Am 11. Oktober 2011 17:05 schrieb Patrick Kiley <[email protected]>: > 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 Ah ok, so what is the output of $ pkg-config --libs libgmx_d then?
> > > > > > On Tue, Oct 11, 2011 at 3:57 PM, Christoph Junghans <[email protected]> > wrote: >> >> 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. >> > > -- > 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.
