Task 38580812

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
 (0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
18:18:37 (28184): wrapper (7.9.26016): starting
18:18:37 (28184): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A14_A09_0.pdb
QB_A14_A09_0.xml
QB_A14_A09_equil.pdb
QB_A14_A09.inpcrd
QB_A14_A09_input.yaml
QB_A14_A09_mdlambda.pdb
QB_A14_A09_min.pdb
QB_A14_A09_npt.pdb
QB_A14_A09_out_merged_nowater.pdb
QB_A14_A09.pdb
QB_A14_A09.prmtop
QB_A14_A09_sys.xml
QB_A14_A09_therm.pdb
run.bat
run.sh
18:18:39 (28184): Library/usr/bin/tar.exe exited; CPU time 0.000000
18:18:39 (28184): 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 'D:\BOINC\slots\0\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 D:\BOINC\slots\0\Lib\site-packages\pip (python 3.11)
  Collecting setuptools
    Obtaining dependency information for setuptools from https://files.pythonhosted.org/packages/a3/dc/17031897dae0efacfea57dfd3a82fdd2a2aeb58e0ff71b77b87e44edc772/setuptools-80.9.0-py3-none-any.whl.metadata
    Using cached setuptools-80.9.0-py3-none-any.whl.metadata (6.6 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/20/12/38679034af332785aac8774540895e234f4d07f7545804097de4b666afd8/packaging-25.0-py3-none-any.whl.metadata
    Using cached packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
  Using cached setuptools-80.9.0-py3-none-any.whl (1.2 MB)
  Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
  Using cached packaging-25.0-py3-none-any.whl (66 kB)
  Installing collected packages: setuptools, packaging, setuptools-scm
    Creating D:\BOINC\slots\0\pip-build-env-whsldgf0\overlay\Scripts
  Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
  Running command Getting requirements to build wheel
  D:\BOINC\slots\0\pip-build-env-whsldgf0\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)
  D:\BOINC\slots\0\pip-build-env-whsldgf0\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 D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info
  writing D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info\dependency_links.txt
  writing entry points to D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info\entry_points.txt
  writing requirements to D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info\requires.txt
  writing top-level names to D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info\top_level.txt
  writing manifest file 'D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm.egg-info\SOURCES.txt'
  creating 'D:\BOINC\slots\0\pip-modern-metadata-otfms4ip\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  D:\BOINC\slots\0\pip-build-env-whsldgf0\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 'D:\BOINC\slots\0\pip-wheel-zw5m0r6y\.tmp-e06ozx4s\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 'D:\BOINC\slots\0\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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835489} normal block at 0x00000206BF178720, 8 bytes long.
 Data: <  S     > 00 00 53 BF 06 02 00 00 
..\lib\diagnostics_win.cpp(417) : {3833952} normal block at 0x00000206C1A53940, 1080 bytes long.
 Data: < '              > D0 27 00 00 CD CD CD CD E8 03 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {308} normal block at 0x00000206BF177460, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
20:19:22 (18944): wrapper (7.9.26016): starting
20:19:22 (18944): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\BOINC\slots\0\tmp already exists.
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 "D:\BOINC\slots\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
  File "D:\BOINC\slots\0\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
    rx.scheduleJobs()
  File "D:\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
    self.transport.ProcessJobQueue(min_time,cycle_time)
  File "D:\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
    self.isDone(repl,0)
  File "D:\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
    retcode = self._update_replica(job)
              ^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
    pot = job['openmm_worker'].get_energy()
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
    return self._worker_getenergy()
           ^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
    state = self.simulation.context.getState(getEnergy = True)
            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "D:\BOINC\slots\0\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
22:26:02 (18944): C:/Windows/system32/cmd.exe exited; CPU time 7689.531250
22:26:02 (18944): app exit status: 0x16
22:26:02 (18944): called boinc_finish(195)
0 bytes in 0 Free Blocks.
346 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: 123024503 bytes.
Dumping objects ->
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{1841} normal block at 0x0000012FE12608A0, 85 bytes long.
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..\api\boinc_api.cpp(309) : {1838} normal block at 0x0000012FE1265150, 8 bytes long.
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{264} normal block at 0x0000012FE1265AB0, 16 bytes long.
 Data: < \& /           > D0 5C 26 E1 2F 01 00 00 00 00 00 00 00 00 00 00 
{263} normal block at 0x0000012FE1265240, 16 bytes long.
 Data: < \& /           > A8 5C 26 E1 2F 01 00 00 00 00 00 00 00 00 00 00 
{262} normal block at 0x0000012FE12658D0, 16 bytes long.
 Data: < \& /           > 80 5C 26 E1 2F 01 00 00 00 00 00 00 00 00 00 00 
{260} normal block at 0x0000012FE1264D90, 16 bytes long.
 Data: <0 & /           > 30 11 26 E1 2F 01 00 00 00 00 00 00 00 00 00 00 
{259} normal block at 0x0000012FE1261130, 40 bytes long.
 Data: < M& /     & /   > 90 4D 26 E1 2F 01 00 00 90 15 26 E1 2F 01 00 00 
{258} normal block at 0x0000012FE1264C50, 16 bytes long.
 Data: <`\& /           > 60 5C 26 E1 2F 01 00 00 00 00 00 00 00 00 00 00 
{257} normal block at 0x0000012FE12651F0, 16 bytes long.
 Data: <8\& /           > 38 5C 26 E1 2F 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x0000012FE125ECB0, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{255} normal block at 0x0000012FE1265830, 16 bytes long.
 Data: < \& /           > 10 5C 26 E1 2F 01 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x0000012FE1265C10, 992 bytes long.
 Data: <0X& /     % /   > 30 58 26 E1 2F 01 00 00 B0 EC 25 E1 2F 01 00 00 
{90} normal block at 0x0000012FE125F010, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{89} normal block at 0x0000012FE1259BD0, 16 bytes long.
 Data: <  & /           > C0 10 26 E1 2F 01 00 00 00 00 00 00 00 00 00 00 
{88} normal block at 0x0000012FE12610C0, 40 bytes long.
 Data: <  % /     % /   > D0 9B 25 E1 2F 01 00 00 10 F0 25 E1 2F 01 00 00 
{67} normal block at 0x0000012FE12593B0, 16 bytes long.
 Data: <                > 80 EA C1 F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000012FE12590E0, 16 bytes long.
 Data: <@               > 40 E9 C1 F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000012FE1259630, 16 bytes long.
 Data: < W              > F8 57 BE F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000012FE1258EB0, 16 bytes long.
 Data: < W              > D8 57 BE F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000012FE1259040, 16 bytes long.
 Data: <P               > 50 04 BE F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000012FE1259AE0, 16 bytes long.
 Data: <0               > 30 04 BE F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000012FE1259270, 16 bytes long.
 Data: <                > E0 02 BE F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x0000012FE1259950, 16 bytes long.
 Data: <                > 10 04 BE F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x0000012FE1259900, 16 bytes long.
 Data: <p               > 70 04 BE F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x0000012FE1258CD0, 16 bytes long.
 Data: <                > 18 C0 BC F1 F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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