Comments (6)
It means that the number of system's file descriptors in use exceeds the limit. This can be changed with 'ulimit' in linux.
It may also be an issue with the code when files are not closed, or temporary files are created on low level (I created a bug report to Python developers as the tempfile documentation doesn't mention that when creating a temporary file, it should be both removed after use and file descriptor closed even though the file was never opened).
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Thanks for the prompt response @amjjbonvin . I'll check my implementation. Btw I need to run 735 complexes instead of the above mentioned 100, and it ran pretty well till around 400 complexes, after which I got these issues.
Anyways, thanks again for your response. And also for building and providing such a powerful tool.
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Most like a Python limitation. It is probably more efficient to run fewer complexes at the same time rather than starting all 100 at the same time.
Thanks for the suggestion @amjjbonvin . I am not running 100 complexes simultaneously. My setup looks like the following.
# Input PDB directory
set z="processed_pdb_batch2/*"
@ run=1
# Iterate over all the proteins in the directory
foreach i (`ls -d $z`)
# Make run.param file for current complex
python makeParam.py --pdb $i --run $run
# 1st haddock initialization
haddock2.4
# Enter run directory
cd run$run
# Edit the run.cns file to use 128 cores
python ../editCNS.py --filename run.cns
# 2st haddock initialization
haddock2.4
cd ..
@ run+=1
echo $i
echo $run
end
It runs well for the initial few complexes, but arbitrarily freezes with the mentioned error or skips the current run and moves over to the next complex (Inferred from the small size ~400MB of such run directory in comparison to a complete run that weighs exactly 1.1GB). I suspect some temp files are not being closed properly during the three step (it0, it1, water) docking process for these incomplete runs, leading to the eventual bottleneck. Pls suggest a way to overcome or an alternative to automate HADDOCK runs for multiple complexes.
Thanks.
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Related Issues (9)
- Typo in the check for multiple molecules in the same chain
- haddock-tools/restrain_bodies.py - seed is constant HOT 11
- floats in restraints file HOT 17
- restrain_ligand.py & restrain_bodies.py not compatible with Python 3 HOT 6
- cif conversion causes unexpected renumbering of residues HOT 1
- molprobity.py gives a TypeError HOT 2
- Please consider publishing `haddock-tools` as a `conda`/`pip` package HOT 8
- Descriptive Headers HOT 1
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