Task 38581924

Stderr output

<core_client_version>8.2.4</core_client_version>
<![CDATA[
<stderr_txt>
18:40:36 (21228): wrapper (7.9.26016): starting
18:40:36 (21228): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A13_A36_0.pdb
QB_A13_A36_0.xml
QB_A13_A36_equil.pdb
QB_A13_A36.inpcrd
QB_A13_A36_input.yaml
QB_A13_A36_mdlambda.pdb
QB_A13_A36_min.pdb
QB_A13_A36_npt.pdb
QB_A13_A36.pdb
QB_A13_A36.prmtop
QB_A13_A36_sys.xml
QB_A13_A36_therm.pdb
run.bat
run.sh
18:40:39 (21228): Library/usr/bin/tar.exe exited; CPU time 0.000000
18:40:39 (21228): 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_GPUGRID\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_GPUGRID\slots\0\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_GPUGRID\slots\0\pip-build-env-x0z6w2pi\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_GPUGRID\slots\0\pip-build-env-x0z6w2pi\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_GPUGRID\slots\0\pip-build-env-x0z6w2pi\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_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info
  writing C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info\SOURCES.txt'
  listing git files failed - pretending there aren't any
  reading manifest file 'C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC_GPUGRID\slots\0\pip-modern-metadata-zgk6w2hi\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC_GPUGRID\slots\0\pip-build-env-x0z6w2pi\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_GPUGRID\slots\0\pip-wheel-sxnqz329\.tmp-jah1uyuu\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_GPUGRID\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) : {3835225} normal block at 0x0000019006DEE5E0, 8 bytes long.
 Data: <  !     > 00 00 21 07 90 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833958} normal block at 0x0000019008C07630, 1080 bytes long.
 Data: < X              > D8 58 00 00 CD CD CD CD 08 02 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {311} normal block at 0x0000019006DE4CE0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
10:51:39 (28116): wrapper (7.9.26016): starting
10:51:39 (28116): 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_GPUGRID\slots\0\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
11:46:23 (28116): C:/Windows/system32/cmd.exe exited; CPU time 3282.140625
11:46:23 (28116): called boinc_finish(0)
0 bytes in 0 Free Blocks.
632 bytes in 8 Normal Blocks.
1144 bytes in 1 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 0 bytes.
Total allocations: 66995098 bytes.
Dumping objects ->
{1660} normal block at 0x0000022AD444EF80, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1649} normal block at 0x0000022AD4465830, 48 bytes long.
 Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1638} normal block at 0x0000022AD4465670, 48 bytes long.
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{1627} normal block at 0x0000022AD44654B0, 48 bytes long.
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{1616} normal block at 0x0000022AD4465980, 48 bytes long.
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{1585} normal block at 0x0000022AD444F4B0, 64 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1574} normal block at 0x0000022AD444F3C0, 180 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
..\api\boinc_api.cpp(309) : {1571} normal block at 0x0000022AD44662F0, 8 bytes long.
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{941} normal block at 0x0000022AD44505A0, 180 bytes long.
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{305} normal block at 0x0000022AD4465E90, 8 bytes long.
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{296} normal block at 0x0000022AD4451DD0, 80 bytes long.
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{295} normal block at 0x0000022AD4465F30, 16 bytes long.
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{294} normal block at 0x0000022AD4465F80, 16 bytes long.
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{293} normal block at 0x0000022AD445FBA0, 32 bytes long.
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{292} normal block at 0x0000022AD4465EE0, 16 bytes long.
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{291} normal block at 0x0000022AD44660C0, 16 bytes long.
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{289} normal block at 0x0000022AD4466070, 16 bytes long.
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{287} normal block at 0x0000022AD4466B60, 16 bytes long.
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{281} normal block at 0x0000022AD4466610, 16 bytes long.
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{279} normal block at 0x0000022AD4466570, 16 bytes long.
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{278} normal block at 0x0000022AD4460620, 32 bytes long.
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{277} normal block at 0x0000022AD4466700, 16 bytes long.
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{275} normal block at 0x0000022AD4466840, 16 bytes long.
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{273} normal block at 0x0000022AD445FEA0, 32 bytes long.
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{272} normal block at 0x0000022AD4466DE0, 16 bytes long.
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{268} normal block at 0x0000022AD4466B10, 16 bytes long.
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{267} normal block at 0x0000022AD4466480, 16 bytes long.
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{266} normal block at 0x0000022AD4466110, 16 bytes long.
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{263} normal block at 0x0000022AD4466CA0, 16 bytes long.
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{262} normal block at 0x0000022AD44652F0, 40 bytes long.
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{261} normal block at 0x0000022AD44663E0, 16 bytes long.
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{258} normal block at 0x0000022AD4466CF0, 16 bytes long.
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{257} normal block at 0x0000022AD4466E50, 992 bytes long.
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{93} normal block at 0x0000022AD4460320, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{92} normal block at 0x0000022AD445E350, 16 bytes long.
 Data: <  D *           > 20 C4 44 D4 2A 02 00 00 00 00 00 00 00 00 00 00 
{91} normal block at 0x0000022AD444C420, 40 bytes long.
 Data: <P E *     F *   > 50 E3 45 D4 2A 02 00 00 20 03 46 D4 2A 02 00 00 
{70} normal block at 0x0000022AD445DF40, 16 bytes long.
 Data: <                > 80 EA C2 FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{69} normal block at 0x0000022AD445DFE0, 16 bytes long.
 Data: <@               > 40 E9 C2 FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{68} normal block at 0x0000022AD445E300, 16 bytes long.
 Data: < W              > F8 57 BF FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{67} normal block at 0x0000022AD445E2B0, 16 bytes long.
 Data: < W              > D8 57 BF FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{66} normal block at 0x0000022AD445DD10, 16 bytes long.
 Data: <P               > 50 04 BF FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{65} normal block at 0x0000022AD445E030, 16 bytes long.
 Data: <0               > 30 04 BF FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{64} normal block at 0x0000022AD445E260, 16 bytes long.
 Data: <                > E0 02 BF FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x0000022AD445D900, 16 bytes long.
 Data: <                > 10 04 BF FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x0000022AD445DC20, 16 bytes long.
 Data: <p               > 70 04 BF FA F7 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x0000022AD445E440, 16 bytes long.
 Data: <                > 18 C0 BD FA F7 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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