Gmxapi* tests segfault in rpmbuild - Redmine #3408
From: https://koji.fedoraproject.org/koji/taskinfo?taskID=42153050
49/52 Test #49: GmxapiExternalInterfaceTests ........***Exception: SegFault 0.90 sec
[==========] Running 9 tests from 2 test cases.
[----------] Global test environment set-u
[----------] 8 tests from GmxApiTest
[ RUN ] GmxApiTest.ApiRunnerRestrainedMD
Setting the LD random seed to 394101933
Generated 331705 of the 331705 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 331705 of the 331705 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 3 bonded neighbours molecule type 'methane'
NOTE 1 [file spc_and_methane.top, line 33]:
The bond in molecule-type methane between atoms 1 C and 2 H1 has an
estimated oscillational period of 1.1e-02 ps, which is less than 10 times
the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Number of degrees of freedom in T-Coupling group System is 18.00
NOTE 2 [file /builddir/build/BUILD/gromacs-2020.1/serial/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 2 notes
Start 50: GmxapiMpiTests
50/52 Test #50: GmxapiMpiTests ......................***Exception: SegFault 0.87 sec
[==========] Running 9 tests from 2 test cases.
[----------] Global test environment set-u
[----------] 8 tests from GmxApiTest
[ RUN ] GmxApiTest.ApiRunnerRestrainedMD
Setting the LD random seed to -369162639
Generated 331705 of the 331705 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 331705 of the 331705 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 3 bonded neighbours molecule type 'methane'
NOTE 1 [file spc_and_methane.top, line 33]:
The bond in molecule-type methane between atoms 1 C and 2 H1 has an
estimated oscillational period of 1.1e-02 ps, which is less than 10 times
the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Number of degrees of freedom in T-Coupling group System is 18.00
NOTE 2 [file /builddir/build/BUILD/gromacs-2020.1/serial/src/api/cpp/tests/Testing/Temporary/GmxApiTest_ApiRunnerRestrainedMD_input.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 2 notes
Start 51: GmxapiInternalInterfaceTests
51/52 Test #51: GmxapiInternalInterfaceTests ........***Exception: SegFault 0.87 sec
[==========] Running 2 tests from 1 test case.
[----------] Global test environment set-u
[----------] 2 tests from GmxApiTest
[ RUN ] GmxApiTest.BuildApiWorkflowImpl
Setting the LD random seed to -1197576397
Generated 331705 of the 331705 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 331705 of the 331705 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 3 bonded neighbours molecule type 'methane'
NOTE 1 [file spc_and_methane.top, line 33]:
The bond in molecule-type methane between atoms 1 C and 2 H1 has an
estimated oscillational period of 1.1e-02 ps, which is less than 10 times
the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Number of degrees of freedom in T-Coupling group System is 18.00
NOTE 2 [file /builddir/build/BUILD/gromacs-2020.1/serial/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 2 notes
Start 52: GmxapiInternalsMpiTests
52/52 Test #52: GmxapiInternalsMpiTests .............***Exception: SegFault 0.85 sec
[==========] Running 2 tests from 1 test case.
[----------] Global test environment set-u
[----------] 2 tests from GmxApiTest
[ RUN ] GmxApiTest.BuildApiWorkflowImpl
Setting the LD random seed to -1980902306
Generated 331705 of the 331705 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 331705 of the 331705 1-4 parameter combinations
Excluding 2 bonded neighbours molecule type 'SOL'
Excluding 3 bonded neighbours molecule type 'methane'
NOTE 1 [file spc_and_methane.top, line 33]:
The bond in molecule-type methane between atoms 1 C and 2 H1 has an
estimated oscillational period of 1.1e-02 ps, which is less than 10 times
the time step of 2.0e-03 ps.
Maybe you forgot to change the constraints mdp option.
Number of degrees of freedom in T-Coupling group System is 18.00
NOTE 2 [file /builddir/build/BUILD/gromacs-2020.1/serial/src/api/cpp/workflow/tests/Testing/Temporary/GmxApiTest_BuildApiWorkflowImpl_input.mdp]:
You are using a plain Coulomb cut-off, which might produce artifacts.
You might want to consider using PME electrostatics.
There were 2 notes
92% tests passed, 4 tests failed out of 52
Label Time Summary:
GTest = 75.32 sec*proc (52 tests)
IntegrationTest = 16.76 sec*proc (9 tests)
MpiTest = 50.27 sec*proc (8 tests)
SlowTest = 46.38 sec*proc (2 tests)
UnitTest = 12.19 sec*proc (41 tests)
Total Test time (real) = 75.39 sec
The following tests FAILED:
49 - GmxapiExternalInterfaceTests (SEGFAULT)
50 - GmxapiMpiTests (SEGFAULT)
51 - GmxapiInternalInterfaceTests (SEGFAULT)
52 - GmxapiInternalsMpiTests (SEGFAULT)
Errors while running CTest
Build log attached.
To reproduce this on fedora do:
git clone https://github.com/junghans/gromacs-rpm.git
cd gromacs-rpm.git
spectool -g gromacs.spec
fedpkg --release f33 srpm
mock -r fedora-rawhide-ppc64le --no-clean gromacs-2020.1-1.fc33.src.rpm
mock -r fedora-rawhide-ppc64le --shell
(from redmine: issue id 3408, created on 2020-03-03 by junghans)
- Relations:
- relates #951 (closed)
- relates #2896 (closed)
- blocks #2756 (closed)
- Changesets:
- Revision 0e1d4376 by Christoph Junghans on 2020-03-07T23:42:05Z:
cmake: use libsuffix on gmxapi as well
Related to #3408
Change-Id: I2f5648321bdea1f1d564b738783092a709429fa8