Open gnthibault opened 8 years ago
Do you still get the segfault when you use libtiff from our conda repos?
conda install libtiff
You'll probably need to remove your custom-compiled version of libtiff.
Thank you for your answer, I receive [SSL: CERTIFICATE_VERIFY_FAILED] when trying to use conda, how can I overcome that problem, I would like to disable ssl certificate checking ?
EDIT: ok the faq covers this problem: https://docs.continuum.io/anaconda-repository/faq
And... the result is exactly the same, importing libtiff generates a segmentation fault on my setup, and gdb reveals that the segfault arise in the same place than previously.
I encounter the same problem with linux conda 3.14.1
platform : linux-64
conda version : 3.14.1
conda-build version : 1.14.1
python version : 2.7.10.final.0
requests version : 2.7.0
root environment : /software/2015/x86_64/anaconda/2.3.0 (read only)
default environment : /mnt/lib/python2.7/conda/envs/safl
envs directories : /home/nemesa/.conda/envs
/home/nemesa/envs
/software/2015/x86_64/anaconda/2.3.0/envs
package cache : /home/nemesa/.conda/envs/.pkgs
/home/nemesa/envs/.pkgs
/software/2015/x86_64/anaconda/2.3.0/pkgs
channel URLs : https://repo.continuum.io/pkgs/free/linux-64/
https://repo.continuum.io/pkgs/free/noarch/
https://repo.continuum.io/pkgs/pro/linux-64/
https://repo.continuum.io/pkgs/pro/noarch/
config file : None
is foreign system : False
with a python2.7.12 install with latest numpy=1.11.1 libtiff=0.4.4
(gdb) r -c "import libtiff"
Starting program: /bin/python -c "import libtiff"
[Thread debugging using libthread_db enabled]
Missing separate debuginfo for /mnt/lib/python2.7/site-packages/numpy/core/../../../../libiomp5.so
Detaching after fork from child process 28514.
Program received signal SIGSEGV, Segmentation fault.
0x00007ffff1211e20 in PyArray_API ()
from /mnt/lib/python2.7/site-packages/numpy/core/multiarray.so
Missing separate debuginfos, use: debuginfo-install glibc-2.12-1.166.el6_7.7.x86_64 libgcc-4.4.7-11.el6.x86_64 libjpeg-turbo-1.2.1-3.el6_5.x86_64 libtiff-3.9.4-10.el6_5.x86_64
The conda install libtiff
command states libtiff is already installed (i think conda install sources the C library?), so to install pylibtiff you have to use pip install libtiff
.
The error is the same if cloned and installed from github. non-conda virtualenv python2.7 with same version numbers works fine.
I still have this problem, and it prevents me from using anaconda... It is really a shame because all other tools packaged into it are really powerfull.
But As I can't even load my data I can't use any through anaconda.
With the hope that someone from ContinuumIO take a look at this, here is the backtrace I get with gdb:
Program received signal SIGSEGV, Segmentation fault. 0x00007fffeff3ede0 in PyArray_API () from /home/user/anaconda2/lib/python2.7/site-packages/numpy/core/multiarray.so Missing separate debuginfos, use: debuginfo-install libgcc-4.8.5-4.el7.x86_64 (gdb) bt
at /home/user/anaconda2/lib/python2.7/site-packages/numpy/core/include/numpy/__multiarray_api.h:1673
pathname=0xa6ca40 "/home/user/anaconda2/lib/python2.7/site-packages/libtiff/tif_lzw.so", fp=<optimized out>) at ./Python/importdl.c:53
at Python/import.c:2722
buf=0xa6ba30 "libtiff.tif_lzw", p_buflen=0x7fffffffc130) at Python/import.c:2537
globals=<optimized out>, name=0x0) at Python/import.c:2246
fromlist=0x7ffff7d92b50 <_Py_NoneStruct>, level=<optimized out>) at Python/import.c:2310
argcount=0, kws=0x0, kwcount=0, defs=0x0, defcount=0, closure=0x0) at Python/ceval.c:3582
pathname=0xa82330 "/home/user/anaconda2/lib/python2.7/site-packages/libtiff/tiff_sample_plane.pyc") at Python/import.c:731
pathname=0xa82330 "/home/user/anaconda2/lib/python2.7/site-packages/libtiff/tiff_sample_plane.pyc", fp=<optimized out>)
at Python/import.c:1121
fullname=0xa87290 "libtiff.tiff_sample_plane") at Python/import.c:2722
buf=0xa87290 "libtiff.tiff_sample_plane", p_buflen=0x7fffffffc6d0) at Python/import.c:2537
globals=<optimized out>, name=0x0) at Python/import.c:2246
level=<optimized out>) at Python/import.c:2310
@gnthibault are you using the libtiff
from conda or pip still?
I installed libtiff from pip, and from source myself, using anaconda 2.7, and everytime I try to import it using import libtiff, I get a nasty segmentation fault.
I am on linux centOS, kernel build 3.10.0-327.13.1.el7.x86_64
My configuration:
Output when using gdb:
Is it a bug, or is there something I am doing wrong ?
Thank you in advance