> /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20' That is the problem, the error basically means that the above gromacs version got compiled using a different, most likely newer, glibc.
You have basically two options: 1.) Compile VOTCA on the same node using the same compiler as gromacs. Or 2.) Compile another version of gromacs specially for VOTCA. See: <https://github.com/votca/csg/wiki/Installing#gromacs> On a side note it doesn't make much sense to link a mpi-enabled version of gromacs into VOTCA anyway. Christoph Am 23.05.2016 18:51 schrieb "rjadrich2" <[email protected]>: > > Hi Christoph, > > Here is the output: > > --------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > Determining if the pthread_create exist failed with the following output: > Change Dir: /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp > > Run Build Command:"/usr/bin/gmake" "cmTryCompileExec510651724/fast" > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec510651724.dir/build.make CMakeFiles/cmTryCompileExec510651724.dir/build > gmake[1]: Entering directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_progress_report /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 > Building C object CMakeFiles/cmTryCompileExec510651724.dir/CheckSymbolExists.c.o > /usr/bin/cc -o CMakeFiles/cmTryCompileExec510651724.dir/CheckSymbolExists.c.o -c /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp/CheckSymbolExists.c > Linking C executable cmTryCompileExec510651724 > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec510651724.dir/link.txt --verbose=1 > /usr/bin/cc CMakeFiles/cmTryCompileExec510651724.dir/CheckSymbolExists.c.o -o cmTryCompileExec510651724 -rdynamic > CMakeFiles/cmTryCompileExec510651724.dir/CheckSymbolExists.c.o: In function `main': > CheckSymbolExists.c:(.text+0xc): undefined reference to `pthread_create' > /usr/bin/ld: link errors found, deleting executable `cmTryCompileExec510651724' > collect2: ld returned 1 exit status > gmake[1]: *** [cmTryCompileExec510651724] Error 1 > gmake[1]: Leaving directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > gmake: *** [cmTryCompileExec510651724/fast] Error 2 > > File /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp/CheckSymbolExists.c: > /* */ > #include <pthread.h> > > int main(int argc, char** argv) > { > (void)argv; > #ifndef pthread_create > return ((int*)(&pthread_create))[argc]; > #else > (void)argc; > return 0; > #endif > } > > Determining if the function pthread_create exists in the pthreads failed with the following output: > Change Dir: /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp > > Run Build Command:"/usr/bin/gmake" "cmTryCompileExec2799678089/fast" > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec2799678089.dir/build.make CMakeFiles/cmTryCompileExec2799678089.dir/build > gmake[1]: Entering directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_progress_report /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 > Building C object CMakeFiles/cmTryCompileExec2799678089.dir/CheckFunctionExists.c.o > /usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create -o CMakeFiles/cmTryCompileExec2799678089.dir/CheckFunctionExists.c.o -c /opt/apps/cmake/3.1.0/share/cmake-3.1/Modules/CheckFunctionExists.c > Linking C executable cmTryCompileExec2799678089 > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec2799678089.dir/link.txt --verbose=1 > /usr/bin/cc -DCHECK_FUNCTION_EXISTS=pthread_create CMakeFiles/cmTryCompileExec2799678089.dir/CheckFunctionExists.c.o -o cmTryCompileExec2799678089 -rdynamic -lpthreads > /usr/bin/ld: cannot find -lpthreads > collect2: ld returned 1 exit status > gmake[1]: *** [cmTryCompileExec2799678089] Error 1 > gmake[1]: Leaving directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > gmake: *** [cmTryCompileExec2799678089/fast] Error 2 > > > Determining if the function gmx_gpu_sharing_supported exists in the /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so failed with the following output: > Change Dir: /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp > > Run Build Command:"/usr/bin/gmake" "cmTryCompileExec4208178029/fast" > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec4208178029.dir/build.make CMakeFiles/cmTryCompileExec4208178029.dir/build > gmake[1]: Entering directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_progress_report /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 > Building C object CMakeFiles/cmTryCompileExec4208178029.dir/CheckFunctionExists.c.o > /usr/bin/cc -DCHECK_FUNCTION_EXISTS=gmx_gpu_sharing_supported -o CMakeFiles/cmTryCompileExec4208178029.dir/CheckFunctionExists.c.o -c /opt/apps/cmake/3.1.0/share/cmake-3.1/Modules/CheckFunctionExists.c > Linking C executable cmTryCompileExec4208178029 > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec4208178029.dir/link.txt --verbose=1 > /usr/bin/cc -DCHECK_FUNCTION_EXISTS=gmx_gpu_sharing_supported CMakeFiles/cmTryCompileExec4208178029.dir/CheckFunctionExists.c.o -o cmTryCompileExec4208178029 -rdynamic /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so -Wl,-rpath,/opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64 > CMakeFiles/cmTryCompileExec4208178029.dir/CheckFunctionExists.c.o: In function `main': > CheckFunctionExists.c:(.text+0x15): undefined reference to `gmx_gpu_sharing_supported' > /usr/bin/ld: link errors found, deleting executable `cmTryCompileExec4208178029' > collect2: ld returned 1 exit status > gmake[1]: *** [cmTryCompileExec4208178029] Error 1 > gmake[1]: Leaving directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > gmake: *** [cmTryCompileExec4208178029/fast] Error 2 > > > Determining if the function gmx_is_single_precision exists in the /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so failed with the following output: > Change Dir: /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp > > Run Build Command:"/usr/bin/gmake" "cmTryCompileExec3948644274/fast" > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec3948644274.dir/build.make CMakeFiles/cmTryCompileExec3948644274.dir/build > gmake[1]: Entering directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_progress_report /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 > Building CXX object CMakeFiles/cmTryCompileExec3948644274.dir/CheckFunctionExists.cpp.o > /usr/bin/c++ -DCHECK_FUNCTION_EXISTS=gmx_is_single_precision -o CMakeFiles/cmTryCompileExec3948644274.dir/CheckFunctionExists.cpp.o -c /home1/03112/bal2488/votca/src/csg/CMakeModules/CheckFunctionExists.cpp > Linking CXX executable cmTryCompileExec3948644274 > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec3948644274.dir/link.txt --verbose=1 > /usr/bin/c++ -DCHECK_FUNCTION_EXISTS=gmx_is_single_precision CMakeFiles/cmTryCompileExec3948644274.dir/CheckFunctionExists.cpp.o -o cmTryCompileExec3948644274 -rdynamic /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so -Wl,-rpath,/opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64 > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::range_error::~range_error()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::out_of_range::~out_of_range()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::length_error::~length_error()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::invalid_argument::~invalid_argument()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::domain_error::~domain_error()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::underflow_error::~underflow_error()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::overflow_error::~overflow_error()@GLIBCXX_3.4.15' > /usr/bin/ld: link errors found, deleting executable `cmTryCompileExec3948644274' > collect2: ld returned 1 exit status > gmake[1]: *** [cmTryCompileExec3948644274] Error 1 > gmake[1]: Leaving directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > gmake: *** [cmTryCompileExec3948644274/fast] Error 2 > > > Determining if the function gmx_is_double_precision exists in the /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so failed with the following output: > Change Dir: /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp > > Run Build Command:"/usr/bin/gmake" "cmTryCompileExec1788432292/fast" > /usr/bin/gmake -f CMakeFiles/cmTryCompileExec1788432292.dir/build.make CMakeFiles/cmTryCompileExec1788432292.dir/build > gmake[1]: Entering directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_progress_report /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp/CMakeFiles 1 > Building CXX object CMakeFiles/cmTryCompileExec1788432292.dir/CheckFunctionExists.cpp.o > /usr/bin/c++ -DCHECK_FUNCTION_EXISTS=gmx_is_double_precision -o CMakeFiles/cmTryCompileExec1788432292.dir/CheckFunctionExists.cpp.o -c /home1/03112/bal2488/votca/src/csg/CMakeModules/CheckFunctionExists.cpp > Linking CXX executable cmTryCompileExec1788432292 > /opt/apps/cmake/3.1.0/bin/cmake -E cmake_link_script CMakeFiles/cmTryCompileExec1788432292.dir/link.txt --verbose=1 > /usr/bin/c++ -DCHECK_FUNCTION_EXISTS=gmx_is_double_precision CMakeFiles/cmTryCompileExec1788432292.dir/CheckFunctionExists.cpp.o -o cmTryCompileExec1788432292 -rdynamic /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so -Wl,-rpath,/opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64 > CMakeFiles/cmTryCompileExec1788432292.dir/CheckFunctionExists.cpp.o: In function `main': > CheckFunctionExists.cpp:(.text+0x10): undefined reference to `gmx_is_double_precision()' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::__detail::_List_node_base::_M_hook(std::__detail::_List_node_base*)@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::__throw_out_of_range_fmt(char const*, ...)@GLIBCXX_3.4.20' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::range_error::~range_error()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::out_of_range::~out_of_range()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::length_error::~length_error()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::invalid_argument::~invalid_argument()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::domain_error::~domain_error()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::underflow_error::~underflow_error()@GLIBCXX_3.4.15' > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so: undefined reference to `std::overflow_error::~overflow_error()@GLIBCXX_3.4.15' > /usr/bin/ld: link errors found, deleting executable `cmTryCompileExec1788432292' > collect2: ld returned 1 exit status > gmake[1]: *** [cmTryCompileExec1788432292] Error 1 > gmake[1]: Leaving directory `/home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeTmp' > gmake: *** [cmTryCompileExec1788432292/fast] Error 2 > > ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- > > > Thanks a lot! > > Best, > > Ryan > > > > > > On Monday, May 23, 2016 at 2:15:59 PM UTC-5, Christoph Junghans wrote: >> >> 2016-05-23 12:05 GMT-06:00 rjadrich2 <[email protected]>: >> > Hello Christoph, >> > >> > Upon trying to install VOTCA I am getting a very strange error message: >> > >> > >> > -- checking for module 'libgromacs_d' >> > -- package 'libgromacs_d' not found >> > -- checking for module 'libgromacs' >> > -- found libgromacs, version 5.0.6 >> > -- Looking for GromacsVersion in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so >> > -- Looking for GromacsVersion in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so - >> > found >> > -- Looking for init_domdec_vsites in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so >> > -- Looking for init_domdec_vsites in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so - >> > found >> > -- Looking for gmx_gpu_sharing_supported in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so >> > -- Looking for gmx_gpu_sharing_supported in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so - >> > not found >> > -- Looking for c++ gmx_is_single_precision in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so >> > -- Looking for c++ gmx_is_single_precision in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so - >> > not found >> > -- Looking for c++ gmx_is_double_precision in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so >> > -- Looking for c++ gmx_is_double_precision in >> > /opt/apps/intel15/mvapich2_2_1/gromacs/5.0.6/x86_64/lib64/libgromacs.so - >> > not found >> > CMake Error at CMakeModules/FindGROMACS.cmake:61 (message): >> > Could not find neither gmx_is_single_precision nor gmx_is_double_precision >> > in the gromacs library, that is very very strange, take look at the error >> > message in /home1/03112/bal2488/votca/src/csg/CMakeFiles/CMakeError.log to >> > find out what was going wrong. This most likely means that your gromacs >> > version is too old, we need at least gromacs 5 ! >> > Call Stack (most recent call first): >> > CMakeLists.txt:82 (find_package) >> > >> > >> > I am using Gromacs 5.0.6 so the "we need at least gromacs 5" is strange. I >> > am also using CMake 3.1.0 to avoid the issue in some earlier versions. Do >> > you have any thoughts on this? >> Which version of VOTCA is that? >> >> Can you post your CMakeError.log? >> >> Thanks, >> >> Christoph >> > >> > Thanks so much! >> > >> > Best, >> > >> > Ryan >> > >> > -- >> > You received this message because you are subscribed to the Google Groups >> > "votca" group. >> > To unsubscribe from this group and stop receiving emails from it, send an >> > email to [email protected]. >> > To post to this group, send email to [email protected]. >> > Visit this group at https://groups.google.com/group/votca. >> > For more options, visit https://groups.google.com/d/optout. >> >> >> >> -- >> Christoph Junghans >> Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. -- You received this message because you are subscribed to the Google Groups "votca" group. To unsubscribe from this group and stop receiving emails from it, send an email to [email protected]. To post to this group, send email to [email protected]. Visit this group at https://groups.google.com/group/votca. For more options, visit https://groups.google.com/d/optout.
