2016-05-24 9:56 GMT-06:00 rjadrich2 <[email protected]>: > Hi Christoph, > > Thanks so much! that fixed my issues. :) Option 1.) or option 2.) ?
Christoph > > 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]>: >> > >> > 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. -- 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.
