On Fri, Apr 3, 2020 at 6:49 PM Ramon Gonzalez Perez <[email protected]> wrote: > > Hello, > > I'm using GROMACS 2019. > > I did "export DYLD_LIBRARY_PATH=/usr/local/votca/lib:/usr/local/gromacs/lib" > and csg_stat and csg_map seem to work but when I run "csg_settings --options > settings.xml" on the hexane/ibi_all tutorial I get: Do you mean csg_inverse? Try "csg_inverse --debug --options settings.xml" and post the end of the output here.
Christoph > > Terminated: 15 > > Thanks, > > Ramón > > On Friday, April 3, 2020 at 11:36:55 AM UTC-6, Christoph Junghans wrote: >> >> On Fri, Apr 3, 2020 at 11:29 AM Ramon Gonzalez Perez >> <[email protected]> wrote: >> > >> > Hello, >> > >> > I added -DENABLE_RPATH_INJECT=ON and moved from zsh to bash but got a new >> > error when running make: >> > >> > error: >> > no member named 'nmolblock' in 'gmx_mtop_t' >> > for(int iblock=0; iblock<mtop.nmolblock; ++iblock) >> > ~~~~ ^ >> Yea, VOTCA-1.4* doesn't support newer versions of gromacs. What >> version of gromacs are you using? >> >> > >> > I tried the stable version and the installation seemed to work but when >> > running csg_stat it says: >> > >> > dyld: Library not loaded: @loader_path/../lib/libgromacs.4.dylib >> > Referenced from: /usr/local/votca/lib/libvotca_csg.6.dylib >> > Reason: image not found >> > Abort trap: 6 >> Did you source VOTCARC.bash and GMXRC.bash? >> >> Alternatively, do "export >> DYLD_LIBRARY_PATH=/usr/local/votca/lib:/usr/local/gromacs/lib" >> >> Christoph >> >> >> > >> > This is the procedure I'm following: >> > >> > sudo rm -rf /usr/local/votca >> > sudo rm -rf votca >> > prefix=/usr/local/votca >> > version=stable >> > git clone -b ${version} --recursive https://github.com/votca/votca.git >> > cd votca >> > mkdir build >> > cd build >> > cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} >> > -DWITH_SQLITE3=OFF -DWITH_GMX=ON >> > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include >> > -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.4.dylib >> > -DENABLE_RPATH_INJECT=ON >> > -DYLD_LIBRARY_PATH=/usr/local/votca/lib/libvotca_csg.6.dylib .. >> > make -j5 >> > sudo make install >> > source /usr/local/votca/bin/VOTCARC.bash >> > >> > And this is the content of the directories where the libraries are located: >> > >> > ls /usr/local/gromacs/lib/ >> > libgromacs.4.0.0.dylib libgromacs.4.dylib libgromacs.dylib >> > pkgconfig >> > >> > ls /usr/local/votca/lib/ >> > cmake libvotca_csg.6.dylib libvotca_csg.dylib >> > libvotca_tools.6.dylib libvotca_tools.dylib >> > >> > Am I missing something? >> > >> > Ramón >> > >> > On Wednesday, April 1, 2020 at 8:41:08 PM UTC-6, Christoph Junghans wrote: >> >> >> >> On Wed, Apr 1, 2020 at 2:52 PM Christoph Junghans <[email protected]> >> >> wrote: >> >> > >> >> > On Wed, Apr 1, 2020 at 2:36 PM Ramon Gonzalez Perez >> >> > <[email protected]> wrote: >> >> > > >> >> > > I'm also getting that file. Did the installation work, then? >> >> > > >> >> > > Because when I try to use csg_stat I get the following message: >> >> > > >> >> > > dyld: Library not loaded: @rpath/libmkl_core.dylib >> >> > > Referenced from: /usr/local/votca/bin/csg_stat >> >> > You could try to adding -DENABLE_RPATH_INJECT=ON on your cmake comment. >> >> > Alternatively, set the DYLD_LIBRARY_PATH variable to where your libmkl >> >> > is located. >> >> > >> >> > > Reason: image not found >> >> > > zsh: abort csg_stat >> >> > Oh, you are using zsh, so the VOTCA.bash won't work for you as it is >> >> > for bash. >> >> > I guess, you could try "setopt NULL_GLOB" in zsh to make the bash file >> >> > work. >> >> Also fixed in the next release: https://github.com/votca/tools/pull/220 >> >> >> >> Christoph >> >> > >> >> > Christoph >> >> > > >> >> > > On Wednesday, April 1, 2020 at 1:56:05 PM UTC-6, Christoph Junghans >> >> > > wrote: >> >> > >> >> >> > >> On Wed, Apr 1, 2020 at 1:30 PM Ramon Gonzalez Perez >> >> > >> <[email protected]> wrote: >> >> > >> > >> >> > >> > v1.4.1 through: >> >> > >> > >> >> > >> > sudo rm -rf /usr/local/votca >> >> > >> > >> >> > >> > prefix=/usr/local/votca >> >> > >> > >> >> > >> > version=v1.4.1 >> >> > >> > >> >> > >> > git clone -b ${version} --recursive >> >> > >> > https://github.com/votca/votca.git >> >> > >> > >> >> > >> > cd votca >> >> > >> > >> >> > >> > mkdir build >> >> > >> > >> >> > >> > cd build >> >> > >> > >> >> > >> > cmake -DBUILD_CSGAPPS=ON -DCMAKE_INSTALL_PREFIX=${prefix} >> >> > >> > -DWITH_SQLITE3=OFF -DWITH_GMX=ON >> >> > >> > -DGROMACS_INCLUDE_DIR=/usr/local/gromacs/include >> >> > >> > -DGROMACS_LIBRARY=/usr/local/gromacs/lib/libgromacs.dylib .. >> >> > >> > >> >> > >> > sudo make -j5 >> >> > >> No sudo needed here. >> >> > >> > >> >> > >> > sudo make install >> >> > >> I did exactly that on Linux and I get the following file: >> >> > >> >> >> > >> $ ls /usr/local/votca/share/votca/rc/ >> >> > >> csg-completion.bash >> >> > >> >> >> > >> Christoph >> >> > >> > >> >> > >> > >> >> > >> > On Wednesday, April 1, 2020 at 1:23:14 PM UTC-6, Christoph >> >> > >> > Junghans wrote: >> >> > >> >> >> >> > >> >> On Wed, Apr 1, 2020 at 1:14 PM Ramon Gonzalez Perez >> >> > >> >> <[email protected]> wrote: >> >> > >> >> > >> >> > >> >> > Hello, >> >> > >> >> > >> >> > >> >> > I installed VOTCA on macOS but when I source >> >> > >> >> > /usr/local/votca/bin/VOTCARC.bash I get this error: >> >> > >> >> > >> >> > >> >> > /usr/local/votca/bin/VOTCARC.bash:29: no matches found: >> >> > >> >> > /usr/local/votca/share/votca/rc/*rc.bash >> >> > >> >> How did you install VOTCA? What version? >> >> > >> >> >> >> > >> >> Christoph >> >> > >> >> > >> >> > >> >> > Thanks, >> >> > >> >> > >> >> > >> >> > Ramón >> >> > >> >> > >> >> > >> >> > -- >> >> > >> >> > You received this message because you are subscribed to the >> >> > >> >> > Google Groups "votca" group. >> >> > >> >> > To unsubscribe from this group and stop receiving emails from >> >> > >> >> > it, send an email to [email protected]. >> >> > >> >> > To view this discussion on the web visit >> >> > >> >> > https://groups.google.com/d/msgid/votca/c19d41b6-7295-41d3-8fac-1366431f7601%40googlegroups.com. >> >> > >> >> >> >> > >> >> >> >> > >> >> >> >> > >> >> -- >> >> > >> >> Christoph Junghans >> >> > >> >> Web: http://www.compphys.de >> >> > >> > >> >> > >> > -- >> >> > >> > You received this message because you are subscribed to the Google >> >> > >> > Groups "votca" group. >> >> > >> > To unsubscribe from this group and stop receiving emails from it, >> >> > >> > send an email to [email protected]. >> >> > >> > To view this discussion on the web visit >> >> > >> > https://groups.google.com/d/msgid/votca/10085817-cd1a-45e6-8054-8e570f7ec1ea%40googlegroups.com. >> >> > >> >> >> > >> >> >> > >> >> >> > >> -- >> >> > >> Christoph Junghans >> >> > >> Web: http://www.compphys.de >> >> > > >> >> > > -- >> >> > > You received this message because you are subscribed to the Google >> >> > > Groups "votca" group. >> >> > > To unsubscribe from this group and stop receiving emails from it, >> >> > > send an email to [email protected]. >> >> > > To view this discussion on the web visit >> >> > > https://groups.google.com/d/msgid/votca/23598d8a-56eb-4a45-a796-5e95a13c469d%40googlegroups.com. >> >> > >> >> > >> >> > >> >> > -- >> >> > Christoph Junghans >> >> > Web: http://www.compphys.de >> >> >> >> >> >> >> >> -- >> >> Christoph Junghans >> >> Web: http://www.compphys.de >> > >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To view this discussion on the web visit >> > https://groups.google.com/d/msgid/votca/9fb7768d-cc06-4e3b-bf93-5c9d227c49ff%40googlegroups.com. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To view this discussion on the web visit > https://groups.google.com/d/msgid/votca/c80e6e02-10c2-4cb6-a871-de091895798e%40googlegroups.com. -- Christoph Junghans Web: http://www.compphys.de -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To view this discussion on the web visit https://groups.google.com/d/msgid/votca/CAHG27e63S2FRMU8V3bh%3DQaeD4bOCVSaPHROhUUbTGB0gPt2dTQ%40mail.gmail.com.
