[gmx-users] stepsize too small: help to solve problem in GROMACS installation

[Anna Marabotti]

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: anna.marabotti at 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"
 
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://maillist.sys.kth.se/pipermail/gromacs.org_gmx-users/attachments/20100526/0875928a/attachment.html>