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Not supporting for multicore in Windows enviroment #5

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o7o opened this issue Dec 19, 2016 · 12 comments
Closed

Not supporting for multicore in Windows enviroment #5

o7o opened this issue Dec 19, 2016 · 12 comments

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@o7o
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o7o commented Dec 19, 2016

when I did not set --maxthread to 1, plip did not work well. I got loop process in something like "..multiprocessing/fork.."
Plip can work again when we set 1 core.

Would you like to add this feature in the future update.

Thanks
@ssalentin
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Could you provide me with the specific error message you get?

@o7o
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o7o commented Dec 21, 2016 •
edited

Sorry for late reply

here it is the screenshoot for error multicore (win7 64bit, python 2.7 32bit)

link: https://goo.gl/NZbe6Z

error multicore-win764bit-py2732bit

different for Ubuntu 16.04, and I am sorry, it used python 2.7 version, right as ricrogz said.

link: https://goo.gl/4lbmR9

plip-ubuntu16 04-py27

Help me, I have tried in other Win 7 64bit system using python 2.7 64bit, but I got some error

link: https://goo.gl/ij9weO

plip-other-win7-64bit-py2764bit

Thank you very much

@ssalentin
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For the first case, try to rename the plipcmd script to plipcmd.py. Sometimes, there seem to be issues with the multiprocessing module in Windows when trying to reimport scripts without the .py ending.
For the second case it seems that you don't have a matching version of your Python bindings for OpenBabel installed.

@o7o
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o7o commented Jan 4, 2017 •
edited

Thank you for your respond.
For my second case, I uninstall standalone openbabel installation first because I had installed it before.
For the first one, as you said, I renamed two files plipcmd to plipcmd.py; in C:\Python27\Scripts and C:\Python27\Lib\site-packages\plip-1.3.3-py2.7.egg\EGG-INFO\scripts.
And edit this:

#!C:\Python27\python.exe
# EASY-INSTALL-SCRIPT: 'plip==1.3.3','plipcmd'
__requires__ = 'plip==1.3.3'
__import__('pkg_resources').run_script('plip==1.3.3', 'plipcmd.py')

in plipcmd.py in C:\Python27\Scripts
It's worked like charmed for my all core, no error showed, but when I checked the result folder, I did not find the .pse and .png files. What should I do to solve the problem?
Thanks
Environment: OS Windows 7 64bit with Python 2.7 64bit

@o7o o7o closed this as completed Jan 4, 2017
@o7o o7o reopened this Jan 4, 2017
@ssalentin
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With which parameters did you run PLIP?

@o7o
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o7o commented Jan 14, 2017 •
edited

all as -vtxyp

v=verbose
t=report in txt
x=report in xml
y=pymol session
p=image
CMIIW

@ssalentin
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Sounds like a problem with PyMOL then. Please start in debug mode (--debug) and post the output here.

@o7o
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o7o commented Jan 21, 2017 •
edited

here the debug result for multicore:

Run PLIP

**********************************************
* Protein-Ligand Interaction Profiler v1.3.3 *
**********************************************

Starting analysis of 1bju.pdb
===============================
13 lines automatically fixed in PDB input file.
[EXPERIMENTAL] Input is PDBQT file. Some features (especially visualization) mig
ht not work as expected. Please consider using PDB format instead.
PDB structure successfully read.
Debug:  Pymol Name set as: '1bju'
Debug:  4 ligand(s) after first filtering step.
Debug:  Finalizing extraction for ligand GP6:A:910
Debug:  Number of isomorphisms: 8
Debug:  Finalizing extraction for ligand SO4:A:901
Debug:  Number of isomorphisms: 24
Debug:  Finalizing extraction for ligand DMS:A:300
Debug:  Number of isomorphisms: 4
Debug:  Finalizing extraction for ligand CA:A:246
Debug:  Number of isomorphisms: 1
Analyzing 4 ligands...

GP6 [SMALLMOLECULE] -- GP6:A:910
---------------------------------
Debug:  Number of aromatic ring candidates: 2
  Contains 2 aromatic ring(s).
  Binding site atoms in vicinity (7.5 A max. dist: 164).
Debug:  Number of aromatic ring candidates: 34
  Reduced number of hydrophobic contacts from 2 to 1.
  Ligand interacts with 6 binding site residue(s) in chain(s) A.
  Complex uses 6 hydrogen bond(s), 1 pi-stacking(s), 1 water bridge(s).

SO4 [SMALLMOLECULE] -- SO4:A:901
---------------------------------
  Info:  may be biologically irrelevant
Debug:  Number of aromatic ring candidates: 0
  Binding site atoms in vicinity (7.5 A max. dist: 62).
Debug:  Number of aromatic ring candidates: 34
  Ligand interacts with 3 binding site residue(s) in chain(s) A.
  Complex uses 1 salt bridge(s), 2 hydrogen bond(s).

DMS [SMALLMOLECULE] -- DMS:A:300
---------------------------------
  Info:  may be biologically irrelevant
Debug:  Number of aromatic ring candidates: 0
  Binding site atoms in vicinity (7.5 A max. dist: 58).
Debug:  Number of aromatic ring candidates: 34
  Ligand interacts with 1 binding site residue(s) in chain(s) A.
  Complex uses 1 hydrogen bond(s).

CA [ION] -- CA:A:246
---------------------
Debug:  Number of aromatic ring candidates: 0
  Binding site atoms in vicinity (7.5 A max. dist: 71).
Debug:  Number of aromatic ring candidates: 34
  Ligand interacts with 1 binding site residue(s) in chain(s) A.

Generating visualizations in parallel on 4 cores ...
Finished analysis. Find the result files in bju1/

Press any key to continue . . .

and here the result for maxthreads activated:

Run PLIP

**********************************************
* Protein-Ligand Interaction Profiler v1.3.3 *
**********************************************

Starting analysis of 1bju.pdb
===============================
13 lines automatically fixed in PDB input file.
[EXPERIMENTAL] Input is PDBQT file. Some features (especially visualization) mig
ht not work as expected. Please consider using PDB format instead.
PDB structure successfully read.
Debug:  Pymol Name set as: '1bju'
Debug:  4 ligand(s) after first filtering step.
Debug:  Finalizing extraction for ligand GP6:A:910
Debug:  Number of isomorphisms: 8
Debug:  Finalizing extraction for ligand SO4:A:901
Debug:  Number of isomorphisms: 24
Debug:  Finalizing extraction for ligand DMS:A:300
Debug:  Number of isomorphisms: 4
Debug:  Finalizing extraction for ligand CA:A:246
Debug:  Number of isomorphisms: 1
Analyzing 4 ligands...

GP6 [SMALLMOLECULE] -- GP6:A:910
---------------------------------
Debug:  Number of aromatic ring candidates: 2
  Contains 2 aromatic ring(s).
  Binding site atoms in vicinity (7.5 A max. dist: 164).
Debug:  Number of aromatic ring candidates: 34
  Reduced number of hydrophobic contacts from 2 to 1.
  Ligand interacts with 6 binding site residue(s) in chain(s) A.
  Complex uses 6 hydrogen bond(s), 1 pi-stacking(s), 1 water bridge(s).

SO4 [SMALLMOLECULE] -- SO4:A:901
---------------------------------
  Info:  may be biologically irrelevant
Debug:  Number of aromatic ring candidates: 0
  Binding site atoms in vicinity (7.5 A max. dist: 62).
Debug:  Number of aromatic ring candidates: 34
  Ligand interacts with 3 binding site residue(s) in chain(s) A.
  Complex uses 1 salt bridge(s), 2 hydrogen bond(s).

DMS [SMALLMOLECULE] -- DMS:A:300
---------------------------------
  Info:  may be biologically irrelevant
Debug:  Number of aromatic ring candidates: 0
  Binding site atoms in vicinity (7.5 A max. dist: 58).
Debug:  Number of aromatic ring candidates: 34
  Ligand interacts with 1 binding site residue(s) in chain(s) A.
  Complex uses 1 hydrogen bond(s).

CA [ION] -- CA:A:246
---------------------
Debug:  Number of aromatic ring candidates: 0
  Binding site atoms in vicinity (7.5 A max. dist: 71).
Debug:  Number of aromatic ring candidates: 34
  Ligand interacts with 1 binding site residue(s) in chain(s) A.
Debug:  Setting current_name to "plipfixed.1bju_cqquyh" and pdbid to "1bju
"Debug:  Selecting ligand for PDBID 1bju and ligand name Ligand_CA with: Debug:
 resn CA and chain A and resi 246* Executive: object "1bjuCartoon" created.
 Executive: object 1bjuCartoon created.
PyMOL>viewport 1200,800
PyMOL>import os
PyMOL>os.environ['NRGSUITE_INSTALLATION'] = "C:\Program Files\NRGsuite"
Imagemagick not available. Images will not be resized or cropped.
Debug:  Setting current_name to "plipfixed.1bju_cqquyh" and pdbid to "1bju
"Debug:  Selecting ligand for PDBID 1bju and ligand name Ligand_DMS with: Debug:
  resn DMS and chain A and resi 300* Executive: object "1bjuCartoon" created.
 Executive: object 1bjuCartoon created.
PyMOL>viewport 1200,800
Imagemagick not available. Images will not be resized or cropped.
Debug:  Setting current_name to "plipfixed.1bju_cqquyh" and pdbid to "1bju
"Debug:  Selecting ligand for PDBID 1bju and ligand name Ligand_GP6 with: Debug:
  resn GP6 and chain A and resi 910* Executive: object "1bjuCartoon" created.
 Executive: object 1bjuCartoon created.
PyMOL>viewport 1200,800
Imagemagick not available. Images will not be resized or cropped.
Debug:  Setting current_name to "plipfixed.1bju_cqquyh" and pdbid to "1bju
"Debug:  Selecting ligand for PDBID 1bju and ligand name Ligand_SO4 with: Debug:
  resn SO4 and chain A and resi 901* Executive: object "1bjuCartoon" created.
 Executive: object 1bjuCartoon created.
PyMOL>viewport 1200,800

Finished analysis. Find the result files in bju/

Press any key to continue . . .

Noted. I have installed both version of ImageMagick-7.0.3-10-Q16-x**-dll in my system.

Thanks

@ssalentin
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Thanks. From the log, I can't see a problem. Is the outputfolder (bju1/ or bju/) completely empty in both cases?

@o7o
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o7o commented Jan 24, 2017

Like as I said at first, I got all files of result (-txyp-) at bju folder when I enable maxthreads to 1 (only 1 core). Otherwise, when I used "all" core (more than 1, of course), I just got two kind of files, txt and xml at bju1 folder, there were no .png and .pse.

Any way, thanks for your time and support for this case. I hope, in the future, plip will be running multicore in windows environment.

@ssalentin
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Okay, thank you again for the clarification. There are some differences in the fork modules of Unix and Windows systems. We will look into the problem for a future release. I will leave the issue open until then.

@o7o
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o7o commented May 31, 2017 •
edited

Hi again Salentin,
I am glad, PLIP version 1.3.4(b) has been released. For your info, I have installed and tested it in my PC, but it is still not working in multi core
My System: Windows 7 64bit, Python 2.7.13 64bit, PyMOL 1.8.6.1, OpenBabel 2.4.1
Thanks

@ssalentin ssalentin mentioned this issue Jan 3, 2018
Closed
ssalentin pushed a commit that referenced this issue Aug 7, 2018
Merge pull request #5 from lkagami/lkagami-4
8237ddd 
Add "include_package_data"
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@o7o @ssalentin