I am new to Rosetta and trying to install in my workstation. After installation when I ran the unit test, and it is showing like a 99% success rate. Is it ok to now run the program or I need to fix the issues? If not can you please help me out to fix that?
After doing this,
python test/run.py --mode=debug -j32
I am getting
-------- Unit test summary --------
Total number of tests: 3469
number tests passed: 3451
number tests failed: 18
failed tests:
core.test: conformation_stored_restypes_tests:test_load_pdb
core.test: conformation_stored_restypes_tests:test_load_pdb_with_pose_copy
core.test: conformation_stored_restypes_tests:test_score_restype_noset
core.test: conformation_stored_restypes_tests:test_pack_restype_noset
core.test: conformation_stored_restypes_tests:test_min_restype_noset
core.test: conformation_stored_restypes_tests:test_load_restype_conf
core.test: conformation_stored_restypes_tests:test_cartmin_restype_noset
core.test: conformation_stored_restypes_tests:test_serialization
protocols.test: StructureDataTests:test_move_segments
protocols.test: StructureDataTests:test_enzdes_remarks
protocols.test: StructureDataTests:test_slice
protocols.test: StructureDataTests:test_non_peptidic_bonds
protocols.test: AlignResiduesMoverTests:test_tomponent_cstfile
protocols.test: GenericSimulatedAnnealerTests:test_boltzmann
protocols.test: StructureDataTests:test_delete_segment
protocols.test: GenericSimulatedAnnealerTests:test_acceptance
protocols.test: GenericSimulatedAnnealerTests:test_checkpointing
protocols.test: AlignResiduesMoverTests:test_align_theozyme
Success rate: 99%
---------- End of Unit test summary
Done!
Please help me out
Thank you in advance
That's concerning -- the pass rate should be 100% on all public releases, and in our hands on our testing server, it is. It suggests a system-specific problem that we need to fix. Which compiler were you using, what is your operating system, and what version of Rosetta are you running? Also could you run one of the tests that failed and post the output here? (For example, ./test/run.py --mode=debug conformation_stored_restypes_tests).
I am having a similiar problem.
I am on a cluster which runs CentOS Linux release 8.2.2004. I am trying to compile Rosetta 3.9 (in order to link with RifDock), mode=release. I thought it might have been a new gcc (9.3) issue so I tried deleting and compiling again with older gcc versions (4.8, 5.5, 8.3.1) but 21-25 unit tests always fail.
Here is the most recent: Rosetta 3.9 and tests were compiled/run with mode=release and gcc 8.3.1
This is the current unit test results:
-------- Unit test summary --------
Total number of tests: 3813
number tests passed: 3792
number tests failed: 21
failed tests:
protocols.test: LoopsFileIOTest:test_LoopsFileIO_read_JSON_loops_file
protocols.test: StructureDataTests:test_enzdes_remarks
protocols.test: StructureDataTests:test_non_peptidic_bonds
protocols.test: GenericSimulatedAnnealerTests:test_boltzmann
protocols.test: StructureDataTests:test_move_segments
protocols.test: AlignResiduesMoverTests:test_align_theozyme
protocols.test: GenericSimulatedAnnealerTests:test_acceptance
protocols.test: StructureDataTests:test_delete_segment
protocols.test: AlignResiduesMoverTests:test_tomponent_cstfile
protocols.test: ScoreTest:test_Score12
protocols.test: GenericSimulatedAnnealerTests:test_checkpointing
protocols.test: StructureDataTests:test_slice
core.test: conformation_stored_restypes_tests:test_load_pdb_with_pose_copy
core.test: conformation_stored_restypes_tests:test_load_pdb
core.test: conformation_stored_restypes_tests:test_load_restype_conf
core.test: conformation_stored_restypes_tests:test_score_restype_noset
core.test: conformation_stored_restypes_tests:test_min_restype_noset
core.test: conformation_stored_restypes_tests:test_serialization
core.test: conformation_stored_restypes_tests:test_pack_restype_noset
core.test: conformation_stored_restypes_tests:test_cartmin_restype_noset
numeric.test: GeneralizedEigenSolverTests:test_4x4_complex_problem
Success rate: 99.4492525570417%
---------- End of Unit test summary
Done!
Here is the output from the failed tests:
Running one suite: conformation_stored_restypes_tests
Test suite: conformation_stored_restypes_tests (test/core/conformation/conformation_stored_restypes.cxxtest.hh)
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/DonStrength.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/ref2015_params/AccStrength.csv
basic.io.database: Database file opened: scoring/score_functions/rama/fd/all.ramaProb
basic.io.database: Database file opened: scoring/score_functions/rama/fd/prepro.ramaProb
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.all.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.gly.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.pro.txt
basic.io.database: Database file opened: scoring/score_functions/omega/omega_ppdep.valile.txt
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/shapovalov/10deg/kappa131/a20.prop
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-lengths.txt
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-angles.txt
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-torsions.txt
basic.io.database: Database file opened: scoring/score_functions/bondlength_bondangle/default-improper.txt
basic.io.database: [ WARNING ] Unable to locate database file chemical/residue_type_sets/fa_standard/residue_types/devel/denovo_design/D2I.params
ERROR: Cannot find file 'devel/denovo_design/D2I.params or /grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/database/chemical/residue_type_sets/fa_standard/residue_types/devel/denovo_design/D2I.params'
ERROR:: Exit from: src/core/chemical/residue_io.cc line: 212
BACKTRACE:
/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/source/build/src/release/linux/4.18/64/x86/gcc/8/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2cd) [0x15554647240d]
/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/source/build/src/release/linux/4.18/64/x86/gcc/8/default/libcore.2.so(core::chemical::read_topology_file(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, std::weak_ptr<core::chemical::AtomTypeSet const>, std::weak_ptr<core::chemical::ElementSet const>, std::weak_ptr<core::chemical::MMAtomTypeSet const>, std::weak_ptr<core::chemical::orbitals::OrbitalTypeSet const>)+0x440) [0x155547a57090]
/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/source/build/src/release/linux/4.18/64/x86/gcc/8/default/libcore.2.so(core::chemical::ResidueTypeSet::add_base_residue_type(std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x130) [0x155547af2e40]
./core.test() [0xcd2e61]
./core.test() [0xf0eda2]
./core.test() [0x56438a]
/lib64/libc.so.6(__libc_start_main+0xf3) [0x1555444716a3]
./core.test() [0x56441e]
ERROR: Unhandled Exception caught by cxxtest:
File: src/core/chemical/residue_io.cc:212
[ ERROR ] UtilityExitException
ERROR: Cannot find file 'devel/denovo_design/D2I.params or /grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/database/chemical/residue_type_sets/fa_standard/residue_types/devel/denovo_design/D2I.params'
Command line: ./core.test conformation_stored_restypes_tests --database=/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/database --mute core
These two also have the same error:
And looking in the database folder there is no 'devel' folder on this path: main/database/chemical/residue_type_sets/fa_standard/residue_types/
Here are the other 4 failed unit tests:
Running one suite: GeneralizedEigenSolverTests
Test suite: GeneralizedEigenSolverTests (test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh)
In GeneralizedEigenSolverTests::test_4x4_complex_problem:
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:382: Error: Expected (actual_1.real() == expected_1_real) up to epsilon (0.0000), found (0.4153 != 0.4153)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:383: Error: Expected (actual_1.imag() == expected_1_imag) up to epsilon (0.0000), found (-0.2293 != -0.2293)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:384: Error: Expected (actual_2.real() == expected_2_real) up to epsilon (0.0000), found (-0.2579 != -0.2579)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:385: Error: Expected (actual_2.imag() == expected_2_imag) up to epsilon (0.0000), found (-0.1653 != -0.1653)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:386: Error: Expected (actual_3.real() == expected_3_real) up to epsilon (0.0000), found (0.5137 != 0.5137)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:387: Error: Expected (actual_3.imag() == expected_3_imag) up to epsilon (0.0000), found (-0.1274 != -0.1274)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:388: Error: Expected (actual_4.real() == expected_4_real) up to epsilon (0.0000), found (-0.6303 != -0.6303)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:389: Error: Expected (actual_4.imag() == expected_4_imag) up to epsilon (0.0000), found (-0.0592 != -0.0592)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:382: Error: Expected (actual_1.real() == expected_1_real) up to epsilon (0.0000), found (0.4153 != 0.4153)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:383: Error: Expected (actual_1.imag() == expected_1_imag) up to epsilon (0.0000), found (0.2293 != 0.2293)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:384: Error: Expected (actual_2.real() == expected_2_real) up to epsilon (0.0000), found (-0.2579 != -0.2579)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:385: Error: Expected (actual_2.imag() == expected_2_imag) up to epsilon (0.0000), found (0.1653 != 0.1653)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:386: Error: Expected (actual_3.real() == expected_3_real) up to epsilon (0.0000), found (0.5137 != 0.5137)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:387: Error: Expected (actual_3.imag() == expected_3_imag) up to epsilon (0.0000), found (0.1274 != 0.1274)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:388: Error: Expected (actual_4.real() == expected_4_real) up to epsilon (0.0000), found (-0.6303 != -0.6303)
./test/numeric/linear_algebra/GeneralizedEigenSolverTests.cxxtest.hh:389: Error: Expected (actual_4.imag() == expected_4_imag) up to epsilon (0.0000), found (0.0592 != 0.0592)
CXXTEST_ERROR: test_4x4_complex_problem Failed!
Failed 1 of 169 tests
Success rate: 99%
Running one suite: LoopsFileIOTest
Test suite: LoopsFileIOTest (test/protocols/loops/LoopsFileIO.cxxtest.hh)
protocols.loops.LoopsFileIO: [ ERROR ] Error parsing bogus ( line 1 ): [WARNING] DEPRECATED old style extended marker X is used
In LoopsFileIOTest::test_LoopsFileIO_read_JSON_loops_file:
./test/protocols/loops/LoopsFileIO.cxxtest.hh:380: Error: Assertion failed: lfd[ 1 ].skip_rate() == 0.5
./test/protocols/loops/LoopsFileIO.cxxtest.hh:391: Error: Assertion failed: sloops[ 1 ].skip_rate == 0.5
CXXTEST_ERROR: test_LoopsFileIO_read_JSON_loops_file Failed!
Failed 1 of 1673 tests
Success rate: 99%
Running one suite: AlignResiduesMoverTests
Test suite: AlignResiduesMoverTests (test/protocols/denovo_design/movers/AlignResiduesMoverTests.cxxtest.hh)
ERROR: Cannot open file devel/denovo_design/cat_residues.pdb
ERROR:: Exit from: src/core/io/pdb/build_pose_as_is.cc line: 176
BACKTRACE:
/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/source/build/src/release/linux/4.18/64/x86/gcc/8/default/libutility.so(utility::exit(char const*, int, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, int)+0x2cd) [0x15554627040d]
/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/source/build/src/release/linux/4.18/64/x86/gcc/8/default/libcore.3.so(core::io::pdb::build_pose_from_pdb_as_is(core::pose::Pose&, core::chemical::ResidueTypeSet const&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::io::StructFileReaderOptions const&)+0x249) [0x1555491ba029]
/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/source/build/src/release/linux/4.18/64/x86/gcc/8/default/libcore.3.so(core::io::pdb::build_pose_from_pdb_as_is(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&, core::io::StructFileReaderOptions const&)+0x40) [0x1555491ba390]
/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/source/build/src/release/linux/4.18/64/x86/gcc/8/default/libcore.3.so(core::io::pdb::build_pose_from_pdb_as_is(core::pose::Pose&, std::__cxx11::basic_string<char, std::char_traits<char>, std::allocator<char> > const&)+0x2a) [0x1555491ba60a]
./protocols.test() [0x59bdc4]
./protocols.test() [0xe6a992]
./protocols.test() [0x58fd5a]
/lib64/libc.so.6(__libc_start_main+0xf3) [0x15554426f6a3]
./protocols.test() [0x58fdee]
ERROR: Unhandled Exception caught by cxxtest:
File: src/core/io/pdb/build_pose_as_is.cc:176
[ ERROR ] UtilityExitException
ERROR: Cannot open file devel/denovo_design/cat_residues.pdb
Command line: ./protocols.test AlignResiduesMoverTests --database=/grid/furukawa/home_norepl/dawood/rosetta_src_3_9/main/database --mute core
Running one suite: ScoreTest
Test suite: ScoreTest (test/protocols/moves/ScoreTest.cxxtest.hh)
Start All Scoring tests
basic.io.database: Database file opened: scoring/score_functions/PairEPotential/pdb_pair_stats_fine
basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBPoly1D.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBFadeIntervals.csv
basic.io.database: Database file opened: scoring/score_functions/hbonds/score12_params/HBEval.csv
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_n
basic.io.database: Database file opened: scoring/score_functions/P_AA_pp/P_AA_pp
basic.io.database: Database file opened: scoring/score_functions/rama/Rama_smooth_dyn.dat_ss_6.4
File: ./test/protocols/moves/ScoreTest.cxxtest.hh Line:82
MoversTest::ScoreMover Files protocols/moves/score12.pdb and protocols/moves/score12.pdb._tmp_ are not equal!
CXXTEST_ERROR: test_AllMovers:ScoreMover Failed!
In ScoreTest::test_Score12:
./test/protocols/moves/ScoreTest.cxxtest.hh:82: Error: Test failed: test_AllMovers
UTracer(protocols/moves/score12.u) line 1 not equal:
protocols.simple_moves.ScoreMover: E fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref != protocols.simple_moves.ScoreMover: E fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref
old: protocols.simple_moves.ScoreMover: E fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref
new: protocols.simple_moves.ScoreMover: E fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref./test/UTracer.hh:100: Error: Test failed: " \x1B[0mprotocols.simple_moves.ScoreMover: \x1B[0mE fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref != protocols.simple_moves.ScoreMover: E fa_atr fa_rep fa_sol fa_intra_rep pro_close fa_pair hbond_sr_bb hbond_lr_bb hbond_bb_sc hbond_sc dslf_ss_dst dslf_cs_ang dslf_ss_dih dslf_ca_dih rama omega fa_dun p_aa_pp ref "
CXXTEST_ERROR: test_Score12 Failed!
Failed 1 of 1673 tests
Success rate: 99%
Would really appreciate your help! Thanks in advance!