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

[Justin A. Lemkul]

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.marabotti at isa.cnr.it <mailto: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"
>  
> 

-- 
========================================

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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