx-thread-opts "$NEWOPTS" \
--cxx-noalias-opts "$NEWOPTS -fno-alias" \
--cc-opts "$NEWOPTS"
cd Linux-x86_64-icc
make -j${PARALLEL}
make release