Description
Hi,
I've got this error while trying to run np.percentile on a series of images in a loop:
Python 2.7.6 (default, May 29 2014, 17:32:27)
[GCC Intel(R) C++ gcc 4.4 mode] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> from skimage.io import ImageCollection
>>> imc = ImageCollection('/share/experiments/ahm/projections/Block_1_*.tiff')
>>> for i in xrange(len(imc)):
... low, hi = np.percentile(imc[i],(0,98))
...
*** glibc detected *** python2.7: double free or corruption (out): 0x000000000379cf60 ***
======= Backtrace: =========
/lib64/libc.so.6[0x3d08876166]
/lib64/libc.so.6[0x3d08878ca3]
/usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so(+0x1c4fc)[0x7f9ffccb84fc]
/usr/local/lib/python2.7/site-packages/numpy/core/multiarray.so(+0x1cfdb)[0x7f9ffccb8fdb]
/usr/local/lib/libpython2.7.so.1.0(__PGOSF184_frame_dealloc+0x542)[0x7fa005221482]
/usr/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x1aa)[0x7fa005243bda]
/usr/local/lib/libpython2.7.so.1.0(__PGOSF292_function_call+0x4a)[0x7fa0051fe03a]
/usr/local/lib/libpython2.7.so.1.0(+0x115a9e)[0x7fa005184a9e]
/usr/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x6b56)[0x7fa00523f046]
/usr/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x180)[0x7fa005243bb0]
/usr/local/lib/libpython2.7.so.1.0(+0x1c789c)[0x7fa00523689c]
/usr/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1a10)[0x7fa005239f00]
/usr/local/lib/libpython2.7.so.1.0(PyEval_EvalCodeEx+0x180)[0x7fa005243bb0]
/usr/local/lib/libpython2.7.so.1.0(+0x1c789c)[0x7fa00523689c]
/usr/local/lib/libpython2.7.so.1.0(PyEval_EvalFrameEx+0x1a10)[0x7fa005239f00]
/usr/local/lib/libpython2.7.so.1.0(PyEval_EvalCode+0x147)[0x7fa0051756f7]
/usr/local/lib/libpython2.7.so.1.0(PyRun_InteractiveOneFlags+0x2c4)[0x7fa0051a62b4]
/usr/local/lib/libpython2.7.so.1.0(PyRun_InteractiveLoopFlags+0x143)[0x7fa0051a5f93]
/usr/local/lib/libpython2.7.so.1.0(PyRun_AnyFileExFlags+0x46)[0x7fa0051a57f6]
/usr/local/lib/libpython2.7.so.1.0(Py_Main+0x613)[0x7fa0051975e3]
python2.7(main+0x2f)[0x40088f]
/lib64/libc.so.6(__libc_start_main+0xfd)[0x3d0881ed1d]
python2.7[0x400799]
======= Memory map: ========
00400000-00401000 r-xp 00000000 fd:00 2490380 /usr/local/bin/python2.7
00600000-00601000 rw-p 00000000 fd:00 2490380 /usr/local/bin/python2.7
020c2000-03bbd000 rw-p 00000000 00:00 0 [heap]
31a5a00000-31a5a83000 r-xp 00000000 fd:00 2359299 /lib64/libm-2.12.so
31a5a83000-31a5c82000 ---p 00083000 fd:00 2359299 /lib64/libm-2.12.so
31a5c82000-31a5c83000 r--p 00082000 fd:00 2359299 /lib64/libm-2.12.so
31a5c83000-31a5c84000 rw-p 00083000 fd:00 2359299 /lib64/libm-2.12.so
322fa00000-322fae8000 r-xp 00000000 fd:00 2522823 /usr/lib64/libstdc++.so.6.0.13
322fae8000-322fce8000 ---p 000e8000 fd:00 2522823 /usr/lib64/libstdc++.so.6.0.13
322fce8000-322fcef000 r--p 000e8000 fd:00 2522823 /usr/lib64/libstdc++.so.6.0.13
322fcef000-322fcf1000 rw-p 000ef000 fd:00 2522823 /usr/lib64/libstdc++.so.6.0.13
322fcf1000-322fd06000 rw-p 00000000 00:00 0
3230200000-3230225000 r-xp 00000000 fd:00 2522830 /usr/lib64/libpng12.so.0.49.0
3230225000-3230425000 ---p 00025000 fd:00 2522830 /usr/lib64/libpng12.so.0.49.0
3230425000-3230426000 rw-p 00025000 fd:00 2522830 /usr/lib64/libpng12.so.0.49.0
3d08400000-3d08420000 r-xp 00000000 fd:00 2359322 /lib64/ld-2.12.so
3d0861f000-3d08620000 r--p 0001f000 fd:00 2359322 /lib64/ld-2.12.so
3d08620000-3d08621000 rw-p 00020000 fd:00 2359322 /lib64/ld-2.12.so
3d08621000-3d08622000 rw-p 00000000 00:00 0
3d08800000-3d0898b000 r-xp 00000000 fd:00 2359343 /lib64/libc-2.12.so
3d0898b000-3d08b8a000 ---p 0018b000 fd:00 2359343 /lib64/libc-2.12.so
3d08b8a000-3d08b8e000 r--p 0018a000 fd:00 2359343 /lib64/libc-2.12.so
3d08b8e000-3d08b8f000 rw-p 0018e000 fd:00 2359343 /lib64/libc-2.12.so
3d08b8f000-3d08b94000 rw-p 00000000 00:00 0
3d09000000-3d09017000 r-xp 00000000 fd:00 2359420 /lib64/libpthread-2.12.so
3d09017000-3d09217000 ---p 00017000 fd:00 2359420 /lib64/libpthread-2.12.so
3d09217000-3d09218000 r--p 00017000 fd:00 2359420 /lib64/libpthread-2.12.so
3d09218000-3d09219000 rw-p 00018000 fd:00 2359420 /lib64/libpthread-2.12.so
3d09219000-3d0921d000 rw-p 00000000 00:00 0
3d09400000-3d09402000 r-xp 00000000 fd:00 2359418 /lib64/libdl-2.12.so
3d09402000-3d09602000 ---p 00002000 fd:00 2359418 /lib64/libdl-2.12.so
3d09602000-3d09603000 r--p 00002000 fd:00 2359418 /lib64/libdl-2.12.so
3d09603000-3d09604000 rw-p 00003000 fd:00 2359418 /lib64/libdl-2.12.so
3d09800000-3d09815000 r-xp 00000000 fd:00 2359437 /lib64/libz.so.1.2.3
3d09815000-3d09a14000 ---p 00015000 fd:00 2359437 /lib64/libz.so.1.2.3
3d09a14000-3d09a15000 r--p 00014000 fd:00 2359437 /lib64/libz.so.1.2.3
3d09a15000-3d09a16000 rw-p 00015000 fd:00 2359437 /lib64/libz.so.1.2.3
3d0a000000-3d0a01d000 r-xp 00000000 fd:00 2359516 /lib64/libselinux.so.1
3d0a01d000-3d0a21c000 ---p 0001d000 fd:00 2359516 /lib64/libselinux.so.1
3d0a21c000-3d0a21d000 r--p 0001c000 fd:00 2359516 /lib64/libselinux.so.1
3d0a21d000-3d0a21e000 rw-p 0001d000 fd:00 2359516 /lib64/libselinux.so.1
3d0a21e000-3d0a21f000 rw-p 00000000 00:00 0
3d0a800000-3d0a816000 r-xp 00000000 fd:00 2359426 /lib64/libresolv-2.12.so
3d0a816000-3d0aa16000 ---p 00016000 fd:00 2359426 /lib64/libresolv-2.12.so
3d0aa16000-3d0aa17000 r--p 00016000 fd:00 2359426 /lib64/libresolv-2.12.so
3d0aa17000-3d0aa18000 rw-p 00017000 fd:00 2359426 /lib64/libresolv-2.12.so
3d0aa18000-3d0aa1a000 rw-p 00000000 00:00 0
3d0b000000-3d0b016000 r-xp 00000000 fd:00 2359411 /lib64/libgcc_s-4.4.7-20120601.so.1
3d0b016000-3d0b215000 ---p 00016000 fd:00 2359411 /lib64/libgcc_s-4.4.7-20120601.so.1
3d0b215000-3d0b216000 rw-p 00015000 fd:00 2359411 /lib64/libgcc_s-4.4.7-20120601.so.1
3d0bc00000-3d0bc03000 r-xp 00000000 fd:00 2359710 /lib64/libcom_err.so.2.1
3d0bc03000-3d0be02000 ---p 00003000 fd:00 2359710 /lib64/libcom_err.so.2.1
3d0be02000-3d0be03000 r--p 00002000 fd:00 2359710 /lib64/libcom_err.so.2.1
3d0be03000-3d0be04000 rw-p 00003000 fd:00 2359710 /lib64/libcom_err.so.2.1Aborted (core dumped)
So I tried running it in different ways:
Python 2.7.6 (default, May 29 2014, 17:32:27)
[GCC Intel(R) C++ gcc 4.4 mode] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> from skimage.io import ImageCollection
>>> imc = ImageCollection('/share/experiments/ahm/projections/Block_1_*.tiff')
>>> for i in xrange(len(imc)):
... low = np.percentile(imc[i],0)
... hi = np.percentile(imc[i],98)
...
*** glibc detected *** python2.7: double free or corruption (out): 0x0000000003525120 ***
But, I have no problem in running it outside loop:
Python 2.7.6 (default, May 29 2014, 17:32:27)
[GCC Intel(R) C++ gcc 4.4 mode] on linux2
Type "help", "copyright", "credits" or "license" for more information.
>>> import numpy as np
>>> from skimage.io import ImageCollection
>>> imc=ImageCollection('/share/experiments/ahm/projections/Block_1_*.tiff')
>>> low, hi = np.percentile(imc[0],(0,98))
>>> low
13783.0
>>> hi
23991.0
It's just when I used np.percentile in loop then things got messy. I used numpy 1.9.0.dev-c24cc4e in this case, but on my other machine with numpy 1.8.0 has no problem at all.
Best regards,
Habib