[gmx-users] installation problems with gromacs-2016.1

sunyeping sunyeping at aliyun.com
Tue Jan 31 13:47:27 CET 2017


Dear all,
I am trying to install the latest version of gromacs ( gromacs-2016.1) into my computer with two C2050 NAVIDIA GPUs. My system is centos 6, and the cuda SDK (version 7.0).I followed the instruction in the gromacs webpage:(1) install gcc-4.9.4 with c++11 support.(2) wget http://ftp.gromacs.org/pub/gromacs/gromacs-2016.1.tar.gz 
(3) tar xfz gromacs-2016.1.tar.gz
(4) cd gromacs-2016.1
(5) mkdir build
(6) cd build
(7) cmake .. -DGMX_GPU=ON -DGMX_BUILD_OWN_FFTW=ON -DCMAKE_INSTALL_PREFIX=/app/build(8) make(9) make check
However, the results of make check show that all 21 tests failed. The output message of every test is similar, which read like:
1/21 Test  #1: TestUtilsUnitTests ...............***Failed    0.00 sec
/app/source/gromacs-2016.1/build/bin/testutils-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /app/source/gromacs-2016.1/build/bin/testutils-test)
/app/source/gromacs-2016.1/build/bin/testutils-test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /app/source/gromacs-2016.1/build/bin/testutils-test)
/app/source/gromacs-2016.1/build/bin/testutils-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /app/source/gromacs-2016.1/build/bin/testutils-test)
/app/source/gromacs-2016.1/build/bin/testutils-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
/app/source/gromacs-2016.1/build/bin/testutils-test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
/app/source/gromacs-2016.1/build/bin/testutils-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
/app/source/gromacs-2016.1/build/bin/testutils-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
/app/source/gromacs-2016.1/build/bin/testutils-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)

      Start  2: MdlibUnitTest
 2/21 Test  #2: MdlibUnitTest ....................***Failed    0.00 sec
/app/source/gromacs-2016.1/build/bin/mdlib-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /app/source/gromacs-2016.1/build/bin/mdlib-test)
/app/source/gromacs-2016.1/build/bin/mdlib-test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /app/source/gromacs-2016.1/build/bin/mdlib-test)
/app/source/gromacs-2016.1/build/bin/mdlib-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /app/source/gromacs-2016.1/build/bin/mdlib-test)
/app/source/gromacs-2016.1/build/bin/mdlib-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.20' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
/app/source/gromacs-2016.1/build/bin/mdlib-test: /usr/lib64/libstdc++.so.6: version `CXXABI_1.3.8' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
/app/source/gromacs-2016.1/build/bin/mdlib-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.18' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
/app/source/gromacs-2016.1/build/bin/mdlib-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.14' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
/app/source/gromacs-2016.1/build/bin/mdlib-test: /usr/lib64/libstdc++.so.6: version `GLIBCXX_3.4.15' not found (required by /app/source/gromacs-2016.1/build/lib/libgromacs.so.2)
......
Is anyone familiar with this situation and could help me with these problems?
Best regards. 
Yeping Sun


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