Task 38580356
| Name | JNK1_A21_A33_r3_1-QUICO_ATM_GAFF2_LOMAP_JNK1_2-0-5-RND7351_0 |
| Workunit | 31545199 |
| Created | 11 Dec 2025, 14:29:39 UTC |
| Sent | 11 Dec 2025, 14:29:44 UTC |
| Report deadline | 16 Dec 2025, 14:29:44 UTC |
| Received | 14 Dec 2025, 6:31:20 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 647947 |
| Run time | 2 days 7 hours 23 min 36 sec |
| CPU time | 1 days 8 hours 49 min 2 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 16,497.02 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 671.80 MB |
| Peak swap size | 3.85 GB |
| Peak disk usage | 3.49 GB |
Stderr output
<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
15:47:05 (2688): wrapper (7.9.26016): starting
15:47:05 (2688): 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
15:47:10 (2688): Library/usr/bin/tar.exe exited; CPU time 0.000000
15:47:10 (2688): 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 'D:\ProgramData\BOINC\slots\2\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 D:\ProgramData\BOINC\slots\2\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 6.7 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 D:\ProgramData\BOINC\slots\2\pip-build-env-nmzrlv53\overlay\Scripts
Successfully installed packaging-25.0 setuptools-80.9.0 setuptools-scm-9.2.2
Running command Getting requirements to build wheel
D:\ProgramData\BOINC\slots\2\pip-build-env-nmzrlv53\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)
D:\ProgramData\BOINC\slots\2\pip-build-env-nmzrlv53\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 D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info
writing D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info\PKG-INFO
writing dependency_links to D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info\dependency_links.txt
writing entry points to D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info\entry_points.txt
writing requirements to D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info\requires.txt
writing top-level names to D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info\top_level.txt
writing manifest file 'D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info\SOURCES.txt'
listing git files failed - pretending there aren't any
reading manifest file 'D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
adding license file 'LICENSE'
writing manifest file 'D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm.egg-info\SOURCES.txt'
creating 'D:\ProgramData\BOINC\slots\2\pip-modern-metadata-up7ce1tp\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
D:\ProgramData\BOINC\slots\2\pip-build-env-nmzrlv53\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 'D:\ProgramData\BOINC\slots\2\pip-wheel-ff2fvd89\.tmp-azd_jopj\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 'D:\ProgramData\BOINC\slots\2\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) : {3835150} normal block at 0x00000265B8B0D860, 8 bytes long.
Data: < S e > 00 00 53 BA 65 02 00 00
..\lib\diagnostics_win.cpp(417) : {3833954} normal block at 0x00000265BA7B8DE0, 1080 bytes long.
Data: < > FC 14 00 00 CD CD CD CD 04 02 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {309} normal block at 0x00000265B8B06470, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
08:10:56 (13084): wrapper (7.9.26016): starting
08:10:56 (13084): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\2\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1498} normal block at 0x0000016925FAB180, 8 bytes long.
Data: < %i > 00 00 F5 25 69 01 00 00
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x0000016925FAB5B0, 1080 bytes long.
Data: < > 00 12 00 00 CD CD CD CD C0 01 00 00 00 00 00 00
Object dump complete.
06:25:31 (5660): wrapper (7.9.26016): starting
06:25:31 (5660): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\2\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1498} normal block at 0x0000020C8BD56070, 8 bytes long.
Data: < > 00 00 0C 8C 0C 02 00 00
..\lib\diagnostics_win.cpp(417) : {302} normal block at 0x0000020C8BD566E0, 1080 bytes long.
Data: <x > 78 0B 00 00 CD CD CD CD A8 01 00 00 00 00 00 00
Object dump complete.
09:13:42 (17100): wrapper (7.9.26016): starting
09:13:42 (17100): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
A subdirectory or file D:\ProgramData\BOINC\slots\2\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
tar: run.log: file changed as we read it
tar: r*/*.dcd: Cannot stat: No such file or directory
tar: Exiting with failure status due to previous errors
07:30:26 (17100): C:/Windows/system32/cmd.exe exited; CPU time 38122.406250
07:30:26 (17100): called boinc_finish(0)
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: 1268367006 bytes.
Dumping objects ->
{1586} normal block at 0x0000022CE5EE32B0, 48 bytes long.
Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44
{1575} normal block at 0x0000022CE5EE2EC0, 48 bytes long.
Data: <HOME=D:\ProgramD> 48 4F 4D 45 3D 44 3A 5C 50 72 6F 67 72 61 6D 44
{1564} normal block at 0x0000022CE5EE2E50, 48 bytes long.
Data: <TMP=D:\ProgramDa> 54 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44 61
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Data: <TEMP=D:\ProgramD> 54 45 4D 50 3D 44 3A 5C 50 72 6F 67 72 61 6D 44
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{1511} normal block at 0x0000022CE5ED1C30, 64 bytes long.
Data: <PATH=D:\ProgramD> 50 41 54 48 3D 44 3A 5C 50 72 6F 67 72 61 6D 44
..\api\boinc_api.cpp(309) : {1498} normal block at 0x0000022CE5EE8FA0, 8 bytes long.
Data: < , > 00 00 7F E7 2C 02 00 00
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{263} normal block at 0x0000022CE5EE9180, 16 bytes long.
Data: < , > A0 98 EE E5 2C 02 00 00 00 00 00 00 00 00 00 00
{261} normal block at 0x0000022CE5EE94A0, 16 bytes long.
Data: <`1 , > 60 31 EE E5 2C 02 00 00 00 00 00 00 00 00 00 00
{260} normal block at 0x0000022CE5EE3160, 40 bytes long.
Data: < , 0 , > A0 94 EE E5 2C 02 00 00 30 1C ED E5 2C 02 00 00
{259} normal block at 0x0000022CE5EE95E0, 16 bytes long.
Data: < , > 80 98 EE E5 2C 02 00 00 00 00 00 00 00 00 00 00
{258} normal block at 0x0000022CE5EE8C80, 16 bytes long.
Data: <X , > 58 98 EE E5 2C 02 00 00 00 00 00 00 00 00 00 00
{257} normal block at 0x0000022CE5EE45B0, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{256} normal block at 0x0000022CE5EE9130, 16 bytes long.
Data: <0 , > 30 98 EE E5 2C 02 00 00 00 00 00 00 00 00 00 00
{255} normal block at 0x0000022CE5EE9830, 992 bytes long.
Data: <0 , E , > 30 91 EE E5 2C 02 00 00 B0 45 EE E5 2C 02 00 00
{91} normal block at 0x0000022CE5EE4DF0, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{90} normal block at 0x0000022CE5EDE620, 16 bytes long.
Data: < 0 , > 80 30 EE E5 2C 02 00 00 00 00 00 00 00 00 00 00
{89} normal block at 0x0000022CE5EE3080, 40 bytes long.
Data: < , M , > 20 E6 ED E5 2C 02 00 00 F0 4D EE E5 2C 02 00 00
{68} normal block at 0x0000022CE5EDE1C0, 16 bytes long.
Data: < ~ > 80 EA 7E DD F6 7F 00 00 00 00 00 00 00 00 00 00
{67} normal block at 0x0000022CE5EDE080, 16 bytes long.
Data: <@ ~ > 40 E9 7E DD F6 7F 00 00 00 00 00 00 00 00 00 00
{66} normal block at 0x0000022CE5EDDC70, 16 bytes long.
Data: < W{ > F8 57 7B DD F6 7F 00 00 00 00 00 00 00 00 00 00
{65} normal block at 0x0000022CE5EDE210, 16 bytes long.
Data: < W{ > D8 57 7B DD F6 7F 00 00 00 00 00 00 00 00 00 00
{64} normal block at 0x0000022CE5EDE3A0, 16 bytes long.
Data: <P { > 50 04 7B DD F6 7F 00 00 00 00 00 00 00 00 00 00
{63} normal block at 0x0000022CE5EDD950, 16 bytes long.
Data: <0 { > 30 04 7B DD F6 7F 00 00 00 00 00 00 00 00 00 00
{62} normal block at 0x0000022CE5EDDFE0, 16 bytes long.
Data: < { > E0 02 7B DD F6 7F 00 00 00 00 00 00 00 00 00 00
{61} normal block at 0x0000022CE5EDE580, 16 bytes long.
Data: < { > 10 04 7B DD F6 7F 00 00 00 00 00 00 00 00 00 00
{60} normal block at 0x0000022CE5EDE3F0, 16 bytes long.
Data: <p { > 70 04 7B DD F6 7F 00 00 00 00 00 00 00 00 00 00
{59} normal block at 0x0000022CE5EDDB80, 16 bytes long.
Data: < y > 18 C0 79 DD F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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