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: 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] <javascript:>> 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] <javascript:>. > > 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.
