search

compomics / ms2pip

MS²PIP: Fast and accurate peptide spectrum prediction for multiple fragmentation methods, instruments, and labeling techniques.
https://ms2pip.readthedocs.io
Apache License 2.0
37 stars 18 forks source link

C memory errors #33

Closed bittremieux closed 5 years ago

bittremieux commented 5 years ago

When I run MS2PIP locally (precompiled MS2PIP release v20190624) I regularly get C memory errors. The specific errors can vary: malloc errors, free errors, corrupted size, unspecified SIGABRT, ...

Such errors where memory is incorrectly accessed or freed are pretty much impossible to debug, so I was wondering whether you've experienced similar errors as well? Any tips on how to fix this?

Sometimes MS2PIP runs correctly, but equally often it crashes for some weird reason.

RalfG commented 5 years ago

Strange, I never had these issues. Maybe there is an incompatibility between your system and the system we used to compile the models?

Can you try the latest commit in the master branch and compile it yourself? With this version compilation should be a bit faster (takes for me 10 minutes). It can be compiled with pip install . or with conda build . -c bioconda; conda install ms2pip --use-local. The models are exactly the same, so results should also be identical to the latest release version.

RalfG commented 5 years ago

@bittremieux, did you manage to build the latest master branch version? If so, did this fix the issues you saw? Thanks!

bittremieux commented 5 years ago

I ran my MS2PIP script on another system instead, and I haven't gotten any errors there. Weird stuff, but whatever. 🤷‍♂️