Great! Thank you very much. I managed to install it on the cluster, there was smth funny with pkg- config indeed. (One more machine to go, but I think I know where the problem lays now)
Valentina On Sep 6, 3:25 pm, Christoph Junghans <[email protected]> wrote: > Hi Valentina, > > after we had recently so much problem with detecting gromacs I cleaned > up cmake's gromacs detection code. > I also added the support for gromacs 4.0.X back. > > You can specify the gromacs include dir and library in GROMACS_LIBRARY > and GROMACS_INCLUDE_DIR independently of their version. > > But>-- checking for module 'libgmx' > > -- package 'libgmx' not found > > shows me that there is something wrong with your pkg-config path. > You can test if it works beforehand by running: > $pkg-config --cflags --libs libgmx > The output should look like this: > -pthread -DGMX_SOFTWARE_INVSQRT -DGMX_THREADS -pthread -lgmx -lm > > Is pkg-config installed? > > And actually GMXRC should set the PKG_CONFIG_PATH for you. > > Cheers, > > Christoph > > 2011/9/6 Valentina <[email protected]>: > > > > > Hello again. > > > I am trying to install Votca on other 2 machines (i am now the > > installer of the lab) and have a similar problem as above. I do have > > pkg-config, I have added pkg-config path, I have the right version > > (4.5.4) of gromacs installed, I have tried specifying the path to the > > gmx include and library by hand, as advised above, but nothing seem to > > work, I get an error of similar type as above (but different): > > > Working on csg > > Source dir (csg) is already there - skipping checkout > > cmake -DCMAKE_INSTALL_PREFIX=/usr/local/votca -DWITH_SQLITE3=NO - > > DCMAKE_INSTALL_RPATH_USE_LINK_PATH=ON . > > -- checking for module 'libgmx' > > -- package 'libgmx' not found > > -- Could NOT find GROMACS (missing: GROMACS_LIBRARY > > GROMACS_INCLUDE_DIR) > > CMake Error at src/libcsg/CMakeLists.txt:25 (message): > > gromacs not found, make sure you have installed at least the > > gromacs-4.0.7 > > and it's dev package. If the gromacs module was not found above, > > make sure > > you have sourced GMXRC or set PKG_CONFIG_PATH yourself. If you have > > a > > double precision version of gromacs enable to build against it with > > -DGMX_DOUBLE=ON. If you have gromacs-5.0 installed enable to build > > against > > it with -DWITH_GMX_DEVEL=ON. Gromacs support can be disable it with > > -DWITH_GMX=OFF. > > > There must be a wise trick, that I don't know. > > Thank you for help, > > Valentina > > > On Aug 5, 8:08 pm, Valentina <[email protected]> wrote: > >> Awesome! Thank you very much, editing PKG_CONFIG_PATH did the trick! > >> V > > >> On Aug 5, 7:20 pm, Christoph Junghans <[email protected]> wrote: > > >> > Hi Valentina, > > >> > You can have a look at CMakeFiles/CMakeError.log. > > >> > I have some ideas what could be the problem: > >> > 1.) Do you have pkg-config installed? > >> > 2.) On some distributions /usr/local/gromacs/lib/pkgconfig is not > >> > included in the search path of pkg-config, you can add it by > >> > export PKG_CONFIG_PATH=/usr/local/gromacs/lib/pkgconfig > >> > 3.) Specify GMX_LIBRARY and GMX_INCLUDE_DIR by hand by adding > >> > -DGMX_LIBRARY=/usr/local/gromacs/lib/libgmx.so > >> > -DGMX_INCLUDE_DIR=/usr/local/include > >> > to the build.sh commandline. > > >> > Cheers, > > >> > Christoph > > >> > 2011/8/5 Valentina <[email protected]>: > > >> > > Hi there, > > >> > > I have reinstalled gromacs 4.5.4 with shared libraries, single > >> > > precision. I have now the following libraries. > > >> > > ls /usr/gromacs/lib > >> > > /usr/local/gromacs/lib/libgmx.a > >> > > /usr/local/gromacs/lib/libgmx.la > >> > > /usr/local/gromacs/lib/libgmx.so > >> > > /usr/local/gromacs/lib/libgmx.so.6 > >> > > /usr/local/gromacs/lib/libgmx.so.6.0.0 > >> > > /usr/local/gromacs/lib/libgmx_d.a > >> > > /usr/local/gromacs/lib/libgmx_d.la > >> > > /usr/local/gromacs/lib/libgmxana.a > >> > > /usr/local/gromacs/lib/libgmxana.la > >> > > /usr/local/gromacs/lib/libgmxana.so > >> > > /usr/local/gromacs/lib/libgmxana.so.6 > >> > > /usr/local/gromacs/lib/libgmxana.so.6.0.0 > >> > > /usr/local/gromacs/lib/libgmxana_d.a > >> > > /usr/local/gromacs/lib/libgmxana_d.la > >> > > /usr/local/gromacs/lib/libgmxpreprocess.a > >> > > /usr/local/gromacs/lib/libgmxpreprocess.la > >> > > /usr/local/gromacs/lib/libgmxpreprocess.so > >> > > /usr/local/gromacs/lib/libgmxpreprocess.so.6 > >> > > /usr/local/gromacs/lib/libgmxpreprocess.so.6.0.0 > >> > > /usr/local/gromacs/lib/libgmxpreprocess_d.a > >> > > /usr/local/gromacs/lib/libgmxpreprocess_d.la > > >> > > LD_LIBRARY_PATH includes the correct path: > > >> > > echo $LD_LIBRARY_PATH > >> > > /usr/local/votca/lib:/usr/local/gromacs/lib > > >> > > Unfortunately, upon compiling votca, I still get the same error: > > >> > > -- checking for module 'libgmx' > >> > > -- package 'libgmx' not found > >> > > -- Could NOT find GMX (missing: GMX_LIBRARY GMX_INCLUDE_DIR) > >> > > CMake Error at src/libcsg/CMakeLists.txt:44 (message): > >> > > gromacs-4.5 (single or double) not found, make sure you have also > >> > > installed > >> > > the gromacs-4.5 and it's dev package or disable it with - > >> > > DWITH_GMX=OFF. If > >> > > you have gromacs-5.0 installed enable to build against it with > >> > > -DWITH_GMX_DEVEL=ON > > >> > > -- Configuring incomplete, errors occurred! > > >> > > Could you advise me how I can solve this? > > >> > > Many thanks, > >> > > V > > >> > > On Aug 4, 6:12 pm, Valentina Erastova <[email protected]> > >> > > wrote: > >> > >> Hello, > > >> > >> I am trying to compile with gromacs, but not being successful, getting > >> > >> this error: > >> > >> -- Could NOT find GMX (missing: GMX_LIBRARY GMX_INCLUDE_DIR) > >> > >> CMake Error at src/libcsg/CMakeLists.txt:44 (message): > >> > >> gromacs-4.5 (single or double) not found, make sure you have also > >> > >> installed > >> > >> the gromacs-5.0 and it's dev package or disable it with - > >> > >> DWITH_GMX=OFF. If > >> > >> you have gromacs-5.0 installed enable to build against it with > >> > >> -DWITH_GMX_DEVEL=ON > > >> > >> I have gromacs 4.5.3 installed on my computer, > > >> > >> my library path seems to be ok: > >> > >> echo $LD_LIBRARY_PATH > >> > >> /usr/local/votca/lib:/usr/local/gromacs/lib:/usr/lib > > >> > >> I can locate gmx libraries there > >> > >> locate libgmx_d > >> > >> /usr/lib/libgmx_d.so.4 > >> > >> /usr/lib/libgmx_d.so.4.0.0 > >> > >> /usr/local/gromacs/lib/libgmx_d.a > >> > >> /usr/local/gromacs/lib/libgmx_d.la > >> > >> /usr/local/gromacs/lib/pkgconfig/libgmx_d.pc > > >> > >> also in build.sh if I echo the LD_LIBRARY_PATH it is correct. > > >> > >> Does anyone have a solution? > > >> > >> Many thanks, > >> > >> V > > >> > >> On Aug 4, 3:03 pm, Christoph Junghans <[email protected]> wrote: > > >> > >> > Hi Valentina, > > >> > >> > it seems like you have compiled VOTCA without gromacs support. > >> > >> > Please check that again. tpr and xtc files need gromacs support. > > >> > >> > Cheers, > > >> > >> > Christoph > > >> > >> > 2011/8/4 Valentina Erastova <[email protected]>: > > >> > >> > > Dear VOTCA Developers, > >> > >> > > I am trying to use VOTCA for GC my system and I have a problem > >> > >> > > with > >> > >> > > running csg_boltzmann. As described in the manual I am providing > >> > >> > > gromacs > >> > >> > > topology, but it seems to to be a supported topology. > >> > >> > > Here is an example, when I try running the tutorial: > >> > >> > > My existing files in the directory (created by running run.sh) > >> > >> > > -rw-r--r-- 1 d47fvj users 3713 2011-05-02 15:35 topol.top > >> > >> > > -rw-r--r-- 1 d47fvj users 739 2011-05-02 15:35 settings.xml > >> > >> > > -rwxr-xr-x 1 d47fvj users 69 2011-05-02 15:35 run.sh > >> > >> > > -rwxr-xr-x 1 d47fvj users 318 2011-05-02 15:35 run_fmatch.sh > >> > >> > > -rwxr-xr-x 1 d47fvj users 219 2011-05-02 15:35 run_boltzmann.sh > >> > >> > > -rw-r--r-- 1 d47fvj users 1171 2011-05-02 15:35 propane.xml > >> > >> > > -rw-r--r-- 1 d47fvj users 575 2011-05-02 15:35 conf.gro > >> > >> > > -rw-r--r-- 1 d47fvj users 157 2011-05-02 15:35 boltzmann_cmds > >> > >> > > -rw-r--r-- 1 d47fvj users 10310 2011-08-04 13:04 mdout.mdp > >> > >> > > -rw-r--r-- 1 d47fvj users 18836 2011-08-04 13:04 topol.tpr > >> > >> > > -rw-r--r-- 1 d47fvj users 192384 2011-08-04 13:05 traj.trr > >> > >> > > -rw-r--r-- 1 d47fvj users 4348 2011-08-04 13:05 state.cpt > >> > >> > > -rw-r--r-- 1 d47fvj users 12897 2011-08-04 13:05 md.log > >> > >> > > -rw-r--r-- 1 d47fvj users 1308 2011-08-04 13:05 ener.edr > >> > >> > > -rw-r--r-- 1 d47fvj users 804 2011-08-04 13:05 confout.gro > >> > >> > > -rw-r--r-- 1 d47fvj users 9864 2011-08-04 13:06 grompp.mdp > >> > >> > > Followed by ./run_boltzmann.sh > >> > >> > > an error occurred: > >> > >> > > input format not supported: topol.tpr > >> > >> > > I also have tried with topol.top but same error. > >> > >> > > Could you advise me how can I solve this problem? > >> > >> > > Many thanks, > > >> > >> > > __________________________ > >> > >> > > Valentina Erastova > >> > >> > > PhD Research Postgraduate > >> > >> > > Computational Chemistry Group > >> > >> > > Department of Chemistry > >> > >> > > Durham University > >> > >> > > Sciences Editor, > >> > >> > > Kaleidoscope > >> > >> > > STEM Ambassador > >> > >> > > Associate Member of RSC > >> > >> > > +44 786 131 6686 > >> > >> > > +7 926 587 6662 > > >> > >> > -- > >> > >> > Dr. Christoph Junghans > >> > >> > Votca Core Developer > > >> > >> > Web:http://www.votca.org > > >> > > -- > >> > > 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. > > >> > -- > >> > Dr. Christoph Junghans > >> > Votca Core Developer > > >> > Web:http://www.votca.org > > > -- > > 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. > > -- > Dr. Christoph Junghans > Votca Core Developer > > Web:http://www.votca.org -- 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.
