AMBER Archive (2009)

Subject: Re: [AMBER] pmemd on BlueGene/P?

From: Hannes Loeffler (hannes.loeffler_at_stfc.ac.uk)
Date: Fri Feb 06 2009 - 03:01:37 CST

Carlos,

thank you very much for coming back to me so rapidly.

Our software is at patch(?) level V1R3M0_460_2008-081112P. The cpp/xlf
expects to find (hard-coded I think) the cat files
in /opt/ibmcmp/xlf/11.1/msg/en_US/ but they are actually installed
in /opt/ibmcmp/xlf/bg/11.1/msg/en_US/. Anyway, looking through the cpp
binary I found that you can set the enviroment variabel XL_DEFMSG to the
proper directory.

The problem was that mpif.h could not be found, so I adjusted the
include paths and also the lib paths (see below). BTW, there appears to
be a "fast" libmpich. Would that one have any effect on performance?

Pmemd/9 compiles now, also with netcdf 4.0, and a few tests finished
successfully.

If you have any comments I would be grateful to hear about them.

Hannes.

===================== config.h for BG/P =========================

MATH_DEFINES =
MATH_LIBS = -L$MASSVP_LIBDIR -lmassv
DIRFRC_DEFINES = -DDIRFRC_EFS -DIRFRC_COMTRANS -DSLOW_INDIRECTVEC

# compilers and linker
F90 = mpixlf90
CC = mpixlc
LOAD = mpixlf90

# FFTW
FFT_INCLUDEDIR = /home/hhl/usr/include
FFT_LIBDIR = /home/hhl/usr/lib
FFT_DEFINES = -DFFTW_FFT
FFT_INCLUDE = -I$(FFT_INCLUDEDIR)
FFT_LIBS = -L$(FFT_LIBDIR) -lfftw3

# netcdf 4.0
NETCDF_HOME = /home/hhl/usr
NETCDF_DEFINES = -DBINTRAJ
NETCDF_MOD = netcdf.mod
NETCDF_LIBS = $(NETCDF_HOME)/lib/libnetcdf.bgp.a

# MPI, there is also /bgsys/drivers/ppcfloor/comm/fast/{lib,include}
MPI_DEFINES = -DMPI
MPI_INCLUDE = -I/bgsys/drivers/ppcfloor/include
-I/bgsys/drivers/ppcfloor/comm/include
MPI_LIBS = -L/bgsys/drivers/ppcfloor/lib
-L/bgsys/drivers/ppcfloor/comm/lib -lmpich.cnk

# preprocessor stuff
CPP = /opt/ibmcmp/xlf/bg/11.1/exe/cpp
CPPFLAGS =
#XL_DEFMSG = /opt/ibmcmp/xlf/bg/11.1/msg/en_US
F90_DEFINES = -DNO_C_UNDERSCORE

# flags for the Fortran 90 compiler, some tweaking may be possible
# e.g. -O4 sets -O3 -qarch -qtune -qcache -qhot -qipa
# -O5 sets -O4 -qipa=level=2
# -qlibansi
MODULE_SUFFIX = mod
CPUFLAGS = -qarch=450d -qtune=450
F90FLAGS = $(CPUFLAGS) -qsuffix=f=f90 -qdpc -c
F90_OPT_DBG = -g -O0
F90_OPT_LO = -qmaxmem=-1
F90_OPT_MED = -qmaxmem=-1 -O
F90_OPT_HI = -O3 -qstrict -qhot
F90_OPT_DFLT = $(F90_OPT_HI)

CFLAGS = $(CPUFLAGS) -DNO_C_UNDERSCORE

LOADFLAGS =
LOADLIBS = -lm

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