Task 38596126
| Name | TYK2_A06_A01_r0_4-QUICO_ATM_OFF23_NAGL_TYK2-0-4-RND2715_1 |
| Workunit | 31552139 |
| Created | 24 Mar 2026, 11:04:28 UTC |
| Sent | 24 Mar 2026, 11:05:00 UTC |
| Report deadline | 29 Mar 2026, 11:05:00 UTC |
| Received | 24 Mar 2026, 11:10:39 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 641009 |
| Run time | 1 min 25 sec |
| CPU time | 22 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 23,198.49 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 647.20 MB |
| Peak swap size | 12.89 GB |
| Peak disk usage | 1.42 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>
06:08:02 (7580): wrapper (7.9.26016): starting
06:08:02 (7580): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A06_A01_0.pdb
QB_A06_A01_0.xml
QB_A06_A01.inpcrd
QB_A06_A01_input.yaml
QB_A06_A01.pdb
QB_A06_A01.prmtop
QB_A06_A01_sys.xml
run.bat
run.sh
06:08:03 (7580): Library/usr/bin/tar.exe exited; CPU time 0.015625
06:08:03 (7580): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
WARNING: Retrying (Retry(total=4, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x000001DA58BDC290>: Failed to establish a new connection: [WinError 10013] An attempt was made to access a socket in a way forbidden by its access permissions')': /simple/pyaml/
WARNING: Retrying (Retry(total=3, connect=None, read=None, redirect=None, status=None)) after connection broken by 'NewConnectionError('<pip._vendor.urllib3.connection.HTTPSConnection object at 0x000001DA58BDCC50>: Failed to establish a new connection: [WinError 10013] An attempt was made to access a socket in a way forbidden by its access permissions')': /simple/pyaml/
WARNING: The script pyaml.exe is installed in 'C:\ProgramData\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 C:\ProgramData\BOINC\slots\0\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 15.8 MB/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\0\pip-build-env-kmf4yekg\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\0\pip-build-env-kmf4yekg\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\0\pip-build-env-kmf4yekg\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\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info
writing C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info\entry_points.txt
writing requirements to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info\requires.txt
writing top-level names to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-gui5bqg3\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
C:\ProgramData\BOINC\slots\0\pip-build-env-kmf4yekg\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\\0\\pip-wheel-1lwz5ugs\\.tmp-ymws23il\\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\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.
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\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
rx.scheduleJobs()
File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
self.transport.ProcessJobQueue(min_time,cycle_time)
File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
self.isDone(repl,0)
File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
retcode = self._update_replica(job)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\0\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\0\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
return self._worker_getenergy()
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
state = self.simulation.context.getState(getEnergy = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\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
06:08:49 (7580): C:/Windows/system32/cmd.exe exited; CPU time 22.484375
06:08:49 (7580): app exit status: 0x16
06:08:49 (7580): called boinc_finish(195)
0 bytes in 0 Free Blocks.
460 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: 785879 bytes.
Dumping objects ->
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Data: < ¨AçE > 90 A8 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{269} normal block at 0x00000245E741A490, 16 bytes long.
Data: <h¨AçE > 68 A8 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{268} normal block at 0x00000245E741A5D0, 16 bytes long.
Data: <@¨AçE > 40 A8 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{267} normal block at 0x00000245E7419A40, 16 bytes long.
Data: < ¨AçE > 18 A8 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{266} normal block at 0x00000245E7419E00, 16 bytes long.
Data: <ð§AçE > F0 A7 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{264} normal block at 0x00000245E7419DB0, 16 bytes long.
Data: < AAçE > 00 41 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{263} normal block at 0x00000245E7414100, 40 bytes long.
Data: <° AçE éE > B0 9D 41 E7 45 02 00 00 80 1B 0C E9 45 02 00 00
{262} normal block at 0x00000245E741A080, 16 bytes long.
Data: <ЧAçE > D0 A7 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{261} normal block at 0x00000245E741A3A0, 16 bytes long.
Data: <¨§AçE > A8 A7 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{260} normal block at 0x00000245E7415740, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{259} normal block at 0x00000245E7419950, 16 bytes long.
Data: < §AçE > 80 A7 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{258} normal block at 0x00000245E741A780, 992 bytes long.
Data: <P AçE @WAçE > 50 99 41 E7 45 02 00 00 40 57 41 E7 45 02 00 00
{94} normal block at 0x00000245E7415B00, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{93} normal block at 0x00000245E740E3F0, 16 bytes long.
Data: < =AçE > 10 3D 41 E7 45 02 00 00 00 00 00 00 00 00 00 00
{92} normal block at 0x00000245E7413D10, 40 bytes long.
Data: <ðã@çE [AçE > F0 E3 40 E7 45 02 00 00 00 5B 41 E7 45 02 00 00
{71} normal block at 0x00000245E740E7B0, 16 bytes long.
Data: < êÆFö > 80 EA C6 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{70} normal block at 0x00000245E740E170, 16 bytes long.
Data: <@éÆFö > 40 E9 C6 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{69} normal block at 0x00000245E740E350, 16 bytes long.
Data: <øWÃFö > F8 57 C3 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{68} normal block at 0x00000245E740E080, 16 bytes long.
Data: <ØWÃFö > D8 57 C3 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{67} normal block at 0x00000245E740E440, 16 bytes long.
Data: <P ÃFö > 50 04 C3 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x00000245E740E120, 16 bytes long.
Data: <0 ÃFö > 30 04 C3 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x00000245E740E030, 16 bytes long.
Data: <à ÃFö > E0 02 C3 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x00000245E740DC20, 16 bytes long.
Data: < ÃFö > 10 04 C3 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x00000245E740E300, 16 bytes long.
Data: <p ÃFö > 70 04 C3 46 F6 7F 00 00 00 00 00 00 00 00 00 00
{62} normal block at 0x00000245E740DDB0, 16 bytes long.
Data: < ÀÁFö > 18 C0 C1 46 F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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