Task 38603438

Stderr output

<core_client_version>8.2.9</core_client_version>
<![CDATA[
<stderr_txt>
18:36:02 (16800): wrapper (7.9.26016): starting
18:36:02 (16800): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A05_A03_0.pdb
QB_A05_A03_0.xml
QB_A05_A03.inpcrd
QB_A05_A03_input.yaml
QB_A05_A03.pdb
QB_A05_A03.prmtop
QB_A05_A03_sys.xml
Detected memory leaks!
Dumping objects ->
..\api\boinc_api.cpp(309) : {3835208} normal block at 0x00000170067D6910, 8 bytes long.
 Data: <  y p   > 00 00 79 06 70 01 00 00 
..\lib\diagnostics_win.cpp(417) : {3833946} normal block at 0x000001700682F770, 1080 bytes long.
 Data: < .              > A4 2E 00 00 CD CD CD CD D8 01 00 00 00 00 00 00 
..\zip\boinc_zip.cpp(122) : {305} normal block at 0x00000170067E10F0, 260 bytes long.
 Data: <                > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 
Object dump complete.
19:41:52 (17348): wrapper (7.9.26016): starting
19:41:52 (17348): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A05_A03_0.pdb
QB_A05_A03_0.xml
QB_A05_A03.inpcrd
QB_A05_A03_input.yaml
QB_A05_A03.pdb
QB_A05_A03.prmtop
QB_A05_A03_sys.xml
run.bat
run.sh
19:41:55 (17348): Library/usr/bin/tar.exe exited; CPU time 0.000000
19:41:55 (17348): 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\1\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\1\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/b7/b9/c538f279a4e237a006a2c98387d081e9eb060d203d8ed34467cc0f0b9b53/packaging-26.0-py3-none-any.whl.metadata
    Downloading packaging-26.0-py3-none-any.whl.metadata (3.3 kB)
  Downloading setuptools-82.0.1-py3-none-any.whl (1.0 MB)
     ---------------------------------------- 1.0/1.0 MB 3.7 MB/s eta 0:00:00
  Downloading setuptools_scm-10.0.5-py3-none-any.whl (21 kB)
  Downloading packaging-26.0-py3-none-any.whl (74 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\1\pip-build-env-hix4bqtn\overlay\Scripts
  Successfully installed packaging-26.0 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\1\pip-build-env-hix4bqtn\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\1\pip-build-env-hix4bqtn\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\1\pip-build-env-hix4bqtn\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\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info
  writing C:\ProgramData\BOINC\slots\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info\PKG-INFO
  writing dependency_links to C:\ProgramData\BOINC\slots\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info\dependency_links.txt
  writing entry points to C:\ProgramData\BOINC\slots\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info\entry_points.txt
  writing requirements to C:\ProgramData\BOINC\slots\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info\requires.txt
  writing top-level names to C:\ProgramData\BOINC\slots\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info\top_level.txt
  writing manifest file 'C:\ProgramData\BOINC\slots\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info\SOURCES.txt'
  C:\ProgramData\BOINC\slots\1\pip-build-env-hix4bqtn\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\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info\SOURCES.txt'
  reading manifest template 'MANIFEST.in'
  adding license file 'LICENSE'
  writing manifest file 'C:\ProgramData\BOINC\slots\1\pip-modern-metadata-gp3zi35c\atom_openmm.egg-info\SOURCES.txt'
  creating 'C:\ProgramData\BOINC\slots\1\pip-modern-metadata-gp3zi35c\atom_openmm-8.4.0.dist-info'
  Running command Building wheel for atom-openmm (pyproject.toml)
  C:\ProgramData\BOINC\slots\1\pip-build-env-hix4bqtn\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\1\pip-build-env-hix4bqtn\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\\1\\pip-wheel-ldh_lgas\\.tmp-8f2eljn2\\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\1\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.
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
07:47:17 (17348): C:/Windows/system32/cmd.exe exited; CPU time 41206.343750
07:47:17 (17348): called boinc_finish(0)
0 bytes in 0 Free Blocks.
460 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: 647826937 bytes.
Dumping objects ->
{1648} normal block at 0x000001BDC605C3A0, 48 bytes long.
 Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 
{1637} normal block at 0x000001BDC605C250, 48 bytes long.
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{1626} normal block at 0x000001BDC605C020, 48 bytes long.
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{1615} normal block at 0x000001BDC605C6B0, 48 bytes long.
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{1604} normal block at 0x000001BDC605C5D0, 48 bytes long.
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{1573} normal block at 0x000001BDC604C9E0, 64 bytes long.
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{1562} normal block at 0x000001BDC60432C0, 102 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) : {1559} normal block at 0x000001BDC60637A0, 8 bytes long.
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{921} normal block at 0x000001BDC6048E00, 102 bytes long.
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{298} normal block at 0x000001BDC6063D90, 8 bytes long.
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{290} normal block at 0x000001BDC604B140, 80 bytes long.
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{289} normal block at 0x000001BDC6063700, 16 bytes long.
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{287} normal block at 0x000001BDC605DAE0, 32 bytes long.
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{286} normal block at 0x000001BDC60636B0, 16 bytes long.
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{285} normal block at 0x000001BDC60642E0, 16 bytes long.
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{284} normal block at 0x000001BDC60638E0, 16 bytes long.
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{283} normal block at 0x000001BDC60641F0, 16 bytes long.
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{266} normal block at 0x000001BDC6063A20, 16 bytes long.
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{264} normal block at 0x000001BDC6063C50, 16 bytes long.
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{263} normal block at 0x000001BDC60643D0, 16 bytes long.
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{259} normal block at 0x000001BDC6063B10, 16 bytes long.
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{257} normal block at 0x000001BDC6063660, 16 bytes long.
 Data: <`               > 60 C5 05 C6 BD 01 00 00 00 00 00 00 00 00 00 00 
{256} normal block at 0x000001BDC605C560, 40 bytes long.
 Data: <`6              > 60 36 06 C6 BD 01 00 00 E0 C9 04 C6 BD 01 00 00 
{255} normal block at 0x000001BDC6063C00, 16 bytes long.
 Data: <@F              > 40 46 06 C6 BD 01 00 00 00 00 00 00 00 00 00 00 
{254} normal block at 0x000001BDC6063ED0, 16 bytes long.
 Data: < F              > 18 46 06 C6 BD 01 00 00 00 00 00 00 00 00 00 00 
{253} normal block at 0x000001BDC605DF00, 32 bytes long.
 Data: <Library/usr/bin/> 4C 69 62 72 61 72 79 2F 75 73 72 2F 62 69 6E 2F 
{252} normal block at 0x000001BDC60639D0, 16 bytes long.
 Data: < E              > F0 45 06 C6 BD 01 00 00 00 00 00 00 00 00 00 00 
{251} normal block at 0x000001BDC60645F0, 992 bytes long.
 Data: < 9              > D0 39 06 C6 BD 01 00 00 00 DF 05 C6 BD 01 00 00 
{87} normal block at 0x000001BDC605E020, 32 bytes long.
 Data: <windows_x86_64__> 77 69 6E 64 6F 77 73 5F 78 38 36 5F 36 34 5F 5F 
{86} normal block at 0x000001BDC60581D0, 16 bytes long.
 Data: <                > E0 C1 05 C6 BD 01 00 00 00 00 00 00 00 00 00 00 
{85} normal block at 0x000001BDC605C1E0, 40 bytes long.
 Data: <                > D0 81 05 C6 BD 01 00 00 20 E0 05 C6 BD 01 00 00 
{64} normal block at 0x000001BDC6057FA0, 16 bytes long.
 Data: <   j            > 80 EA 95 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{63} normal block at 0x000001BDC6058040, 16 bytes long.
 Data: <@  j            > 40 E9 95 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{62} normal block at 0x000001BDC60580E0, 16 bytes long.
 Data: < W j            > F8 57 92 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{61} normal block at 0x000001BDC6057A50, 16 bytes long.
 Data: < W j            > D8 57 92 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{60} normal block at 0x000001BDC6057410, 16 bytes long.
 Data: <P  j            > 50 04 92 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{59} normal block at 0x000001BDC6057A00, 16 bytes long.
 Data: <0  j            > 30 04 92 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{58} normal block at 0x000001BDC6057E60, 16 bytes long.
 Data: <   j            > E0 02 92 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{57} normal block at 0x000001BDC6057F50, 16 bytes long.
 Data: <   j            > 10 04 92 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{56} normal block at 0x000001BDC6057BE0, 16 bytes long.
 Data: <p  j            > 70 04 92 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
{55} normal block at 0x000001BDC6057DC0, 16 bytes long.
 Data: <   j            > 18 C0 90 6A F6 7F 00 00 00 00 00 00 00 00 00 00 
Object dump complete.

</stderr_txt>
]]>

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