Error during compilation #3
Comments
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It is errors when launching Do you have the same errors with a 'vanilla' GROMACS source tree ? (e.g without applying the colvars patch) |
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No, not at all! For un patched Gromacs... no error.. @gromacs Version 2019
to 2023. No error with -DGMX_GPU=CUDA flag
…On Mon, 28 Aug 2023, 7:33 pm Hub, ***@***.***> wrote:
It is errors when launching make test after compiling GROMACS.
Do you have the same errors with a 'vanilla' GROMACS source tree ? (e.g
without applying the colvars patch)
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okay thanks. I'll look into it. |
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thanks for your kind consideration |
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I'm not able to reproduce the errors in the test. I tried with an Ubuntu 22.04, gcc and with or without CUDA (v.12) but all tests passed in my case (with GROMACS 2022 with or without colvars path) Can you give us the command line you used and the version of the OS and gcc/CUDA installed? |
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CUDA 11.7, OS Linuxmint
…On Thu, 31 Aug 2023, 2:42 pm Giacomo Fiorin, ***@***.***> wrote:
Also, please include the OS and CUDA version, and compiler version if it's
not the gcc that comes with the OS
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can you provide a bit more information please ? (command line executed, gcc version). |
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Sure I will send you on Tuesday.
…On Fri, 1 Sept 2023, 2:42 pm Hub, ***@***.***> wrote:
can you provide a bit more information please ? (command line executed,
gcc version).
Does it happen also on a CPU-only build?
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@debanjansen48 Were you able to gather the information? |
Conventional gromacs alrady installed and working with gpu accelaration. Why I am receivibg this error during compilation of colver patched gromacs. Is there ant tutorial for installation?
or.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -5.9555001258850098
Expected: forces[i][m]
Which is: -5.9527950286865234
Difference: 0.0027051 (5673 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -5.9555001258850098
Expected: forces[i][m]
Which is: -5.9527950286865234
Difference: 0.0027051 (5673 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 5.9554991722106934
Expected: forces[i][m]
Which is: 5.9527950286865234
Difference: 0.00270414 (5671 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 5.9554991722106934
Expected: forces[i][m]
Which is: 5.9527950286865234
Difference: 0.00270414 (5671 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 5.9554991722106934
Expected: forces[i][m]
Which is: 5.9527950286865234
Difference: 0.00270414 (5671 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -5.9555001258850098
Expected: forces[i][m]
Which is: -5.9527950286865234
Difference: 0.0027051 (5673 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -5.9555001258850098
Expected: forces[i][m]
Which is: -5.9527950286865234
Difference: 0.0027051 (5673 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -5.9555001258850098
Expected: forces[i][m]
Which is: -5.9527950286865234
Difference: 0.0027051 (5673 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -6.6088199615478516
Expected: forces[i][m]
Which is: -6.6120624542236328
Difference: 0.00324249 (6800 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -6.6088199615478516
Expected: forces[i][m]
Which is: -6.6120624542236328
Difference: 0.00324249 (6800 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -6.6088199615478516
Expected: forces[i][m]
Which is: -6.6120624542236328
Difference: 0.00324249 (6800 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 6.6088194847106934
Expected: forces[i][m]
Which is: 6.6120624542236328
Difference: 0.00324297 (6801 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 6.6088194847106934
Expected: forces[i][m]
Which is: 6.6120624542236328
Difference: 0.00324297 (6801 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 6.6088194847106934
Expected: forces[i][m]
Which is: 6.6120624542236328
Difference: 0.00324297 (6801 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -6.6088199615478516
Expected: forces[i][m]
Which is: -6.6120624542236328
Difference: 0.00324249 (6800 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -6.6088199615478516
Expected: forces[i][m]
Which is: -6.6120624542236328
Difference: 0.00324249 (6800 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -6.6088199615478516
Expected: forces[i][m]
Which is: -6.6120624542236328
Difference: 0.00324249 (6800 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 6.6088194847106934
Expected: forces[i][m]
Which is: 6.6120624542236328
Difference: 0.00324297 (6801 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 6.6088194847106934
Expected: forces[i][m]
Which is: 6.6120624542236328
Difference: 0.00324297 (6801 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 6.6088194847106934
Expected: forces[i][m]
Which is: 6.6120624542236328
Difference: 0.00324297 (6801 single-prec. ULPs, rel. 0.00049)
Tolerance: abs. 0.000330441, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 5.9554991722106934
Expected: forces[i][m]
Which is: 5.9527950286865234
Difference: 0.00270414 (5671 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 5.9554991722106934
Expected: forces[i][m]
Which is: 5.9527950286865234
Difference: 0.00270414 (5671 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: 5.9554991722106934
Expected: forces[i][m]
Which is: 5.9527950286865234
Difference: 0.00270414 (5671 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -5.9555001258850098
Expected: forces[i][m]
Which is: -5.9527950286865234
Difference: 0.0027051 (5673 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -5.9555001258850098
Expected: forces[i][m]
Which is: -5.9527950286865234
Difference: 0.0027051 (5673 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
/home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/api/nblib/listed_forces/tests/calculator.cpp:84: Failure
Value of: refForcesFloat[i][m]
Actual: -5.9555001258850098
Expected: forces[i][m]
Which is: -5.9527950286865234
Difference: 0.0027051 (5673 single-prec. ULPs, rel. 0.000454)
Tolerance: abs. 0.000297775, rel. 5e-05
[ FAILED ] LinearChainDataFixture.Multithreading (5 ms)
[----------] 1 test from LinearChainDataFixture (5 ms total)
[----------] 2 tests from ListedShims
[ RUN ] ListedShims.ParameterConversion
[ OK ] ListedShims.ParameterConversion (0 ms)
[ RUN ] ListedShims.GmxToNblibConversion
[ OK ] ListedShims.GmxToNblibConversion (0 ms)
[----------] 2 tests from ListedShims (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0, where TypeParam = nblib::TwoParameterInteractionnblib::HarmonicBondTypeParameter
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/0.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/0 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1, where TypeParam = nblib::G96BondType
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/1.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/1 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2, where TypeParam = nblib::CubicBondType
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/2.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/2 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3, where TypeParam = nblib::MorseBondType
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/3.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/3 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4, where TypeParam = nblib::TwoParameterInteractionnblib::FENEBondTypeParameter
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/4.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/4 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5, where TypeParam = nblib::AngleInteractionTypenblib::HarmonicAngleParameter
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/5.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/5 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6, where TypeParam = nblib::CosineParamAnglenblib::G96AngleParameter
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/6.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/6 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7, where TypeParam = nblib::CosineParamAnglenblib::RestrictedAngleParameter
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/7.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/7 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8, where TypeParam = nblib::TwoParameterInteractionnblib::LinearAngleParameter
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/8.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/8 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9, where TypeParam = nblib::QuarticAngle
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/9.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/9 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10, where TypeParam = nblib::CrossBondBond
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/10.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/10 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11, where TypeParam = nblib::CrossBondAngle
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/11.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/11 (0 ms total)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12, where TypeParam = nblib::ProperDihedral
[ RUN ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth
[ OK ] CompareEachTypeInNblibAndGmx/NblibGmxListed/12.SameForcesOnBoth (0 ms)
[----------] 1 test from CompareEachTypeInNblibAndGmx/NblibGmxListed/12 (0 ms total)
[----------] 1 test from ListedTransformations
[ RUN ] ListedTransformations.SortInteractionIndices
[ OK ] ListedTransformations.SortInteractionIndices (0 ms)
[----------] 1 test from ListedTransformations (0 ms total)
[----------] Global test environment tear-down
[==========] 44 tests from 22 test suites ran. (83 ms total)
[ PASSED ] 43 tests.
[ FAILED ] 1 test, listed below:
[ FAILED ] LinearChainDataFixture.Multithreading
1 FAILED TEST
double free or corruption (fasttop)
4/88 Test #4: NbLibSamplesTestArgon .......................... Passed 0.06 sec
Start 5: NbLibSamplesTestMethaneWater
5/88 Test gromacs#5: NbLibSamplesTestMethaneWater ................... Passed 0.05 sec
Start 6: NbLibUtilTests
6/88 Test gromacs#6: NbLibUtilTests ................................. Passed 0.05 sec
Start 7: NbLibSetupTests
7/88 Test gromacs#7: NbLibSetupTests ................................Subprocess aborted***Exception: 2.69 sec
[==========] Running 58 tests from 3 test suites.
[----------] Global test environment set-up.
[----------] 41 tests from NBlibTest
[ RUN ] NBlibTest.CubicBoxCannotHaveNaN
[ OK ] NBlibTest.CubicBoxCannotHaveNaN (0 ms)
[ RUN ] NBlibTest.CubicBoxCannotHaveInf
[ OK ] NBlibTest.CubicBoxCannotHaveInf (0 ms)
[ RUN ] NBlibTest.RectangularBoxCannotHaveNaN
[ OK ] NBlibTest.RectangularBoxCannotHaveNaN (0 ms)
[ RUN ] NBlibTest.RectangularBoxCannotHaveInf
[ OK ] NBlibTest.RectangularBoxCannotHaveInf (0 ms)
[ RUN ] NBlibTest.CubicBoxWorks
[ OK ] NBlibTest.CubicBoxWorks (0 ms)
[ RUN ] NBlibTest.BoxEqual
[ OK ] NBlibTest.BoxEqual (0 ms)
[ RUN ] NBlibTest.NonBondedForceParamsCorrect
[ OK ] NBlibTest.NonBondedForceParamsCorrect (0 ms)
[ RUN ] NBlibTest.CanMergeInteractions
[ OK ] NBlibTest.CanMergeInteractions (0 ms)
[ RUN ] NBlibTest.ParticleTypeNameCanBeConstructed
[ OK ] NBlibTest.ParticleTypeNameCanBeConstructed (0 ms)
[ RUN ] NBlibTest.ParticleTypeMassCanBeConstructed
[ OK ] NBlibTest.ParticleTypeMassCanBeConstructed (0 ms)
[ RUN ] NBlibTest.PbcHolderWorks
[ OK ] NBlibTest.PbcHolderWorks (0 ms)
[ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName
[ OK ] NBlibTest.CanConstructMoleculeWithoutChargeOrResidueName (0 ms)
[ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName
[ OK ] NBlibTest.CanConstructMoleculeWithChargeWithoutResidueName (0 ms)
[ RUN ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName
[ OK ] NBlibTest.CanConstructMoleculeWithoutChargeWithResidueName (0 ms)
[ RUN ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName
[ OK ] NBlibTest.CanConstructMoleculeWithChargeWithResidueName (0 ms)
[ RUN ] NBlibTest.CanGetNumParticlesInMolecule
[ OK ] NBlibTest.CanGetNumParticlesInMolecule (0 ms)
[ RUN ] NBlibTest.CanConstructExclusionListFromNames
[ OK ] NBlibTest.CanConstructExclusionListFromNames (0 ms)
[ RUN ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed
[ OK ] NBlibTest.CanConstructExclusionListFromNamesAndIndicesMixed (0 ms)
[ RUN ] NBlibTest.AtWorks
[ OK ] NBlibTest.AtWorks (0 ms)
[ RUN ] NBlibTest.AtThrows
[ OK ] NBlibTest.AtThrows (1 ms)
[ RUN ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass
[ OK ] NBlibTest.MoleculeThrowsSameParticleTypeNameDifferentMass (0 ms)
[ RUN ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass
[ OK ] NBlibTest.MoleculeDontThrowsSameParticleTypeNameDifferentMass (0 ms)
[ RUN ] NBlibTest.MoleculeNoThrowsSameParticleTypeName
[ OK ] NBlibTest.MoleculeNoThrowsSameParticleTypeName (0 ms)
[ RUN ] NBlibTest.CanAddInteractions
[ OK ] NBlibTest.CanAddInteractions (0 ms)
[ RUN ] NBlibTest.CanAddUreyBradley
[ OK ] NBlibTest.CanAddUreyBradley (0 ms)
[ RUN ] NBlibTest.TopologyHasNumParticles
[ OK ] NBlibTest.TopologyHasNumParticles (2 ms)
[ RUN ] NBlibTest.TopologyHasCharges
[ OK ] NBlibTest.TopologyHasCharges (0 ms)
[ RUN ] NBlibTest.TopologyHasMasses
[ OK ] NBlibTest.TopologyHasMasses (0 ms)
[ RUN ] NBlibTest.TopologyHasParticleTypes
[ OK ] NBlibTest.TopologyHasParticleTypes (0 ms)
[ RUN ] NBlibTest.TopologyHasParticleTypeIds
[ OK ] NBlibTest.TopologyHasParticleTypeIds (0 ms)
[ RUN ] NBlibTest.TopologyThrowsIdenticalParticleType
[ OK ] NBlibTest.TopologyThrowsIdenticalParticleType (0 ms)
[ RUN ] NBlibTest.TopologyHasExclusions
[ OK ] NBlibTest.TopologyHasExclusions (0 ms)
[ RUN ] NBlibTest.TopologyHasSequencing
[ OK ] NBlibTest.TopologyHasSequencing (0 ms)
[ RUN ] NBlibTest.TopologyCanAggregateBonds
[ OK ] NBlibTest.TopologyCanAggregateBonds (0 ms)
[ RUN ] NBlibTest.TopologyCanSequencePairIDs
[ OK ] NBlibTest.TopologyCanSequencePairIDs (0 ms)
[ RUN ] NBlibTest.TopologySequenceIdThrows
No particle O-Atom in residue SOL in molecule SOL found
[ OK ] NBlibTest.TopologySequenceIdThrows (0 ms)
[ RUN ] NBlibTest.TopologyCanEliminateDuplicateBonds
[ OK ] NBlibTest.TopologyCanEliminateDuplicateBonds (0 ms)
[ RUN ] NBlibTest.TopologyListedInteractions
[ OK ] NBlibTest.TopologyListedInteractions (0 ms)
[ RUN ] NBlibTest.TopologyListedInteractionsMultipleTypes
[ OK ] NBlibTest.TopologyListedInteractionsMultipleTypes (0 ms)
[ RUN ] NBlibTest.TopologyInvalidParticleInInteractionThrows
No particle Iron in residue SOL in molecule SOL found
[ OK ] NBlibTest.TopologyInvalidParticleInInteractionThrows (0 ms)
[ RUN ] NBlibTest.toGmxExclusionBlockWorks
[ OK ] NBlibTest.toGmxExclusionBlockWorks (0 ms)
[----------] 41 tests from NBlibTest (13 ms total)
[----------] 16 tests from NbnxmSetupTest
[ RUN ] NbnxmSetupTest.findNumEnergyGroups
[ OK ] NbnxmSetupTest.findNumEnergyGroups (0 ms)
[ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto
[ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumAuto (0 ms)
[ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnumNo
[ OK ] NbnxmSetupTest.canTranslateBenchmarkEnumNo (0 ms)
[ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM
[ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum2XM (0 ms)
[ RUN ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM
[ OK ] NbnxmSetupTest.canTranslateBenchmarkEnum4XM (0 ms)
[ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsAuto
[ OK ] NbnxmSetupTest.CheckKernelSetupThrowsAuto (0 ms)
[ RUN ] NbnxmSetupTest.CheckKernelSetupThrowsCount
[ OK ] NbnxmSetupTest.CheckKernelSetupThrowsCount (0 ms)
[ RUN ] NbnxmSetupTest.canCreateKernelSetupPlain
[ OK ] NbnxmSetupTest.canCreateKernelSetupPlain (0 ms)
[ RUN ] NbnxmSetupTest.canCreateParticleInfoAllVdv
[ OK ] NbnxmSetupTest.canCreateParticleInfoAllVdv (0 ms)
[ RUN ] NbnxmSetupTest.ewaldCoeffWorks
[ OK ] NbnxmSetupTest.ewaldCoeffWorks (0 ms)
[ RUN ] NbnxmSetupTest.updateForcerecWorks
[ OK ] NbnxmSetupTest.updateForcerecWorks (0 ms)
[ RUN ] NbnxmSetupTest.canCheckKernelSetup
[ OK ] NbnxmSetupTest.canCheckKernelSetup (0 ms)
[ RUN ] NbnxmSetupTest.CanCreateNbnxmCPU
[ OK ] NbnxmSetupTest.CanCreateNbnxmCPU (0 ms)
[ RUN ] NbnxmSetupTest.canCreateKernelSetupGPU
[ OK ] NbnxmSetupTest.canCreateKernelSetupGPU (0 ms)
[ RUN ] NbnxmSetupTest.CanCreateDeviceStreamManager
corrupted size vs. prev_size in fastbins
8/88 Test gromacs#8: NbLibTprTests ..................................***Timeout 30.03 sec
[==========] Running 4 tests from 1 test suite.
[----------] Global test environment set-up.
[----------] 4 tests from TprReaderTest
[ RUN ] TprReaderTest.SimDBTprIsCreated
NOTE 1 [file /home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/build/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]:
With Verlet lists the optimal nstlist is >= 10, with GPUs >= 20. Note
that with the Verlet scheme, nstlist has no effect on the accuracy of
your simulation.
NOTE 2 [file /home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/build/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]:
Setting nstcalcenergy (100) equal to nstenergy (4)
Number of degrees of freedom in T-Coupling group System is 33.00
NOTE 3 [file /home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/build/api/nblib/tests/Testing/Temporary/TprReaderTest_SimDBTprIsCreated_input.mdp]:
NVE simulation: will use the initial temperature of 68.810 K for
determining the Verlet buffer size
There were 3 notes
9/88 Test gromacs#9: NbLibIntegrationTests .......................... Passed 0.05 sec
Start 10: NbLibIntegratorTests
10/88 Test gromacs#10: NbLibIntegratorTests ...........................Subprocess aborted***Exception: 1.35 sec
[==========] Running 1 test from 1 test suite.
[----------] Global test environment set-up.
[----------] 1 test from NBlibTest
[ RUN ] NBlibTest.IntegratorWorks
[ OK ] NBlibTest.IntegratorWorks (2 ms)
[----------] 1 test from NBlibTest (2 ms total)
[----------] Global test environment tear-down
[==========] 1 test from 1 test suite ran. (2 ms total)
[ PASSED ] 1 test.
double free or corruption (fasttop)
11/88 Test gromacs#11: TestUtilsUnitTests ............................. Passed 0.03 sec
Start 12: TestUtilsMpiUnitTests
12/88 Test gromacs#12: TestUtilsMpiUnitTests .......................... Passed 0.03 sec
Start 13: UtilityUnitTests
13/88 Test gromacs#13: UtilityUnitTests ............................... Passed 0.03 sec
Start 14: UtilityMpiUnitTests
14/88 Test gromacs#14: UtilityMpiUnitTests ............................ Passed 0.03 sec
Start 15: GmxlibTests
15/88 Test gromacs#15: GmxlibTests .................................... Passed 0.03 sec
Start 16: MdlibUnitTest
16/88 Test gromacs#16: MdlibUnitTest .................................. Passed 0.45 sec
Start 17: AwhTest
17/88 Test gromacs#17: AwhTest ........................................ Passed 0.04 sec
Start 18: DensityFittingAppliedForcesUnitTest
18/88 Test gromacs#18: DensityFittingAppliedForcesUnitTest ............ Passed 0.03 sec
Start 19: QMMMAppliedForcesUnitTest
19/88 Test gromacs#19: QMMMAppliedForcesUnitTest ...................... Passed 0.05 sec
Start 20: AppliedForcesUnitTest
20/88 Test gromacs#20: AppliedForcesUnitTest .......................... Passed 0.03 sec
Start 21: ListedForcesTest
21/88 Test #21: ListedForcesTest ............................... Passed 0.04 sec
Start 22: NbnxmTests
22/88 Test #22: NbnxmTests ..................................... Passed 0.03 sec
Start 23: CommandLineUnitTests
23/88 Test #23: CommandLineUnitTests ........................... Passed 0.03 sec
Start 24: DomDecTests
24/88 Test #24: DomDecTests .................................... Passed 0.03 sec
Start 25: DomDecMpiTests
25/88 Test #25: DomDecMpiTests ................................. Passed 0.29 sec
Start 26: EwaldUnitTests
26/88 Test #26: EwaldUnitTests ................................. Passed 0.60 sec
Start 27: FFTUnitTests
27/88 Test #27: FFTUnitTests ................................... Passed 0.37 sec
Start 28: GpuUtilsUnitTests
28/88 Test #28: GpuUtilsUnitTests .............................. Passed 0.28 sec
Start 29: HardwareUnitTests
29/88 Test #29: HardwareUnitTests .............................. Passed 0.16 sec
Start 30: MathUnitTests
30/88 Test #30: MathUnitTests .................................. Passed 0.07 sec
Start 31: MdrunUtilityUnitTests
31/88 Test #31: MdrunUtilityUnitTests .......................... Passed 0.03 sec
Start 32: MdrunUtilityMpiUnitTests
32/88 Test #32: MdrunUtilityMpiUnitTests ....................... Passed 0.03 sec
Start 33: MDSpanTests
33/88 Test #33: MDSpanTests .................................... Passed 0.03 sec
Start 34: MdtypesUnitTest
34/88 Test #34: MdtypesUnitTest ................................ Passed 0.04 sec
Start 35: OnlineHelpUnitTests
35/88 Test #35: OnlineHelpUnitTests ............................ Passed 0.03 sec
Start 36: OptionsUnitTests
36/88 Test #36: OptionsUnitTests ............................... Passed 0.03 sec
Start 37: PbcutilUnitTest
37/88 Test #37: PbcutilUnitTest ................................ Passed 0.03 sec
Start 38: RandomUnitTests
38/88 Test #38: RandomUnitTests ................................ Passed 0.03 sec
Start 39: RestraintTests
39/88 Test #39: RestraintTests ................................. Passed 0.03 sec
Start 40: TableUnitTests
40/88 Test #40: TableUnitTests ................................. Passed 0.07 sec
Start 41: TaskAssignmentUnitTests
41/88 Test #41: TaskAssignmentUnitTests ........................ Passed 0.03 sec
Start 42: GmxTimingTests
42/88 Test #42: GmxTimingTests ................................. Passed 0.03 sec
Start 43: TopologyTest
43/88 Test #43: TopologyTest ................................... Passed 0.03 sec
Start 44: PullTest
44/88 Test #44: PullTest ....................................... Passed 0.03 sec
Start 45: SimdUnitTests
45/88 Test #45: SimdUnitTests .................................. Passed 0.05 sec
Start 46: CompatibilityHelpersTests
46/88 Test #46: CompatibilityHelpersTests ...................... Passed 0.03 sec
Start 47: GmxAnaTest
47/88 Test #47: GmxAnaTest ..................................... Passed 0.43 sec
Start 48: GmxPreprocessTests
48/88 Test #48: GmxPreprocessTests ............................. Passed 0.51 sec
Start 49: Pdb2gmx1Test
49/88 Test #49: Pdb2gmx1Test ................................... Passed 0.93 sec
Start 50: Pdb2gmx2Test
50/88 Test #50: Pdb2gmx2Test ................................... Passed 0.96 sec
Start 51: Pdb2gmx3Test
51/88 Test #51: Pdb2gmx3Test ................................... Passed 3.79 sec
Start 52: CorrelationsTest
52/88 Test #52: CorrelationsTest ............................... Passed 0.18 sec
Start 53: AnalysisDataUnitTests
53/88 Test #53: AnalysisDataUnitTests .......................... Passed 0.06 sec
Start 54: CoordinateIOTests
54/88 Test #54: CoordinateIOTests .............................. Passed 0.13 sec
Start 55: TrajectoryAnalysisUnitTests
55/88 Test #55: TrajectoryAnalysisUnitTests .................... Passed 2.00 sec
Start 56: EnergyAnalysisUnitTests
56/88 Test #56: EnergyAnalysisUnitTests ........................ Passed 0.25 sec
Start 57: ToolUnitTests
57/88 Test #57: ToolUnitTests .................................. Passed 3.51 sec
Start 58: FileIOTests
58/88 Test #58: FileIOTests .................................... Passed 0.14 sec
Start 59: SelectionUnitTests
59/88 Test #59: SelectionUnitTests ............................. Passed 0.53 sec
Start 60: ParserTest
60/88 Test #60: ParserTest ..................................... Passed 1.05 sec
Start 61: MdrunOutputTests
61/88 Test #61: MdrunOutputTests ............................... Passed 5.27 sec
Start 62: MdrunModulesTests
62/88 Test #62: MdrunModulesTests .............................. Passed 5.62 sec
Start 63: MdrunIOTests
63/88 Test #63: MdrunIOTests ................................... Passed 48.18 sec
Start 64: MdrunTestsOneRank
64/88 Test #64: MdrunTestsOneRank .............................. Passed 4.60 sec
Start 65: MdrunTestsTwoRanks
65/88 Test #65: MdrunTestsTwoRanks ............................. Passed 4.63 sec
Start 66: MdrunSingleRankAlgorithmsTests
66/88 Test #66: MdrunSingleRankAlgorithmsTests ................. Passed 1.52 sec
Start 67: MdrunNonIntegratorTests
67/88 Test #67: MdrunNonIntegratorTests ........................ Passed 24.78 sec
Start 68: MdrunTpiTests
68/88 Test #68: MdrunTpiTests .................................. Passed 1.83 sec
Start 69: MdrunMpiTests
69/88 Test #69: MdrunMpiTests .................................. Passed 8.52 sec
Start 70: MdrunMultiSimTests
70/88 Test #70: MdrunMultiSimTests ............................. Passed 0.50 sec
Start 71: MdrunMultiSimReplexTests
71/88 Test #71: MdrunMultiSimReplexTests ....................... Passed 0.48 sec
Start 72: MdrunMultiSimReplexEquivalenceTests
72/88 Test #72: MdrunMultiSimReplexEquivalenceTests ............ Passed 0.13 sec
Start 73: MdrunMpi1RankPmeTests
73/88 Test #73: MdrunMpi1RankPmeTests .......................... Passed 5.52 sec
Start 74: MdrunMpi2RankPmeTests
74/88 Test #74: MdrunMpi2RankPmeTests .......................... Passed 6.55 sec
Start 75: MdrunMpiCoordinationBasicTestsOneRank
75/88 Test #75: MdrunMpiCoordinationBasicTestsOneRank .......... Passed 2.44 sec
Start 76: MdrunMpiCoordinationBasicTestsTwoRanks
76/88 Test #76: MdrunMpiCoordinationBasicTestsTwoRanks ......... Passed 2.60 sec
Start 77: MdrunMpiCoordinationCouplingTestsOneRank
77/88 Test #77: MdrunMpiCoordinationCouplingTestsOneRank ....... Passed 39.97 sec
Start 78: MdrunMpiCoordinationCouplingTestsTwoRanks
78/88 Test #78: MdrunMpiCoordinationCouplingTestsTwoRanks ...... Passed 19.09 sec
Start 79: MdrunMpiCoordinationConstraintsTestsOneRank
79/88 Test #79: MdrunMpiCoordinationConstraintsTestsOneRank .... Passed 46.64 sec
Start 80: MdrunMpiCoordinationConstraintsTestsTwoRanks
80/88 Test #80: MdrunMpiCoordinationConstraintsTestsTwoRanks ... Passed 43.09 sec
Start 81: MdrunFEPTests
81/88 Test #81: MdrunFEPTests .................................. Passed 2.00 sec
Start 82: MdrunPullTests
82/88 Test #82: MdrunPullTests ................................. Passed 1.25 sec
Start 83: MdrunSimulatorComparison
83/88 Test #83: MdrunSimulatorComparison ....................... Passed 0.03 sec
Start 84: MdrunVirtualSiteTests
84/88 Test #84: MdrunVirtualSiteTests .......................... Passed 2.91 sec
Start 85: regressiontests/complex
85/88 Test #85: regressiontests/complex ........................***Failed 183.86 sec
Re-running aminoacids using only CPU-based non-bonded kernels
Re-running awh_multidim using only CPU-based non-bonded kernels
Re-running butane using only CPU-based non-bonded kernels
Re-running dd121 using only CPU-based non-bonded kernels
Re-running distance_restraints using only CPU-based non-bonded kernels
Re-running ethyleenglycol using only CPU-based non-bonded kernels
Re-running field using only CPU-based non-bonded kernels
Re-running nacl using only CPU-based non-bonded kernels
Re-running nbnxn-free-energy using only CPU-based non-bonded kernels
Re-running nbnxn-free-energy-vv using only CPU-based non-bonded kernels
Re-running nbnxn-ljpme-geometric using only CPU-based non-bonded kernels
Re-running nbnxn-ljpme-LB using only CPU-based non-bonded kernels
Re-running nbnxn-ljpme-LB-geometric using only CPU-based non-bonded kernels
Re-running nbnxn-vdw-force-switch using only CPU-based non-bonded kernels
Re-running nbnxn-vdw-potential-switch using only CPU-based non-bonded kernels
Re-running nbnxn-vdw-potential-switch-argon using only CPU-based non-bonded kernels
Re-running nbnxn_pme using only CPU-based non-bonded kernels
Re-running nbnxn_pme_order5 using only CPU-based non-bonded kernels
Re-running nbnxn_pme_order6 using only CPU-based non-bonded kernels
Re-running nbnxn_rf using only CPU-based non-bonded kernels
Re-running nbnxn_rzero using only CPU-based non-bonded kernels
Re-running nbnxn_vsite using only CPU-based non-bonded kernels
gmx check failed on the .edr file while checking the forces
Abnormal return value for 'gmx check -f /home/debanjan/Downloads/Colvers/gromacs-2022.4-colvars/build/tests/gromacs-regressiontests-release-2022/complex/nbnxn_vsite/reference_s.trr -f2 traj.trr -tol 0.001 -abstol 0.05 >checkforce.out 2>checkforce.err' was 1
FAILED. Check checkforce.out (1 errors) file(s) in nbnxn_vsite/nb-cpu for nbnxn_vsite-nb-cpu
Re-running nst_mismatch using only CPU-based non-bonded kernels
Re-running octahedron using only CPU-based non-bonded kernels
Re-running orientation-restraints using only CPU-based non-bonded kernels
Re-running position-restraints using only CPU-based non-bonded kernels
Re-running pr-vrescale using only CPU-based non-bonded kernels
Re-running pull_constraint using only CPU-based non-bonded kernels
Re-running pull_cylinder using only CPU-based non-bonded kernels
Re-running pull_geometry_angle using only CPU-based non-bonded kernels
Re-running pull_geometry_angle-axis using only CPU-based non-bonded kernels
Re-running pull_geometry_dihedral using only CPU-based non-bonded kernels
Re-running sw using only CPU-based non-bonded kernels
Re-running swap_x using only CPU-based non-bonded kernels
Re-running swap_y using only CPU-based non-bonded kernels
Re-running swap_z using only CPU-based non-bonded kernels
Re-running tip4p using only CPU-based non-bonded kernels
Re-running tip4pflex using only CPU-based non-bonded kernels
Re-running urea using only CPU-based non-bonded kernels
Re-running walls using only CPU-based non-bonded kernels
1 out of 88 complex tests FAILED
86/88 Test #86: regressiontests/freeenergy ..................... Passed 59.60 sec
Start 87: regressiontests/rotation
87/88 Test #87: regressiontests/rotation ....................... Passed 10.37 sec
Start 88: regressiontests/essentialdynamics
88/88 Test #88: regressiontests/essentialdynamics .............. Passed 3.12 sec
93% tests passed, 6 tests failed out of 88
Label Time Summary:
GTest = 332.88 secproc (81 tests)
IntegrationTest = 132.77 secproc (25 tests)
MpiTest = 188.05 secproc (19 tests)
QuickGpuTest = 34.95 secproc (17 tests)
SlowTest = 165.90 secproc (13 tests)
UnitTest = 34.21 secproc (43 tests)
Total Test time (real) = 591.06 sec
The following tests FAILED:
1 - GmxapiExternalInterfaceTests (Failed)
3 - NbLibListedForcesTests (Subprocess aborted)
7 - NbLibSetupTests (Subprocess aborted)
8 - NbLibTprTests (Timeout)
10 - NbLibIntegratorTests (Subprocess aborted)
85 - regressiontests/complex (Failed)
Errors while running CTest
make[3]: *** [CMakeFiles/run-ctest-nophys.dir/build.make:71: CMakeFiles/run-ctest-nophys] Error 8
make[2]: *** [CMakeFiles/Makefile2:3301: CMakeFiles/run-ctest-nophys.dir/all] Error 2
make[1]: *** [CMakeFiles/Makefile2:3334: CMakeFiles/check.dir/rule] Error 2
make: *** [Makefile:641: check] Error 2
The text was updated successfully, but these errors were encountered: