----- Original Message -----
From: Pinchas Aped <[email protected]>
Date: Monday, June 28, 2010 3:43
Subject: [gmx-users] Problems with installing mpi-version of Gromacs
To: Discussion list for GROMACS users <[email protected]>
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> Dear All: > > I have installed Gromacs on a Linux (RedHat) cluster, using
> the following csh script - > >
> -------------------------------------------------------------------------------------
> > #! /bin/csh > > set DIR=/private/gnss/Gromacs > > setenv SOFT
> ${DIR}/software
> setenv CPPFLAGS "-I$SOFT/include"
> setenv LDFLAGS "-L$SOFT/lib"
> setenv NCPU 4
> setenv PATH "$PATH":$SOFT/bin
> cd openmpi-1.2.8; ./configure --prefix=$SOFT; make -j $NCPU; make install
> cd ../fftw-3.1.3; ./configure --prefix=$SOFT --enable-float; make -j $NCPU;
> make install
> cd ../gsl-1.11; ./configure --prefix=$SOFT; make -j $NCPU; make install
> cd ../gromacs-4.0.7; ./configure --prefix=$SOFT --with-gsl; make -j $NCPU;
> make install
> make distclean; ./configure --prefix=$SOFT --program-suffix=_mpi
> --enable-mpi --with-gsl; make mdrun -j $NCPU; make install-mdrun >
> -------------------------------------------------------------------------------------
> > > It seemed to have worked OK, and we could run Gromacs on a single
> processor. > > When I tried to create a parallel version with the script -
> > >
> -------------------------------------------------------------------------------------
> > #! /bin/csh > > set DIR=/private/gnss/Gromacs > > setenv SOFT
> ${DIR}/software
> setenv CPPFLAGS "-I$SOFT/include"
> setenv LDFLAGS "-L$SOFT/lib"
> setenv NCPU 4
> setenv PATH "$PATH":$SOFT/bin > > cd gromacs-4.0.7; ./configure
> --prefix=$SOFT --with-gsl --enable-mpi; make -j $NCPU mdrun; make
> install-mdrun >
> -------------------------------------------------------------------------------------
> > > - the installation log ended with - > > ......... > checking
> whether the MPI cc command works... configure: error: Cannot compile and
> link MPI code with mpicc
> make: *** No rule to make target `mdrun'. Stop.
> make: *** No rule to make target `install-mdrun'. Stop. > > I can't
> figure out from this message what is wrong or missing with my MPI.
It looks like you included the scripts the wrong way around, or something.
Both scripts should build MPI-enabled mdrun, with the second not naming it with
_mpi. See
http://www.gromacs.org/index.php?title=Download_%26_Installation/Installation_Instructions
for the usual procedure.
You can inspect the last 100 or so lines of config.log to see the actual error
issue.
The issue has probably got nothing to do with GROMACS. Try compiling and
running some MPI test program to establish this.
Mark
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