Anna Marabotti wrote:
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/include
-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?
Assuming that "gcc-412" implies that the compiler is gcc-4.1.2, then you should
take note of the big, bold warning on the Gromacs Downloads page:
"WARNING: do not use the gcc 4.1.x set of compilers. They are broken. These
compilers come with recent Linux distrubutions like Fedora 5/6 etc."
-Justin
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: anna.marabo...@isa.cnr.it <mailto:anna.marabo...@isa.cnr.it>
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"
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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