error in ATM work units

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kcharuso

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watwatwatwatwatwatwatwatwatwatwatwat
Message 62281 - Posted: 27 Mar 2025, 4:19:43 UTC

hi all, i got numbers of ATM computation errors and i dont know why or how to fix it but here is the log from one of it. i apologize for it being too long but i do not know any other way.

<core_client_version>8.0.2</core_client_version>
<![CDATA[
<message>
The operating system cannot run (null).
(0xc3) - exit code 195 (0xc3)</message>
<stderr_txt>
01:40:50 (5900): wrapper (7.9.26016): starting
01:40:50 (5900): wrapper: running Library/usr/bin/tar.exe (xjvf input.tar.bz2)
QB_A03_A26_0.xml
QB_A03_A26.inpcrd
QB_A03_A26_input.yaml
QB_A03_A26.prmtop
run.bat
run.sh
01:40:51 (5900): Library/usr/bin/tar.exe exited; CPU time 0.000000
01:40:51 (5900): 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\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 git version
git version 2.47.0.windows.1
Running command git clone --filter=blob:none https://github.com/Acellera/atm.git 'C:\ProgramData\BOINC\slots\0\pip-req-build-x_5mq4bw'
Cloning into 'C:\ProgramData\BOINC\slots\0\pip-req-build-x_5mq4bw'...
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Updating files: 100% (140/140), done.
Running command git rev-parse HEAD
1fb570c42d487468a2c42ad1db1d264f19d49e95
Running command git rev-parse HEAD
1fb570c42d487468a2c42ad1db1d264f19d49e95
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/54/21/f43f0a1fa8b06b32812e0975981f4677d28e0f3271601dc88ac5a5b83220/setuptools-78.1.0-py3-none-any.whl.metadata
Using cached setuptools-78.1.0-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/10/7c/5a9799042320242c383c4485a2771a37d49e8ce2312ca647653d2fd1a7a4/setuptools_scm-8.2.0-py3-none-any.whl.metadata
Using cached setuptools_scm-8.2.0-py3-none-any.whl.metadata (6.8 kB)
Collecting packaging>=20 (from setuptools-scm>=8)
Obtaining dependency information for packaging>=20 from https://files.pythonhosted.org/packages/88/ef/eb23f262cca3c0c4eb7ab1933c3b1f03d021f2c48f54763065b6f0e321be/packaging-24.2-py3-none-any.whl.metadata
Using cached packaging-24.2-py3-none-any.whl.metadata (3.2 kB)
Using cached setuptools-78.1.0-py3-none-any.whl (1.3 MB)
Using cached setuptools_scm-8.2.0-py3-none-any.whl (43 kB)
Using cached packaging-24.2-py3-none-any.whl (65 kB)
Installing collected packages: setuptools, packaging, setuptools-scm
Successfully installed packaging-24.2 setuptools-78.1.0 setuptools-scm-8.2.0
Running command Getting requirements to build wheel
running egg_info
creating acellera_atm.egg-info
writing acellera_atm.egg-info\PKG-INFO
writing dependency_links to acellera_atm.egg-info\dependency_links.txt
writing entry points to acellera_atm.egg-info\entry_points.txt
writing top-level names to acellera_atm.egg-info\top_level.txt
writing manifest file 'acellera_atm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'manifest.json' under directory 'atm\apps'
warning: manifest_maker: MANIFEST.in, line 3: 'prune' expects a single <dir_pattern>

adding license file 'LICENSE'
writing manifest file 'acellera_atm.egg-info\SOURCES.txt'
Running command Preparing metadata (pyproject.toml)
running dist_info
creating C:\ProgramData\BOINC\slots\0\pip-modern-metadata-8rlbn0i7\acellera_atm.egg-info
writing C:\ProgramData\BOINC\slots\0\pip-modern-metadata-8rlbn0i7\acellera_atm.egg-info\PKG-INFO
writing dependency_links to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-8rlbn0i7\acellera_atm.egg-info\dependency_links.txt
writing entry points to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-8rlbn0i7\acellera_atm.egg-info\entry_points.txt
writing top-level names to C:\ProgramData\BOINC\slots\0\pip-modern-metadata-8rlbn0i7\acellera_atm.egg-info\top_level.txt
writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-8rlbn0i7\acellera_atm.egg-info\SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'manifest.json' under directory 'atm\apps'
warning: manifest_maker: MANIFEST.in, line 3: 'prune' expects a single <dir_pattern>

adding license file 'LICENSE'
writing manifest file 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-8rlbn0i7\acellera_atm.egg-info\SOURCES.txt'
creating 'C:\ProgramData\BOINC\slots\0\pip-modern-metadata-8rlbn0i7\acellera_atm-0.0.18.dist-info'
Running command Building wheel for acellera-atm (pyproject.toml)
running bdist_wheel
running build
running build_py
creating build\lib\atm
copying atm\atomutils.py -> build\lib\atm
copying atm\atom_nnp_wrapper.py -> build\lib\atm
copying atm\ommreplica.py -> build\lib\atm
copying atm\ommsystem.py -> build\lib\atm
copying atm\rbfe_production.py -> build\lib\atm
copying atm\rbfe_structprep.py -> build\lib\atm
copying atm\utils.py -> build\lib\atm
copying atm\uwham.py -> build\lib\atm
copying atm\worker.py -> build\lib\atm
copying atm\__init__.py -> build\lib\atm
running egg_info
writing acellera_atm.egg-info\PKG-INFO
writing dependency_links to acellera_atm.egg-info\dependency_links.txt
writing entry points to acellera_atm.egg-info\entry_points.txt
writing top-level names to acellera_atm.egg-info\top_level.txt
reading manifest template 'MANIFEST.in'
warning: no files found matching 'manifest.json' under directory 'atm\apps'
warning: manifest_maker: MANIFEST.in, line 3: 'prune' expects a single <dir_pattern>

adding license file 'LICENSE'
writing manifest file 'acellera_atm.egg-info\SOURCES.txt'
copying atm\logging.ini -> build\lib\atm
installing to build\bdist.win-amd64\wheel
running install
running install_lib
creating build\bdist.win-amd64\wheel
creating build\bdist.win-amd64\wheel\atm
copying build\lib\atm\atomutils.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\atom_nnp_wrapper.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\logging.ini -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\ommreplica.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\ommsystem.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\rbfe_production.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\rbfe_structprep.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\utils.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\uwham.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\worker.py -> build\bdist.win-amd64\wheel\.\atm
copying build\lib\atm\__init__.py -> build\bdist.win-amd64\wheel\.\atm
running install_egg_info
Copying acellera_atm.egg-info to build\bdist.win-amd64\wheel\.\acellera_atm-0.0.18-py3.11.egg-info
running install_scripts
creating build\bdist.win-amd64\wheel\acellera_atm-0.0.18.dist-info\WHEEL
creating 'C:\ProgramData\BOINC\slots\0\pip-wheel-cq7bh12n\.tmp-dlmu3idl\acellera_atm-0.0.18-py3-none-any.whl' and adding 'build\bdist.win-amd64\wheel' to it
adding 'acellera_atm-0.0.18.dist-info/licenses/LICENSE'
adding 'atm/__init__.py'
adding 'atm/atom_nnp_wrapper.py'
adding 'atm/atomutils.py'
adding 'atm/logging.ini'
adding 'atm/ommreplica.py'
adding 'atm/ommsystem.py'
adding 'atm/rbfe_production.py'
adding 'atm/rbfe_structprep.py'
adding 'atm/utils.py'
adding 'atm/uwham.py'
adding 'atm/worker.py'
adding 'acellera_atm-0.0.18.dist-info/METADATA'
adding 'acellera_atm-0.0.18.dist-info/WHEEL'
adding 'acellera_atm-0.0.18.dist-info/entry_points.txt'
adding 'acellera_atm-0.0.18.dist-info/top_level.txt'
adding 'acellera_atm-0.0.18.dist-info/RECORD'
removing build\bdist.win-amd64\wheel
WARNING: The scripts 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.
2025-03-27 01:41:20,318 - atm.rbfe_production - INFO - Configuration:
Traceback (most recent call last):
File "<frozen runpy>", line 198, in _run_module_as_main
File "<frozen runpy>", line 88, in _run_code
File "C:\ProgramData\BOINC\slots\0\Scripts\rbfe_production.exe\__main__.py", line 7, in <module>
File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atm\rbfe_production.py", line 323, in rbfe_production
rx = OpenmmJobAmberRBFE(os.path.basename(os.path.abspath(config_file)))
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "C:\ProgramData\BOINC\slots\0\Lib\site-packages\atm\rbfe_production.py", line 30, in __init__
raise ValueError("Invalid configuration file format")
ValueError: Invalid configuration file format
01:41:20 (5900): C:/Windows/system32/cmd.exe exited; CPU time 1.937500
01:41:20 (5900): app exit status: 0x16
01:41:20 (5900): called boinc_finish(195)
0 bytes in 0 Free Blocks.
426 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: 389456 bytes.
Dumping objects ->
{3835393} normal block at 0x000001CCD1251410, 48 bytes long.
Data: <PATH=C:\ProgramD> 50 41 54 48 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{3835382} normal block at 0x000001CCD12507D0, 48 bytes long.
Data: <HOME=C:\ProgramD> 48 4F 4D 45 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{3835371} normal block at 0x000001CCD1251640, 48 bytes long.
Data: <TMP=C:\ProgramDa> 54 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44 61
{3835360} normal block at 0x000001CCD1251560, 48 bytes long.
Data: <TEMP=C:\ProgramD> 54 45 4D 50 3D 43 3A 5C 50 72 6F 67 72 61 6D 44
{3835349} normal block at 0x000001CCD1251090, 48 bytes long.
Data: <TMPDIR=C:\Progra> 54 4D 50 44 49 52 3D 43 3A 5C 50 72 6F 67 72 61
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{3835307} normal block at 0x000001CCD13CCBE0, 85 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) : {3835304} normal block at 0x000001CCCF768F60, 8 bytes long.
Data: < &&#209;&#204; > 00 00 26 D1 CC 01 00 00
{3834625} normal block at 0x000001CCD13CC0A0, 85 bytes long.
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..\zip\boinc_zip.cpp(122) : {312} normal block at 0x000001CCCF7602A0, 260 bytes long.
Data: < > 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00
{297} normal block at 0x000001CCCF75E150, 80 bytes long.
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{296} normal block at 0x000001CCCF773CB0, 16 bytes long.
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{295} normal block at 0x000001CCCF774930, 16 bytes long.
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{293} normal block at 0x000001CCCF7745C0, 16 bytes long.
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{292} normal block at 0x000001CCCF774160, 16 bytes long.
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{291} normal block at 0x000001CCCF773C60, 16 bytes long.
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{290} normal block at 0x000001CCCF770A00, 48 bytes long.
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{289} normal block at 0x000001CCCF774110, 16 bytes long.
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{288} normal block at 0x000001CCCF76E2F0, 32 bytes long.
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{285} normal block at 0x000001CCCF773BC0, 16 bytes long.
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{284} normal block at 0x000001CCCF7744D0, 16 bytes long.
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{283} normal block at 0x000001CCCF773E40, 16 bytes long.
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{282} normal block at 0x000001CCCF773FD0, 16 bytes long.
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{277} normal block at 0x000001CCCF774890, 16 bytes long.
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{275} normal block at 0x000001CCCF76E6B0, 32 bytes long.
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{80} normal block at 0x000001CCCF7699B0, 16 bytes long.
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{79} normal block at 0x000001CCCF768E70, 16 bytes long.
Data: <@&#233; &#196;&#247; > 40 E9 0C C4 F7 7F 00 00 00 00 00 00 00 00 00 00
{78} normal block at 0x000001CCCF768D80, 16 bytes long.
Data: <&#248;W &#196;&#247; > F8 57 09 C4 F7 7F 00 00 00 00 00 00 00 00 00 00
{77} normal block at 0x000001CCCF769370, 16 bytes long.
Data: <&#216;W &#196;&#247; > D8 57 09 C4 F7 7F 00 00 00 00 00 00 00 00 00 00
{76} normal block at 0x000001CCCF769820, 16 bytes long.
Data: <P &#196;&#247; > 50 04 09 C4 F7 7F 00 00 00 00 00 00 00 00 00 00
{75} normal block at 0x000001CCCF769320, 16 bytes long.
Data: <0 &#196;&#247; > 30 04 09 C4 F7 7F 00 00 00 00 00 00 00 00 00 00
{74} normal block at 0x000001CCCF769960, 16 bytes long.
Data: <&#224; &#196;&#247; > E0 02 09 C4 F7 7F 00 00 00 00 00 00 00 00 00 00
{73} normal block at 0x000001CCCF769280, 16 bytes long.
Data: < &#196;&#247; > 10 04 09 C4 F7 7F 00 00 00 00 00 00 00 00 00 00
{72} normal block at 0x000001CCCF768D30, 16 bytes long.
Data: <p &#196;&#247; > 70 04 09 C4 F7 7F 00 00 00 00 00 00 00 00 00 00
{71} normal block at 0x000001CCCF768E20, 16 bytes long.
Data: < &#192; &#196;&#247; > 18 C0 07 C4 F7 7F 00 00 00 00 00 00 00 00 00 00
Object dump complete.

</stderr_txt>
]]>
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William Albert

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Message 62284 - Posted: 27 Mar 2025, 9:17:53 UTC

ValueError: Invalid configuration file format


This is almost certainly a problem with that particular work unit, and is something that would have to be fixed by whoever creates these work units.

If you look at the information about this particular work unit, you'll likely see other computers failing similar to the way that yours did.
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kcharuso

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Message 62286 - Posted: 27 Mar 2025, 11:21:39 UTC - in response to Message 62284.  

so, i did not crashed it or caused the error right? i kind of thought so too at first but i want confirmation from the community. thank you for the clearification.
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W-Fred

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Message 62290 - Posted: 28 Mar 2025, 13:41:58 UTC - in response to Message 62286.  

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William Albert

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Message 62291 - Posted: 28 Mar 2025, 16:39:11 UTC - in response to Message 62290.  

I have 100% error rate...
https://gpugrid.net/gpugrid/results.php?userid=580353


Looking at an example of one of your failed WUs (https://gpugrid.net/gpugrid/result.php?resultid=38401921), this looks like a problem with your setup (although many other WUs that failed are legitimately broken).

In particular:

19:51:42 (16096): wrapper: running C:/Windows/system32/cmd.exe (/c call Scripts\activate.bat && Scripts\conda-unpack.exe && run.bat)
'G:\-' is not recognized as an internal or external command,
operable program or batch file.


As well as:

{3835265} normal block at 0x0000016B0C26D300, 64 bytes long.
 Data: <PATH=G:\-=Utils=> 50 41 54 48 3D 47 3A 5C 2D 3D 55 74 69 6C 73 3D 


I'm not familiar Windows file and directory naming conventions/limitations, but it seems that BOINC is having problems with how you've set your PATH variable.

If removing the directory BOINC is stumbling on from your main system PATH isn't feasible, you may need to set a custom PATH specifically for BOINC. If you're running BOINC as a service, here's a link that describes how to set custom environment variables for services: https://serverfault.com/a/1103091
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W-Fred

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Message 62292 - Posted: 28 Mar 2025, 20:42:19 UTC - in response to Message 62291.  
Last modified: 28 Mar 2025, 20:51:01 UTC

Thank you, good catch. I reinstall Boinc into another directory that does not contain "-" or "=" characters. Maybe that's the problem.
Edit: Yes, that was the problem. Now it seems the GPU is working.
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Ryan Munro

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Message 62319 - Posted: 31 Mar 2025, 13:14:05 UTC

Looks like the apps may be starting to error out on my Linux box

https://gpugrid.net/gpugrid/result.php?resultid=38420069

"note: This error originates from a subprocess, and is likely not a problem with pip."
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KeithBriggs

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Message 62320 - Posted: 31 Mar 2025, 16:26:24 UTC - in response to Message 62319.  

We wont have any evidence that it's a Linux only problem for a while as its at the bottom of Stacie's pile of tasks. There's lots of coding issues.
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