Task 38582311

Stderr output

<core_client_version>8.2.8</core_client_version>
<![CDATA[
<stderr_txt>
20:01:50 (6420): wrapper (7.9.26016): starting
20:01:50 (6420): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A40_A05_0.pdb
QB_A40_A05_0.xml
QB_A40_A05_equil.pdb
QB_A40_A05.inpcrd
QB_A40_A05_input.yaml
QB_A40_A05_mdlambda.pdb
QB_A40_A05_min.pdb
QB_A40_A05_npt.pdb
QB_A40_A05.pdb
QB_A40_A05.prmtop
QB_A40_A05_sys.xml
QB_A40_A05_therm.pdb
run.bat
run.sh
20:02:14 (6420): Library/usr/bin/tar.exe exited; CPU time 0.203125
20:02:14 (6420): 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\7\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\7\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\7\pip-build-env-ts5xfrv8\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\7\pip-build-env-ts5xfrv8\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\7\pip-build-env-ts5xfrv8\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\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\7\pip-modern-metadata-skpbzs4j\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\7\pip-build-env-ts5xfrv8\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\7\pip-wheel-32_hrsx_\.tmp-49fv5gpj\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\7\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.
23:46:35 (3284): wrapper (7.9.26016): starting
23:46:35 (3284): 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\7\tmp already exists.
Warning: importing 'simtk.openmm' is deprecated.  Import 'openmm' instead.
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {1444} normal block at 0x00000167444B3D30, 8 bytes long.
 Data: <   Eg   > 00 00 D3 45 67 01 00 00 
..\lib\diagnostics_win.cpp(417) : {297} normal block at 0x00000167444B4A30, 1080 bytes long.
 Data: <                > 88 1D 00 00 CD CD CD CD 9C 00 00 00 00 00 00 00 
Object dump complete.
20:00:00 (13084): wrapper (7.9.26016): starting
20:00:00 (13084): 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\7\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
00:42:20 (13084): C:/Windows/system32/cmd.exe exited; CPU time 16637.406250
00:42:20 (13084): 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: 255962486 bytes.
Dumping objects ->
{1532} normal block at 0x000001E70D90BE40, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1521} normal block at 0x000001E70D90BB30, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1510} normal block at 0x000001E70D90BEB0, 48 bytes long.
 Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61 
{1499} normal block at 0x000001E70D90BC10, 48 bytes long.
 Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1488} normal block at 0x000001E70D90BAC0, 48 bytes long.
 Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61 
{1457} normal block at 0x000001E70D8F61C0, 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) : {1444} normal block at 0x000001E70D912FE0, 8 bytes long.
 Data: <        > 00 00 1D 0F E7 01 00 00 
{298} normal block at 0x000001E70D912A90, 8 bytes long.
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{289} normal block at 0x000001E70D8F5BD0, 80 bytes long.
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{288} normal block at 0x000001E70D912B30, 16 bytes long.
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{287} normal block at 0x000001E70D9138F0, 16 bytes long.
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{286} normal block at 0x000001E70D90D080, 32 bytes long.
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{285} normal block at 0x000001E70D9133A0, 16 bytes long.
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{284} normal block at 0x000001E70D913080, 16 bytes long.
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{283} normal block at 0x000001E70D912A40, 16 bytes long.
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{282} normal block at 0x000001E70D912EF0, 16 bytes long.
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{281} normal block at 0x000001E70D90B820, 48 bytes long.
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{280} normal block at 0x000001E70D9133F0, 16 bytes long.
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{278} normal block at 0x000001E70D913760, 16 bytes long.
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{273} normal block at 0x000001E70D912EA0, 16 bytes long.
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{272} normal block at 0x000001E70D913670, 16 bytes long.
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{271} normal block at 0x000001E70D90CBA0, 32 bytes long.
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{270} normal block at 0x000001E70D913710, 16 bytes long.
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{269} normal block at 0x000001E70D90C850, 320 bytes long.
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{268} normal block at 0x000001E70D9132B0, 16 bytes long.
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{267} normal block at 0x000001E70D9135D0, 16 bytes long.
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{266} normal block at 0x000001E70D90D2C0, 32 bytes long.
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{265} normal block at 0x000001E70D912C20, 16 bytes long.
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{264} normal block at 0x000001E70D90CC60, 32 bytes long.
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{263} normal block at 0x000001E70D913030, 16 bytes long.
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{262} normal block at 0x000001E70D912E50, 16 bytes long.
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{261} normal block at 0x000001E70D912E00, 16 bytes long.
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{260} normal block at 0x000001E70D913260, 16 bytes long.
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{259} normal block at 0x000001E70D912AE0, 16 bytes long.
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{258} normal block at 0x000001E70D912BD0, 16 bytes long.
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{256} normal block at 0x000001E70D912F40, 16 bytes long.
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{255} normal block at 0x000001E70D90BA50, 40 bytes long.
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{254} normal block at 0x000001E70D913350, 16 bytes long.
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{253} normal block at 0x000001E70D913170, 16 bytes long.
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{252} normal block at 0x000001E70D90D020, 32 bytes long.
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{251} normal block at 0x000001E70D9138A0, 16 bytes long.
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{250} normal block at 0x000001E70D9139B0, 992 bytes long.
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{86} normal block at 0x000001E70D90D980, 32 bytes long.
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{85} normal block at 0x000001E70D907220, 16 bytes long.
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{84} normal block at 0x000001E70D90BC80, 40 bytes long.
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{63} normal block at 0x000001E70D907630, 16 bytes long.
 Data: <  A=            > 80 EA 41 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001E70D906BE0, 16 bytes long.
 Data: <@ A=            > 40 E9 41 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001E70D906E10, 16 bytes long.
 Data: < W>=            > F8 57 3E 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001E70D907360, 16 bytes long.
 Data: < W>=            > D8 57 3E 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001E70D907590, 16 bytes long.
 Data: <P >=            > 50 04 3E 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x000001E70D9070E0, 16 bytes long.
 Data: <0 >=            > 30 04 3E 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x000001E70D906B90, 16 bytes long.
 Data: <  >=            > E0 02 3E 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x000001E70D907770, 16 bytes long.
 Data: <  >=            > 10 04 3E 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{55} normal block at 0x000001E70D906EB0, 16 bytes long.
 Data: <p >=            > 70 04 3E 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
{54} normal block at 0x000001E70D906DC0, 16 bytes long.
 Data: <  <=            > 18 C0 3C 3D F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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