Am 11. Oktober 2011 18:08 schrieb Patrick Kiley <[email protected]>: > 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 <[email protected]> > wrote: >> >> Am 11. Oktober 2011 17:40 schrieb Patrick Kiley <[email protected]>: >> > 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 <[email protected]> >> > wrote: >> >> >> >> 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. >> >> >> > >> > -- >> > 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.
