Core dump revisited
Sheldon
shejo284 at gmail.com
Sun Dec 17 05:01:12 EST 2006
Hi,
I have a python script that uses a C extention. I keep getting a
recurring problem that causes a core dump a few lines after the C
extention return data back tp python. I tried using pbd and gdb but I
have not succeeded in understanding what went wrong and where. I post
the python script here is the error message and gdb output after
reading the core file:
..... printout from with C extention....
Completed freeing 2D arrays.
Now freeing 1D arrays
freed 1D arrays
freeing 15km arrays
Complete
Returning data back to Python!
In python: assigning tuple data to numeric arrays!
Time to do the coastal effects
Segmentation fault (core dumped)
......
Now there next step after "Time to do the coastal effects" was never
executed. And even if I put another print statement there the same
thing happens. I am using python 2.3 and I have set my stacksize to
unlimited. When reading the core dump file with gdb I get:
gdb msgppscomp.py core.3203
GNU gdb 6.0-2mdk (Mandrake Linux)
Copyright 2003 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and
you are
welcome to change it and/or distribute copies of it under certain
conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB. Type "show warranty" for
details.
This GDB was configured as
"i586-mandrake-linux-gnu"..."/data/proj_ns1/safworks/sheldon/msgppscomp.py":
not in executable format: File format not recognized
Core was generated by `python msgppscomp.py'.
Program terminated with signal 11, Segmentation fault.
#0 0x40079dfa in ?? ()
(gdb)
.................
I am not very familiar with using gdb with python and C extentions. I
would like to get some ideas about where the problem might be. I have
made sure that all the arrays in the C extention are freed before
exiting so I doubt that this might be the problem. Here is the python
script:
#!/usr/bin/env python
#!-*-coding: UTF-8 -*-
class WriteHdfFile:
def __init__(self,outfile):
self.outfile = outfile
self.COMPRESS_LVL = 6
def writeAreainfo(self):
import _pyhl
import sys
sys.float_output_precision = 2
aList = _pyhl.nodelist()
aNode = _pyhl.node(_pyhl.GROUP_ID,"/PPS_MSG_COMP")
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/LAT")
aNode.setArrayValue(1,lat.shape,lat,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/LON")
aNode.setArrayValue(1,lon.shape,lon,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/VALCONCEN")
aNode.setArrayValue(1,valconcen.shape,valconcen,"int",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/LIGHTCON")
aNode.setArrayValue(1,lightcon.shape,lightcon,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/BIAS100")
aNode.setArrayValue(1,bias100.shape,bias100,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/BIAS75")
aNode.setArrayValue(1,bias75.shape,bias75,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/BIAS50")
aNode.setArrayValue(1,bias50.shape,bias50,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/BIAS25")
aNode.setArrayValue(1,bias25.shape,bias25,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/COAST")
aNode.setArrayValue(1,coast.shape,coast,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/STATISTICS")
aNode.setArrayValue(1,stats.shape,stats,"int",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/PERCENTAGE")
aNode.setArrayValue(1,percentage.shape,percentage,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/VA_vs_BIAS")
aNode.setArrayValue(1,va_area.shape,va_area,"float",-1)
aList.addNode(aNode)
aNode=_pyhl.node(_pyhl.DATASET_ID,"/VANUM")
aNode.setArrayValue(1,vanum.shape,vanum,"float",-1)
aList.addNode(aNode)
aNode = _pyhl.node(_pyhl.ATTRIBUTE_ID,"/NSCENES")
aNode.setScalarValue(-1,areascenes,"int",-1)
aList.addNode(aNode)
aNode = _pyhl.node(_pyhl.ATTRIBUTE_ID,"/SATELLITE")
aNode.setScalarValue(-1,satid,"string",-1)
aList.addNode(aNode)
self.status = aList.write(self.outfile,self.COMPRESS_LVL)
return self.status
#---------------------------------------------------------------------------------------------------------------------------
if __name__ == "__main__":
from Numeric import *
import sys, os, string, math, glob
import msgppsarea,msgppscoast
import shelve
date = str(200510)
#date = sys.argv[1]
#s = sys.argv[2]
cp = 'cfc'
global
valconcen,bias100,bias75,lightcon,bias50,bias25,percentage,va_area,lat,lon
global stats,areascenes,satid,vanum,coast
valconcen = zeros((324,243),'i')
bias100 = zeros((324,243),'f')
bias75 = zeros((324,243),'f')
lightcon = zeros((324,243),'f')
bias50 = zeros((324,243),'f')
bias25 = zeros((324,243),'f')
coast = zeros((324,243),'f')
percentage = zeros((60,1),'f')
va_area = zeros((90,1),'f')
vanum = zeros((90,1),'f')
lat = zeros((324,243),'f')
lon = zeros((324,243),'f')
stats = zeros((60,1), 'i')
d =
shelve.open("/data/proj/safworks/sheldon/MSG_PPS_COMP/c_codes/"+"_"+date+".shelve")
msglist = d["Area.msglist"]
tilescenes = d["Area.tilescenes"]
tiles = d["Area.tiles"]
ppslist = d["Area.ppslist"]
lllist = d["Area.lllist"]
areascenes = d["Area.areascenes"]
d.close()
print "Deleting file pointer and calling C function"
RES =
msgppsarea.msgppsarea(tilescenes,tiles,msglist,ppslist,lllist,int(date),areascenes)
print "In python: assigning tuple data to numeric arrays!"
for x in range(324):
bias100[x] = (RES[0])[x*243:x*243+243]
bias75[x] = (RES[1])[x*243:x*243+243]
bias50[x] = (RES[2])[x*243:x*243+243]
bias25[x] = (RES[3])[x*243:x*243+243]
lat[x] = (RES[4])[x*243:x*243+243]
lon[x] = (RES[5])[x*243:x*243+243]
lightcon[x] = (RES[6])[x*243:x*243+243]
valconcen[x] = (RES[7])[x*243:x*243+243]
for x in range(90):
va_area[x] = (RES[10])[x]
vanum[x] = (RES[11])[x]
for x in range(60):
stats[x] = (RES[8])[x]
percentage[x] = (RES[9])[x]
print "Time to do the coastal effects"
RES = msgppscoast.msgppscoast(ravel(bias100),tiles)
for x in range(324):
coast[x] = (RES[0])[x*243:x*243+243]
outfile =
"/data/proj/safworks/sheldon/MSG_PPS_COMP/results/"+'CFC'+'_'+ '_' +
date + '.h5'
print outfile
chk = WriteHdfFile(outfile)
res = chk.writeAreainfo()
print "File written!"
print "Complete!"
********************************
The C extention is very large so I will include it if anyone wants to
see it.
Thanks for any advice,
Sheldon
More information about the Python-list
mailing list