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OpenMS is not working #7333

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clin888 opened this issue Feb 5, 2024 · 14 comments
Open

OpenMS is not working #7333

clin888 opened this issue Feb 5, 2024 · 14 comments

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@clin888
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clin888 commented Feb 5, 2024

Hi,

The following message was found when generated a spectrum library using DDA data. Please help
Thanks

Traceback (most recent call last):
File "C:\ProgramData\Python_3.9\Scripts\easypqp-script.py", line 33, in
sys.exit(load_entry_point('easypqp==0.1.42', 'console_scripts', 'easypqp')())
File "C:\ProgramData\Python_3.9\Scripts\easypqp-script.py", line 25, in importlib_load_entry_point
return next(matches).load()
File "C:\ProgramData\Python_3.9\lib\importlib\metadata.py", line 86, in load
module = import_module(match.group('module'))
File "C:\ProgramData\Python_3.9\lib\importlib_init_.py", line 127, in import_module
return _bootstrap._gcd_import(name[level:], package, level)
File "", line 1030, in _gcd_import
File "", line 1007, in _find_and_load
File "", line 986, in _find_and_load_unlocked
File "", line 680, in load_unlocked
File "", line 850, in exec_module
File "", line 228, in call_with_frames_removed
File "C:\ProgramData\Python_3.9\lib\site-packages\easypqp\main.py", line 9, in
from .convert import conversion, basename_spectralfile
File "C:\ProgramData\Python_3.9\lib\site-packages\easypqp\convert.py", line 18, in
import pyopenms as po
File "C:\ProgramData\Python_3.9\lib\site-packages\pyopenms_init.py", line 107, in
raise e
File "C:\ProgramData\Python_3.9\lib\site-packages\pyopenms_init.py", line 65, in
from ._all_modules import * # pylint: disable=wildcard-import; lgtm(py/polluting-import)
File "C:\ProgramData\Python_3.9\lib\site-packages\pyopenms_all_modules.py", line 1, in
from ._pyopenms_1 import * # pylint: disable=wildcard-import; lgtm(py/polluting-import)
ImportError: DLL load failed while importing _pyopenms_1: A dynamic link library (DLL) initialization routine failed.

======================================================================
Error when loading pyOpenMS libraries!
Libraries could not be found / could not be loaded.

To debug this error, please run ldd (on linux), otool -L (on macOS) or dependency walker (on windows) on

C:\ProgramData\Python_3.9\lib\site-packages\pyopenms\pyopenms*.so

======================================================================
Traceback (most recent call last):
File "C:\Fragpipe\FragPipe-jre-21.1\fragpipe\tools\speclib\gen_con_spec_lib.py", line 724, in
main_easypqp()
File "C:\Fragpipe\FragPipe-jre-21.1\fragpipe\tools\speclib\gen_con_spec_lib.py", line 566, in main_easypqp
subprocess.run([os.fspath(easypqp), '--version'], check=True)
File "C:\ProgramData\Python_3.9\lib\subprocess.py", line 528, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['C:\ProgramData\Python_3.9\Scripts\easypqp.exe', '--version']' returned non-zero exit status 1.
Process 'SpecLibGen' finished, exit code: 1
Process returned non-zero exit code, stopping

log_2024-02-04_16-55-51.txt
@jpfeuffer
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Hi!

I think you might be getting this error because of one of the following reasons:

  • You are running 32-bit Python or a 32-bit Windows
  • You have not installed the Microsoft Visual C++ Redistributable package
  • Your CPU does not support certain SIMD (AVX?) instructions

Let us know if you need help checking any of those facts.

Tagging @cbielow as a windows and SIMD expert.

@clin888
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clin888 commented Feb 5, 2024

Hi,

Thank you for your help,

You are running 32-bit Python or a 32-bit Windows
--I run 64-bit Python with 64-bit window 10 enterprise
You have not installed the Microsoft Visual C++ Redistributable package
--I have Microsoft Visual C++ Redistributable package installed
Your CPU does not support certain SIMD (AVX?) instructions
--The CPU is intel Xeon ES 530 and it should support AVX

Thanks

@jpfeuffer
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jpfeuffer commented Feb 5, 2024 •
edited

Hm ok.
Can you list the DLLs or pyds in C:\ProgramData\Python_3.9\lib\site-packages\pyopenms?
And potentially even run DependencyWalker on any of the _pyopenms.dlls or .pyds and post a screenshot? https://lucasg.github.io/Dependencies/

@clin888
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clin888 commented Feb 5, 2024

Hi,

Thank you for your efforts. Enclosed is a screenshot for Dependency and Pyopenms

pyopenms_file_list.docx
.

@jpfeuffer
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Thank you very much for your quick and helpful debugging.
Unfortunately, your screenshots actually look very much correct. I think "Dependencies" should show some dependent DLLs as red, in case they are missing or incompatible.
Maybe run dependencies on _pyopenms_1.cp39-win_amd64 and quickly scroll through the dependency list to check that there is nothing marked in the color red.

@guoci guoci mentioned this issue Feb 9, 2024
Closed
@fcyu fcyu mentioned this issue Apr 18, 2024
Closed
@jkennedy-hutch
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Good afternoon,

I'd like to take over where clin888 left off - he's currently out of the lab for a while. Attached is a screenshot of the dependencies for _pyopenms_1.cp39-win_amd64. It looks like there's one in red and a couple libraries with bad checksums. Are these our culprits?

Thanks,
-Jake
dependencies

@jpfeuffer
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jpfeuffer commented Apr 20, 2024 •
edited

Hi!

Maybe the missing ordinals are a problem, but they are from a system library, not anything that we ship.
The incorrect checksums are less likely to be a problem, I don't think they are checked by default during loading (I think a checksum of 0 just means we don't encode any into the DLL).

Can you try in whatever python (environment) this code is called by fragpipe to run:

import dlltracer
import sys
with dlltracer.Trace(out=sys.stdout):
    import pyopenms
    print(pyopenms.__version__)

To potentially debug at which library it really crashes.
(I found this somewhere, never tried myself)

@jkennedy-hutch
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jkennedy-hutch commented Apr 22, 2024 via email

@jpfeuffer
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Oh yes, you need to pip install dlltracer into that env first. I forgot.

@jkennedy-hutch
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jkennedy-hutch commented Apr 22, 2024 via email

@jpfeuffer
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Hmmm can you try running it from an elevated/admin command line or python Run as Administrator?
Do you have those permissions? I think they are unfortunately necessary for this kind of debugging.

@jkennedy-hutch
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jkennedy-hutch commented Apr 22, 2024 via email

@jpfeuffer
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In theory it should not affect the execution but I cannot guarantee. Maybe it's also the way that fragpipe calls easypqp that calls pyopenms.. (and the permissions involved in spawning those subprocesses or accessing files/dlls)

Can you try just importing pyopenms in the python env? This should "work" without admin permissions (or at least fail with the initial error).

Other options are trying a fresh Windows virtual machine or so, to see if it's reproducible.

Unfortunately I do not have Windows, therefore we depend on GitHub's public runners, on which pyopenms works on a fresh "installation"

@jkennedy-hutch
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jkennedy-hutch commented Apr 23, 2024 via email

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3 participants
@jpfeuffer @clin888 @jkennedy-hutch