Task 38580856
| Name | JNK1_A01_A04_r2_1-QUICO_ATM_GAFF2_LOMAP_JNK1_3-2-5-RND9210_0 |
| Workunit | 31545455 |
| Created | 12 Dec 2025, 2:15:25 UTC |
| Sent | 12 Dec 2025, 2:15:31 UTC |
| Report deadline | 17 Dec 2025, 2:15:31 UTC |
| Received | 14 Dec 2025, 1:09:03 UTC |
| Server state | Over |
| Outcome | Computation error |
| Client state | Compute error |
| Exit status | 194 (0x000000C2) EXIT_ABORTED_BY_CLIENT |
| Computer ID | 630770 |
| Run time | 3 min 41 sec |
| CPU time | 31 sec |
| Validate state | Invalid |
| Credit | 0.00 |
| Device peak FLOPS | 9,335.88 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 639.32 MB |
| Peak swap size | 3.02 GB |
| Peak disk usage | 3.79 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<message>
Process still present 5 min after writing finish file; aborting</message>
<stderr_txt>
10:47:25 (21064): wrapper (7.9.26016): starting
10:47:25 (21064): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A01_A04_0.pdb
QB_A01_A04_0.xml
QB_A01_A04_equil.pdb
QB_A01_A04.inpcrd
QB_A01_A04_input.yaml
QB_A01_A04_mdlambda.pdb
QB_A01_A04_min.pdb
QB_A01_A04_npt.pdb
QB_A01_A04_out_merged_nowater.pdb
QB_A01_A04.pdb
QB_A01_A04.prmtop
QB_A01_A04_sys.xml
QB_A01_A04_therm.pdb
run.bat
run.sh
10:47:29 (21064): Library/usr/bin/tar.exe exited; CPU time 0.000000
10:47:29 (21064): 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\3\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\3\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 C:\ProgramData\BOINC\slots\3\pip-build-env-m_5hikyo\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\3\pip-build-env-m_5hikyo\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\3\pip-build-env-m_5hikyo\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\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info
writing C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info\entry_points.txt
writing requirements to C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info\requires.txt
writing top-level names to C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\3\pip-modern-metadata-gl6q5rlb\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
C:\ProgramData\BOINC\slots\3\pip-build-env-m_5hikyo\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\3\pip-wheel-h4vm_ti_\.tmp-ptjvk66e\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\3\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) : {3840863} normal block at 0x000002806328DF60, 8 bytes long.
Data: < pc > 00 00 70 63 80 02 00 00
..\lib\diagnostics_win.cpp(417) : {3839703} normal block at 0x000002806327DC60, 1080 bytes long.
Data: < > 84 10 00 00 CD CD CD CD 80 02 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {313} normal block at 0x0000028063281590, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
12:58:48 (10036): wrapper (7.9.26016): starting
12:58:48 (10036): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x00000226F7115980, 8 bytes long.
Data: < H & > 00 00 48 F7 26 02 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x00000226F7116D60, 1080 bytes long.
Data: < > B8 1F 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
13:05:37 (7928): wrapper (7.9.26016): starting
13:05:37 (7928): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x000002D5C64F5AB0, 8 bytes long.
Data: < K > 00 00 4B C6 D5 02 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000002D5C64F6A30, 1080 bytes long.
Data: < > F4 1E 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
13:12:13 (12136): wrapper (7.9.26016): starting
13:12:13 (12136): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x0000024FBC8E6930, 8 bytes long.
Data: < O > 00 00 CF BC 4F 02 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x0000024FBC8E76D0, 1080 bytes long.
Data: < N > A8 4E 00 00 CD CD CD CD BC 01 00 00 00 00 00 00
Object dump complete.
13:27:26 (18236): wrapper (7.9.26016): starting
13:27:26 (18236): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x0000018D0F995C80, 8 bytes long.
Data: < > 00 00 DE 0F 8D 01 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x0000018D0F996D90, 1080 bytes long.
Data: <<B > 3C 42 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
13:57:05 (11160): wrapper (7.9.26016): starting
13:57:05 (11160): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x000001E6046A5E30, 8 bytes long.
Data: < > 00 00 AB 04 E6 01 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000001E6046A6D60, 1080 bytes long.
Data: < > BC 13 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
16:02:14 (12524): wrapper (7.9.26016): starting
16:02:14 (12524): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x000002A61A346830, 8 bytes long.
Data: < / > 00 00 2F 1A A6 02 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000002A61A346D60, 1080 bytes long.
Data: << > 3C 14 00 00 CD CD CD CD B4 01 00 00 00 00 00 00
Object dump complete.
16:32:03 (22128): wrapper (7.9.26016): starting
16:32:03 (22128): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x0000017EF4A985A0, 8 bytes long.
Data: < ~ > 00 00 F6 F4 7E 01 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x0000017EF4A99610, 1080 bytes long.
Data: <X' > 58 27 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
18:40:17 (5968): wrapper (7.9.26016): starting
18:40:17 (5968): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x000002C823DF5DF0, 8 bytes long.
Data: < "$ > 00 00 22 24 C8 02 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000002C823DF6D70, 1080 bytes long.
Data: <8O > 38 4F 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
19:51:23 (24308): wrapper (7.9.26016): starting
19:51:23 (24308): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x000001C1A7E465E0, 8 bytes long.
Data: < > 00 00 DE A7 C1 01 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x000001C1A7E46D90, 1080 bytes long.
Data: < X > 90 58 00 00 CD CD CD CD B8 01 00 00 00 00 00 00
Object dump complete.
22:08:08 (21828): wrapper (7.9.26016): starting
22:08:08 (21828): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1466} normal block at 0x00000255C03B70C0, 8 bytes long.
Data: < 6 U > 00 00 36 C0 55 02 00 00
..\lib\diagnostics_win.cpp(417) : {306} normal block at 0x00000255C03B7AA0, 1080 bytes long.
Data: < > EC 1A 00 00 CD CD CD CD B4 01 00 00 00 00 00 00
Object dump complete.
08:29:10 (13920): wrapper (7.9.26016): starting
08:29:10 (13920): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1465} normal block at 0x000001E483EB6280, 8 bytes long.
Data: < > 00 00 1E 84 E4 01 00 00
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000001E483EB6E40, 1080 bytes long.
Data: <` \ > 60 20 00 00 CD CD CD CD 5C 00 00 00 00 00 00 00
Object dump complete.
09:50:10 (1524): wrapper (7.9.26016): starting
09:50:10 (1524): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1465} normal block at 0x0000025F7A8A6690, 8 bytes long.
Data: < z_ > 00 00 85 7A 5F 02 00 00
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000025F7A8A6E40, 1080 bytes long.
Data: <T/ > 54 2F 00 00 CD CD CD CD BC 00 00 00 00 00 00 00
Object dump complete.
12:10:26 (8144): wrapper (7.9.26016): starting
12:10:26 (8144): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1465} normal block at 0x0000028A025060D0, 8 bytes long.
Data: < > 00 00 98 02 8A 02 00 00
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x0000028A02506E70, 1080 bytes long.
Data: <x > 78 19 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
12:35:52 (2332): wrapper (7.9.26016): starting
12:35:52 (2332): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1465} normal block at 0x000001796DF55BC0, 8 bytes long.
Data: < my > 00 00 F2 6D 79 01 00 00
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000001796DF56E60, 1080 bytes long.
Data: < , > 04 2C 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
12:56:15 (5356): wrapper (7.9.26016): starting
12:56:15 (5356): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1465} normal block at 0x000001AD242F5900, 8 bytes long.
Data: < *$ > 00 00 2A 24 AD 01 00 00
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000001AD242F6830, 1080 bytes long.
Data: < " > C8 22 00 00 CD CD CD CD AC 01 00 00 00 00 00 00
Object dump complete.
18:15:02 (25540): wrapper (7.9.26016): starting
18:15:02 (25540): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1465} normal block at 0x00000224BAE45E90, 8 bytes long.
Data: < $ > 00 00 20 BB 24 02 00 00
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x00000224BAE46E60, 1080 bytes long.
Data: <T^ > 54 5E 00 00 CD CD CD CD B4 01 00 00 00 00 00 00
Object dump complete.
18:24:38 (22708): wrapper (7.9.26016): starting
18:24:38 (22708): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\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 "C:\ProgramData\BOINC\slots\3\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
File "C:\ProgramData\BOINC\slots\3\Lib\site-packages\atom_openmm\rbfe_production.py", line 33, in rbfe_production
rx.scheduleJobs()
File "C:\ProgramData\BOINC\slots\3\Lib\site-packages\atom_openmm\async_re.py", line 321, in scheduleJobs
self.transport.ProcessJobQueue(min_time,cycle_time)
File "C:\ProgramData\BOINC\slots\3\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 186, in ProcessJobQueue
self.isDone(repl,0)
File "C:\ProgramData\BOINC\slots\3\Lib\site-packages\atom_openmm\local_openmm_transport.py", line 287, in isDone
retcode = self._update_replica(job)
^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\3\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\3\Lib\site-packages\atom_openmm\ommworker.py", line 451, in get_energy
return self._worker_getenergy()
^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\3\Lib\site-packages\atom_openmm\ommworker.py", line 400, in _worker_getenergy
state = self.simulation.context.getState(getEnergy = True)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\3\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
18:42:20 (22708): C:/Windows/system32/cmd.exe exited; CPU time 794.953125
18:42:20 (22708): app exit status: 0x16
18:42:20 (22708): 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: 17167478 bytes.
Dumping objects ->
{1553} normal block at 0x000001C483534CC0, 48 bytes long.
Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1542} normal block at 0x000001C483534A20, 48 bytes long.
Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1531} normal block at 0x000001C483534B00, 48 bytes long.
Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61
{1520} normal block at 0x000001C4835349B0, 48 bytes long.
Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1509} normal block at 0x000001C483534BE0, 48 bytes long.
Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61
{1478} normal block at 0x000001C4835228B0, 64 bytes long.
Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
..\api\boinc_api.cpp(309) : {1465} normal block at 0x000001C483535630, 8 bytes long.
Data: < > 00 00 87 83 C4 01 00 00
{306} normal block at 0x000001C483536030, 8 bytes long.
Data: < iS > 90 69 53 83 C4 01 00 00
{297} normal block at 0x000001C48351F910, 80 bytes long.
Data: </c call Scripts\> 2F 63 20 63 61 6C 6C 20 53 63 72 69 70 74 73 5C
{296} normal block at 0x000001C483535A90, 16 bytes long.
Data: < hS > 98 68 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{295} normal block at 0x000001C483535590, 16 bytes long.
Data: <phS > 70 68 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{294} normal block at 0x000001C48352FBE0, 32 bytes long.
Data: <r0/checkpoint.xm> 72 30 2F 63 68 65 63 6B 70 6F 69 6E 74 2E 78 6D
{293} normal block at 0x000001C483535E50, 16 bytes long.
Data: <HhS > 48 68 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{292} normal block at 0x000001C4835359A0, 16 bytes long.
Data: < hS > 20 68 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{291} normal block at 0x000001C4835354A0, 16 bytes long.
Data: < gS > F8 67 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{290} normal block at 0x000001C483535EA0, 16 bytes long.
Data: < gS > D0 67 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{289} normal block at 0x000001C4835348D0, 48 bytes long.
Data: <ComSpec=C:\Windo> 43 6F 6D 53 70 65 63 3D 43 3A 5C 57 69 6E 64 6F
{288} normal block at 0x000001C4835355E0, 16 bytes long.
Data: < Q > C8 B9 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{287} normal block at 0x000001C483530240, 32 bytes long.
Data: <SystemRoot=C:\Wi> 53 79 73 74 65 6D 52 6F 6F 74 3D 43 3A 5C 57 69
{286} normal block at 0x000001C483536350, 16 bytes long.
Data: < Q > A0 B9 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{284} normal block at 0x000001C483535FE0, 16 bytes long.
Data: <x Q > 78 B9 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{283} normal block at 0x000001C483535A40, 16 bytes long.
Data: <P Q > 50 B9 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{282} normal block at 0x000001C483536260, 16 bytes long.
Data: <( Q > 28 B9 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{281} normal block at 0x000001C483535450, 16 bytes long.
Data: < Q > 00 B9 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{280} normal block at 0x000001C483536080, 16 bytes long.
Data: < Q > D8 B8 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{279} normal block at 0x000001C48352FB20, 32 bytes long.
Data: <CUDA_DEVICE=0 PU> 43 55 44 41 5F 44 45 56 49 43 45 3D 30 00 50 55
{278} normal block at 0x000001C483535400, 16 bytes long.
Data: < Q > B0 B8 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{277} normal block at 0x000001C48351B8B0, 320 bytes long.
Data: < TS R > 00 54 53 83 C4 01 00 00 20 FB 52 83 C4 01 00 00
{276} normal block at 0x000001C483535950, 16 bytes long.
Data: < gS > B0 67 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{275} normal block at 0x000001C483535B30, 16 bytes long.
Data: < gS > 88 67 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{274} normal block at 0x000001C48352FD00, 32 bytes long.
Data: <C:/Windows/syste> 43 3A 2F 57 69 6E 64 6F 77 73 2F 73 79 73 74 65
{273} normal block at 0x000001C483535860, 16 bytes long.
Data: <`gS > 60 67 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{272} normal block at 0x000001C48352FA60, 32 bytes long.
Data: <xjvf input.tar.b> 78 6A 76 66 20 69 6E 70 75 74 2E 74 61 72 2E 62
{271} normal block at 0x000001C483535D60, 16 bytes long.
Data: < fS > A8 66 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{270} normal block at 0x000001C4835361C0, 16 bytes long.
Data: < fS > 80 66 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{269} normal block at 0x000001C483535D10, 16 bytes long.
Data: <XfS > 58 66 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{268} normal block at 0x000001C483535680, 16 bytes long.
Data: <0fS > 30 66 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{267} normal block at 0x000001C483535CC0, 16 bytes long.
Data: < fS > 08 66 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{266} normal block at 0x000001C483535E00, 16 bytes long.
Data: < eS > E0 65 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{264} normal block at 0x000001C4835359F0, 16 bytes long.
Data: < JS > 90 4A 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{263} normal block at 0x000001C483534A90, 40 bytes long.
Data: < YS (R > F0 59 53 83 C4 01 00 00 B0 28 52 83 C4 01 00 00
{262} normal block at 0x000001C483535540, 16 bytes long.
Data: < eS > C0 65 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{261} normal block at 0x000001C4835354F0, 16 bytes long.
Data: < eS > 98 65 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{260} normal block at 0x000001C48352F460, 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 0x000001C483535C20, 16 bytes long.
Data: <peS > 70 65 53 83 C4 01 00 00 00 00 00 00 00 00 00 00
{258} normal block at 0x000001C483536570, 992 bytes long.
Data: < \S ` R > 20 5C 53 83 C4 01 00 00 60 F4 52 83 C4 01 00 00
{94} normal block at 0x000001C483530120, 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 0x000001C48352D7E0, 16 bytes long.
Data: < Q > A0 CB 51 83 C4 01 00 00 00 00 00 00 00 00 00 00
{92} normal block at 0x000001C48351CBA0, 40 bytes long.
Data: < R S > E0 D7 52 83 C4 01 00 00 20 01 53 83 C4 01 00 00
{71} normal block at 0x000001C48352DFB0, 16 bytes long.
Data: < @ > 80 EA C3 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{70} normal block at 0x000001C48352DDD0, 16 bytes long.
Data: <@ @ > 40 E9 C3 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{69} normal block at 0x000001C48352D240, 16 bytes long.
Data: < W @ > F8 57 C0 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{68} normal block at 0x000001C48352D560, 16 bytes long.
Data: < W @ > D8 57 C0 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{67} normal block at 0x000001C48352DB50, 16 bytes long.
Data: <P @ > 50 04 C0 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x000001C48352DA60, 16 bytes long.
Data: <0 @ > 30 04 C0 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x000001C48352D790, 16 bytes long.
Data: < @ > E0 02 C0 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x000001C48352D8D0, 16 bytes long.
Data: < @ > 10 04 C0 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x000001C48352D4C0, 16 bytes long.
Data: <p @ > 70 04 C0 40 F6 7F 00 00 00 00 00 00 00 00 00 00
{62} normal block at 0x000001C48352D3D0, 16 bytes long.
Data: < @ > 18 C0 BE 40 F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
18:50:39 (9828): wrapper (7.9.26016): starting
18:50:39 (9828): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1465} normal block at 0x000001C276D968C0, 8 bytes long.
Data: < w > 00 00 1B 77 C2 01 00 00
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000001C276D96E40, 1080 bytes long.
Data: < 1 > F8 31 00 00 CD CD CD CD 90 01 00 00 00 00 00 00
Object dump complete.
20:07:31 (2184): wrapper (7.9.26016): starting
20:07:31 (2184): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file C:\ProgramData\BOINC\slots\3\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1465} normal block at 0x000001DD84BD5AE0, 8 bytes long.
Data: < N > 00 00 4E 86 DD 01 00 00
..\lib\diagnostics_win.cpp(417) : {305} normal block at 0x000001DD84BD6BC0, 1080 bytes long.
Data: < 8 > D4 38 00 00 CD CD CD CD C4 01 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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