Task 38611713
| Name | tnks2_A21_A11_r0_5-QUICO_ATM_GAFF2_NAGL_TNKS2-4-6-RND5519_0 |
| Workunit | 31564408 |
| Created | 15 Apr 2026, 22:33:55 UTC |
| Sent | 15 Apr 2026, 22:34:02 UTC |
| Report deadline | 20 Apr 2026, 22:34:02 UTC |
| Received | 16 Apr 2026, 4:10:30 UTC |
| Server state | Over |
| Outcome | Success |
| Client state | Done |
| Exit status | 0 (0x00000000) |
| Computer ID | 652075 |
| Run time | 3 hours 59 min 10 sec |
| CPU time | 3 hours 59 min 10 sec |
| Validate state | Valid |
| Credit | 750,000.00 |
| Device peak FLOPS | 6,746.53 GFLOPS |
| Application version | ATM: Free energy calculations of protein-ligand binding v1.20 (cuda1121) windows_x86_64 |
| Peak working set size | 479.66 MB |
| Peak swap size | 6.50 GB |
| Peak disk usage | 3.64 GB |
Stderr output
<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
16:38:05 (9432): wrapper (7.9.26016): starting
16:38:05 (9432): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A21_A11_0.pdb
QB_A21_A11_0.xml
QB_A21_A11.inpcrd
QB_A21_A11_input.yaml
QB_A21_A11.pdb
QB_A21_A11.prmtop
QB_A21_A11_sys.xml
run.bat
run.sh
16:38:06 (9432): Library/usr/bin/tar.exe exited; CPU time 0.000000
16:38:06 (9432): 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 0x000001DFE0E4FB50>: Failed to establish a new connection: [Errno 11001] getaddrinfo failed')': /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/5c/e1/342c4434df56aa537f6ce7647eefee521d96fbb828b08acd709865767652/setuptools_scm-10.0.5-py3-none-any.whl.metadata
Downloading setuptools_scm-10.0.5-py3-none-any.whl.metadata (6.5 kB)
Collecting vcs-versioning>=1.0.0.dev0 (from setuptools-scm>=8)
Obtaining dependency information for vcs-versioning>=1.0.0.dev0 from https://files.pythonhosted.org/packages/e6/60/73603fbcdbe5e803855bcce4414f94eaeed449083bd8183e67161af78188/vcs_versioning-1.1.1-py3-none-any.whl.metadata
Downloading vcs_versioning-1.1.1-py3-none-any.whl.metadata (1.6 kB)
Collecting packaging>=20 (from setuptools-scm>=8)
Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/7a/c2/920ef838e2f0028c8262f16101ec09ebd5969864e5a64c4c05fad0617c56/packaging-26.1-py3-none-any.whl.metadata
Downloading packaging-26.1-py3-none-any.whl.metadata (3.5 kB)
Downloading setuptools-82.0.1-py3-none-any.whl (1.0 MB)
---------------------------------------- 1.0/1.0 MB 252.0 kB/s eta 0:00:00
Downloading setuptools_scm-10.0.5-py3-none-any.whl (21 kB)
Downloading packaging-26.1-py3-none-any.whl (95 kB)
Downloading vcs_versioning-1.1.1-py3-none-any.whl (79 kB)
Installing collected packages: setuptools, packaging, vcs-versioning, setuptools-scm
Creating C:\ProgramData\BOINC\slots\0\pip-build-env-ud1mky0a\overlay\Scripts
Successfully installed packaging-26.1 setuptools-82.0.1 setuptools-scm-10.0.5 vcs-versioning-1.1.1
Running command Getting requirements to build wheel
C:\ProgramData\BOINC\slots\0\pip-build-env-ud1mky0a\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: UserWarning: version of None already set
warnings.warn(f"version of {self.dist_name} already set")
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
C:\ProgramData\BOINC\slots\0\pip-build-env-ud1mky0a\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
return get_active_overrides().subprocess_timeout
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-ud1mky0a\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: UserWarning: version of None already set
warnings.warn(f"version of {self.dist_name} already set")
running dist_info
creating C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\atom_openmm.egg-info
writing C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\atom_openmm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\atom_openmm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\atom_openmm.egg-info\entry_points.txt
writing requirements to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\atom_openmm.egg-info\requires.txt
writing top-level names to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\atom_openmm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\atom_openmm.egg-info\SOURCES.txt'
C:\ProgramData\BOINC\slots\0\pip-build-env-ud1mky0a\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
return get_active_overrides().subprocess_timeout
listing git files failed - pretending there aren't any
reading manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\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-emui9vbu\atom_openmm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-emui9vbu\atom_openmm-8.4.0.dist-info'
Running command Building wheel for atom-openmm (pyproject.toml)
C:\ProgramData\BOINC\slots\0\pip-build-env-ud1mky0a\overlay\Lib\site-packages\setuptools_scm\_integration\version_inference.py:151: UserWarning: version of None already set
warnings.warn(f"version of {self.dist_name} already set")
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
C:\ProgramData\BOINC\slots\0\pip-build-env-ud1mky0a\overlay\Lib\site-packages\vcs_versioning\overrides.py:609: UserWarning: No GlobalOverrides context is active. Auto-creating one with SETUPTOOLS_SCM prefix for backwards compatibility. Consider using 'with GlobalOverrides.from_env("YOUR_TOOL"):' explicitly.
return get_active_overrides().subprocess_timeout
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-hevia05q\\.tmp-jk3mtcin\\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.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835091} normal block at 0x0000028469D0C130, 8 bytes long.
Data: < i > 00 00 CB 69 84 02 00 00
..\lib\diagnostics_win.cpp(417) : {3833940} normal block at 0x0000028469CFF990, 1080 bytes long.
Data: < , h > F0 2C 00 00 CD CD CD CD 68 01 00 00 00 00 00 00
..\zip\boinc_zip.cpp(122) : {302} normal block at 0x0000028469D15D10, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
Object dump complete.
20:06:30 (13376): wrapper (7.9.26016): starting
20:06:30 (13376): 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\0\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated. Import 'openmm' instead.
tar: run.log: file changed as we read it
21:05:21 (13376): C:/Windows/system32/cmd.exe exited; CPU time 3592.359375
21:05:21 (13376): 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: 44745684 bytes.
Dumping objects ->
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Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1523} normal block at 0x000002228194AC30, 48 bytes long.
Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{1512} normal block at 0x000002228194AF40, 48 bytes long.
Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61
{1501} normal block at 0x000002228194AED0, 48 bytes long.
Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
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Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61
{1459} normal block at 0x000002228193AF10, 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) : {1446} normal block at 0x0000022281945EC0, 8 bytes long.
Data: < % " > 00 00 25 83 22 02 00 00
{296} normal block at 0x0000022281946870, 8 bytes long.
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{254} normal block at 0x000002228194DF50, 16 bytes long.
Data: < " > 20 B0 94 81 22 02 00 00 00 00 00 00 00 00 00 00
{253} normal block at 0x000002228194B020, 40 bytes long.
Data: <P " " > 50 DF 94 81 22 02 00 00 10 AF 93 81 22 02 00 00
{252} normal block at 0x000002228194DF00, 16 bytes long.
Data: < $ " > 10 24 95 81 22 02 00 00 00 00 00 00 00 00 00 00
{251} normal block at 0x000002228194E0E0, 16 bytes long.
Data: < # " > E8 23 95 81 22 02 00 00 00 00 00 00 00 00 00 00
{250} normal block at 0x000002228194C490, 32 bytes long.
Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F
{249} normal block at 0x000002228194DEB0, 16 bytes long.
Data: < # " > C0 23 95 81 22 02 00 00 00 00 00 00 00 00 00 00
{248} normal block at 0x00000222819523C0, 992 bytes long.
Data: < " " > B0 DE 94 81 22 02 00 00 90 C4 94 81 22 02 00 00
{84} normal block at 0x000002228194C610, 32 bytes long.
Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F
{83} normal block at 0x0000022281946910, 16 bytes long.
Data: < " > F0 AD 94 81 22 02 00 00 00 00 00 00 00 00 00 00
{82} normal block at 0x000002228194ADF0, 40 bytes long.
Data: < i " " > 10 69 94 81 22 02 00 00 10 C6 94 81 22 02 00 00
{61} normal block at 0x00000222819460A0, 16 bytes long.
Data: < u > 80 EA 75 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{60} normal block at 0x0000022281945F10, 16 bytes long.
Data: <@ u > 40 E9 75 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{59} normal block at 0x0000022281946320, 16 bytes long.
Data: < Wr > F8 57 72 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{58} normal block at 0x0000022281946820, 16 bytes long.
Data: < Wr > D8 57 72 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{57} normal block at 0x00000222819469B0, 16 bytes long.
Data: <P r > 50 04 72 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{56} normal block at 0x0000022281945E20, 16 bytes long.
Data: <0 r > 30 04 72 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{55} normal block at 0x0000022281945DD0, 16 bytes long.
Data: < r > E0 02 72 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{54} normal block at 0x0000022281946AF0, 16 bytes long.
Data: < r > 10 04 72 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{53} normal block at 0x00000222819466E0, 16 bytes long.
Data: <p r > 70 04 72 EE F6 7F 00 00 00 00 00 00 00 00 00 00
{52} normal block at 0x0000022281945FB0, 16 bytes long.
Data: < p > 18 C0 70 EE F6 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.
</stderr_txt>
]]>
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