Hello! Thanks for the email, I was about to write you about it.
Unfortunately I don't have root rights on the cluster :( I will capture the guy tomorrow (he already left office), and will do as you said, and email you back. V __________________________ Valentina Erastova PhD Research Postgraduate Computational Chemistry Group Department of Chemistry Durham University Sciences Editor, Kaleidoscope STEM Ambassador Associate Member of RSC www.dur.ac.uk/valentina.erastova +44 786 131 6686 On 28 Jun 2012, at 16:35, Christoph Junghans wrote: > Thanks Valentina, > > The segfault when doing "make install" is the only weird things, but > that must be inside cmake somehow. > Maybe cmake 2.8.8 is too cutting-edge Votca only requires cmake 2.6 > (,but Gromacs 4.6 will require cmake-2.8). > > Can you run > $ make install VERBOSE=1 > and have a look at which exact command the segfault happens? > > Cheers, > > Christoph > > 2012/6/28 <[email protected]>: >> Comment by [email protected]: >> >> ==== Installing VOTCA 1.2.2 (on Rocks 6 Cluster) ==== >> >> >> Make sure *gsl* and *cmake* are installed on the system. >> >> *gsl* >> Installing by hand: >> Get a copy of gsl-1.15 from http://ftp.heanet.ie/mirrors/gnu/gsl/ and >> extract: >> {{{ tar -xzvf gsl-*.tar.gz >> ./configure --enable-shared --prefix=/share/apps/gsl >> make >> make install}}} >> Please note, we install to the folder /share/apps/ on out cluster, but it >> does not necessarily have to be it. >> >> >> >> *cmake* >> >> Next get a copy of cmake-2.8.8: >> {{{wget http://www.cmake.org/files/v2.8/cmake-2.8.8.tar.gz >> tar -xvf cmake-2.8.8.tar.gz >> cd cmake-2.8.8 >> ./configure --prefix=/share/apps/.cmake >> make >> make install}}} >> >> Add this directory to your path in .bashrc >> {{{ export PATH=$PATH:/share/apps/.cmake/bin }}} >> >> Also you (might) need to make sure the *expat* package is installed. >> >> You will also of course need *Gromacs* and *fftw3* installed, following the >> instructions in [[install_gromacs|Installing Gromacs]]. >> >> >> >> Now we can install *VOTCA*. Get a copy of the newest VOTCA from >> http://www.votca.org/download, then get build.sh and make sure it is >> executable: >> {{{tar -xzvf votca*.tar.gz >> wget http://votca.googlecode.com/hg/build.sh >> chmod +x build.sh}}} >> >> VOTCA (with all flags) should be installed like: >> >> {{{ ./build.sh -DWITH_SQLITE3=NO -DEXTERNAL_BOOST=OFF >> -DGSL_INCLUDE_DIR=/share/apps/gsl/include >> -DGSL_LIBRARY=/share/apps/gsl/lib/libgsl.so >> -DGSLCBLAS_LIBRARY=/share/apps/gsl/lib/libgslcblas.so >> -DFFTW3_INCLUDE_DIR=/share/apps/fftw3_d/include >> -DFFTW3_LIBRARY=/share/apps/fftw3_d/lib/libfftw3.so >> -DGROMACS_INCLUDE_DIR=/share/apps/gromacs/include >> -DGROMACS_LIBRARY=/share/apps/gromacs/lib/libgmx.so >> -DGROMACS_DEP_LIBARIES=/share/apps/gsl/lib/libgslcblas.so;/share/apps/gsl/lib/libgsl.so >> --prefix /share/apps/votca tools csg }}} >> >> *BUT* we got segmentation fault (?) so we have manually edited *tools* and >> *csg* install files: >> >> Move into the tools folder >> {{{ cd tools }}} >> and edit the cmake script >> {{{ nano cmake_install.cmake }}} >> by changing any reference to the path '/root/votca' to '/share/apps/votca'. >> Then run >> {{{ make >> make install }}} >> >> The move to the csg folder >> {{{ cd ../csg }}} >> and again edit the make script >> {{{ nano cmake_install.cmake }}} >> by changing any reference to the path '/root/votca' to '/share/apps/votca'. >> Then run >> {{{ make >> make install }}} >> >> Then add the VOTCA install directory to the path. Add to your .bashrc file >> {{{ export >> LD_LIBRARY_PATH=${LD_LIBRARY_PATH}:/share/apps/votca/lib:/usr/lib64/openmpi/lib/ >> export PATH=$PATH:/share/apps/votca/bin:share/apps/votca }}} >> >> Ta-Da! >> >> For more information: >> http://code.google.com/p/votca/wiki/Installing >> >> -- >> 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. >> > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > 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. > -- 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.
