Hi All,
I've built Gromacs 2019 on both a CentOS 7 and SLES12 machine.
Built using gcc@7.2.0
Dependencies:
fftw@3.3.8
openmpi@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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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>
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