Task 38580890
| Name | JNK1_A21_A33_r4_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-3-5-RND7888_0 |
| Workunit | 31545474 |
| Created | 12 Dec 2025, 4:49:24 UTC |
| Sent | 12 Dec 2025, 4:49:29 UTC |
| Report deadline | 17 Dec 2025, 4:49:29 UTC |
| Received | 12 Dec 2025, 6:01:15 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 195 (0x000000C3) EXIT_CHILD_FAILED |
| Computer ID | 541192 |
| Run time | 50 min 26 sec |
| CPU time | 36 min 17 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 52,230.32 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 648.86 MB |
| Peak swap size | 12.93 GB |
| Peak disk usage | 3.13 GB |
Stderr output
<core_client_version>8.0.2</core_client_version>
<![CDATA[
<message>
Das Betriebssystem kann (null) nicht ausf�hren.
(0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
06:11:00 (49128): wrapper (7.9.26016): starting
06:11:00 (49128): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A21_A33_0.pdb
QB_A21_A33_0.xml
QB_A21_A33_equil.pdb
QB_A21_A33.inpcrd
QB_A21_A33_input.yaml
QB_A21_A33_mdlambda.pdb
QB_A21_A33_min.pdb
QB_A21_A33_npt.pdb
QB_A21_A33_out_merged_nowater.pdb
QB_A21_A33.pdb
QB_A21_A33.prmtop
QB_A21_A33_sys.xml
QB_A21_A33_therm.pdb
run.bat
run.sh
06:11:03 (49128): Library/usr/bin/tar.exe exited; CPU time 0.000000
06:11:03 (49128): 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 'J:\BOINC\data\slots\23\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 J:\BOINC\data\slots\23\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 J:\BOINC\data\slots\23\pip-build-env-amilv34f\overlay\Scripts
Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
Running command Getting requirements to build wheel
J:\BOINC\data\slots\23\pip-build-env-amilv34f\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)
J:\BOINC\data\slots\23\pip-build-env-amilv34f\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 J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info
writing J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info\PKG-INFO
writing dependency_links to J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info\dependency_links.txt
writing entry points to J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info\entry_points.txt
writing requirements to J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info\requires.txt
writing top-level names to J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info\top_level.txt
writing manifest file 'J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm.egg-info\SOURCES.txt'
creating 'J:\BOINC\data\slots\23\pip-modern-metadata-qiaw2iae\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
J:\BOINC\data\slots\23\pip-build-env-amilv34f\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 'J:\BOINC\data\slots\23\pip-wheel-0y155752\.tmp-a8yhhq07\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 'J:\BOINC\data\slots\23\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 "J:\BOINC\data\slots\23\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
File "J:\BOINC\data\slots\23\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
rx.scheduleJobs()
File "J:\BOINC\data\slots\23\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
self.transport.ProcessJobQueue(min_time,cycle_time)
File "J:\BOINC\data\slots\23\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
self.isDone(repl,0)
File "J:\BOINC\data\slots\23\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
retcode = self._update_replica(job)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "J:\BOINC\data\slots\23\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 212, in _update_replica
pot = job['openmm_worker'].get_energy()
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "J:\BOINC\data\slots\23\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
return self._worker_getenergy()
^^^^^^^^^^^^^^^^^^^^^^^^
File "J:\BOINC\data\slots\23\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
state = self.simulation.context.getState(getEnergy = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "J:\BOINC\data\slots\23\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
06:59:55 (49128): C:/Windows/system32/cmd.exe exited; CPU time 2177.875000
06:59:55 (49128): app exit status: 0x16
06:59:55 (49128): 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: 73628806 bytes.
Dumping objects ->
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Data: <¸¿Ój¸ > B8 BF D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{284} normal block at 0x000001B86AD3BA00, 16 bytes long.
Data: < ¿Ój¸ > 90 BF D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{283} normal block at 0x000001B86AD3B640, 16 bytes long.
Data: <h¿Ój¸ > 68 BF D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{282} normal block at 0x000001B86AD3B9B0, 16 bytes long.
Data: <@¿Ój¸ > 40 BF D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{280} normal block at 0x000001B86AD3AF60, 16 bytes long.
Data: < aÓj¸ > 00 61 D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{279} normal block at 0x000001B86AD36100, 40 bytes long.
Data: <`¯Ój¸ ðÕj¸ > 60 AF D3 6A B8 01 00 00 00 F0 D5 6A B8 01 00 00
{278} normal block at 0x000001B86AD3B5F0, 16 bytes long.
Data: < ¿Ój¸ > 20 BF D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{277} normal block at 0x000001B86AD3BB40, 16 bytes long.
Data: <ø¾Ój¸ > F8 BE D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{276} normal block at 0x000001B86AD35110, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{275} normal block at 0x000001B86AD3B870, 16 bytes long.
Data: <оÓj¸ > D0 BE D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{274} normal block at 0x000001B86AD3BED0, 992 bytes long.
Data: <p¸Ój¸ QÓj¸ > 70 B8 D3 6A B8 01 00 00 10 51 D3 6A B8 01 00 00
{110} normal block at 0x000001B86AD356B0, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{109} normal block at 0x000001B86AD2BD60, 16 bytes long.
Data: < `Ój¸ > 20 60 D3 6A B8 01 00 00 00 00 00 00 00 00 00 00
{108} normal block at 0x000001B86AD36020, 40 bytes long.
Data: <`½Òj¸ °VÓj¸ > 60 BD D2 6A B8 01 00 00 B0 56 D3 6A B8 01 00 00
{87} normal block at 0x000001B86AD2C120, 16 bytes long.
Data: < 꽇÷ > 80 EA BD 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{86} normal block at 0x000001B86AD2C030, 16 bytes long.
Data: <@齇÷ > 40 E9 BD 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{85} normal block at 0x000001B86AD2BBD0, 16 bytes long.
Data: <øWº‡÷ > F8 57 BA 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{84} normal block at 0x000001B86AD2C0D0, 16 bytes long.
Data: <ØWº‡÷ > D8 57 BA 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{83} normal block at 0x000001B86AD2C6C0, 16 bytes long.
Data: <P º‡÷ > 50 04 BA 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{82} normal block at 0x000001B86AD2BB30, 16 bytes long.
Data: <0 º‡÷ > 30 04 BA 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{81} normal block at 0x000001B86AD2B810, 16 bytes long.
Data: <à º‡÷ > E0 02 BA 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{80} normal block at 0x000001B86AD2C2B0, 16 bytes long.
Data: < º‡÷ > 10 04 BA 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{79} normal block at 0x000001B86AD2BF90, 16 bytes long.
Data: <p º‡÷ > 70 04 BA 87 F7 7F 00 00 00 00 00 00 00 00 00 00
{78} normal block at 0x000001B86AD2C210, 16 bytes long.
Data: < À¸‡÷ > 18 C0 B8 87 F7 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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