Unverified Commit c49a9ef3 authored by mvdbeek's avatar mvdbeek
Browse files

Fix seek in slurm memory check 

Fixes
https://sentry.galaxyproject.org/share/issue/e196a12836fe40da83c5e9e24c4c8329/:
```
UnsupportedOperation: can't do nonzero end-relative seeks
  File "galaxy/jobs/runners/slurm.py", line 217, in __check_memory_limit
    f.seek(-2048, os.SEEK_END)
```
which has probably been broken since we moved to python 3.
parent dc145ed4

lib/galaxy/jobs/runners/slurm.py

+6 −3
Original line number Diff line number Diff line
@@ -7,7 +7,10 @@ import time 


from galaxy import model

from galaxy.jobs.runners.drmaa import DRMAAJobRunner

from galaxy.util import commands

from galaxy.util import (

    commands,

    unicodify,

)

from galaxy.util.custom_logging import get_logger



log = get_logger(__name__)
@@ -212,12 +215,12 @@ class SlurmJobRunner(DRMAAJobRunner): 
        """

        try:

            log.debug("Checking %s for exceeded memory message from SLURM", efile_path)

            with open(efile_path) as f:

            with open(efile_path, "rb") as f:

                if os.path.getsize(efile_path) > 2048:

                    f.seek(-2048, os.SEEK_END)

                    f.readline()

                for line in f.readlines():

                    stripped_line = line.strip()

                    stripped_line = unicodify(line)

                    if stripped_line == SLURM_MEMORY_LIMIT_EXCEEDED_MSG:

                        return OUT_OF_MEMORY_MSG

                    elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS):