Task 38580595
| Name | JNK1_A20_A33_r2_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-0-5-RND4287_0 |
| Workunit | 31545328 |
| Created | 11 Dec 2025, 16:09:14 UTC |
| Sent | 11 Dec 2025, 16:09:16 UTC |
| Report deadline | 16 Dec 2025, 16:09:16 UTC |
| Received | 11 Dec 2025, 16:42:02 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 645421 |
| Run time | 11 min 21 sec |
| CPU time | 9 min |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 1,392.51 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 587.83 MB |
| Peak swap size | 5.08 GB |
| Peak disk usage | 2.81 GB |
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>
08:24:44 (25084): wrapper (7.9.26016): starting
08:24:44 (25084): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A20_A33_0.pdb
QB_A20_A33_0.xml
QB_A20_A33_equil.pdb
QB_A20_A33.inpcrd
QB_A20_A33_input.yaml
QB_A20_A33_mdlambda.pdb
QB_A20_A33_min.pdb
QB_A20_A33_npt.pdb
QB_A20_A33_out_merged_nowater.pdb
QB_A20_A33.pdb
QB_A20_A33.prmtop
QB_A20_A33_sys.xml
QB_A20_A33_therm.pdb
run.bat
run.sh
08:24:46 (25084): Library/usr/bin/tar.exe exited; CPU time 0.000000
08:24:46 (25084): 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\12\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\12\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
Downloading 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
Downloading packaging-25.0-py3-none-any.whl.metadata (3.3 kB)
Downloading setuptools-80.9.0-py3-none-any.whl (1.2 MB)
---------------------------------------- 1.2/1.2 MB 5.0 MB/s eta 0:00:00
Downloading setuptools_scm-9.2.2-py3-none-any.whl (62 kB)
Downloading packaging-25.0-py3-none-any.whl (66 kB)
Installing collected packages: setuptools, packaging, setuptools-scm
Creating C:\ProgramData\BOINC\slots\12\pip-build-env-zwwk3mx5\overlay\Scripts
Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
Running command Getting requirements to build wheel
C:\ProgramData\BOINC\slots\12\pip-build-env-zwwk3mx5\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\12\pip-build-env-zwwk3mx5\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\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info
writing C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info\entry_points.txt
writing requirements to C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info\requires.txt
writing top-level names to C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\12\pip-modern-metadata-elk9op5p\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
C:\ProgramData\BOINC\slots\12\pip-build-env-zwwk3mx5\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\12\pip-wheel-z_mmypeh\.tmp-s77wvvh8\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\12\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\12\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
rx.scheduleJobs()
File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
self.transport.ProcessJobQueue(min_time,cycle_time)
File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
self.isDone(repl,0)
File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
retcode = self._update_replica(job)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\12\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\12\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
return self._worker_getenergy()
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\12\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
state = self.simulation.context.getState(getEnergy = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\12\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
08:34:47 (25084): C:/Windows/system32/cmd.exe exited; CPU time 540.093750
08:34:47 (25084): app exit status: 0x16
08:34:47 (25084): called boinc_finish(195)
0 bytes in 0 Free Blocks.
256 bytes in 6 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: 10458421 bytes.
Dumping objects ->
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{264} normal block at 0x0000024D3989A6C0, 16 bytes long.
Data: < ¨‰9M > 90 A8 89 39 4D 02 00 00 00 00 00 00 00 00 00 00
{262} normal block at 0x0000024D39899950, 16 bytes long.
Data: <°‚‰9M > B0 82 89 39 4D 02 00 00 00 00 00 00 00 00 00 00
{261} normal block at 0x0000024D398982B0, 40 bytes long.
Data: <P ‰9M f;M > 50 99 89 39 4D 02 00 00 20 02 66 3B 4D 02 00 00
{260} normal block at 0x0000024D3989A300, 16 bytes long.
Data: <p¨‰9M > 70 A8 89 39 4D 02 00 00 00 00 00 00 00 00 00 00
{259} normal block at 0x0000024D3989A350, 16 bytes long.
Data: <H¨‰9M > 48 A8 89 39 4D 02 00 00 00 00 00 00 00 00 00 00
{258} normal block at 0x0000024D39894360, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{257} normal block at 0x0000024D398998B0, 16 bytes long.
Data: < ¨‰9M > 20 A8 89 39 4D 02 00 00 00 00 00 00 00 00 00 00
{256} normal block at 0x0000024D3989A820, 992 bytes long.
Data: <° ‰9M `C‰9M > B0 98 89 39 4D 02 00 00 60 43 89 39 4D 02 00 00
{92} normal block at 0x0000024D39894720, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{91} normal block at 0x0000024D3988D7E0, 16 bytes long.
Data: <` ‰9M > 60 81 89 39 4D 02 00 00 00 00 00 00 00 00 00 00
{90} normal block at 0x0000024D39898160, 40 bytes long.
Data: <à× 9M G‰9M > E0 D7 88 39 4D 02 00 00 20 47 89 39 4D 02 00 00
{69} normal block at 0x0000024D3988DAB0, 16 bytes long.
Data: < ê>ª÷ > 80 EA 3E AA F7 7F 00 00 00 00 00 00 00 00 00 00
{68} normal block at 0x0000024D3988E230, 16 bytes long.
Data: <@é>ª÷ > 40 E9 3E AA F7 7F 00 00 00 00 00 00 00 00 00 00
{67} normal block at 0x0000024D3988E370, 16 bytes long.
Data: <øW;ª÷ > F8 57 3B AA F7 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x0000024D3988DA60, 16 bytes long.
Data: <ØW;ª÷ > D8 57 3B AA F7 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x0000024D3988E050, 16 bytes long.
Data: <P ;ª÷ > 50 04 3B AA F7 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x0000024D3988D920, 16 bytes long.
Data: <0 ;ª÷ > 30 04 3B AA F7 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x0000024D3988D8D0, 16 bytes long.
Data: <à ;ª÷ > E0 02 3B AA F7 7F 00 00 00 00 00 00 00 00 00 00
{62} normal block at 0x0000024D3988D5B0, 16 bytes long.
Data: < ;ª÷ > 10 04 3B AA F7 7F 00 00 00 00 00 00 00 00 00 00
{61} normal block at 0x0000024D3988DBF0, 16 bytes long.
Data: <p ;ª÷ > 70 04 3B AA F7 7F 00 00 00 00 00 00 00 00 00 00
{60} normal block at 0x0000024D3988E4B0, 16 bytes long.
Data: < À9ª÷ > 18 C0 39 AA F7 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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