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Amber-MD / pytraj

Python interface of cpptraj
https://amber-md.github.io/pytraj
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mindist stops working when called multiple times #1572

Closed hherce closed 3 years ago

hherce commented 3 years ago

I am using a for loop to analyze a the minimum distance of a series of individual atoms to a group. I am doing it in the following manner:

alldist = []
for j in range(40):
    dist = []
    frame_indices = [j]
    traj0 = pt.load('tmp.trr', 'tmp.pdb', frame_indices=frame_indices)
    for i in resatoms:
        dist.append(pt.mindist(traj0,':RES&@'+i+' @1-242')[0])
    alldist.append(dist)

It runs fine until the loop reaches 21 frames (j=21) and gets stuck there. The problem is specifically with pt.mindist. I could stop the calculation and try to run again the distances for j=1 and it wont do it, I need to restart python for mindist to work again. I also run j=21 just to be sure that there is nothing wrong with the trajectory itself. Is it possible that mindist contains a variable that keeps increasing with each iteration of the function and this ends up saturating my computer memory? I would also appreciate if you could let me know a way around it while you fix the code. Thanks! Henry

hherce commented 3 years ago

I am almost sure that it is a memory issue, if I reduce the number of atoms in resatoms by half, the loop hangs now in frame 35.

hainm commented 3 years ago

thanks @hherce for your report. I can reproduce the issue with below code (to use pytraj's data):

import pytraj as pt

alldist = []
resatoms = range(10) # works fine with range(8)

for j in range(40):
    dist = []
    frame_indices = [j]
    traj0 = pt.load('tz2.nc', 'tz2.parm7', frame_indices=frame_indices)
    for i in resatoms:
        dist.append(pt.mindist(traj0,':2 :3')[0])
    alldist.append(dist)

print(alldist)
hainm commented 3 years ago

I am investigating now.

hherce commented 3 years ago

Awesome! just let me know if you have any questions. Thanks! Henry

From: Hai Nguyen notifications@github.com Sent: Tuesday, February 9, 2021 11:40 PM To: Amber-MD/pytraj pytraj@noreply.github.com Cc: Herce, Henry D. Henry_Herce@DFCI.HARVARD.EDU; Mention mention@noreply.github.com Subject: Re: [Amber-MD/pytraj] mindist stops working when called multiple times (#1572)

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I am investigating now.

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hainm commented 3 years ago

@hherce Please turn off the capture_stdout, which is problematic:

import pytraj as pt
from contextlib import contextmanager

class Dummy:
    def __enter__(self):
        return self

    def __exit__(self):
        return

    def read(self):
        return ""

@contextmanager
def mock_capture():
    yield Dummy(), ""

pt.analysis.c_action.capture_stdout = mock_capture

alldist = []
resatoms = range(40)

for j in range(40):
    dist = []
    frame_indices = [j]
    traj0 = pt.load('tz2.nc', 'tz2.parm7', frame_indices=frame_indices)
    for i in resatoms:
        dist.append(pt.mindist(traj0,':2 :3')[0])
    alldist.append(dist)

print(alldist)

Related issues:

  1. https://github.com/Amber-MD/pytraj/issues/1498#issuecomment-558360392
  2. https://github.com/Amber-MD/pytraj/issues/1569
hherce commented 3 years ago

Great! Thanks so much! It seems that is working now and I would have never figured out a way around this. Thanks again and best regards, Henry

From: Hai Nguyen notifications@github.com Sent: Tuesday, February 9, 2021 11:55 PM To: Amber-MD/pytraj pytraj@noreply.github.com Cc: Herce, Henry D. Henry_Herce@DFCI.HARVARD.EDU; Mention mention@noreply.github.com Subject: Re: [Amber-MD/pytraj] mindist stops working when called multiple times (#1572)

    External Email - Use Caution

@hhercehttps://secure-web.cisco.com/1d39ahEo-ykQCNMwK8HwjWmfYEwGI2yVQq8jAFPqlb888SfSHIqlvomi8c3RXd1j8CcLgx7Vr867pfDfxkQzrgBxoBTyfyjlL74H_y-NqTDB_4f-7Bn34T3pCbHvDEP-eRuNJCijyUT-z7L3uDQOBzrzqFcXEEgmccWSICBupl-QvAXnxzmDec1jWQM2cmZqZwC1bkcYsBmIBI9ECvewjRNacWZGsFcsG8-Z8yQ6Nb1wKCzXOTF_Pk7VxyPvkKctf/https%3A%2F%2Fgithub.com%2Fhherce Please turn off the capture_stdout, which is problematic:

import pytraj as pt

from contextlib import contextmanager

class Dummy:

def __enter__(self):

    return self

def __exit__(self):

    return

def read(self):

    return ""

@contextmanager

def mock_capture():

yield Dummy(), ""

pt.analysis.c_action.capture_stdout = mock_capture

alldist = []

resatoms = range(40)

for j in range(40):

dist = []

frame_indices = [j]

traj0 = pt.load('tz2.nc', 'tz2.parm7', frame_indices=frame_indices)

for i in resatoms:

    dist.append(pt.mindist(traj0,':2 :3')[0])

alldist.append(dist)

print(alldist)

Related issues:

  1. 1498 (comment)https://secure-web.cisco.com/1DEVWSHsqnonSx4nm9YJFSP42B4hIzcNVPl8Mcu4FbrQ5WCnf9ouOvva_kVN4LzW_e8H1joFOEkjxCclMdEXwTlLmMXF7kN0gN84P2MVgJKVb-ypdxr26ACAMWyVDHokT9ye7oUYT140qb-kDwRPxQ9JdUEuue146mOnpWOE42H43uReGef3h66BO4bWW0aBLFIZMnKaIPQF7iY45GHLJZrtQmEY-jvEivc9batVWNR94YISG8DZFwv7VibvRJzJW/https%3A%2F%2Fgithub.com%2FAmber-MD%2Fpytraj%2Fissues%2F1498%23issuecomment-558360392

  2. 1569https://secure-web.cisco.com/1E97pQ0ngdFa_HJkxaO3osuejGpVJKenSNoWa16-AcL0NJn-FECiF0hCsrghwW-MNItzp7p_YZ5oA_hPnwZMsSweTekFJ_i43L_5et4QopxkL0UNszJpDzojKl2Zych1DS6YntYD9ozDmpk2fajifocXq_u4C_WDiq0PieOLreAXPIi2X6DIy8z3iHKYexhoTh7p0F9oJA_0LWZJtcwTWAWhzqvUOFTZ35dm7WQ8vOFJdYtWKG_1Y3e0xsNPY6ytN/https%3A%2F%2Fgithub.com%2FAmber-MD%2Fpytraj%2Fissues%2F1569

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