I am running with gromacs 4.5.4 myself (as 4.5.5 wasn't out when I compiled on all my machines). But it seems that build.sh was changed (?) to automatically download gromacs - something new to me then, sorry.
I still think that what happened is that your libraries are linking to older version, so mb find where is gromacs 4.5.5 is and make sure that you manually specify paths correctly? Sorry it wasn't much use. V On Oct 21, 11:13 pm, Marc Segovia <[email protected]> wrote: > Hi Valentina > > Thanks by your reply, I try your suggestion, but the problem > persist.IMHO is about that when build.sh takes gromacs from his site, > is 4.5.5, and the actual version of votca is compiled with 4.5.3. > One way to turn around is compile gromacs 4.5.3, but as installation > with build.sh is pretty friendly I guess can be solved in other way. > Nice weekend > Marc > > marc@marc ~/votca/src $ sudo ./build.sh -DEXTERNAL_BOOST=OFF > -DWITH_SQLITE3=OFF -DTXT2TAGS_EXECUTABLE="" > -DGMX_INCLUDE_DIR=/usr/local/gromacs-4.5.3/include > -DGMX_LIBRARY=/usr/local/gromacs-4.5.3/lib gromacs tools csg > > This is VOTCA build.sh, version 1.7.6 > Install prefix is '/home/marc/votca' > Using 5 jobs for make > Working on gromacs > Download tarball gromacs-4.5.5.tar.gz > fromftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz > --2011-10-22 19:55:43-- > ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz > => `gromacs-4.5.5.tar.gz' > > On Fri, Oct 21, 2011 at 6:44 PM, Valentina > > > > > > > > <[email protected]> wrote: > > Hi Marc, > > > Make sure all of paths are to correct places (ie 4.5.3) when > > compiling. You may need to specify this paths in ./build.sh > > -DGMX_INCLUDE_DIR=/usr/local/gromacs-4.5.3/include > > -DGMX_LIBRARY=/usr/local/gromacs-4.5.3/lib > > > also mb make sure it's consistent here too: export PKG_CONFIG_PATH=/ > > usr/local/gromacs-4.5.3/lib/pkgconfig > > > Hope it works:) > > V > > > On Oct 21, 9:27 pm, Marc Segovia <[email protected]> wrote: > >> Hi all > > >> Executing the following command to install Votca > >> sudo ./build.sh -DEXTERNAL_BOOST=OFF -DWITH_SQLITE3=OFF > >> -DTXT2TAGS_EXECUTABLE="" gromacs tools csg > > >> installation is pretty perfect , but a problem with gromacs arise when > >> try to use csg_map. > >> seems that download and installation from gromacs site brings 4.5.5 > >> version and votca is compiled to 4.5.3. > >> As this way to install gromacs is easy and soft than usual, someone > >> could give a tip how to compile 4.5.3 through votca ? > >> I source .bash files as usual. > > >> Best regards > >> Marc > > >> csg_map --top topol.tpr --trj confout.gro --cg hexane.xml --out > >> conf_cg.gro > >> WARNING: VOTCA was compiled using a different Gromacs library version > >> compiled: VERSION 4.5.3 (single precision) > >> loaded:VERSION 4.5.5 (single precision) > >> Try to source another GMXRC or be prepared for unexpectred behaviour. > >> Reading file topol.tpr, VERSION 4.5.5 (single precision) > >> I have 20000 beads in 1000 molecules > >> I have 3000 beads in 1000 molecules for the coarsegraining > >> WARNING: VOTCA was compiled using a different Gromacs library version > >> compiled: VERSION 4.5.3 (single precision) > >> loaded:VERSION 4.5.5 (single precision) > >> Try to source another GMXRC or be prepared for unexpectred behaviour. > > >> ------------------------------------------------------- > >> Program VOTCA, VERSION 4.5.5 > >> Source code file: /home/marc/votca/src/gromacs/src/gmxlib/futil.c, line: > >> 491 > > >> File input/output error: > >> confout.gro > >> For more information and tips for troubleshooting, please check the GROMACS > >> website athttp://www.gromacs.org/Documentation/Errors > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To post to this group, send email to [email protected]. > > To unsubscribe from this group, send email to > > [email protected]. > > For more options, visit this group > > athttp://groups.google.com/group/votca?hl=en. -- You received this message because you are subscribed to the Google Groups "votca" group. To post to this group, send email to [email protected]. To unsubscribe from this group, send email to [email protected]. For more options, visit this group at http://groups.google.com/group/votca?hl=en.
