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

[Mark Abraham]

Hi,

The tests are not using python at all. You had your path set up so that you
can find that version of python, but it looks like it was built by some
ancient gcc, so finding it in (probably) the LD_LIBRARY_PATH is still going
poorly for GROMACS. I would hope there is a more robust way to install
anaconda, but I'm outside my expertise, there.

Mark

On Wed, Jan 18, 2017 at 11:54 PM Matthew Barcus <mb2293 at cornell.edu> wrote:

> 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
> --
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