Re: [gmx-users] Gromacs Install problem
Hello, if you have found a bug in the multi-dimensional array please report it on redmine.gromacs.org so we can fix it, together with the build configuration that causes it. Cheers Paul On 14/03/2020 00:51, Alexander Tzanov wrote: The new version from March 2020.1 is buggy. Try version 2020. There is another bug in multidimensional array ... Alex On Mar 13, 2020 1:54 PM, xuan Zhang wrote: Hi, When I install the Gromacs on Linux, the cmake occurs error like below. I am a newer on this software. I appreciate very much that you can help me. Best regards, Xuan **/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CMake Error at cmake/FindLibStdCpp.cmake:162 (message): GROMACS requires C++14, but a test of such functionality in the C++ standard library failed to compile. The g++ found at /usr/bin/g++ had a suitable version, so ;something else must be the problem Call Stack (most recent call first): CMakeLists.txt:69 (find_package) -- Configuring incomplete, errors occurred! See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". *#cmakeerror.log as below:* Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following output: Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build make[1]: Entering directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o CMakeFiles/cmTC_203a2.dir/src.cxx.o -c /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: namespace "std" has no member "cbegin" int main() { int a[2]; std::cbegin(a); } ^ compilation aborted for /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 make[1]: Leaving directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Makefile:138: recipe for target 'cmTC_203a2/fast' failed make: *** [cmTC_203a2/fast] Error 2 Source file was: #include int main() { int a[2]; std::cbegin(a); } -- *Xuan Zhang* PhD Candidate China University of Petroleum(East China) School of Petroleum Engineering No.66 Changjiang West Road, Qingdao Visiting scholar (2017.12-2018.12) The University of Texas at Austin Cockrell School of Engineering McKetta Department of Chemical Engineering 200 E Dean Keeton St. Stop C0400 CPE 5.428 *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Paul Bauer, PhD GROMACS Development Manager KTH Stockholm, SciLifeLab 0046737308594 -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs Install problem
The new version from March 2020.1 is buggy. Try version 2020. There is another bug in multidimensional array ... Alex On Mar 13, 2020 1:54 PM, xuan Zhang wrote: Hi, When I install the Gromacs on Linux, the cmake occurs error like below. I am a newer on this software. I appreciate very much that you can help me. Best regards, Xuan **/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CMake Error at cmake/FindLibStdCpp.cmake:162 (message): GROMACS requires C++14, but a test of such functionality in the C++ standard library failed to compile. The g++ found at /usr/bin/g++ had a suitable version, so ;something else must be the problem Call Stack (most recent call first): CMakeLists.txt:69 (find_package) -- Configuring incomplete, errors occurred! See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". *#cmakeerror.log as below:* Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following output: Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build make[1]: Entering directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o CMakeFiles/cmTC_203a2.dir/src.cxx.o -c /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: namespace "std" has no member "cbegin" int main() { int a[2]; std::cbegin(a); } ^ compilation aborted for /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 make[1]: Leaving directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Makefile:138: recipe for target 'cmTC_203a2/fast' failed make: *** [cmTC_203a2/fast] Error 2 Source file was: #include int main() { int a[2]; std::cbegin(a); } -- *Xuan Zhang* PhD Candidate China University of Petroleum(East China) School of Petroleum Engineering No.66 Changjiang West Road, Qingdao Visiting scholar (2017.12-2018.12) The University of Texas at Austin Cockrell School of Engineering McKetta Department of Chemical Engineering 200 E Dean Keeton St. Stop C0400 CPE 5.428 *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs Install problem
For that error you may use normal and better Intel compiler or gcc above 6.3. The 2020.1 compiles well after correcting stupid bug in multidimensional array routine and with use of Intel 19 and gcc above 6. I use 7.3 Your compiler is too old to support C++14 but there other problem as well Alex On Mar 13, 2020 1:54 PM, xuan Zhang wrote: Hi, When I install the Gromacs on Linux, the cmake occurs error like below. I am a newer on this software. I appreciate very much that you can help me. Best regards, Xuan **/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON CMake Error at cmake/FindLibStdCpp.cmake:162 (message): GROMACS requires C++14, but a test of such functionality in the C++ standard library failed to compile. The g++ found at /usr/bin/g++ had a suitable version, so ;something else must be the problem Call Stack (most recent call first): CMakeLists.txt:69 (find_package) -- Configuring incomplete, errors occurred! See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". *#cmakeerror.log as below:* Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following output: Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build make[1]: Entering directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o CMakeFiles/cmTC_203a2.dir/src.cxx.o -c /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: namespace "std" has no member "cbegin" int main() { int a[2]; std::cbegin(a); } ^ compilation aborted for /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 make[1]: Leaving directory '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' Makefile:138: recipe for target 'cmTC_203a2/fast' failed make: *** [cmTC_203a2/fast] Error 2 Source file was: #include int main() { int a[2]; std::cbegin(a); } -- *Xuan Zhang* PhD Candidate China University of Petroleum(East China) School of Petroleum Engineering No.66 Changjiang West Road, Qingdao Visiting scholar (2017.12-2018.12) The University of Texas at Austin Cockrell School of Engineering McKetta Department of Chemical Engineering 200 E Dean Keeton St. Stop C0400 CPE 5.428 *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
Re: [gmx-users] Gromacs Install problem
Hi, For now, I have added the compiler to cmake and it works. But in the *make *step, the errors were shown as below. Thank you very much. Best regards, Xuan src/gromacs/CMakeFiles/lmfit_objlib.dir/build.make:79: recipe for target 'src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o' failed make[2]: *** [src/gromacs/CMakeFiles/lmfit_objlib.dir/__/external/lmfit/lmmin.cpp.o] Error 1 CMakeFiles/Makefile2:4229: recipe for target 'src/gromacs/CMakeFiles/lmfit_objlib.dir/all' failed make[1]: *** [src/gromacs/CMakeFiles/lmfit_objlib.dir/all] Error 2 Makefile:179: recipe for target 'all' failed make: *** [all] Error 2 liy0i@kw60520:/data16/XUAN/gromacs-2020.1/build$ ./configure -bash: ./configure: No such file or directory On Sat, Mar 14, 2020 at 1:53 AM xuan Zhang wrote: > Hi, > > When I install the Gromacs on Linux, the cmake occurs error like below. I > am a newer on this software. I appreciate very much that you can help me. > > Best regards, > Xuan > > **/gromacs-2020.1/build$ cmake .. -DGMX_BUILD_OWN_FFTW=ON > -DREGRESSIONTEST_DOWNLOAD=ON > CMake Error at cmake/FindLibStdCpp.cmake:162 (message): > GROMACS requires C++14, but a test of such functionality in the C++ > standard library failed to compile. The g++ found at /usr/bin/g++ had a > suitable version, so ;something else must be the problem > Call Stack (most recent call first): > CMakeLists.txt:69 (find_package) > > > -- Configuring incomplete, errors occurred! > See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeOutput.log". > See also "/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeError.log". > > > *#cmakeerror.log as below:* > > Performing C++ SOURCE FILE Test CXX14_COMPILES failed with the following > output: > Change Dir: /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp > > Run Build Command(s):/usr/bin/make cmTC_203a2/fast && /usr/bin/make -f > CMakeFiles/cmTC_203a2.dir/build.make CMakeFiles/cmTC_203a2.dir/build > make[1]: Entering directory > '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' > Building CXX object CMakeFiles/cmTC_203a2.dir/src.cxx.o > /sw/workstations/apps/linux-ubuntu16.04-x86_64/openmpi/3.1.1/intel-18.0.1/lqdls6jj3oauixvl4rbbpnljxr6sd6zs/bin/mpic++ > -gcc-name=/usr/bin/g++ -DCXX14_COMPILES -std=c++14 -o > CMakeFiles/cmTC_203a2.dir/src.cxx.o -c > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx(2): error: > namespace "std" has no member "cbegin" > int main() { int a[2]; std::cbegin(a); } > ^ > > compilation aborted for > /data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp/src.cxx (code 2) > CMakeFiles/cmTC_203a2.dir/build.make:82: recipe for target > 'CMakeFiles/cmTC_203a2.dir/src.cxx.o' failed > make[1]: *** [CMakeFiles/cmTC_203a2.dir/src.cxx.o] Error 2 > make[1]: Leaving directory > '/data16/XUAN/gromacs-2020.1/build/CMakeFiles/CMakeTmp' > Makefile:138: recipe for target 'cmTC_203a2/fast' failed > make: *** [cmTC_203a2/fast] Error 2 > > > Source file was: > #include > int main() { int a[2]; std::cbegin(a); } > > -- > *Xuan Zhang* > > PhD Candidate > China University of Petroleum(East China) > School of Petroleum Engineering > No.66 Changjiang West Road, Qingdao > > > Visiting scholar (2017.12-2018.12) > The University of Texas at Austin > Cockrell School of Engineering > McKetta Department of Chemical Engineering > 200 E Dean Keeton St. Stop C0400 > CPE 5.428 > > *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com > -- *Xuan Zhang* PhD Candidate China University of Petroleum(East China) School of Petroleum Engineering No.66 Changjiang West Road, Qingdao Visiting scholar (2017.12-2018.12) The University of Texas at Austin Cockrell School of Engineering McKetta Department of Chemical Engineering 200 E Dean Keeton St. Stop C0400 CPE 5.428 *(+86) 15563945098 <(571)%20346-9770>* | zhangxuan7...@gmail.com -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.