[gmx-developers] Error Gromacs Install from Git and gromacs tar

David van der Spoel spoel at xray.bmc.uu.se
Sun Jul 12 22:26:21 CEST 2009

Rodrigo faccioli wrote:
> Hello,
> I've tried to install the Gromacs from git repository. For this, I read 
> http://www.gromacs.org/Developers/Git/Git_Tutorial . In this way, I 
> executed the commands: git clone --mirror git://git.gromacs.org/gromacs 
> and git clone git://git.gromacs.org/gromacs
> After that, I read quick and dirty installation in 
> http://oldwiki.gromacs.org/index.php/quick_and_dirty_installation. I 
> downloaded all programs which are listed there, except Gromacs because I 
> got it from git repository :). The other change that I made was: I 
> change the NCPU value for 2.
> I executed the commands which are shown for bash box. Moreover, when I 
> execute the command ./configure --prefix=$SOFT --enable-mpi --with-gsl, 
> I receive the error message: checking size of int... configure: error: 
> cannot compute sizeof (int)
> See `config.log' for more details.
> I opened the config.log file and its last line shows configure: exit 77
> After this error, I downloaded the others Gromacs versions (4.05 and 
> 4.0.4) from 
> http://www.gromacs.org/index.php?title=Download_%26_Installation. 
> Moreover, these versions show the same error.
> So, I tried to understand where can be my error. When I remove the 
> --enable-mpi option from configure command above, the command works fine.
> My doubt is what I made wrong. Unfortunately, I can't understand.
> My Operation System is Ubuntu 9.04 and I'm running on laptop Dell XPS.
> I thank any help and sorry if my question is so obvious and my English 
> mistakes.

Hi Rodrigo,

do you have mpi installed?
Check the config.log, it looks like an MPI problem.

With the git sources you need to start by typing

> --
> Rodrigo Antonio Faccioli
> Ph.D Student in Electrical Engineering
> University of Sao Paulo - USP
> Engineering School of Sao Carlos - EESC
> Department of Electrical Engineering - SEL
> Intelligent System in Structure Bioinformatics
> http://laips.sel.eesc.usp.br
> Phone: 55 (16) 3373-9366 Ext 229
> Curriculum Lattes - http://lattes.cnpq.br/1025157978990218
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David van der Spoel, Ph.D., Professor of Biology
Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
Box 596, 75124 Uppsala, Sweden. Phone:	+46184714205. Fax: +4618511755.
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se

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