I didn't specify anything by hand in the case above. Since I am using double precision gmx, should I specify -DGMX_D_LIBRARY rather than _DGMX_LIBRARY?
patrick On Tue, Oct 11, 2011 at 5:17 PM, Christoph Junghans <jungh...@votca.org>wrote: > Am 11. Oktober 2011 18:08 schrieb Patrick Kiley <pjki...@gmail.com>: > > Here is the contents of the entire file: > .... > > > > Determining if the function GromacsVersion exists in the > > /usr/local/gromacs/lib failed with the following output: > That looks strange to me, did you specify GMX_LIBRARY by hand? > > For very odd systems you can specify all libs by hand, for examples see > the build.sh line in <https://code.google.com/p/votca/wiki/compiling_AIX> > > Christoph > > > > Change Dir: /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp > > > > Run Build Command:/usr/bin/make "cmTryCompileExec/fast" > > /usr/bin/make -f CMakeFiles/cmTryCompileExec.dir/build.make > > CMakeFiles/cmTryCompileExec.dir/build > > make[1]: Entering directory > > `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' > > /usr/local/bin/cmake -E cmake_progress_report > > /home/patrick/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 > > Building C object CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o > > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion -o > > CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -c > > /usr/local/share/cmake-2.8/Modules/CheckFunctionExists.c > > Linking C executable cmTryCompileExec > > /usr/local/bin/cmake -E cmake_link_script > > CMakeFiles/cmTryCompileExec.dir/link.txt --verbose=1 > > /usr/bin/gcc -DCHECK_FUNCTION_EXISTS=GromacsVersion > > CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o -o > cmTryCompileExec > > -rdynamic > > CMakeFiles/cmTryCompileExec.dir/CheckFunctionExists.c.o: In function > `main': > > CheckFunctionExists.c:(.text+0x15): undefined reference to > `GromacsVersion' > > collect2: ld returned 1 exit status > > make[1]: Leaving directory > `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' > > make[1]: *** [cmTryCompileExec] Error 1 > > make: *** [cmTryCompileExec/fast] Error 2 > > > > > > > > On Tue, Oct 11, 2011 at 5:02 PM, Christoph Junghans <jungh...@votca.org> > > wrote: > >> > >> Am 11. Oktober 2011 17:40 schrieb Patrick Kiley <pjki...@gmail.com>: > >> > Sorry! I should have realized that was what you were asking > >> > $ pkg-config --libs libgmx_d produces: > >> > -L/usr/local/gromacs/lib -lgmx_d > >> That looks ok to me, but it doesn't fit with > >> > -- package 'libgmx_d' not found > >> From your email above. > >> > >> What kind of error does csg/CMakeFiles/CMakeError.log report at the end? > >> > >> Christoph > >> > >> > > >> > Patrick > >> > > >> > > >> > On Tue, Oct 11, 2011 at 4:24 PM, Christoph Junghans < > jungh...@votca.org> > >> > wrote: > >> >> > >> >> Am 11. Oktober 2011 17:05 schrieb Patrick Kiley <pjki...@gmail.com>: > >> >> > 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 > >> >> > <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 > >> >> >> >> >>> 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