[gmx-users] Make check not passing tests on 2018.5

Fri Feb 1 05:00:14 CET 2019

Hello,

I've compiled gromacs 2018.5 in double precision a couple times now and it
keeps on failing the same tests every time. This is on Ubuntu 18.04 with an
i9 7900X.

The cmake I used was:
cmake .. -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=on -DGMX_BUILD_OWN_FFTW=ON
-DCMAKE_BUILD_TYPE=Release -DGMX_BUILD_UNITTESTS=ON
-DCMAKE_INSTALL_PREFIX=/usr/local/gromacs-2018.5

The problem with make check is:

34/39 Test #34: regressiontests/simple ...........   Passed    3.01 sec
      Start 35: regressiontests/complex
35/39 Test #35: regressiontests/complex ..........***Failed   34.69 sec
Will test using executable suffix _d
             :-) GROMACS - gmx mdrun, 2018.5 (double precision) (-:

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GROMACS:      gmx mdrun, version 2018.5 (double precision)
Executable:   /home/david/gromacs-2018.5/build/bin/gmx_d
Data prefix:  /home/david/gromacs-2018.5 (source tree)
Working dir:  /home/david/gromacs-2018.5/build/tests/regressiontests-2018.5
Command line:
  gmx_d mdrun -h

Thanx for Using GROMACS - Have a Nice Day

Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8.

Abnormal return value for ' gmx_d mdrun    -nb cpu   -notunepme
>mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8.

Abnormal return value for ' gmx_d mdrun    -nb cpu   -notunepme
>mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
FAILED. Check checkpot.out (69 errors), checkforce.out (224 errors)
file(s) in distance_restraints for distance_restraints
Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8.

Abnormal return value for ' gmx_d mdrun    -nb cpu   -notunepme
>mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8.

Abnormal return value for ' gmx_d mdrun       -notunepme >mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
Mdrun cannot use the requested (or automatic) number of ranks, retrying with 8.

Abnormal return value for ' gmx_d mdrun       -notunepme >mdrun.out 2>&1' was 1
Retrying mdrun with better settings...
FAILED. Check checkpot.out (16 errors), checkforce.out (1362 errors)
file(s) in orientation-restraints for orientation-restraints
2 out of 51 complex tests FAILED

      Start 36: regressiontests/kernel
36/39 Test #36: regressiontests/kernel ...........   Passed   55.12 sec
      Start 37: regressiontests/freeenergy
37/39 Test #37: regressiontests/freeenergy .......   Passed    9.27 sec
      Start 38: regressiontests/pdb2gmx
38/39 Test #38: regressiontests/pdb2gmx ..........   Passed   16.95 sec
      Start 39: regressiontests/rotation
39/39 Test #39: regressiontests/rotation .........   Passed    3.60 sec

97% tests passed, 1 tests failed out of 39

Label Time Summary:
GTest              =   4.54 sec*proc (33 tests)
IntegrationTest    =   2.03 sec*proc (3 tests)
MpiTest            =   0.20 sec*proc (3 tests)
UnitTest           =   2.51 sec*proc (30 tests)

Total Test time (real) = 127.19 sec

The following tests FAILED:
	 35 - regressiontests/complex (Failed)
Errors while running CTest
CMakeFiles/run-ctest-nophys.dir/build.make:57: recipe for target
'CMakeFiles/run-ctest-nophys' failed
make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8
CMakeFiles/Makefile2:1385: recipe for target
'CMakeFiles/run-ctest-nophys.dir/all' failed
make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2
CMakeFiles/Makefile2:1165: recipe for target 'CMakeFiles/check.dir/rule' failed
make[1]: *** [CMakeFiles/check.dir/rule] Error 2
Makefile:626: recipe for target 'check' failed
make: *** [check] Error 2

Looking at the log file for the orientation-restraints test shows
different energies calculated for some terms. The different terms are
bolded, but if that doesn't carry the LJ, Coulomb, Potential, Kinetic,
Total, Conserved, Temperature, Pressure and Constr rmsd are all
different. In most cases significantly.

>From reference_d.log:
   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    8.49937e+02    2.39137e+03    1.86371e+03    1.57563e+02   -3.65191e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    9.32112e+02    1.40820e+04   -*1.21790e+03*   *-2.01406e+04*    4.96236e+01
  Orient. Rest.   Ori. R. RMSD      Potential    Kinetic En.   Total Energy
    2.68612e+00    1.95988e+00   *-1.39474e+03*    *3.19608e+03*
*1.80134e+03*
  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
    *1.80134e+03*    *3.03394e+02*   *-4.01423e+01*    *6.77807e-09*

And from my system:
   Energies (kJ/mol)
           Bond            U-B    Proper Dih.  Improper Dih.      CMAP Dih.
    8.49937e+02    2.39137e+03    1.86371e+03    1.57563e+02   -3.65191e+02
          LJ-14     Coulomb-14        LJ (SR)   Coulomb (SR)   Coul. recip.
    9.32112e+02    1.40820e+04   *-3.34280e+02   -3.70272e+03*    4.96236e+01
  Orient. Rest.   Ori. R. RMSD      Potential    Kinetic En.   Total Energy
    2.68612e+00    1.95988e+00    *1.59268e+04    3.21311e+03*    *1.91399e+04*
  Conserved En.    Temperature Pressure (bar)   Constr. rmsd
    *1.91399e+04    3.05010e+02    1.11267e+02    7.18413e-09*

Any help on how resolve this would be greatly appreciated.

Cheers,

David