Hi Christoph, Thanks so much! that fixed my issues. :)
Best, Ryan On Tuesday, May 24, 2016 at 7:31:56 AM UTC-5, Christoph Junghans wrote: > > > /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] <javascript:>>: > > > > 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] <javascript:>. > > To post to this group, send email to [email protected] > <javascript:>. > > 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.
