Hi,
this post is bit misorganized. so you have passed ./configure stage? I
tackle the obvious first.
1. On Compaq platform, use export MPICC="gcc
-L/usr/lib/mpi/mpi_compaq/lib -lmpifarg -lmpi -lelan"
2. it seems that the compiler doesn't receive Macro definition from
commandline, so you may go into the files to hard code the string values
(e.g. GMXLIBDIR are present in tools/futil.c and kernel/topio.c)
Regards,
Yang Ye
On 11/15/2007 6:59 AM, Chris Neale wrote:
I am having difficulty installing the mpi version of gromacs 3.3.2 on
a new computer. I have the same problems for 3.3.1. The serial
version appears to have worked fine. The cluster uses elan for MPI I
have parsed some values from config.log
configure:3291: ccc -V >&5
Compaq C T6.5-002 on Linux 2.4.21-3.7qsnet alpha
Installed as ccc-6.5.6.002-1
Red Hat Linux release 7.2 (Enigma)
Using /usr/lib/gcc-lib/alpha-redhat-linux/2.96 (4).
Compiler Driver T6.5-001 (Linux) cc Driver
I believe my previous post was rejected since it was >2000 lines so I
have put the
entire config.log here:
http://www.pomeslab.com/CN_GromacsPost_111407.html
and reposted.
mpicc appears to link like this (although the script is complicated
enough
that I am not sure if this variable gets modified later):
my %mpilibs ='-L/usr/lib/mpi/mpi_compaq/lib -lmpifarg -lmpi -lelan'
I think that I must have autoconf somewhere since the Makefile was
created, however:
$automake --version
automake (GNU automake) 1.4-p5
$ autoconf --version
bash: autoconf: command not found
I have found some posts related to futil.c including the following
potential fix
http://www.gromacs.org/pipermail/gmx-users/2005-January/013806.html
but I didn't understand where the quotes were intended to go and the
next reply indicates that this is not a good idea in any event.
Another post indicates that I may be required to link it myself and
avoid the mpicc wrapper. I have tried including the following lines
in my compilation script before calling configure
export CC=gcc
export MPICC=gcc
export LIBS="-lmpi"
but configure ends very quickly with the error message:
checking for C compiler default output file name... configure: error:
C compiler cannot create executables
Thanks for any assistance.
Chris.
########
I ran it like this:
#!/bin/bash
MD=/scratch/cneale/exe/gromacs-3.3.2
cd $MD
mkdir exec
export FFTW_LOCATION=/home/cneale/exe/fftw-3.1.2/exec
export GROMACS_LOCATION=${MD}/exec
export CPPFLAGS="-I$FFTW_LOCATION/include"
export LDFLAGS="-L$FFTW_LOCATION/lib"
./configure --prefix=$GROMACS_LOCATION --enable-mpi
--program-suffix="_mpi" --disable-nice > output.mpi_configure 2>&1
make mdrun > output.mpi_make_mdrun 2>&1
make install-mdrun > output.mpi_make_install_mdrun 2>&1
#make distclean
########
The first error in the 'make mdrun' output is:
source='futil.c' object='futil.lo' libtool=yes \
DEPDIR=.deps depmode=none /bin/sh ../../config/depcomp \
/bin/sh ../../libtool --tag=CC --mode=compile mpicc -DHAVE_CONFIG_H
-I. -I../../src -I../../include
-DGMXLIBDIR=\"/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\"
-I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo
-arch ev6 -unroll 2 -fp_reorder -c -o futil.lo futil.c
mpicc -DHAVE_CONFIG_H -I. -I../../src -I../../include
-DGMXLIBDIR=\"/scratch/cneale/exe/gromacs-3.3.2/exec/share/top\"
-I/home/cneale/exe/fftw-3.1.2/exec/include -std1 -fast -O4 -no_ifo
-arch ev6 -unroll 2 -fp_reorder -c futil.c -o futil.o
cc: Error: futil.c, line 521: Invalid expression. (badexpr)
strcpy(libpath,GMXLIBDIR);
---------------------^
cc: Warning: futil.c, line 521: Invalid token discarded. (invaltoken)
strcpy(libpath,GMXLIBDIR);
---------------------^
make[2]: *** [futil.lo] Error 1
make[2]: Leaving directory
`/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory
`/mnt/scratch/cneale/exe/gromacs-3.3.2/src/gmxlib'
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