CFD Online Discussion Forums - [OpenFOAM] Paraview Free/Delete all memory

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Paraview Free/Delete all memory

Hello,

I am encountering some difficulties to remove all the data from paraview.
After loading several time steps of a pvd files (Multi-Block Data) using a python script, the pc runs out of memory and paraview crashes. However, after each time steps, I delete all the variables with instructions "Delete(var)" and "del var".
It is the same problem if I do a Edit/Delete all, I still have the memory used according to the Memory inspector "client"...
The only way I see to free the memory is to kill the process paraview from a terminal or to kill the client in the memory inspector. Nevertheless, this also closes paraview.

Does someone knows how to delete all the memory between the first time-step and the second load? Maybe there is a way using server connections.
My idea would be :
1) create a connection.
2) load the data and run a job.
3) close the server before reopening a new one to compute the second load...

Do you have a solution, suggestions or other ideas?
Have a good day,
Eric

Greetings Eric,

I know that ParaView is known to have memory leaking problems, but last reports I've seen indicate that ParaView 3.98.0 no longer has this problem... it's here: http://www.cfd-online.com/Forums/ope...ls-my-ram.html

Best regards,
Bruno

Dear Bruno,
Thank you a lot for your comment. Indeed, I read that too and I am currently using this version of paraview (3.98) because of this problem and because it has additional export possibilities in vectorial format...

Nevertheless, I still get memory leaking problems with this version. Maybe because I am controlling paraview from python scripts... In fact, I am using scripts because I did not find some capabilities like saving automatically contours in new vtk files using filters, or computing and saving computed area of surfaces or volumes but I know how to do that using scripts...

Thanks again and best regards,
Eric

Dear Foamers,

this discussion is a little old, but maybe somebody may still be interested in the topic.

I'm using Paraview 4.1.0 (the version that comes with OF 2.4.0) and I'm trying to export in batch some data (from vtk files to csv files) using pvpython.

The script loops over some 1000s of files in several directories and after 6000-7000 files a memory leak error happens, which is quite annoying considering that I'm using a 32 GB workstation...:(

In the script loop I delete all the objects I generated within a single loop instance to try free memory but this doesn't help.

Has anybody found a solution to this memory leak issue?
Thanks and Best Regards
Cristian

Quick answer: Without example code for reproducing the same error, it's pretty hard to try and diagnose the issue. Either way, have you seen this answer: http://stackoverflow.com/a/26514796 ?

Dear wyldckat,

thanks for your reply.

I was already aware of the solution proposed in the link you posted. I actually found it on the main Paraview wiki: http://www.paraview.org/Wiki/ParaView/Python_Scripting

I am not a python expert and maybe I made some mistakes with the Delete() and del functions. I here report my script (I hope I am doing it in the right way):

Code:

#Script used to export csv from vtk datafiles

import fnmatch

import os

import sys

import re

from paraview.simple import *

#servermanager.Connect()



# Directories where to run

#dirs = ["01mm", "02mm", "03mm", "04mm", "05mm"]

dirs = ["01mm"]



# VTK file names

rhoBasename = "rho_sampleSurf_"  

rhoOutName =  "rho_coord."          



# Generate the list of files on which to operate

# and the corresponding output csv names

files = []

for dd in dirs:

    for ff in os.listdir("./"+dd):

        if fnmatch.fnmatch(ff, rhoBasename+"*"):

            nameRead = "./" + dd + "/" + ff

            numb = (re.findall("\d+", nameRead))[1]

            nameWrite = "./" + dd + "/" + rhoOutName + numb + ".csv"

            files.append([nameRead,nameWrite])



#print files

#sys.exit()





print "Start export"

zz = 1

for ff in files:

    if (zz%1000==0):

        print "written " + str(zz) + " csv files\n"

    # Open the correct file

    reader = OpenDataFile(ff[0])

    # Apply filters to it

    pd2cd = PointDatatoCellData(Input = reader)

    cc = CellCenters(Input = pd2cd)

    # Prepare the output name



    # Write the file

    writer = CreateWriter(ff[1], cc)

    # NO NEED IF LOOP DONE EXPLICITLY writer.WriteAllTimeSteps = 1

    writer.FieldAssociation = "Points"

    writer.UpdatePipeline()



    # Delete the generated objects

    del writer

    cc.Input = []

    Delete(cc)

    del cc

    pd2cd.Input = []

    Delete(pd2cd)

    del pd2cd

    Delete(reader)

    del reader



    zz += 1



print "Export completed"

I run the script by using "pvpython script.py" without any particular option.

Thanks for the help,
Best Regards,
Cristian

Hi Cristian,

Probably a better way to loop over files is to first build the pipeline and then only change the reader's and writer's filenames. Here is an example script:

Code:

reader = OpenDataFile(files[0][0])

pd2cd = PointDatatoCellData(Input = reader)

cc = CellCenters(Input = pd2cd)

writer = CreateWriter(files[0][1], cc)

writer.FieldAssociation = "Points"

for ff in files:     

   reader.FileNames = ff[0]

   writer.FileName = ff[1]

   writer.UpdatePipeline()

Now you don't have to worry about deleting the filters because you are using same filters all the time.

-Mikko

Dear Mikko,

Thanks for your suggestion.

Your snippet made my day! :)

Now paraview doesn't leak memory while the script is running!.

Maybe creating / deleting a reader and a writer at any loop instance (as I used to do) made paraview leaving some garbage in memory...

I report here the new version of the script since maybe it could be useful to others having similar needs/issues:

Code:

#Script used to export csv from rho datafiles

import fnmatch

import os

import sys

import re

from paraview.simple import *



# Directories where to run

dirs = ["01mm", "02mm", "03mm", "04mm", "05mm"]



# File rho names

rhoBasename = "rho_sampleSurf_"     #rho_sampleSurf_2576.vtk 

rhoOutName =  "rho_coord."          #rho_coord.550.csv



# Generate the list of files on which to operate

# and the corresponding output csv names

files = []

for dd in dirs:

    for ff in os.listdir("./"+dd):

        if fnmatch.fnmatch(ff, rhoBasename+"*"):

            nameRead = "./" + dd + "/" + ff

            numb = (re.findall("\d+", nameRead))[1]

            nameWrite = "./" + dd + "/" + rhoOutName + numb + ".csv"

            files.append([nameRead,nameWrite])



print "Start export"



# Generate the export pipeline

reader = OpenDataFile(files[0][0])

pd2cd = PointDatatoCellData(Input = reader)

cc = CellCenters(Input = pd2cd)

writer = CreateWriter(files[0][1], cc)

writer.FieldAssociation = "Points"



# Processed files counter

zz = 1



for ff in files:

    # Print out the counter value from time to time

    if (zz%1000==0):

        print "written " + str(zz) + " csv files\n"



    # Update the pipeline and write the csv file

    reader.FileNames = ff[0]

    writer.FileName = ff[1]

    writer.UpdatePipeline()



    # Update counter

    zz += 1



print "Export completed"

Thanks again,
Best regards,
Cristian

I'm glad that it worked. :)

I just wanted to add that I think Paraview is not leaking because I've made same kind of loops with big datasets and for many files. I think you are not deleting the writer. Thus at the end of your loop you should delete all the sources in inverse order than generating them:

Code:

    # Delete the generated objects     

   Delete(writer)     

   Delete(cc)     

   Delete(pd2cd)

   Delete(reader)

If you are deleting all the filters like in your case, you can also:

Code:

for key, value in GetSources().items():

   Delete(value)

   print 'Deleted:', key, value

Dear Mikko,

Thanks again for your reply.

I actually tried several combination of del / Delete() deleting the pipeline objects in reverse order, but without success.

In particular paraview complained for the "Delete(writer)" line...
You can see an attempt of that in my second post where I just do "del writer"

Probably I made some mistakes somewhere....

I anyway prefer the solution you posted since changing with a loop the reader input seems to me more clever and efficient rather than creating/deleting the reader at every time.

I actually wasn't aware of that possibility...good to know for my next scripts :)

Thanks and Best Regards,
Cristian