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branch: master 「№60596」
Commited by: Vikram K. Mulligan
GitHub commit link: 「fd666910a5edac95」 「№3771」
Difference from previous tested commit:  code diff
Commit date: 2019-01-22 15:55:37
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.addsan integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release

Merge pull request #3771 from RosettaCommons/vmullig/fix_xcode_yet_again Fixing a few more xcode build errors. (Same thing: missing ampersands.)

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branch: master 「№60595」
Commited by: Vikram K. Mulligan
GitHub commit link: 「2787c928a326c3bd」 「№3773」
Difference from previous tested commit:  code diff
Commit date: 2019-01-22 15:46:32
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release

Merge pull request #3773 from RosettaCommons/vmullig/debug_mode_mathvector_overruns Correct bounds-checking on MathVectors MathVectors are zero-based, not one-based, but the bounds checking on the class assumes that indices 0 through (size) are valid. This corrects that. This turns out to be exactly what was wrong with my PolycubicSpline unit tests, too. This pull request corrects the indexing in the MathVector that I use in that test, so that I don't write past the end of an array. Finally, the bounds check was being performed in release and debug modes. This adds an #ifdef to ensure that the bounds check only happens in debug mode, for speed.

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Test: mac.clang.build.xcode

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branch: master 「№60594」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「228f5dcc86e55ec9」 「№3769」
Difference from previous tested commit:  code diff
Commit date: 2019-01-22 15:45:18
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release

Merge pull request #3769 from RosettaCommons/aleaverfay/slim_lkball2 ifndef-wrap a unit test which relies on a debug-mode assertion failure This PR fixes a currently-failing release-mode unit test that I added in the last PR (#3729)

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Test: mac.clang.build.xcode

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branch: master 「№60593」
Commited by: Vikram K. Mulligan
GitHub commit link: 「90b0b9f2010f8dd4」 「№3767」
Difference from previous tested commit:  code diff
Commit date: 2019-01-21 04:07:56
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.addsan integration.mpi integration.release_debug integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan

Merge pull request #3767 from RosettaCommons/vmullig/fix_spline_tests Trying to fix PolycubicSplineTest intermittent failure on Mac/clang build

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Test: mac.clang.build.xcode

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Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
advanced_protein-protein_docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
broker
Test: ubuntu.gcc.unit.addsan

Failed sub-tests (click for more details):
core:ApproximateBuriedUnsatPenaltyTests:test_burial_sanity_check core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_packing_4SER core:ApproximateBuriedUnsatPenaltyTests:test_packing_APA core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_IGReweight core:ApproximateBuriedUnsatPenaltyTests:test_packing_proline_nh_test core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET_O core:ApproximateBuriedUnsatPenaltyTests:test_scoring_4SER core:ApproximateBuriedUnsatPenaltyTests:test_scoring_APA core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_proline_nh_test core:AtomTypeDatabaseIOTests:test_atom_type_set_name numeric:PolycubicSplineTests:test_bicubic_spline_symmetry numeric:PolycubicSplineTests:test_cubic_spline_symmetry numeric:PolycubicSplineTests:test_polycubic_spline_3_data_access numeric:PolycubicSplineTests:test_polycubic_spline_4_data_access numeric:PolycubicSplineTests:test_tetracubic_spline_symmetry numeric:PolycubicSplineTests:test_tricubic_polycubic_3_identical numeric:PolycubicSplineTests:test_tricubic_spline_symmetry protocols:ClusterTests:test_cluster_identification protocols:ClusterTests:test_features


branch: master 「№60592」
Commited by: Vikram K. Mulligan
GitHub commit link: 「bd734379f5721f3c」 「№3768」
Difference from previous tested commit:  code diff
Commit date: 2019-01-20 19:55:23
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration.tutorials integration.ubsan integration.valgrind integration performance profile release.PyRosetta4.MinSizeRel release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan

Merge pull request #3768 from RosettaCommons/vmullig/fix_xcode_build_after_jd3 Trying to fix xcode build after JD3 refactor. Xcode flags cases in which `auto` is misused, causing objects to be copied inadvertently. For example: `for ( auto const larvaljob: larvaljobs_ ) { ... }` This should be `auto const & larvaljob`.

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Test: mac.clang.build.xcode

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Test: linux.clang.integration.tutorials

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advanced_protein-protein_docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
broker
Test: ubuntu.gcc.unit.addsan

Failed sub-tests (click for more details):
core:ApproximateBuriedUnsatPenaltyTests:test_burial_sanity_check core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_packing_4SER core:ApproximateBuriedUnsatPenaltyTests:test_packing_APA core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_IGReweight core:ApproximateBuriedUnsatPenaltyTests:test_packing_proline_nh_test core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET_O core:ApproximateBuriedUnsatPenaltyTests:test_scoring_4SER core:ApproximateBuriedUnsatPenaltyTests:test_scoring_APA core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_proline_nh_test core:AtomTypeDatabaseIOTests:test_atom_type_set_name numeric:PolycubicSplineTests:test_bicubic_spline_symmetry numeric:PolycubicSplineTests:test_cubic_spline_symmetry numeric:PolycubicSplineTests:test_polycubic_spline_3_data_access numeric:PolycubicSplineTests:test_polycubic_spline_4_data_access numeric:PolycubicSplineTests:test_tetracubic_spline_symmetry numeric:PolycubicSplineTests:test_tricubic_polycubic_3_identical numeric:PolycubicSplineTests:test_tricubic_spline_symmetry protocols:ClusterTests:test_cluster_identification protocols:ClusterTests:test_features


branch: master 「№60591」
Commited by: P. Douglas Renfrew
GitHub commit link: 「81a573a47f791407」 「№3761」
Difference from previous tested commit:  code diff
Commit date: 2019-01-18 10:21:39
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.addsan integration.mpi integration.release_debug integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug mac.clang.python27.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan unit.valgrind

Merge pull request #3761 from RosettaCommons/dougrenfrew/restore_oop_design This PR adds back a mc->recover_low( pose ) that was accidentally removed in 67479d1. The removal resulted in identical poses being output for each nstruct. It was found by an external user who contacted the original author @ksdrew .

P. Douglas Renfrew 4 days
I forgot to add in the commit message, changes to the oop_design and hbs_design integration tests are expected.
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Test: mac.clang.build.xcode

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Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
advanced_protein-protein_docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
broker
Test: mac.clang.integration

Failed sub-tests (click for more details):
hbs_design oop_design
Test: ubuntu.gcc.unit.addsan

Failed sub-tests (click for more details):
core:ApproximateBuriedUnsatPenaltyTests:test_burial_sanity_check core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_packing_4SER core:ApproximateBuriedUnsatPenaltyTests:test_packing_APA core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_IGReweight core:ApproximateBuriedUnsatPenaltyTests:test_packing_proline_nh_test core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET_O core:ApproximateBuriedUnsatPenaltyTests:test_scoring_4SER core:ApproximateBuriedUnsatPenaltyTests:test_scoring_APA core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_proline_nh_test core:AtomTypeDatabaseIOTests:test_atom_type_set_name numeric:PolycubicSplineTests:test_bicubic_spline_symmetry numeric:PolycubicSplineTests:test_cubic_spline_symmetry numeric:PolycubicSplineTests:test_polycubic_spline_3_data_access numeric:PolycubicSplineTests:test_polycubic_spline_4_data_access numeric:PolycubicSplineTests:test_tetracubic_spline_symmetry numeric:PolycubicSplineTests:test_tricubic_polycubic_3_identical numeric:PolycubicSplineTests:test_tricubic_spline_symmetry protocols:ClusterTests:test_cluster_identification protocols:ClusterTests:test_features


branch: master 「№60590」
Commited by: Jack Maguire
GitHub commit link: 「06851be071db1027」 「№3759」
Difference from previous tested commit:  code diff
Commit date: 2019-01-18 07:34:23
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release

Merge pull request #3759 from RosettaCommons/JackMaguire/FastDesignScriptsInDatabase Fixing Tests That I Broke Rocco noticed that the changes I made to FastRelax broke integration tests that used custom scorefxn weight files. This PR adds a patch that handles that case. Sorry for not noticing the failed tests! Not sure why it gave me a green checkmark.

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Test: mac.clang.build.xcode

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branch: master 「№60589」
Commited by: Jared Adolf-Bryfogle
GitHub commit link: 「8442bff4fb7bf2cc」 「№3709」
Difference from previous tested commit:  code diff
Commit date: 2019-01-17 20:09:48
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.addsan integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release

Merge pull request #3709 from RosettaCommons/jadolfbr/jd3_updates JD3 Simplification/Refactor Code Changes: ===== - Code templates have been added for common JD3 classes. - Transferred `StandardInnerLarvalJob`s use of `prelim_job_node` as` job_node` into the `InnerLarvalJob`. Since the ILJ is passed with the LarvalJob, this makes every function in the SJQ easier to use as you know which job_node you have - and this is not limited to `PreliminaryLarvalJobs`. - - This makes the StandardInnerLarvalJob obsolete as that was the only extra thing about it. It has been removed and classes refactored to call the InnerLarvalJob. - Moved `PreliminaryLarvalJob` to its own file in `jd3/standard`, changed it to a struct as per conventions, as everything was public. - Added the `PreliminaryLarvalJobTracker`, which the SJQ now uses to track the progress of the PJNs. This is a full class, with private data and initialization methods and is in `jd3/standard` - Added the `JobTracker` class. This class tracks completed and assigned jobs in the SJQ. This JobTracker is now updated by the JQ base class - through a wrapper/decorator function that is called by the JD. This means that SJQ developers can be ensured that the `JobTracker` is up to date and they are not responsible for updating it. Protected accessor methods have been added. - The JQ now holds an OP to the `JobDigraph`. This OP is stored during the JQs version of `initial_job_digraph`, which is a wrapper/decorator to derived class functions - ensuring that the SJQ developer is not responsible for setting it, and protected accessor methods have been added. - `JobNode `now has an optional variable, job_label - this is to better delineate how jobs are constructed. We can now ask the `JobDigraph` which job_label a particular job_node is for - IE this is useful for multiple stages, such as if all Prelim jobs undergo some stage 1, and all jobs from global index i -> j undergo job_type "2". This reduces the amount of logging needed so we do not have to track all the global index ranges to simply start a job of some type. - `EnergyJobSummary` is now in its own file, and the **4?** places where it was copied have been removed! - Add a new `StandardPoseJobSummary`, which is a JobSummary that extracts the Energy and SimpleMetricData from a pose. This should cover Most data needed for a summary ;) - `MoverAndPoseJob` has now been changed to `MoverJob`. The `pose` part of the job is inferred - no need to add that to the name. The `MoverJob` has been expanded to use the `StandardPoseJobSummary` and run a set of optional simple metrics on the final pose before returning the `PoseJobResult` and `StandardPoseJobSummary` pair. MoverJob is now aware of a SequenceMover to make it easier to either set a mover or add movers (which is extremely common). - `InputSource` pose_id variable and function are now source_id to go with the more generalized interface. General SJQ Edits ============= - The SJQ header interface is completely re-organized to have typical derived functions at the top, and mainly unused/specialized functions at the bottom. - Move some SJQ function bulk out of the SJQ and into JD3 util files. - **The number of SJQ private variables has been reduced from 50 members to 32 members** !! - All function briefs in the SJQ have been updated to separate briefs from details (almost all of it was details before). The descriptions have been updated/simplified where possible, and instructions for override behavior or gotchas have been added. Tests ==== A full suite of unit tests have been added for the new main classes, the SJQ tests have been updated to fully test the `JobTracker` and the `PreliminaryLarvalJobTracker`.

Vikram K. Mulligan 3 days
The JD3 refactor broke the xcode build. [list]
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branch: master 「№60588」
Commited by: Brandon Frenz
GitHub commit link: 「b562f8be42fa979f」 「№3737」
Difference from previous tested commit:  code diff
Commit date: 2019-01-17 15:26:41
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration.ubsan integration performance profile release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release

Merge pull request #3737 from CyrusBiotechnology/bfrenz/fix_pro_terminal_ddg fix to prolines near an internal breakpoint

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Test: ubuntu.gcc.unit.addsan

Failed sub-tests (click for more details):
core:ApproximateBuriedUnsatPenaltyTests:test_burial_sanity_check core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_packing_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_packing_4SER core:ApproximateBuriedUnsatPenaltyTests:test_packing_APA core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_packing_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_packing_IGReweight core:ApproximateBuriedUnsatPenaltyTests:test_packing_proline_nh_test core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET core:ApproximateBuriedUnsatPenaltyTests:test_scoring_1ARG_bbMET_O core:ApproximateBuriedUnsatPenaltyTests:test_scoring_4SER core:ApproximateBuriedUnsatPenaltyTests:test_scoring_APA core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_asn core:ApproximateBuriedUnsatPenaltyTests:test_scoring_C3_super_NN core:ApproximateBuriedUnsatPenaltyTests:test_scoring_proline_nh_test core:AtomTypeDatabaseIOTests:test_atom_type_set_name numeric:PolycubicSplineTests:test_bicubic_spline_symmetry numeric:PolycubicSplineTests:test_cubic_spline_symmetry numeric:PolycubicSplineTests:test_polycubic_spline_3_data_access numeric:PolycubicSplineTests:test_polycubic_spline_4_data_access numeric:PolycubicSplineTests:test_tetracubic_spline_symmetry numeric:PolycubicSplineTests:test_tricubic_polycubic_3_identical numeric:PolycubicSplineTests:test_tricubic_spline_symmetry protocols:ClusterTests:test_cluster_identification protocols:ClusterTests:test_features
Test: mac.clang.unit

Failed sub-tests (click for more details):
numeric:PolycubicSplineTests:test_bicubic_spline_symmetry


branch: master 「№60587」
Commited by: Vikram K. Mulligan
GitHub commit link: 「87eed4233e420312」 「№3754」
Difference from previous tested commit:  code diff
Commit date: 2019-01-17 13:00:49
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release unit.ubsan

Merge pull request #3754 from RosettaCommons/vmullig/splinetests Add unit test to determine whether polycubic interpolation of symmetric points is symmetric for N>2

...


branch: master 「№60586」
Commited by: Brandon Frenz
GitHub commit link: 「b5398dc5ab664997」 「№3755」
Difference from previous tested commit:  code diff
Commit date: 2019-01-17 12:47:01
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release

Merge pull request #3755 from CyrusBiotechnology/bfrenz/hybrid_add_hetatm_setter Bfrenz/hybrid add hetatm setter



branch: master 「№60585」
Commited by: Jack Maguire
GitHub commit link: 「110da19b7a791487」 「№3662」
Difference from previous tested commit:  code diff
Commit date: 2019-01-15 17:26:09
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.addsan integration.mpi integration.release_debug integration.tutorials integration.ubsan integration.valgrind integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug mac.clang.python35.release.PyRosetta4.Debug mac.clang.python36.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python27.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel mac.clang.python36.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan

Merge pull request #3662 from RosettaCommons/JackMaguire/FastDesignScriptsInDatabase Adding new non-default FastDesign scripts. Update to the docs wiki coming soon to describe them. Thanks to Vikram for the review.

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Test: linux.gcc.mpi.serialization.integration.mpi

Failed sub-tests (click for more details):
threefold_symm_peptide_design
Test: linux.clang.integration.release_debug_no_symbols

Failed sub-tests (click for more details):
KIC_with_fragments add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup buried_unsat_voids_hbnet_design_symm cart_min_glycans cartesianddg crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cyclization cycpep_design_pipeline d_workflow dcys_disulfidize density_refine density_refine_symm docking_ensemble_prepack enzdes farnesyl fast_relax fast_relax_scripts fiber_diffraction_fad fold_and_dock ga_ligand_dock glycan_anomers hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm helix_from_sequence homodimer_fnd_ref2015_memb hybridization hydrate_relax jrelax membrane_relax membrane_relax_hbond metalloprotein_abrelax mirror_symm mp_relax mp_relax_w_ligand mr_protocols oligourea_design oligourea_predict pna pocket_relax ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG relax_w_allatom_cst remodel_disulfides remodel_disulfides_rosettascripts rnp_ddg_finalize rosetta_scripts_info rs_flexbbmoves rs_loophash sdf_reader simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal stored_residue_subset swm_protein_move_inside_helix_by_bond symm_rotamer_boltzmann threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric vancomycin vip
Test: mac.clang.integration

Failed sub-tests (click for more details):
add_helix_sequence_constraints add_helix_sequence_constraints_advanced_setup buried_unsat_voids_hbnet_design_symm cart_min_glycans cartesianddg crosslinkermover_octahedral crosslinkermover_octahedral_s2_symm crosslinkermover_square_planar crosslinkermover_square_planar_d2_symm crosslinkermover_square_pyramidal crosslinkermover_tetrahedral_metal crosslinkermover_tetrahedral_metal_asp crosslinkermover_tetrahedral_metal_c2_symmetry crosslinkermover_tetrahedral_metal_d2_symmetry crosslinkermover_tma crosslinkermover_tma_symm crosslinkermover_trigonal_planar crosslinkermover_trigonal_planar_c3_symm crosslinkermover_trigonal_pyramidal crosslinkermover_trigonal_pyramidal_c3_symm cyclization cycpep_design_pipeline d_workflow dcys_disulfidize density_refine density_refine_symm docking_ensemble_prepack farnesyl fast_relax fast_relax_scripts fiber_diffraction_fad fold_and_dock ga_ligand_dock glycan_anomers hbnet_energy hbnet_energy_rosettascripts_linear hbnet_energy_symm homodimer_fnd_ref2015_memb hybridization hydrate_relax jrelax membrane_relax membrane_relax_hbond metalloprotein_abrelax mirror_symm mp_relax mp_relax_w_ligand mr_protocols oligourea_design oligourea_predict pna pocket_relax ppi_v3_suiteA ppi_v3_suiteB ppi_v3_suiteC ppi_v3_suiteD ppi_v3_suiteE ppi_v3_suiteF ppi_v3_suiteG relax_w_allatom_cst remodel_disulfides rosetta_scripts_info rs_flexbbmoves rs_loophash simple_cycpep_predict simple_cycpep_predict_angle simple_cycpep_predict_anglelength simple_cycpep_predict_cartesian simple_cycpep_predict_cispro simple_cycpep_predict_cterm_isopeptide_lariat simple_cycpep_predict_cterm_isopeptide_lariat_tailless simple_cycpep_predict_design simple_cycpep_predict_nmethyl simple_cycpep_predict_nterm_isopeptide_lariat simple_cycpep_predict_nterm_isopeptide_lariat_tailless simple_cycpep_predict_octahedral_metal simple_cycpep_predict_peptoid simple_cycpep_predict_setting simple_cycpep_predict_sidechain_isopeptide simple_cycpep_predict_sidechain_isopeptide_reverse simple_cycpep_predict_square_planar_metal simple_cycpep_predict_square_pyramidal_metal simple_cycpep_predict_symm_gly simple_cycpep_predict_tbmb simple_cycpep_predict_terminal_disulfide simple_cycpep_predict_terminal_disulfide_internal_permutations simple_cycpep_predict_terminal_disulfide_tails simple_cycpep_predict_tetrahedral_metal simple_cycpep_predict_tetrahedral_metal_asp simple_cycpep_predict_tma simple_cycpep_predict_trigonal_planar_metal simple_cycpep_predict_trigonal_pyramidal_metal stored_residue_subset symm_rotamer_boltzmann threefold_symm_peptide_design threefoldlinkermover_tbmb threefoldlinkermover_tbmb_symmetric vip
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol


branch: master 「№60584」
Commited by: Jack Maguire
GitHub commit link: 「eea2a5b248f13479」 「№3753」
Difference from previous tested commit:  code diff
Commit date: 2019-01-14 18:26:57
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.addsan integration.mpi integration.release_debug integration.tutorials integration.ubsan integration maintenance.documentation performance profile release.PyRosetta4.Debug ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.Release mac.clang.python35.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan

Merge pull request #3753 from RosettaCommons/JackMaguire/ExFlagProfileTest2 This corrects behavior from #3745 I added a very short profile test that was intended to track memory usage and not focus on speed. Turns out that it is too short for the benchmark server and now it always fails with the warning "Execution time is below 128s, marking test as failed!". This PR increases the nstruct of that test so that it takes longer (still only a few minutes).

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Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
advanced_protein-protein_docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
broker
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol
Test: linux.clang.profile

Failed sub-tests (click for more details):
build_rotamers


branch: master 「№60583」
Commited by: P. Douglas Renfrew
GitHub commit link: 「18118395c4bb9152」 「№3736」
Difference from previous tested commit:  code diff
Commit date: 2019-01-11 15:33:07
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static mac.clang.static.build.release linux.ui mac.ui build.xcode beautification code_quality.clang_analysis serialization integration.addsan integration.mpi integration.release_debug integration.tutorials integration.ubsan integration maintenance.documentation performance profile linux.clang.python27.release.PyRosetta4.Debug linux.clang.python35.release.PyRosetta4.Debug linux.clang.python36.release.PyRosetta4.Debug linux.clang.python27.release.PyRosetta4.MinSizeRel linux.clang.python35.release.PyRosetta4.MinSizeRel linux.clang.python36.release.PyRosetta4.MinSizeRel mac.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python27.release.PyRosetta4.MinSizeRel ubuntu.clang.python35.release.PyRosetta4.MinSizeRel ubuntu.clang.python36.release.PyRosetta4.MinSizeRel linux.clang.python27.release.PyRosetta4.Release linux.clang.python35.release.PyRosetta4.Release linux.clang.python36.release.PyRosetta4.Release mac.clang.python27.release.PyRosetta4.Release mac.clang.python36.release.PyRosetta4.Release ubuntu.clang.python27.release.PyRosetta4.Release ubuntu.clang.python35.release.PyRosetta4.Release ubuntu.clang.python36.release.PyRosetta4.Release release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify unit.addsan linux.clang.unit.release linux.gcc.unit.release unit.ubsan unit.valgrind

Merge pull request #3736 from RosettaCommons/dougrenfrew/conf_residue_full_to_fwd_header Convert some full headers to forward headers. May improve compile times slightly.

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Test: linux.clang.integration.tutorials

Failed sub-tests (click for more details):
advanced_protein-protein_docking
Test: ubuntu.gcc.integration.ubsan

Failed sub-tests (click for more details):
broker
Test: linux.clang.performance

Failed sub-tests (click for more details):
protocols_ligand_docking_LigandDockProtocol
Test: linux.clang.profile

Failed sub-tests (click for more details):
build_rotamers


branch: master 「№60582」
Commited by: Andrew Leaver-Fay
GitHub commit link: 「449d3383852c468b」
Difference from previous tested commit:  code diff
Commit date: 2019-01-11 15:00:05
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration performance profile release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release

Merge aleaverfay/slim_lkball2 (PR #3729) @JackMaguire noticed that the per-residue memory use has increased substantially and tracked it down to the arrays used to store the water coordinates and water-derivative matrices in the Residue data cache for the LK_BallEnergy. Previously the coordinates were held in natoms x max_waters_per_atom x 3 arrays, and the derivative matrices in three natoms x max_waters_per_atom x 3 x 3 arrays. In the case of TRP, this was nearly 15KB per Residue. This memory allocation is 100% my fault from a few years back when trying to make LK_Ball faster, which it did, but not in the most space efficient format. The new code allocates the coordinates in nwaters_actual x 3 arrays, and the derivative matrices in nwaters_actual x 3 x 3 arrays and only when derivatives are actually being calculated. The memory use is now ~200 bytes per Residue in the context of the packer and ~2KB per Residue in the context of the minimizer. Integration tests are clean except for one cosmetic test change.

Vikram K. Mulligan 2 weeks
Note: this merge resulted in a release-mode unit test failure. [list]


branch: master 「№60581」
Commited by: Jack Maguire
GitHub commit link: 「bf29ea89714ac680」 「№3745」
Difference from previous tested commit:  code diff
Commit date: 2019-01-11 11:21:20
linux.clang linux.gcc linux.srlz mac.clang
debug
release
unit
linux.PyRosetta.unit linux.gcc.python36.PyRosetta4.unit mac.PyRosetta.unit build.clean.debug cppcheck mysql postgres linux.zeromq.debug mpi mpi.serialization linux.icc.build.debug OpenCL build.header build.levels ninja graphics static linux.ui mac.ui build.xcode beautification serialization integration.mpi integration.release_debug integration performance profile release.PyRosetta4.MinSizeRel release.source linux.clang.score linux.gcc.score mac.clang.score linux.scripts.pyrosetta scripts.rosetta.parse scripts.rosetta.validate scripts.rosetta.verify linux.clang.unit.release linux.gcc.unit.release

Merge pull request #3745 from RosettaCommons/JackMaguire/ExFlagProfileTest Andrew's PR #3729 fixes an issue that increases Rosetta's memory usage by a factor of 4*. This issue doesn't stand out on the testing server because our test cases tend to be small enough to run quickly (this issue only presents itself when memory usage is dominated by Residue objects). This PR adds a profile test that sets up to perform a large packing run but stops after the setup. All of the Residue objects get made but no sampling takes place. Only takes a few seconds. *when packing with linmem_ig Thanks Steven and Sergey for reviewing!

...
Test: linux.clang.profile

Failed sub-tests (click for more details):
build_rotamers


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Legend:
queued Queued Test
queued for comparison Test finished running but not yet compared
running Test is Running right now
comparing Test results is now comparing with previous results
finished Test is finished without errors
failed Test failed
build Failed Test could not be run because build failed
script failed Test results is unknow because test-script failed
canceled Test was canceled