Task 38580668
| Name | JNK1_A28_A21_r2_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-0-5-RND1862_1 |
| Workunit | 31545373 |
| Created | 11 Dec 2025, 16:25:25 UTC |
| Sent | 11 Dec 2025, 16:25:33 UTC |
| Report deadline | 16 Dec 2025, 16:25:33 UTC |
| Received | 12 Dec 2025, 8:45:11 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 523478 |
| Run time | 4 hours 58 min 43 sec |
| CPU time | 4 hours 42 min 25 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 8,370.90 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 641.74 MB |
| Peak swap size | 3.75 GB |
| Peak disk usage | 3.18 GB |
Stderr output
<core_client_version>8.2.4</core_client_version>
<![CDATA[
<message>
Operativsystemet kan ikke k�re (null).
(0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
04:46:45 (15776): wrapper (7.9.26016): starting
04:46:45 (15776): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A28_A21_0.pdb
QB_A28_A21_0.xml
QB_A28_A21_equil.pdb
QB_A28_A21.inpcrd
QB_A28_A21_input.yaml
QB_A28_A21_mdlambda.pdb
QB_A28_A21_min.pdb
QB_A28_A21_npt.pdb
QB_A28_A21_out_merged_nowater.pdb
QB_A28_A21.pdb
QB_A28_A21.prmtop
QB_A28_A21_sys.xml
QB_A28_A21_therm.pdb
run.bat
run.sh
04:46:55 (15776): Library/usr/bin/tar.exe exited; CPU time 0.000000
04:46:55 (15776): 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\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/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
Using cached 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)
Using cached 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 C:\ProgramData\BOINC\slots\0\pip-build-env-q4zt1e3q\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\0\pip-build-env-q4zt1e3q\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-q4zt1e3q\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-3etatbfe\atom_openmm.egg-info
writing C:\ProgramData\BOINC\slots\0\pip-modern-metadata-3etatbfe\atom_openmm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-3etatbfe\atom_openmm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-3etatbfe\atom_openmm.egg-info\entry_points.txt
writing requirements to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-3etatbfe\atom_openmm.egg-info\requires.txt
writing top-level names to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-3etatbfe\atom_openmm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-3etatbfe\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-3etatbfe\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-3etatbfe\atom_openmm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-3etatbfe\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
C:\ProgramData\BOINC\slots\0\pip-build-env-q4zt1e3q\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-130c8i93\.tmp-8qyavpqq\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
09:44:00 (15776): C:/Windows/system32/cmd.exe exited; CPU time 16945.578125
09:44:00 (15776): app exit status: 0x16
09:44:00 (15776): called boinc_finish(195)
0 bytes in 0 Free Blocks.
626 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: 216820867 bytes.
Dumping objects ->
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Data: <àC=v! > E0 43 3D 76 21 02 00 00 00 00 00 00 00 00 00 00
{260} normal block at 0x00000221763D3400, 16 bytes long.
Data: <¸C=v! > B8 43 3D 76 21 02 00 00 00 00 00 00 00 00 00 00
{259} normal block at 0x00000221763D3770, 16 bytes long.
Data: < C=v! > 90 43 3D 76 21 02 00 00 00 00 00 00 00 00 00 00
{257} normal block at 0x00000221763D3540, 16 bytes long.
Data: <˱<v! > C0 B1 3C 76 21 02 00 00 00 00 00 00 00 00 00 00
{256} normal block at 0x00000221763CB1C0, 40 bytes long.
Data: <@5=v! ÐÇúw! > 40 35 3D 76 21 02 00 00 D0 C7 FA 77 21 02 00 00
{255} normal block at 0x00000221763D34F0, 16 bytes long.
Data: <pC=v! > 70 43 3D 76 21 02 00 00 00 00 00 00 00 00 00 00
{254} normal block at 0x00000221763D3F90, 16 bytes long.
Data: <HC=v! > 48 43 3D 76 21 02 00 00 00 00 00 00 00 00 00 00
{253} normal block at 0x00000221763CC690, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{252} normal block at 0x00000221763D3BD0, 16 bytes long.
Data: < C=v! > 20 43 3D 76 21 02 00 00 00 00 00 00 00 00 00 00
{251} normal block at 0x00000221763D4320, 992 bytes long.
Data: <Ð;=v! Æ<v! > D0 3B 3D 76 21 02 00 00 90 C6 3C 76 21 02 00 00
{87} normal block at 0x00000221763CC750, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{86} normal block at 0x00000221763C67C0, 16 bytes long.
Data: <P±<v! > 50 B1 3C 76 21 02 00 00 00 00 00 00 00 00 00 00
{85} normal block at 0x00000221763CB150, 40 bytes long.
Data: <Àg<v! PÇ<v! > C0 67 3C 76 21 02 00 00 50 C7 3C 76 21 02 00 00
{64} normal block at 0x00000221763C6C70, 16 bytes long.
Data: < êñ!ö > 80 EA F1 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x00000221763C6900, 16 bytes long.
Data: <@éñ!ö > 40 E9 F1 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{62} normal block at 0x00000221763C66D0, 16 bytes long.
Data: <øWî!ö > F8 57 EE 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{61} normal block at 0x00000221763C6720, 16 bytes long.
Data: <ØWî!ö > D8 57 EE 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{60} normal block at 0x00000221763C65E0, 16 bytes long.
Data: <P î!ö > 50 04 EE 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{59} normal block at 0x00000221763C6EA0, 16 bytes long.
Data: <0 î!ö > 30 04 EE 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{58} normal block at 0x00000221763C6D60, 16 bytes long.
Data: <à î!ö > E0 02 EE 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{57} normal block at 0x00000221763C6C20, 16 bytes long.
Data: < î!ö > 10 04 EE 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{56} normal block at 0x00000221763C6680, 16 bytes long.
Data: <p î!ö > 70 04 EE 21 F6 7F 00 00 00 00 00 00 00 00 00 00
{55} normal block at 0x00000221763C6450, 16 bytes long.
Data: < Àì!ö > 18 C0 EC 21 F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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