Re: [Rdkit-discuss] tests failed on Cygwin
Yes, it is definitely a rounding error, I will just have to make that check slightly more tolerant. For the time being, you may safely consider that test as passed. Cheers, p. > On 18 Mar 2015, at 11:10, Michal Krompiec wrote: > > Dear Paolo, >> regarding test 13, would you mind trying to change line 1400 in >> /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from [...] >> and tell me what the return value of >> MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) actually is? > > The return value is -9 (is it a rounding error then?). This is the > full output from the test: > > test 13 > Start 13: testUFFForceField > > 13: Test command: > /home/M212767/RDKit/build/Code/ForceField/UFF/testUFFForceField > 13: Test timeout computed to be: 9.99988e+06 > 13: - > 13: Unit tests for force field basics. > 13: done > 13: - > 13: Unit tests for basics of UFF bond-stretch terms. > 13: done > 13: - > 13: Unit tests for UFF bond-stretch terms. > 13: done > 13: - > 13: Unit tests for basics of UFF angle terms. > 13: done > 13: - > 13: Unit tests for UFF angle-bend terms. > 13: theta = 3.14159; theta0 = 3.14159 > 13: theta = 2.094395, param1.theta0 = 2.094395 > 13: done > 13: - > 13: Test Simple UFF molecule optimizations. > 13: done > 13: - > 13: Unit tests for UFF nonbonded terms. > 13: done > 13: - > 13: Test UFF torsional terms. > 13: done > 13: - > 13: Test UFF Parameter objects > 13: - > 13: Test Simple UFF molecule optimization, part 2. > 13: done > 13: - > 13: Test UFF Torsion Conflicts. > 13: C 0.4783 -0.7477 -0.0753 > 13: C -0.5465 -0.0176 0.3519 > 13: C -0.5114 1.4472 0.0870 > 13: H -1.5201 -0.4838 0.2485 > 13: H 0.4696 1.8363 0.3367 > 13: O -1.2618 1.9423 0.6934 > 13: F -0.7163 1.6298 -0.9622 > 13: done > 13: - > 13: Unit tests for UFF distance constraint terms. > 13: done > 13: - > 13: Unit tests for all UFF constraint terms. > 13: -9 > 13: done > 13: - > 13: Unit tests for copying UFF ForceFields. > 13: done > 13/85 Test #13: testUFFForceField Passed0.35 sec > > Best wishes, > Michal > >> On 17 March 2015 at 23:27, Paolo Tosco wrote: >> Hi Michal, >> >> regarding test 13, would you mind trying to change line 1400 in >> /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from >> >> TEST_ASSERT((int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, >> 8) == -10); >> >> to >> >> std::cout << (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, >> 6, 8) << std::endl; >> >> and tell me what the return value of >> MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) actually is? >> It might just be a periodicity problem. >> >> Thanks for your collaboration, kind regards >> Paolo >> >> >>> On 17/03/2015 14:48, Michal Krompiec wrote: >>> >>> Hello, >>> I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current >>> GitHub version). >>> So far, everything looked fine, but some tests failed: >>> >>> The following tests FAILED: >>> 13 - testUFFForceField (OTHER_FAULT) >>> 66 - testFMCS (SEGFAULT) >>> 79 - pythonTestDbCLI (Failed) - that's not a problem, as the >>> db is not set up (yet) >>> >>> I repeated using --output-on-failure, and that's what I got: >>> >>> testUFFForceField: >>> Test Assert >>> Expression Failed: >>> Violation occurred on line 1400 in file >>> /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp >>> Failed Expression: >>> (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) == >>> -10 >>> >>> 66/85 Test #66: testFMCS .***Exception: >>> SegFault 0.28 sec >>> [14:16:12] *** >>> [14:16:12] FMCS Unit Test >>> [14:16:12] - >>> [14:16:12] FMCS test1Basics() >>> >>> System reboot and /bin/rebaseall did not help. >>> >>> Moreover, tests for the cartridge also failed: >>> >>> $ make && make install && make installcheck >>> make: Nothing to be done for 'all'. >>> /usr/bin/mkdir -p '/usr/lib/postgresql' >>> /usr/bin/mkdir -p '/usr/share/postgresql/extension' >>> /usr/bin/mkdir -p '/usr/share/postgresql/extension' >>> /usr/bin/install -c -m 755 rdkit.dll '/usr/lib/postgresql/rdkit.dll' >>> /usr/bin/install -c -m 644 rdkit.control >>> '/usr/share/postgresql/extension/' >>> /usr/bin/install -c -m 644 rdkit--3.4.sql >>> '/usr/share/postgresql/extension/' >>> /usr/lib/postgresql/pgxs/src/makefiles/../
Re: [Rdkit-discuss] tests failed on Cygwin
Hello, I'm still struggling with the Cygwin build. gdb shows that the segfault in FMCS (test 66) is caused by: #0 0x67d0115a in RDKit::MCSProgressCallbackTimeout(RDKit::MCSProgressData const&, RDKit::MCSParameters const&, void*) () from C:\cygwin\home\path\RDKit\lib\cygFMCS-1.dll What could it be? My suspicion is that it a wrong version of some dll is loaded, but how do I trace it? Best wishes, Michal On 17 March 2015 at 14:48, Michal Krompiec wrote: > Hello, > I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current > GitHub version). > So far, everything looked fine, but some tests failed: > > The following tests FAILED: > 13 - testUFFForceField (OTHER_FAULT) > 66 - testFMCS (SEGFAULT) > 79 - pythonTestDbCLI (Failed) - that's not a problem, as the > db is not set up (yet) > > I repeated using --output-on-failure, and that's what I got: > > testUFFForceField: > Test Assert > Expression Failed: > Violation occurred on line 1400 in file > /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp > Failed Expression: > (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) == > -10 > > 66/85 Test #66: testFMCS .***Exception: > SegFault 0.28 sec > [14:16:12] *** > [14:16:12] FMCS Unit Test > [14:16:12] - > [14:16:12] FMCS test1Basics() > > System reboot and /bin/rebaseall did not help. > > Moreover, tests for the cartridge also failed: > > $ make && make install && make installcheck > make: Nothing to be done for 'all'. > /usr/bin/mkdir -p '/usr/lib/postgresql' > /usr/bin/mkdir -p '/usr/share/postgresql/extension' > /usr/bin/mkdir -p '/usr/share/postgresql/extension' > /usr/bin/install -c -m 755 rdkit.dll '/usr/lib/postgresql/rdkit.dll' > /usr/bin/install -c -m 644 rdkit.control '/usr/share/postgresql/extension/' > /usr/bin/install -c -m 644 rdkit--3.4.sql '/usr/share/postgresql/extension/' > /usr/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress > --inputdir=./ --psqldir='/usr/bin'--dbname=contrib_regression > rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps reaction > (using postmaster on Unix socket, default port) > == dropping database "contrib_regression" == > NOTICE: database "contrib_regression" does not exist, skipping > DROP DATABASE > == creating database "contrib_regression" == > CREATE DATABASE > ALTER DATABASE > == running regression test queries== > test rdkit-91 ... LOG: server process (PID 9076) was > terminated by signal 11: Segmentation fault > DETAIL: Failed process was running: CREATE EXTENSION rdkit; > > Has anybody else encountered such problems? Any idea what to do? > > Thanks, > Michal -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] tests failed on Cygwin
Dear Paolo, > regarding test 13, would you mind trying to change line 1400 in > /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from [...] > and tell me what the return value of > MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) actually is? The return value is -9 (is it a rounding error then?). This is the full output from the test: test 13 Start 13: testUFFForceField 13: Test command: /home/M212767/RDKit/build/Code/ForceField/UFF/testUFFForceField 13: Test timeout computed to be: 9.99988e+06 13: - 13: Unit tests for force field basics. 13: done 13: - 13: Unit tests for basics of UFF bond-stretch terms. 13: done 13: - 13: Unit tests for UFF bond-stretch terms. 13: done 13: - 13: Unit tests for basics of UFF angle terms. 13: done 13: - 13: Unit tests for UFF angle-bend terms. 13: theta = 3.14159; theta0 = 3.14159 13: theta = 2.094395, param1.theta0 = 2.094395 13: done 13: - 13: Test Simple UFF molecule optimizations. 13: done 13: - 13: Unit tests for UFF nonbonded terms. 13: done 13: - 13: Test UFF torsional terms. 13: done 13: - 13: Test UFF Parameter objects 13: - 13: Test Simple UFF molecule optimization, part 2. 13: done 13: - 13: Test UFF Torsion Conflicts. 13: C 0.4783 -0.7477 -0.0753 13: C -0.5465 -0.0176 0.3519 13: C -0.5114 1.4472 0.0870 13: H -1.5201 -0.4838 0.2485 13: H 0.4696 1.8363 0.3367 13: O -1.2618 1.9423 0.6934 13: F -0.7163 1.6298 -0.9622 13: done 13: - 13: Unit tests for UFF distance constraint terms. 13: done 13: - 13: Unit tests for all UFF constraint terms. 13: -9 13: done 13: - 13: Unit tests for copying UFF ForceFields. 13: done 13/85 Test #13: testUFFForceField Passed0.35 sec Best wishes, Michal On 17 March 2015 at 23:27, Paolo Tosco wrote: > Hi Michal, > > regarding test 13, would you mind trying to change line 1400 in > /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from > > TEST_ASSERT((int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, > 8) == -10); > > to > > std::cout << (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, > 6, 8) << std::endl; > > and tell me what the return value of > MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) actually is? > It might just be a periodicity problem. > > Thanks for your collaboration, kind regards > Paolo > > > On 17/03/2015 14:48, Michal Krompiec wrote: >> >> Hello, >> I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current >> GitHub version). >> So far, everything looked fine, but some tests failed: >> >> The following tests FAILED: >> 13 - testUFFForceField (OTHER_FAULT) >> 66 - testFMCS (SEGFAULT) >> 79 - pythonTestDbCLI (Failed) - that's not a problem, as the >> db is not set up (yet) >> >> I repeated using --output-on-failure, and that's what I got: >> >> testUFFForceField: >> Test Assert >> Expression Failed: >> Violation occurred on line 1400 in file >> /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp >> Failed Expression: >> (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) == >> -10 >> >> 66/85 Test #66: testFMCS .***Exception: >> SegFault 0.28 sec >> [14:16:12] *** >> [14:16:12] FMCS Unit Test >> [14:16:12] - >> [14:16:12] FMCS test1Basics() >> >> System reboot and /bin/rebaseall did not help. >> >> Moreover, tests for the cartridge also failed: >> >> $ make && make install && make installcheck >> make: Nothing to be done for 'all'. >> /usr/bin/mkdir -p '/usr/lib/postgresql' >> /usr/bin/mkdir -p '/usr/share/postgresql/extension' >> /usr/bin/mkdir -p '/usr/share/postgresql/extension' >> /usr/bin/install -c -m 755 rdkit.dll '/usr/lib/postgresql/rdkit.dll' >> /usr/bin/install -c -m 644 rdkit.control >> '/usr/share/postgresql/extension/' >> /usr/bin/install -c -m 644 rdkit--3.4.sql >> '/usr/share/postgresql/extension/' >> /usr/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress >> --inputdir=./ --psqldir='/usr/bin'--dbname=contrib_regression >> rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps reaction >> (using postmaster on Unix socket, default port) >> == dropping database "contrib_regression" == >> NOTICE: database "contrib_regression" does not exist, skipping >> DROP DATABASE >> == creating database "contrib_regression" == >> C
Re: [Rdkit-discuss] tests failed on Cygwin
Hi Michal, regarding test 13, would you mind trying to change line 1400 in /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp from TEST_ASSERT((int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) == -10); to std::cout << (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) << std::endl; and tell me what the return value of MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) actually is? It might just be a periodicity problem. Thanks for your collaboration, kind regards Paolo On 17/03/2015 14:48, Michal Krompiec wrote: > Hello, > I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current > GitHub version). > So far, everything looked fine, but some tests failed: > > The following tests FAILED: > 13 - testUFFForceField (OTHER_FAULT) > 66 - testFMCS (SEGFAULT) > 79 - pythonTestDbCLI (Failed) - that's not a problem, as the > db is not set up (yet) > > I repeated using --output-on-failure, and that's what I got: > > testUFFForceField: > Test Assert > Expression Failed: > Violation occurred on line 1400 in file > /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp > Failed Expression: > (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) == > -10 > > 66/85 Test #66: testFMCS .***Exception: > SegFault 0.28 sec > [14:16:12] *** > [14:16:12] FMCS Unit Test > [14:16:12] - > [14:16:12] FMCS test1Basics() > > System reboot and /bin/rebaseall did not help. > > Moreover, tests for the cartridge also failed: > > $ make && make install && make installcheck > make: Nothing to be done for 'all'. > /usr/bin/mkdir -p '/usr/lib/postgresql' > /usr/bin/mkdir -p '/usr/share/postgresql/extension' > /usr/bin/mkdir -p '/usr/share/postgresql/extension' > /usr/bin/install -c -m 755 rdkit.dll '/usr/lib/postgresql/rdkit.dll' > /usr/bin/install -c -m 644 rdkit.control '/usr/share/postgresql/extension/' > /usr/bin/install -c -m 644 rdkit--3.4.sql '/usr/share/postgresql/extension/' > /usr/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress > --inputdir=./ --psqldir='/usr/bin'--dbname=contrib_regression > rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps reaction > (using postmaster on Unix socket, default port) > == dropping database "contrib_regression" == > NOTICE: database "contrib_regression" does not exist, skipping > DROP DATABASE > == creating database "contrib_regression" == > CREATE DATABASE > ALTER DATABASE > == running regression test queries== > test rdkit-91 ... LOG: server process (PID 9076) was > terminated by signal 11: Segmentation fault > DETAIL: Failed process was running: CREATE EXTENSION rdkit; > > Has anybody else encountered such problems? Any idea what to do? > > Thanks, > Michal > > -- > Dive into the World of Parallel Programming The Go Parallel Website, sponsored > by Intel and developed in partnership with Slashdot Media, is your hub for all > things parallel software development, from weekly thought leadership blogs to > news, videos, case studies, tutorials and more. Take a look and join the > conversation now. http://goparallel.sourceforge.net/ > ___ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] tests failed on Cygwin
Hello, I'm trying to build RDKit on Cygwin, on Windows 7 32-bit (current GitHub version). So far, everything looked fine, but some tests failed: The following tests FAILED: 13 - testUFFForceField (OTHER_FAULT) 66 - testFMCS (SEGFAULT) 79 - pythonTestDbCLI (Failed) - that's not a problem, as the db is not set up (yet) I repeated using --output-on-failure, and that's what I got: testUFFForceField: Test Assert Expression Failed: Violation occurred on line 1400 in file /home/m212767/RDKit/Code/ForceField/UFF/testUFFForceField.cpp Failed Expression: (int)MolTransforms::getDihedralDeg(mol->getConformer(), 1, 3, 6, 8) == -10 66/85 Test #66: testFMCS .***Exception: SegFault 0.28 sec [14:16:12] *** [14:16:12] FMCS Unit Test [14:16:12] - [14:16:12] FMCS test1Basics() System reboot and /bin/rebaseall did not help. Moreover, tests for the cartridge also failed: $ make && make install && make installcheck make: Nothing to be done for 'all'. /usr/bin/mkdir -p '/usr/lib/postgresql' /usr/bin/mkdir -p '/usr/share/postgresql/extension' /usr/bin/mkdir -p '/usr/share/postgresql/extension' /usr/bin/install -c -m 755 rdkit.dll '/usr/lib/postgresql/rdkit.dll' /usr/bin/install -c -m 644 rdkit.control '/usr/share/postgresql/extension/' /usr/bin/install -c -m 644 rdkit--3.4.sql '/usr/share/postgresql/extension/' /usr/lib/postgresql/pgxs/src/makefiles/../../src/test/regress/pg_regress --inputdir=./ --psqldir='/usr/bin'--dbname=contrib_regression rdkit-91 props btree molgist bfpgist-91 sfpgist slfpgist fps reaction (using postmaster on Unix socket, default port) == dropping database "contrib_regression" == NOTICE: database "contrib_regression" does not exist, skipping DROP DATABASE == creating database "contrib_regression" == CREATE DATABASE ALTER DATABASE == running regression test queries== test rdkit-91 ... LOG: server process (PID 9076) was terminated by signal 11: Segmentation fault DETAIL: Failed process was running: CREATE EXTENSION rdkit; Has anybody else encountered such problems? Any idea what to do? Thanks, Michal -- Dive into the World of Parallel Programming The Go Parallel Website, sponsored by Intel and developed in partnership with Slashdot Media, is your hub for all things parallel software development, from weekly thought leadership blogs to news, videos, case studies, tutorials and more. Take a look and join the conversation now. http://goparallel.sourceforge.net/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
