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.
