Comments (2)
Currently, there is no way to set the number of cores. pmx itself is not using multiple threads. Maybe it is one of the rdkit functions that parallelizes on more threads, but so far I have not been able to reproduce the issue. Could you share your inputs for this case?
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Hi Vytautas,
Sorry for my slow reply. So I think it must be one of the underlying modules. I tried setting OS NUM_EXPR_THREADS but this had no effect.
The reason why I wanted to do this was because I was encountering issues with multiprocessing pmx atomMapping and pmx ligandHybrid commands. Today I've realised that the issue was caused by the temporary naming system that was being used in reformatPDB function. I haven't dug into it too much but I think the issue was that when multiple processes were run in parallel, they ended up writing to the same file, and so things were getting messy and more often than not breaking.
I've therefore forked the module and used the tempfile.NamedTemporaryFile() to deal with this, allowing multiprocessing to occur. (I also removed some print statement, for my own purpose)
Thanks,
Noah
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Related Issues (20)
- Error in atom.py
- IndexError: list index out of range HOT 2
- Error with Zn atom HOT 1
- Error in ligand_alchemy.py HOT 2
- develop branch - Multiple indentation errors
- Using pmx with parmed generated gromacs topologies HOT 4
- Gromacs 4.6 with an alternative soft-core function HOT 8
- Why does PMX ligandHybrid fail for this specific ligand? HOT 2
- Using hydrogen mass repartitioning and non-equilibrium FEP. HOT 14
- Request to add branch
- Is it possible to run non-equilibrium FEP from pre-equilibrated end points? HOT 2
- Confusion in [ dihedrals ] section in hybrid topology HOT 1
- AttributeError: module 'configparser' has no attribute 'SafeConfigParser'. Did you mean: 'RawConfigParser'? HOT 3
- the calculation of transitions between ligands with different total charges HOT 2
- How to interpret wplots? HOT 1
- charmm36mut force field failed with Fatal error: Atom type ON2 (residue TPO) not found in atomtype database HOT 2
- add special ions
- Repartitioning dummy atom hydrogen mass HOT 3
- Hydrogen mapping
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