[gmx-users] Gomacs 2019 build on sles12 and centos

[Szilárd Páll]

Hi,

I assume the timeout does not happen with non-MPI builds, right? Have you
tried a different MPI flavor?

Cheers,
--
Szilárd


On Mon, Mar 11, 2019 at 10:54 AM Nelson Chris AWE <Chris.Nelson at awe.co.uk>
wrote:

> Hi All,
> I've built Gromacs 2019 on both a CentOS 7 and SLES12 machine.
> Built using gcc at 7.2.0
> Dependencies:
> fftw at 3.3.8
> openmpi at 3.1.3
>
> When running "make check" on both machines, I'm getting the same timeout
> error for test 29 - see below for extract and attached for full test output
> anyone got any ideas?
>
> Thanks,
> Chris.
>
> ===================================================================
> 29/40 Test #29: GmxPreprocessTests ...............***Timeout  30.15 sec
> [==========] Running 26 tests from 4 test cases.
> [----------] Global test environment set-up.
> [----------] 4 tests from GenconfTest
> [ RUN      ] GenconfTest.nbox_Works
> [       OK ] GenconfTest.nbox_Works (186 ms)
> [ RUN      ] GenconfTest.nbox_norenumber_Works
> [       OK ] GenconfTest.nbox_norenumber_Works (92 ms)
> [ RUN      ] GenconfTest.nbox_dist_Works
> [       OK ] GenconfTest.nbox_dist_Works (372 ms)
> [ RUN      ] GenconfTest.nbox_rot_Works
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> center of geometry: 1.733667, 1.477000, 0.905167
> [       OK ] GenconfTest.nbox_rot_Works (471 ms)
> [----------] 4 tests from GenconfTest (1121 ms total)
>
> [----------] 5 tests from InsertMoleculesTest
> [ RUN      ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration
> Reading solute configuration
> Reading molecule configuration
> Initialising inter-atomic distances...
>
> WARNING: Masses and atomic (Van der Waals) radii will be guessed
>          based on residue and atom names, since they could not be
>          definitively assigned from the information in your input
>          files. These guessed numbers might deviate from the mass
>          and radius of the atom type. Please check the output
>          files if necessary.
>
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