Branch: rosetta:commits 「revision: №20788」
Test: ubuntu.gcc.cxx11thread.serialization.python312.PyRosetta.unit
SubTest: T900_distributed
SubTest files: 「file-system-view」
Daemon: nobu-4    
State: T900_distributed

sys.version_info: sys.version_info(major=3, minor=12, micro=0, releaselevel='final', serial=0) Conda environment is not detected, skipping some tests... Executing: /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/bin/python -m unittest pyrosetta.tests.bindings.core.test_pose Output: ./home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/tests/bindings/core/test_pose.py:30: DeprecationWarning: Pose.__len__ is deprecated, prefer 'pose.residues.__len__'. self.assertEqual(8, len(pose1)) # Deprecated /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/tests/bindings/core/test_pose.py:35: DeprecationWarning: Pose.__iter__ is deprecated, prefer 'pose.residues.__iter__'. self.assertEqual(8, len(list(pose1))) # Deprecated /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/tests/bindings/core/test_pose.py:35: DeprecationWarning: Pose.__len__ is deprecated, prefer 'pose.residues.__len__'. self.assertEqual(8, len(list(pose1))) # Deprecated /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/tests/bindings/core/test_pose.py:67: DeprecationWarning: Pose.__getitem__ is deprecated, prefer 'pose.residues.__getitem__'. ''.join([res.annotated_name() for res in pose1[1:9]]), 'A[ALA:NtermProteinFull]CDEFGHI[ILE:CtermProteinFull]') # Deprecated /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/tests/bindings/core/test_pose.py:69: DeprecationWarning: Pose.__getitem__ is deprecated, prefer 'pose.residues.__getitem__'. ''.join([res.annotated_name() for res in pose1[-6:8]]), 'DEFGH') # Deprecated ../home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } .. ---------------------------------------------------------------------- Ran 5 tests in 3.617s OK ┌──────────────────────────────────────────────────────────────────────────────┐ │ PyRosetta-4 │ │ Created in JHU by Sergey Lyskov and PyRosetta Team │ │ (C) Copyright Rosetta Commons Member Institutions │ │ │ │ NOTE: USE OF PyRosetta FOR COMMERCIAL PURPOSES REQUIRE PURCHASE OF A LICENSE │ │ See LICENSE.PyRosetta.md or email license@uw.edu for details │ └──────────────────────────────────────────────────────────────────────────────┘ PyRosetta-4 2025 [Rosetta devel 2025.23.post.dev+5.HEAD.b8285423cda1908f1f3a04583ed64a5be7c87b5b 2025-06-03T14:39:06] retrieved from: git@github.com:RosettaCommons/rosetta.git Executing: /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/bin/python -m unittest pyrosetta.tests.distributed.cluster.test_logging Output: WARNING:root:`conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef` did not run successfully, so the active conda environment YML file string was not saved! It is recommended to run: `conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef > environment.yml` to reproduce this simulation later. Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install . ---------------------------------------------------------------------- Ran 1 test in 16.721s OK Executing: /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/bin/python -m unittest pyrosetta.tests.distributed.cluster.test_reproducibility Output: WARNING:root:`conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef` did not run successfully, so the active conda environment YML file string was not saved! It is recommended to run: `conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef > environment.yml` to reproduce this simulation later. Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } .WARNING:root:`conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef` did not run successfully, so the active conda environment YML file string was not saved! It is recommended to run: `conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef > environment.yml` to reproduce this simulation later. Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } .WARNING:root:`conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef` did not run successfully, so the active conda environment YML file string was not saved! It is recommended to run: `conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef > environment.yml` to reproduce this simulation later. Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } WARNING:root:`conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef` did not run successfully, so the active conda environment YML file string was not saved! It is recommended to run: `conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef > environment.yml` to reproduce this simulation later. Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } .WARNING:root:`conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef` did not run successfully, so the active conda environment YML file string was not saved! It is recommended to run: `conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef > environment.yml` to reproduce this simulation later. Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } WARNING:root:The input 'environment' parameter argument is an empty string, which is not a valid YML file string capturing the active conda environment! Reproduction simulations may not necessarily reproduce the original decoy(s)! Please verify that your active conda environment is identical to the original conda environment that generated the decoy(s) you wish to reproduce! Bypassing conda environment validation... Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } WARNING:root:The input 'environment' parameter argument is an empty string, which is not a valid YML file string capturing the active conda environment! Reproduction simulations may not necessarily reproduce the original decoy(s)! Please verify that your active conda environment is identical to the original conda environment that generated the decoy(s) you wish to reproduce! Bypassing conda environment validation... Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } .WARNING:root:`conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef` did not run successfully, so the active conda environment YML file string was not saved! It is recommended to run: `conda env export --prefix /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef > environment.yml` to reproduce this simulation later. Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install Process Process-3: Traceback (most recent call last): File "/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/lib/python3.12/site-packages/billiard/process.py", line 323, in _bootstrap self.run() File "/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/lib/python3.12/site-packages/billiard/process.py", line 110, in run self._target(*self._args, **self._kwargs) File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/logging_support.py", line 108, in wrapper result = func( ^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/__init__.py", line 119, in fwrap return func(*args, **kwargs) ^^^^^^^^^^^^^^^^^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/multiprocessing.py", line 150, in target results = run_protocol( ^^^^^^^^^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/base.py", line 224, in wrapper return func( ^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/multiprocessing.py", line 100, in run_protocol result = user_protocol(packed_pose, protocol, ignore_errors, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/exceptions.py", line 116, in wrapper result = func(compressed_packed_pose, protocol, ignore_errors, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/multiprocessing.py", line 82, in user_protocol result = protocol(packed_pose, **kwargs) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/tools.py", line 405, in wrapper _output = func(pose, **kwargs) ^^^^^^^^^^^^^^^^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/tests/distributed/cluster/test_reproducibility.py", line 419, in my_second_protocol self.assertDictContainsSubset( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ AttributeError: 'TestReproducibilityMulti' object has no attribute 'assertDictContainsSubset' 2025-06-03 17:22:56,481 - distributed.worker - ERROR - Compute Failed Key: user_spawn_thread-7733e682-ae73-43ef-af92-072345b542bc State: executing Task: <Task 'user_spawn_thread-7733e682-ae73-43ef-af92-072345b542bc' user_spawn_thread(...)> Exception: 'WorkerError("Worker thread killed due to an error or segmentation fault encountered in the user-provided PyRosetta protocol \'my_second_protocol\'.")' Traceback: ' File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/multiprocessing.py", line 200, in user_spawn_thread\n results = get_target_results_kwargs(\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/exceptions.py", line 152, in wrapper\n raise WorkerError(protocol_name)\n' EProcess Process-4: Traceback (most recent call last): File "/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/lib/python3.12/site-packages/billiard/process.py", line 323, in _bootstrap self.run() File "/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/lib/python3.12/site-packages/billiard/process.py", line 110, in run self._target(*self._args, **self._kwargs) File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/logging_support.py", line 92, in wrapper fh = logging.FileHandler(logging_file) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/benchmark/prefix/nobu-4/ubuntu/python-3.12.gcc/ecfa3a6b6e6057c10cb0c7825a20544c/lib/python3.12/logging/__init__.py", line 1231, in __init__ StreamHandler.__init__(self, self._open()) ^^^^^^^^^^^^ File "/home/benchmark/prefix/nobu-4/ubuntu/python-3.12.gcc/ecfa3a6b6e6057c10cb0c7825a20544c/lib/python3.12/logging/__init__.py", line 1263, in _open return open_func(self.baseFilename, self.mode, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ FileNotFoundError: [Errno 2] No such file or directory: '/tmp/tmpwv4ebdpy/outputs/logs/PyRosettaCluster_Tests_PyRosettaCluster.log' /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/logging_support.py:41: ResourceWarning: unclosed file <_io.TextIOWrapper name='/tmp/tmpwv4ebdpy/outputs/logs/PyRosettaCluster.log' mode='a' encoding='UTF-8'> logger.handlers = [] ResourceWarning: Enable tracemalloc to get the object allocation traceback /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/lib/python3.12/site-packages/distributed/node.py:187: UserWarning: Port 8787 is already in use. Perhaps you already have a cluster running? Hosting the HTTP server on port 44779 instead warnings.warn( 2025-06-03 17:22:56,593 - distributed.worker - ERROR - Compute Failed Key: user_spawn_thread-bafa7383-2dc0-4660-8f6b-3de8a7f85406 State: executing Task: <Task 'user_spawn_thread-bafa7383-2dc0-4660-8f6b-3de8a7f85406' user_spawn_thread(...)> Exception: 'WorkerError("Worker thread killed due to an error or segmentation fault encountered in the user-provided PyRosetta protocol \'my_second_protocol\'.")' Traceback: ' File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/multiprocessing.py", line 200, in user_spawn_thread\n results = get_target_results_kwargs(\n ^^^^^^^^^^^^^^^^^^^^^^^^^^\n File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/exceptions.py", line 152, in wrapper\n raise WorkerError(protocol_name)\n' Warning: Use of `pyrosetta.distributed.cluster` namespace requires Anaconda (or Miniconda) to be properly installed for reproducibility of PyRosetta simulations. Please install Anaconda (or Miniconda) onto your system to enable running `which conda`. For installation instructions, visit: https://docs.anaconda.com/anaconda/install /home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/bindings/energies.py:166: DeprecationWarning: Conversion of an array with ndim > 0 to a scalar is deprecated, and will error in future. Ensure you extract a single element from your array before performing this operation. (Deprecated NumPy 1.25.) return { n : float(total_array[n]) for n in total_array.dtype.names } . ====================================================================== ERROR: test_reproducibility_packer_nstruct_multi (pyrosetta.tests.distributed.cluster.test_reproducibility.TestReproducibilityMulti.test_reproducibility_packer_nstruct_multi) Test for PyRosettaCluster decoy reproducibility with an nstruct of 2 ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/exceptions.py", line 139, in wrapper _results = func( File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/multiprocessing.py", line 119, in get_target_results_kwargs [obj for obj in iter(q.get(block=True, timeout=timeout))] ^^^^^^^^^^^^^^^^^ File "/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/lib/python3.12/site-packages/billiard/queues.py", line 111, in get raise Empty _queue.Empty During handling of the above exception, another exception occurred: Traceback (most recent call last): File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/tests/distributed/cluster/test_reproducibility.py", line 467, in test_reproducibility_packer_nstruct_multi PyRosettaCluster( File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/core.py", line 729, in distribute results = future.result() ^^^^^^^^^^^^^^^ File "/home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/lib/python3.12/site-packages/distributed/client.py", line 392, in result return self.client.sync(self._result, callback_timeout=timeout) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/multiprocessing.py", line 200, in user_spawn_thread results = get_target_results_kwargs( ^^^^^^^^^^^^^^^^^ File "/home/benchmark/rosetta/source/build/PyRosetta/Linux-5.4.0-84-generic-x86_64-with-glibc2.27/gcc-7.5.0/python-3.12/minsizerel.serialization.thread/build/pyrosetta/distributed/cluster/exceptions.py", line 152, in wrapper raise WorkerError(protocol_name) ^^^^^^^^^^^^^^^^^ pyrosetta.distributed.cluster.exceptions.WorkerError: Worker thread killed due to an error or segmentation fault encountered in the user-provided PyRosetta protocol 'Worker thread killed due to an error or segmentation fault encountered in the user-provided PyRosetta protocol 'my_second_protocol'.'. ---------------------------------------------------------------------- Ran 6 tests in 187.472s FAILED (errors=1) 2025-06-03 17:23:46,185 - distributed.scheduler - ERROR - Removing worker 'tcp://127.0.0.1:46311' caused the cluster to lose scattered data, which can't be recovered: {'bool-a11de1f2009b4e289b03bbb34a9b232b', 'str-580175012954456ba7dae0076f149e4f', 'set-af0adf30bff7407bbae81b96022bea71', 'str-622479e742c5487f8558c709279d15e0', 'float-3fa177cb2ebd4a96b1d884ff50a26f7b', 'str-f6ca1c2ea3ae4920bdc53ecabebf9543', 'bool-bf7946767c9f44068d965ce21e448f91', 'bytes-a3c0025bceb2445ab9bacee7a7dcd4b6', 'bytes-6dc2a4ebdf034a7a8b98974be5f3280d', 'dict-262a17e14fcf42d9804109015e3daa32', 'str-7377ccd477de4a77b616a60a39497bf5', 'float-f9c42c3770f74a23882143fbe384d582', 'function-1fcd7b02b20c46dfaebec31452e2a91f', 'NoneType-e00d9d06be6a40ac861b1ac00338e055'} (stimulus_id='handle-worker-cleanup-1748985826.1849303') 2025-06-03 17:23:46,186 - distributed.diskutils - ERROR - Failed to remove '/tmp/tmpwv4ebdpy/dask-scratch-space/worker-4z7685dx' (failed in <built-in function lstat>): [Errno 2] No such file or directory: '/tmp/tmpwv4ebdpy/dask-scratch-space/worker-4z7685dx' Encountered error(s) with exit code 1 while running: /home/benchmark/prefix/nobu-4/ubuntu/python_virtual_environments/python-3.12/f458842e9e4485f9c32976b24d6f92ef/bin/python -m unittest pyrosetta.tests.distributed.cluster.test_reproducibility Terminating... Finished T900_distributed in 0:03:39.836741