Am 11. Oktober 2011 16:50 schrieb Patrick Kiley <[email protected]>: > 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 <[email protected]> > wrote: >> >> Am 11. Oktober 2011 16:24 schrieb Patrick Kiley <[email protected]>: >> > 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 <[email protected]> >> > 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 >> >> <[email protected]> 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 <[email protected]> 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 <[email protected]> >> >>> > 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 < >> >>> > > [email protected]> 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 [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. >> >>> >> >> >> > >> > -- >> > 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 >> 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. >> > > -- > 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 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.
