Here is the contents of the entire file: Determining if the function GromacsVersion exists in the /usr/local/gromacs/lib/libgmx.a failed with the following output: 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 make[1]: Leaving directory `/home/patrick/votca/src/csg/CMakeFiles/CMakeTmp' make[1]: *** No rule to make target `/usr/local/gromacs/lib/libgmx.a', needed by `cmTryCompileExec'. Stop. make: *** [cmTryCompileExec/fast] Error 2 Determining if the function GromacsVersion exists in the /usr/local/gromacs/lib failed with the following output: 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 > >> >> >> >>> > >>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. > >> > 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. 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.
