I have definitely sourced gromacs. So many times . . . Here is the output of "ls /usr/local/gromacs/lib/pkgconfig/": libgmxana_d.pc libgmx_d.pc libgmxpreprocess_d.pc libmd_d.pc
On Tue, Oct 11, 2011 at 3:57 PM, Christoph Junghans <jungh...@votca.org>wrote: > Am 11. Oktober 2011 16:50 schrieb Patrick Kiley <pjki...@gmail.com>: > > Hi Christoph, > > > > Here is the output of $ pkg-config --libs libgmx: > > Package libgmx was not found in the pkg-config search path. > > Perhaps you should add the directory containing `libgmx.pc' > > to the PKG_CONFIG_PATH environment variable > > No package 'libgmx' found > what does contain /usr/local/gromacs/lib/pkgconfig then? > Have you sourced GMXRC? > > Cheers, > > Christoph > > > > > > > > > On Tue, Oct 11, 2011 at 3:45 PM, Christoph Junghans <jungh...@votca.org> > > wrote: > >> > >> Am 11. Oktober 2011 16:24 schrieb Patrick Kiley <pjki...@gmail.com>: > >> > Hi Christoph, > >> > > >> > I tried your suggestion, but it doesn't work. I get this error: > >> > "relocation > >> > R_X86_64_32 against `.rodata' can not be used when making a shared > >> > object; > >> > recompile with -fPIC". > >> Hmm, that could be the fPIC bug of gcc, but this looks more like a > >> mixture of 64 and 32 bit libraries. > >> Are all dependence libraries (gsl, fftw, libgmx ...) are compiled in > >> 64bit? e.g. > >> $ file ~/votca/lib/libgmx.so.6 > >> libgmx.so.6: ELF 64-bit LSB shared object, x86-64.... > >> > >> > > >> > I tried a fresh install of the normal gromacs compiled as static, and > >> > tried > >> Well, I hope you have a good reason to go through the pain of > >> compiling statically! > >> Even the gromacs people now compile shared by default. > >> > >> In case you still want to do it, here is a thread with hints: > >> > >> < > https://groups.google.com/group/votca/browse_thread/thread/c4a847aabfa5f643/054959940df46f > > > >> > >> > >> > recompiling votca against it and finally I get this error: > >> > -- package 'libgmx_d' not found > >> > -- Could NOT find GMX_D (missing: GMX_D_LIBRARY GMX_D_INCLUDE_DIR) > >> > CMake Warning at src/libcsg/CMakeLists.txt:41 (message): > >> > gromacs-4.5 double precision not found failback to single precision > >> > > >> > > >> > -- 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 > installed > >> > the > >> > gromacs-4.5 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. > >> > gromacs support can be 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! > >> > > >> > According to Valentina's link: > >> > echo $PKG_CONFIG_PATH produces: > >> > /usr/local/gromacs/lib/pkgconfig > >> > > >> > which I believe is correct. > >> Can you post the output of > >> $ pkg-config --libs libgmx > >> > >> Cheers, > >> > >> Christoph > >> > >> > > >> > Any other ideas? > >> > >> > > >> > Kind regards, > >> > Patrick > >> > On Tue, Oct 11, 2011 at 1:23 PM, Patrick Kiley <pjki...@gmail.com> > >> > wrote: > >> >> > >> >> Hi Valentina, > >> >> > >> >> Thanks for the link, but unfortunately, I get zero errors during > >> >> compilation, so I think this case is a little different from yours, > but > >> >> someone please correct me if I am wrong. > >> >> > >> >> Patrick > >> >> > >> >> On Tue, Oct 11, 2011 at 1:12 PM, Valentina > >> >> <valentina_erast...@yahoo.co.uk> wrote: > >> >>> > >> >>> Oh, sorry, I read topol.tpr at the beginning. > >> >>> > >> >>> I had a similar problem before. This may be useful? > >> >>> > >> >>> > >> >>> > http://groups.google.com/group/votca/browse_thread/thread/d24203fb92647bb9 > >> >>> > >> >>> Valentina > >> >>> > >> >>> > >> >>> On Oct 11, 12:52 pm, Patrick Kiley <pjki...@gmail.com> wrote: > >> >>> > I seem to remember that there used to be a --conf-opts option for > >> >>> > build.sh > >> >>> > that enabled me to build static libs. Does this still exist? I > >> >>> > just > >> >>> > tried > >> >>> > using it, but it doesn't seem to be recognized. > >> >>> > > >> >>> > Patrick > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > > >> >>> > On Tue, Oct 11, 2011 at 12:48 PM, Patrick Kiley < > pjki...@gmail.com> > >> >>> > wrote: > >> >>> > > Dear all, > >> >>> > > >> >>> > > Sorry, that was a mistake on my part. I am actually using the > >> >>> > > .tpr > >> >>> > > files. > >> >>> > > The command was: > >> >>> > > csg_boltzmann --top topol.tpr --cg map5-gly-pro-pro.xml --excl > >> >>> > > --trj > >> >>> > > traj.trr > >> >>> > > >> >>> > > sorry for the confusion. > >> >>> > > >> >>> > > Patrick > >> >>> > > >> >>> > > On Tue, Oct 11, 2011 at 12:40 PM, Sebastian Fritsch < > >> >>> > > frit...@mpip-mainz.mpg.de> wrote: > >> >>> > > >> >>> > >> Hello Patrick, > >> >>> > > >> >>> > >> you need to use the topol.tpr which is the binary form of the > >> >>> > >> topol.top. > >> >>> > >> To get the .tpr you have to run the gromacs preprocessor > >> >>> > >> (grompp). > >> >>> > > >> >>> > >> -Sebastian > >> >>> > >> > Dear all, > >> >>> > > >> >>> > >> > I have recently recompiled GROMACS on my machine, and > therefore > >> >>> > >> > have > >> >>> > >> > needed to recompile VOTCA. > >> >>> > > >> >>> > >> > Here is how I did it: > >> >>> > >> > 1) source gromacs > >> >>> > >> > 2) sudo ./build.sh -R -dcu --release 1.2.1 > >> >>> > >> > --prefix=/home/votca/ > >> >>> > >> > tools csg > >> >>> > > >> >>> > >> > This finishes with no errors, so I thought everything should > be > >> >>> > >> > OK. > >> >>> > >> > However, when I run this command: > >> >>> > >> > csg_boltzmann --top topol.top --cg map.xml --excl --trj > >> >>> > >> > traj.trr > >> >>> > > >> >>> > >> > I get this error: > >> >>> > >> > an error occurred: > >> >>> > >> > input format not supported: topol.top > >> >>> > > >> >>> > >> > To me this means I have somehow compiled without GMX support, > >> >>> > >> > but > >> >>> > >> > how > >> >>> > >> > could this be and how can I fix it? One other thing, I have > >> >>> > >> > compiled > >> >>> > >> > gromacs with static libs, so maybe I need to tell the build > >> >>> > >> > script > >> >>> > >> > this explicitly? > >> >>> > > >> >>> > >> > Thanks for any help you can give, > >> >>> > > >> >>> > >> > Patrick Kiley > >> >>> > > >> >>> > >> -- > >> >>> > >> You received this message because you are subscribed to the > >> >>> > >> Google > >> >>> > >> Groups > >> >>> > >> "votca" group. > >> >>> > >> To post to this group, send email to votca@googlegroups.com. > >> >>> > >> To unsubscribe from this group, send email to > >> >>> > >> votca+unsubscr...@googlegroups.com. > >> >>> > >> 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 votca@googlegroups.com. > >> >>> To unsubscribe from this group, send email to > >> >>> votca+unsubscr...@googlegroups.com. > >> >>> 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 votca@googlegroups.com. > >> > To unsubscribe from this group, send email to > >> > votca+unsubscr...@googlegroups.com. > >> > For more options, visit this group at > >> > http://groups.google.com/group/votca?hl=en. > >> > > >> > >> > >> > >> -- > >> 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 votca@googlegroups.com. > >> To unsubscribe from this group, send email to > >> votca+unsubscr...@googlegroups.com. > >> 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 votca@googlegroups.com. > > To unsubscribe from this group, send email to > > votca+unsubscr...@googlegroups.com. > > For more options, visit this group at > > http://groups.google.com/group/votca?hl=en. > > > > > > -- > 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 votca@googlegroups.com. > To unsubscribe from this group, send email to > votca+unsubscr...@googlegroups.com. > 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. 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