Dear gmx-users, after my last message yesterday on the gmx-user list, I contacted the administrators of the machine on which Gromacs 4.0.7 has been installed. We performed several checks and concluded that probably the command mdrun_d on that machine has been badly compiled (Gromacs has been installed in double precision), whereas the command mdrun_mpi has been compiled correctly and works correctly. They have some problems in finding the error in that installation because they don't know GROMACS in details, so they would like to check the installation they made with people more expert on GROMACS installation. I'm pasting below the steps they made to install Gromacs 4.0.7 on this machine: : GSL INSTALLATION:
./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19 --enable-static --enable-shared && make && make install FFTW INSTALLATION: ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322 --enable-mpi --enable-static --enable-shared --enable-threads --enable-sse2 && make && make install GROMACS INSTALLATION: export LDFLAGS="-L/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322/lib -L/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19/lib" export CPPFLAGS="-I/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_fftw-322/incl ude -I/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gsl-19/include" export NCPU=8 ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gromacs-407 --with-gsl --enable-shared --enable-double && make -j $NCPU && make install make distclean && ./configure --prefix=/afs/enea.it/project/sysbiolab/soft/cresco/gcc-412_gromacs-407 --program-suffix=_mpi --with-gsl --enable-mpi --enable-double && make mdrun -j $NCPU && make install-mdrun Could anybody of you help us for the debugging of this installation? Many thanks again and best regards Anna ____________________________________________________ Anna Marabotti, Ph.D. Laboratory of Bioinformatics and Computational Biology Institute of Food Science, CNR Via Roma, 64 83100 Avellino (Italy) Phone: +39 0825 299651 Fax: +39 0825 781585 Email: [email protected] Skype account: annam1972 Web page: http://bioinformatica.isa.cnr.it/anna/anna.htm "If you think you are too small to make a difference, try sleeping with a mosquito"
-- gmx-users mailing list [email protected] http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to [email protected]. Can't post? Read http://www.gromacs.org/mailing_lists/users.php
