NAMD for Intel Xeon Cluster with MPICH

From: DimitryASuplatov (genesup_at_gmail.com)
Date: Mon Dec 22 2008 - 06:33:48 CST

Hello,

I want to compile NAMD on Intel Xeon cluster running with mpich.

I build fftw and tcp from sources downloaded from http://www.ks.uiuc.edu
site. No problems here.

Thet I download NAMD-2.6, untar it and charm-5.9.
Then I cd to charm-5.9 and edit mpi config file

echo "CMK_CPP_CHARM='/lib/cpp -P'
CMK_CPP_C='gcc -E'
CMK_CC="mpicc $CMK_INCDIR"
CMK_CXX="mpicxx $CMK_INCDIR"
CMK_CXXPP="$CMK_CXX -E "
CMK_CF77="mpif77"
CMK_CF90="mpif90"
CMK_NATIVE_CC="gcc "
CMK_NATIVE_LD="gcc "
CMK_NATIVE_CXX="g++ "
CMK_NATIVE_LDXX="g++ "
CMK_RANLIB='ranlib'
CMK_LIBS='-L/usr/lib/mvapich-intel-x86_64/lib/ -lckqt -lpmpich -lmpich'
CMK_XIOPTS=''
CMK_F90LIBS='-L/usr/absoft/lib -lf90math -lfio -lU77 -lf77math '
CMK_MOD_NAME_ALLCAPS=1
CMK_MOD_EXT="mod"
CMK_F90_USE_MODDIR=1
CMK_F90_MODINC="-p"

" > src/arch/mpi-linux-ia64/conv-mach.sh

Then I run

./build charm++ mpi-linux-ia64 --no-shared -O -DCMK_OPTIMIZE=1
-L/usr/lib/mvapich-intel-x86_64/lib/
-I/usr/lib/mvapich-intel-x86_64/include/

Compilation ends with "charm++ built successfully".
But when I try to run megatest I get the error like this

ld: Warning: size of symbol `valloc' changed from 672
in ../../../bin/../lib/libmemory-default.o to 144
in /usr/lib/mvapich-intel-x86_64/lib/libpmpich.a(malloc.o)
Fatal Error by charmc in
directory /home/suplatov/dist/namd/NAMD_2.6_Source/charm-5.9/tests/charm
++/megatest
  Command mpicxx -rdynamic -o pgm -L../../../bin/../lib
-I../../../bin/../include ../../../bin/../lib/libldb-rand.o megatest.o
groupring.o nodering.o varsizetest.o varraystest.o groupcast.o
nodecast.o synctest.o fib.o arrayring.o tempotest.o packtest.o queens.o
migration.o marshall.o priomsg.o priotest.o rotest.o statistics.o
templates.o inherit.o reduction.o callback.o immediatering.o bitvector.o
moduleinit23805.o ../../../bin/../lib/libmemory-default.o
./../../bin/../lib/libthreads-default.o -lck -lconv-cplus-y
-lconv-core -lconv-util -L/usr/lib/mvapich-intel-x86_64/lib/ -lckqt
-lpmpich -lmpich -ldl -lm returned error code 1
charmc exiting...
make: *** [pgm] Error 1

Perhaps as a consequence namd itself does not compile with this charm.
-------------------------------------------------------------------------------------------------

1. What am I doing wrong? I could not find any simple and
straightforward explanation of compiling namd with mpi in the mail list
or the internet. Did I miss something?

2. Should I use ia64 or amd64 for Intel Quad/Xeon CPU?

Thank you!

mpiCC for 1.2.7 (release) of : 2005/11/04 11:54:51 Version 11.0
Linux T60-2.parallel.ru 2.6.18-hpc-alt1.M41.1 #1 SMP Fri Sep 26 13:28:44
MSD 2008 x86_64 GNU/Linux

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