sprucea5:spack-build>make check [100%] Running all tests except physical validation /scratch/prod-spruce/acs/spack/opt/linux-sles12-x86_64/gcc-7.2.0/cmake-3.13.4-ocbi3jb2k4zbyt2lx7yvrm2ysb65nix6/bin/ctest --output-on-failure -E physicalvalidationtests Test project /ROWAN/group/pts/spack/dev-2019-02-19/var/spack/stage/gromacs-2019-55qcdjpc4twm5abmvt4kghka3eanxdc6/gromacs-2019/spack-build Start 1: TestUtilsUnitTests 1/40 Test #1: TestUtilsUnitTests ............... Passed 1.99 sec Start 2: TestUtilsMpiUnitTests 2/40 Test #2: TestUtilsMpiUnitTests ............ Passed 0.41 sec Start 3: MdlibUnitTest 3/40 Test #3: MdlibUnitTest .................... Passed 0.39 sec Start 4: AppliedForcesUnitTest 4/40 Test #4: AppliedForcesUnitTest ............ Passed 2.24 sec Start 5: ListedForcesTest 5/40 Test #5: ListedForcesTest ................. Passed 1.29 sec Start 6: CommandLineUnitTests 6/40 Test #6: CommandLineUnitTests ............. Passed 0.42 sec Start 7: DomDecTests 7/40 Test #7: DomDecTests ...................... Passed 0.24 sec Start 8: EwaldUnitTests 8/40 Test #8: EwaldUnitTests ................... Passed 9.78 sec Start 9: FFTUnitTests 9/40 Test #9: FFTUnitTests ..................... Passed 0.48 sec Start 10: GpuUtilsUnitTests 10/40 Test #10: GpuUtilsUnitTests ................ Passed 0.23 sec Start 11: HardwareUnitTests 11/40 Test #11: HardwareUnitTests ................ Passed 0.24 sec Start 12: MathUnitTests 12/40 Test #12: MathUnitTests .................... Passed 4.02 sec Start 13: MdrunUtilityUnitTests 13/40 Test #13: MdrunUtilityUnitTests ............ Passed 0.25 sec Start 14: MdrunUtilityMpiUnitTests 14/40 Test #14: MdrunUtilityMpiUnitTests ......... Passed 0.27 sec Start 15: OnlineHelpUnitTests 15/40 Test #15: OnlineHelpUnitTests .............. Passed 0.53 sec Start 16: OptionsUnitTests 16/40 Test #16: OptionsUnitTests ................. Passed 2.04 sec Start 17: RandomUnitTests 17/40 Test #17: RandomUnitTests .................. Passed 0.50 sec Start 18: RestraintTests 18/40 Test #18: RestraintTests ................... Passed 0.86 sec Start 19: TableUnitTests 19/40 Test #19: TableUnitTests ................... Passed 2.33 sec Start 20: TaskAssignmentUnitTests 20/40 Test #20: TaskAssignmentUnitTests .......... Passed 0.24 sec Start 21: UtilityUnitTests 21/40 Test #21: UtilityUnitTests ................. Passed 0.55 sec Start 22: UtilityMpiUnitTests 22/40 Test #22: UtilityMpiUnitTests .............. Passed 1.88 sec Start 23: FileIOTests 23/40 Test #23: FileIOTests ...................... Passed 0.31 sec Start 24: PullTest 24/40 Test #24: PullTest ......................... Passed 0.24 sec Start 25: AwhTest 25/40 Test #25: AwhTest .......................... Passed 0.35 sec Start 26: SimdUnitTests 26/40 Test #26: SimdUnitTests .................... Passed 1.73 sec Start 27: CompatibilityHelpersTests 27/40 Test #27: CompatibilityHelpersTests ........ Passed 1.43 sec Start 28: GmxAnaTest 28/40 Test #28: GmxAnaTest ....................... Passed 1.00 sec Start 29: GmxPreprocessTests 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. 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. 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. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 8 atoms)! Added 1 molecules (out of 1 requested) Writing generated configuration to /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoExistingConfiguration_out.gro Output configuration contains 8 atoms in 4 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoExistingConfiguration (525 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox 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. 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. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 2 atoms)! Try 2 success (now 4 atoms)! Try 3 success (now 6 atoms)! Try 4 success (now 8 atoms)! Try 5 success (now 10 atoms)! Added 5 molecules (out of 5 requested) Writing generated configuration to /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEmptyBox_out.gro Output configuration contains 10 atoms in 10 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEmptyBox (17 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox 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. 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. 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. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 8 atoms)! Try 2 success (now 10 atoms)! Added 2 molecules (out of 2 requested) Writing generated configuration to /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoEnlargedBox_out.gro Output configuration contains 10 atoms in 4 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoEnlargedBox (31 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesWithReplacement 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. 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. 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. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Try 1 success (now 650 atoms)! Try 2 success (now 652 atoms)! Try 3 success (now 654 atoms)! Try 4 success (now 656 atoms)! Added 4 molecules (out of 4 requested) Replaced 8 residues (24 atoms) Writing generated configuration to /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesWithReplacement_out.gro Output configuration contains 632 atoms in 212 residues [ OK ] InsertMoleculesTest.InsertsMoleculesWithReplacement (88 ms) [ RUN ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions 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. 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. NOTE: From version 5.0 gmxpreprocess-test uses the Van der Waals radii from the source below. This means the results may be different compared to previous GROMACS versions. ++++ PLEASE READ AND CITE THE FOLLOWING REFERENCE ++++ A. Bondi van der Waals Volumes and Radii J. Phys. Chem. 68 (1964) pp. 441-451 -------- -------- --- Thank You --- -------- -------- Using random seed 1997 Read 4 positions from file /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_5.dat Try 1 success (now 2 atoms)! Try 2 success (now 4 atoms)! Try 12 skipped position (0.990, 2.010, 3.000) Try 13 success (now 6 atoms)! Added 3 molecules (out of 4 requested) Writing generated configuration to /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/InsertMoleculesTest_InsertsMoleculesIntoFixedPositions_out.gro Output configuration contains 6 atoms in 3 residues [ OK ] InsertMoleculesTest.InsertsMoleculesIntoFixedPositions (30 ms) [----------] 5 tests from InsertMoleculesTest (691 ms total) [----------] 12 tests from GetIrTest [ RUN ] GetIrTest.HandlesDifferentKindsOfMdpLines NOTE 1 [file /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp, line 12]: /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_HandlesDifferentKindsOfMdpLines_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. Ignoring obsolete mdp entry 'title' Replacing old mdp entry 'xtc_grps' by 'compressed-x-grps' [ OK ] GetIrTest.HandlesDifferentKindsOfMdpLines (43 ms) [ RUN ] GetIrTest.HandlesOnlyCutoffScheme [ OK ] GetIrTest.HandlesOnlyCutoffScheme (16 ms) [ RUN ] GetIrTest.UserErrorsSilentlyTolerated NOTE 1 [file /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp, line 5]: /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_UserErrorsSilentlyTolerated_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.UserErrorsSilentlyTolerated (78 ms) [ RUN ] GetIrTest.DefineHandlesAssignmentOnRhs NOTE 1 [file /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp, line 2]: /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_DefineHandlesAssignmentOnRhs_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.DefineHandlesAssignmentOnRhs (11 ms) [ RUN ] GetIrTest.EmptyInputWorks NOTE 1 [file /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp, line 1]: /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_EmptyInputWorks_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.EmptyInputWorks (20 ms) [ RUN ] GetIrTest.ProducesOutputFromElectricField NOTE 1 [file /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp, line 2]: /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricField_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.ProducesOutputFromElectricField (24 ms) [ RUN ] GetIrTest.ProducesOutputFromElectricFieldPulsed NOTE 1 [file /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp, line 2]: /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldPulsed_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.ProducesOutputFromElectricFieldPulsed (12 ms) [ RUN ] GetIrTest.ProducesOutputFromElectricFieldOscillating NOTE 1 [file /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp, line 2]: /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build/src/gromacs/gmxpreprocess/tests/Testing/Temporary/GetIrTest_ProducesOutputFromElectricFieldOscillating_input.mdp did not specify a value for the .mdp option "cutoff-scheme". Probably it was first intended for use with GROMACS before 4.6. In 4.6, the Verlet scheme was introduced, but the group scheme was still the default. The default is now the Verlet scheme, so you will observe different behaviour. [ OK ] GetIrTest.ProducesOutputFromElectricFieldOscillating (14 ms) [ RUN ] GetIrTest.TerminatesOnDuplicateOldAndNewKeys [WARNING] /scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/src/external/googletest/googletest/src/gtest-death-test.cc:836:: Death tests use fork(), which is unsafe particularly in a threaded context. For this test, Google Test detected 3 threads. Start 30: Pdb2gmxTest 30/40 Test #30: Pdb2gmxTest ...................... Passed 51.07 sec Start 31: CorrelationsTest 31/40 Test #31: CorrelationsTest ................. Passed 1.90 sec Start 32: AnalysisDataUnitTests 32/40 Test #32: AnalysisDataUnitTests ............ Passed 2.24 sec Start 33: SelectionUnitTests 33/40 Test #33: SelectionUnitTests ............... Passed 3.65 sec Start 34: TrajectoryAnalysisUnitTests 34/40 Test #34: TrajectoryAnalysisUnitTests ...... Passed 7.25 sec Start 35: EnergyAnalysisUnitTests 35/40 Test #35: EnergyAnalysisUnitTests .......... Passed 0.58 sec Start 36: ToolUnitTests 36/40 Test #36: ToolUnitTests .................... Passed 4.61 sec Start 37: MdrunTests 37/40 Test #37: MdrunTests ....................... Passed 10.40 sec Start 38: MdrunNonIntegratorTests 38/40 Test #38: MdrunNonIntegratorTests .......... Passed 24.38 sec Start 39: LegacyGroupSchemeMdrunTests 39/40 Test #39: LegacyGroupSchemeMdrunTests ...... Passed 3.61 sec Start 40: MdrunMpiTests 40/40 Test #40: MdrunMpiTests .................... Passed 3.49 sec 98% tests passed, 1 tests failed out of 40 Label Time Summary: GTest = 179.56 sec*proc (40 tests) IntegrationTest = 42.87 sec*proc (5 tests) MpiTest = 2.56 sec*proc (3 tests) SlowTest = 51.07 sec*proc (1 test) UnitTest = 85.62 sec*proc (34 tests) Total Test time (real) = 185.62 sec The following tests FAILED: 29 - GmxPreprocessTests (Timeout) Errors while running CTest CMakeFiles/run-ctest-nophys.dir/build.make:60: recipe for target 'CMakeFiles/run-ctest-nophys' failed make[3]: *** [CMakeFiles/run-ctest-nophys] Error 8 make[3]: Leaving directory '/scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build' CMakeFiles/Makefile2:1400: recipe for target 'CMakeFiles/run-ctest-nophys.dir/all' failed make[2]: *** [CMakeFiles/run-ctest-nophys.dir/all] Error 2 make[2]: Leaving directory '/scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build' CMakeFiles/Makefile2:1181: recipe for target 'CMakeFiles/check.dir/rule' failed make[1]: *** [CMakeFiles/check.dir/rule] Error 2 make[1]: Leaving directory '/scratch/cjn/.spack/var/spack/stage/spack-stage/spack-stage-xkrP6s/gromacs-2019/spack-build' Makefile:629: recipe for target 'check' failed make: *** [check] Error 2 sprucea5:spack-build>