[gmx-users] Problems with installing mpi-version of Gromacs

[Mark Abraham]

----- Original Message -----
From: Pinchas Aped <aped at mail.biu.ac.il>
Date: Monday, June 28, 2010 3:43
Subject: [gmx-users] Problems with installing mpi-version of Gromacs
To: Discussion list for GROMACS users <gmx-users at gromacs.org>

 
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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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