Task 38596107

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
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 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
19:11:39 (28840): wrapper (7.9.26016): starting
19:11:39 (28840): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A11_A16_0.pdb
QB_A11_A16_0.xml
QB_A11_A16.inpcrd
QB_A11_A16_input.yaml
QB_A11_A16.pdb
QB_A11_A16.prmtop
QB_A11_A16_sys.xml
run.bat
run.sh
19:11:41 (28840): Library/usr/bin/tar.exe exited; CPU time 0.015625
19:11:41 (28840): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
  WARNING: The script pyaml.exe is installed in 'C:\ProgramData\BOINC\slots\4\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
  Running command pip subprocess to install build dependencies
  Using pip 24.3.1 from C:\ProgramData\BOINC\slots\4\Lib\site-packages\pip (python 3.11)
  Collecting setuptools
    Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/9d/76/f789f7a86709c6b087c5a2f52f911838cad707cc613162401badc665acfe/setuptools-82.0.1-py3-none-any.whl.metadata
    Downloading setuptools-82.0.1-py3-none-any.whl.metadata (6.5 kB)
  Collecting setuptools-scm>=8
    Obtaining dependency information for setuptools-scm>=8 from https://files.pythonhosted.org/packages/3d/ea/ac2bf868899d0d2e82ef72d350d97a846110c709bacf2d968431576ca915/setuptools_scm-9.2.2-py3-none-any.whl.metadata
    Downloading setuptools_scm-9.2.2-py3-none-any.whl.metadata (7.7 kB)
  Collecting packaging>=20 (from setuptools-scm>=8)
    Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl.metadata
    Downloading packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
  Downloading setuptools-82.0.1-py3-none-any.whl (1.0 MB)
     ---------------------------------------- 1.0/1.0 MB 57.1 kB/s eta 0:00:00
  Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
  Downloading packaging-26.0-py3-none-any.whl (74 kB)
  Installing collected packages: setuptools, packaging, setuptools-scm
    Creating C:\ProgramData\BOINC\slots\4\pip-build-env-l7ejtnwh\overlay\Scripts
  Successfully installed packaging-26.0 setuptools-82.0.1 setuptools-scm-9.2.2
  Running command Getting requirements to build wheel
  C:\ProgramData\BOINC\slots\4\pip-build-env-l7ejtnwh\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
    warnings.warn(self.message)
  running egg_info
  writing atom_openmm.egg-info\PKG-INFO
  writing dependency_links to atom_openmm.egg-info\dependency_links.txt
  writing entry points to atom_openmm.egg-info\entry_points.txt
  writing requirements to atom_openmm.egg-info\requires.txt
  writing top-level names to atom_openmm.egg-info\top_level.txt
  listing git files failed - pretending there aren't any
  reading manifest file 'atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'atom_openmm.egg-info\SOURCES.txt'
  Running command Preparing metadata (pyproject.toml)
  C:\ProgramData\BOINC\slots\4\pip-build-env-l7ejtnwh\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
    warnings.warn(self.message)
  running dist_info
  creating C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\4\pip-modern-metadata-1kvoh_zj\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\4\pip-build-env-l7ejtnwh\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:51: UserWarning: version of None already set
    warnings.warn(self.message)
  running bdist_wheel
  running build
  running build_py
  creating build\lib\atom_openmm
  copying atom_openmm\abfe_explicit.py -> build\lib\atom_openmm
  copying atom_openmm\abfe_production.py -> build\lib\atom_openmm
  copying atom_openmm\abfe_structprep.py -> build\lib\atom_openmm
  copying atom_openmm\async_re.py -> build\lib\atom_openmm
  copying atom_openmm\gibbs_sampling.py -> build\lib\atom_openmm
  copying atom_openmm\local_openmm_transport.py -> build\lib\atom_openmm
  copying atom_openmm\make_atm_system_from_amber.py -> build\lib\atom_openmm
  copying atom_openmm\make_atm_system_from_pdb.py -> build\lib\atom_openmm
  copying atom_openmm\make_atm_system_from_rcpt_lig.py -> build\lib\atom_openmm
  copying atom_openmm\ommreplica.py -> build\lib\atom_openmm
  copying atom_openmm\ommsystem.py -> build\lib\atom_openmm
  copying atom_openmm\ommworker.py -> build\lib\atom_openmm
  copying atom_openmm\openmm_async_re.py -> build\lib\atom_openmm
  copying atom_openmm\rbfe_explicit.py -> build\lib\atom_openmm
  copying atom_openmm\rbfe_production.py -> build\lib\atom_openmm
  copying atom_openmm\rbfe_structprep.py -> build\lib\atom_openmm
  copying atom_openmm\temperatureRE_explicit.py -> build\lib\atom_openmm
  copying atom_openmm\transport.py -> build\lib\atom_openmm
  copying atom_openmm\uwham.py -> build\lib\atom_openmm
  copying atom_openmm\__init__.py -> build\lib\atom_openmm
  creating build\lib\atom_openmm\utils
  copying atom_openmm\utils\AtomUtils.py -> build\lib\atom_openmm\utils
  copying atom_openmm\utils\config.py -> build\lib\atom_openmm\utils
  copying atom_openmm\utils\singal_guard.py -> build\lib\atom_openmm\utils
  copying atom_openmm\utils\timer.py -> build\lib\atom_openmm\utils
  copying atom_openmm\utils\__init__.py -> build\lib\atom_openmm\utils
  running egg_info
  writing atom_openmm.egg-info\PKG-INFO
  writing dependency_links to atom_openmm.egg-info\dependency_links.txt
  writing entry points to atom_openmm.egg-info\entry_points.txt
  writing requirements to atom_openmm.egg-info\requires.txt
  writing top-level names to atom_openmm.egg-info\top_level.txt
  listing git files failed - pretending there aren't any
  reading manifest file 'atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'atom_openmm.egg-info\SOURCES.txt'
  copying atom_openmm\utils\logging.conf -> build\lib\atom_openmm\utils
  installing to build\bdist.win-amd64\wheel
  running install
  running install_lib
  creating build\bdist.win-amd64\wheel
  creating build\bdist.win-amd64\wheel\atom_openmm
  copying build\lib\atom_openmm\abfe_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\abfe_production.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\abfe_structprep.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\async_re.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\gibbs_sampling.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\local_openmm_transport.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\make_atm_system_from_amber.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\make_atm_system_from_pdb.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\make_atm_system_from_rcpt_lig.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\ommreplica.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\ommsystem.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\ommworker.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\openmm_async_re.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\rbfe_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\rbfe_production.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\rbfe_structprep.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\temperatureRE_explicit.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\transport.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  creating build\bdist.win-amd64\wheel\atom_openmm\utils
  copying build\lib\atom_openmm\utils\AtomUtils.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\config.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\logging.conf -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\singal_guard.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\timer.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\utils\__init__.py -> build\bdist.win-amd64\wheel\.\atom_openmm\utils
  copying build\lib\atom_openmm\uwham.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  copying build\lib\atom_openmm\__init__.py -> build\bdist.win-amd64\wheel\.\atom_openmm
  running install_egg_info
  Copying atom_openmm.egg-info to build\bdist.win-amd64\wheel\.\atom_openmm-8.4.0-py3.11.egg-info
  running install_scripts
  creating build\bdist.win-amd64\wheel\atom_openmm-8.4.0.dist-info\WHEEL
  creating 'C:\\ProgramData\\BOINC\\slots\\4\\pip-wheel-b52my4_4\\.tmp-8k728ogg\\atom_openmm-8.4.0-py3-none-any.whl' and adding 'build\\bdist.win-amd64\\wheel' to it
  adding 'atom_openmm/__init__.py'
  adding 'atom_openmm/abfe_explicit.py'
  adding 'atom_openmm/abfe_production.py'
  adding 'atom_openmm/abfe_structprep.py'
  adding 'atom_openmm/async_re.py'
  adding 'atom_openmm/gibbs_sampling.py'
  adding 'atom_openmm/local_openmm_transport.py'
  adding 'atom_openmm/make_atm_system_from_amber.py'
  adding 'atom_openmm/make_atm_system_from_pdb.py'
  adding 'atom_openmm/make_atm_system_from_rcpt_lig.py'
  adding 'atom_openmm/ommreplica.py'
  adding 'atom_openmm/ommsystem.py'
  adding 'atom_openmm/ommworker.py'
  adding 'atom_openmm/openmm_async_re.py'
  adding 'atom_openmm/rbfe_explicit.py'
  adding 'atom_openmm/rbfe_production.py'
  adding 'atom_openmm/rbfe_structprep.py'
  adding 'atom_openmm/temperatureRE_explicit.py'
  adding 'atom_openmm/transport.py'
  adding 'atom_openmm/uwham.py'
  adding 'atom_openmm/utils/AtomUtils.py'
  adding 'atom_openmm/utils/__init__.py'
  adding 'atom_openmm/utils/config.py'
  adding 'atom_openmm/utils/logging.conf'
  adding 'atom_openmm/utils/singal_guard.py'
  adding 'atom_openmm/utils/timer.py'
  adding 'atom_openmm-8.4.0.dist-info/licenses/LICENSE'
  adding 'atom_openmm-8.4.0.dist-info/METADATA'
  adding 'atom_openmm-8.4.0.dist-info/WHEEL'
  adding 'atom_openmm-8.4.0.dist-info/entry_points.txt'
  adding 'atom_openmm-8.4.0.dist-info/top_level.txt'
  adding 'atom_openmm-8.4.0.dist-info/RECORD'
  removing build\bdist.win-amd64\wheel
  WARNING: The scripts abfe_production.exe, abfe_structprep.exe, make_atm_system_from_amber.exe, make_atm_system_from_pdb.exe, make_atm_system_from_rcpt_lig.exe, rbfe_production.exe and rbfe_structprep.exe are installed in 'C:\ProgramData\BOINC\slots\4\Scripts' which is not on PATH.
  Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Traceback (most recent call last):
  File "<frozen runpy>", line 198, in _run_module_as_main
  File "<frozen runpy>", line 88, in _run_code
  File "C:\ProgramData\BOINC\slots\4\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "C:\ProgramData\BOINC\slots\4\Lib\site-packages\openmm\openmm.py", line 5022, in getState
    state = _openmm.Context_getState(self, types, enforcePeriodicBox, groups_mask)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
openmm.OpenMMException: Particle coordinate is NaN.  For more information, see https://github.com/openmm/openmm/wiki/Frequently-Asked-Questions#nan
19:23:51 (28840): C:/Windows/system32/cmd.exe exited; CPU time 76.046875
19:23:51 (28840): app exit status: 0x16
19:23:51 (28840): called boinc_finish(195)
0 bytes in 0 Free Blocks.
536 bytes in 8 Normal Blocks.
1144 bytes in 1 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 11010401 bytes.
Dumping objects ->
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{274} normal block at 0x000001F3D0A9F590, 40 bytes long.
 Data: < 9      @W      > B0 39 AA D0 F3 01 00 00 40 57 A9 D0 F3 01 00 00 
{273} normal block at 0x000001F3D0AA38C0, 16 bytes long.
 Data: <P               > 50 ED A9 D0 F3 01 00 00 00 00 00 00 00 00 00 00 
{272} normal block at 0x000001F3D0AA31E0, 16 bytes long.
 Data: <(               > 28 ED A9 D0 F3 01 00 00 00 00 00 00 00 00 00 00 
{271} normal block at 0x000001F3D0A97360, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{270} normal block at 0x000001F3D0AA2FB0, 16 bytes long.
 Data: <                > 00 ED A9 D0 F3 01 00 00 00 00 00 00 00 00 00 00 
{269} normal block at 0x000001F3D0A9ED00, 992 bytes long.
 Data: < /      `s      > B0 2F AA D0 F3 01 00 00 60 73 A9 D0 F3 01 00 00 
{105} normal block at 0x000001F3D0A97A80, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{104} normal block at 0x000001F3D0A8E910, 16 bytes long.
 Data: <                > F0 F9 A9 D0 F3 01 00 00 00 00 00 00 00 00 00 00 
{103} normal block at 0x000001F3D0A9F9F0, 40 bytes long.
 Data: <         z      > 10 E9 A8 D0 F3 01 00 00 80 7A A9 D0 F3 01 00 00 
{80} normal block at 0x000001F3D0A8E550, 16 bytes long.
 Data: <                > 80 EA E4 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{79} normal block at 0x000001F3D0A8E500, 16 bytes long.
 Data: <@               > 40 E9 E4 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{78} normal block at 0x000001F3D0A8EC30, 16 bytes long.
 Data: < W              > F8 57 E1 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{77} normal block at 0x000001F3D0A8E4B0, 16 bytes long.
 Data: < W              > D8 57 E1 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{76} normal block at 0x000001F3D0A8E460, 16 bytes long.
 Data: <P               > 50 04 E1 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{75} normal block at 0x000001F3D0A8E410, 16 bytes long.
 Data: <0               > 30 04 E1 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{74} normal block at 0x000001F3D0A8E3C0, 16 bytes long.
 Data: <                > E0 02 E1 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{73} normal block at 0x000001F3D0A8E320, 16 bytes long.
 Data: <                > 10 04 E1 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{72} normal block at 0x000001F3D0A8E370, 16 bytes long.
 Data: <p               > 70 04 E1 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
{71} normal block at 0x000001F3D0A8E2D0, 16 bytes long.
 Data: <                > 18 C0 DF 93 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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