python - Memory Leak in Matplotlib save fig with PDFPages -


edit: update

i used objgraph print out back reference graphs 'reference' items appeared in memory leak. seems pdfpages holding onto of images iterate thorough them , save them each page (so perhaps inherent pdfpages module). think i'm going modify code write small pdf file on each iteration , use pypdf merge these files desired larger pdf file.

edit: running python 2.7.3 matplotlib 1.3.1. have tried printing out gc.garbage, returns empty list, doesn't appear there uncollectable objects. have tried using both pdf , agg backends, memory leak still present in both of these. tried closing axes (ax1 , cbaxes1) , explicitly using del on of variables (which had effect of removing +3 list after closing increasing +2 list after saving +5 list).

i trying create multiple heatmaps via pcolormesh , save them single page in pdf , repeat process create multiple pages figures in pdf file (i've dropped down 1 figure per page sake of example).

there seems memory leak occurring savefig function, seems small @ first, adds want able save large pdf files.

import matplotlib matplotlib.use('agg') import matplotlib.pyplot plt matplotlib.backends.backend_pdf import pdfpages matplotlib import gridspec matplotlib.backends.backend_agg import figurecanvasagg figurecanvas import numpy np  import resource import gc import objgraph  def plotfunction(i,pdf):      fig = plt.figure()     fig.set_figheight(25)     fig.set_figwidth(64)      gs = gridspec.gridspec(1,2)     ax1 = plt.subplot(gs[0],rasterized=true)      heatmap1 = ax1.pcolormesh(np.random.uniform(size=(10,10)))      cbaxes1 = plt.subplot(gs[1],rasterized=true)      cb1 = plt.colorbar(heatmap1, cax= cbaxes1, use_gridspec = true)      gc.collect()      print 'memory growth before savefig  {round}: %s ({mb} mb)' .format(round=i,mb=resource.getrusage(resource.rusage_self).ru_maxrss/1024/1024) % resource.getrusage(resource.rusage_self).ru_maxrss     objgraph.show_growth()      pdf.savefig(fig) # memory leak seems occur here      gc.collect()      print 'memory growth after savefig  {round}: %s ({mb} mb)' .format(round=i,mb=resource.getrusage(resource.rusage_self).ru_maxrss/1024/1024) % resource.getrusage(resource.rusage_self).ru_maxrss     objgraph.show_growth()      fig.clf()     plt.close(fig)     plt.close('all')     gc.collect()      print 'memory growth after closing  {round}: %s ({mb} mb)' .format(round=i,mb=resource.getrusage(resource.rusage_self).ru_maxrss/1024/1024) % resource.getrusage(resource.rusage_self).ru_maxrss     objgraph.show_growth()   def main():      pdf = pdfpages('output.pdf')     in range(15):         plotfunction(i,pdf)         print 'memory growth outside function {round}: %s ({mb} mb)' .format(round=i,mb=resource.getrusage(resource.rusage_self).ru_maxrss/1024/1024) % resource.getrusage(resource.rusage_self).ru_maxrss         gc.collect()         objgraph.show_growth()     pdf.close()  if __name__ == "__main__":      main()

here's output showing memory leak:

memory growth before savefig  7: 877674496 (837 mb) memory growth after savefig  7: 988385280 (942 mb) reference       32        +3 list          1839        +2 name            16        +2 tuple         2384        +2 memory growth after closing  7: 988385280 (942 mb) list     1842        +3 memory growth outside function 7: 988385280 (942 mb) memory growth before savefig  8: 988651520 (942 mb) memory growth after savefig  8: 1099231232 (1048 mb) reference       35        +3 list          1844        +2 name            18        +2 tuple         2386        +2 memory growth after closing  8: 1099231232 (1048 mb) list     1847        +3 memory growth outside function 8: 1099231232 (1048 mb)

i have tried using multiprocessing, avoiding pyplot, , moving save function suggested in other posts, none of these solutions have solved memory leak problem.

thanks.


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