[gmx-users] question about Gromacs 5.0.4 build

Susan Chacko susanc at helix.nih.gov
Wed Jun 6 19:08:02 CEST 2018

Hi all,

I had installed Gromacs 5.0.4  on a Centos6 system a few years ago, and 
it was fine. We recently migrated our systems to Centos7, where Gromacs 
2018 was installed, also without problems.  A user requested the old 
Gromacs 5.0.4 on the Centos7 system to complete a project.

I worked through the identical install process, but of course with a 
newer compiler. The build of Gromacs went fine, but when I got to 'make 
check', one of the tests gave an error.

	->  13 - SelectionUnitTests (Failed)
[ RUN      ] SelectionCollectionDataTest.HandlesCharge
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:868: Failure
Value of: strValue
   Actual: "6"
Expected: refStrValue
Which is: "5"
Google Test trace:
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:861: Checking '/Compiled/Selection1/Atoms/Length'
/usr/local/src/gromacs/gromacs-5.0.4/src/gromacs/selection/tests/selectioncollection.cpp:312: Checking selection "charge < 0.5"
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:575: Failure
Reference data item not found
Google Test trace:
/usr/local/src/gromacs/gromacs-5.0.4/src/testutils/refdata.cpp:861: Checking '/Compiled/Selection1/Atoms/[5]'
/usr/local/src/gromacs/gromacs-5.0.4/src/gromacs/selection/tests/selectioncollection.cpp:312: Checking selection "charge < 0.5"
[  FAILED  ] SelectionCollectionDataTest.HandlesCharge (1 ms)

The build completed ok, and the user reports that all their tests ran 
fine. Here are the differences between the compiles:

Centos6: Intel compiler 2015.1.133, OpenMPI 1.8.4, instruction set AVX256

Centos7: Intel compiler 2017.4.196, OpenMPI 2.1.2, instruction set SSE4.1

The cmake versions were also different, but that seems minor.

Does anyone have any thoughts about the error above? Should I try 
rebuilding with GCC? Is the Gromacs that I built safe to use :-)?

All suggestions much appreciated,


Susan Chacko, Ph.D.
HPC @ NIH Staff

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