[gmx-users] GROMACS 2016.1 install fails 21/27 tests from 'make check'

[Matthew Barcus]

Hello,

I am trying to install gromacs 2016.1 on a ubuntu 16.04 system. The cmake
command was as follows:

cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda
-DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON

after running 'make' i did not get any errors and proceeded with 'make
check'. It was here that across all the failed tests, it appears the tests
were incidentely accessing my anaconda python and not the system python
(see results from failed test #1):

[100%] Running all tests
Test project /home/matthew/Downloads/gromacs-2016.1/build-gromacs
      Start  1: TestUtilsUnitTests
 1/27 Test  #1: TestUtilsUnitTests ...............***Failed    0.00 sec
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test:
/home/matthew/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not
found (required by
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test)
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test:
/home/matthew/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.8' not
found (required by
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test)
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test:
/home/matthew/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not
found (required by
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test)
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test:
/home/matthew/anaconda3/lib/libgomp.so.1: version `GOMP_4.0' not found
(required by
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/../lib/libgromacs.so.2)
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test:
/home/matthew/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.20' not
found (required by
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/../lib/libgromacs.so.2)
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test:
/home/matthew/anaconda3/lib/libstdc++.so.6: version `CXXABI_1.3.8' not
found (required by
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/../lib/libgromacs.so.2)
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/testutils-test:
/home/matthew/anaconda3/lib/libstdc++.so.6: version `GLIBCXX_3.4.21' not
found (required by
/home/matthew/Downloads/gromacs-2016.1/build-gromacs/bin/../lib/libgromacs.so.2)


I redefined the path variable without the anaconda python:

echo $PATH
/usr/local/cuda-8.0/bin:/home/matthew/bin:/home/matthew/.local/bin:/usr/local/cuda-8.0/bin/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games:/usr/local/games:/snap/bin

then ran 'make clean' and started back at 'cmake ...' only to get the same
results. Executing 'python' uses the system python now (2.7.12), so I do
not know why the tests were calling the anaconda python (3.5.2) still. Any
suggestions are greatly appreciated.

Thanks,

Matt