Cube combination core dump
Hi, I have been trying to combine a few cubes (well, I started with a lot but cut it down to only three now), and I keep getting a core dump.
I have tried various solutions, installed mpdaf in a clean python environment, and used two different python versions, but the core dump happens no matter what. What I show here has mpdaf version 3.5 installed via pip install mpdaf[all] (but I have also used the github one) and python v3.11.2 with GCC 11.2.0 on a CentOS 7 box.
The script is very basic:
import glob
from mpdaf.obj import CubeList
cubes = glob.glob("scipost/*/DATACUBE*.fits")
l = CubeList(cubes[7:9])
cube, expmap, statpix = l.median()
and trying to debug this is not throwing a lot of light on it:
GNU gdb (GDB) Red Hat Enterprise Linux 7.6.1-120.el7
Copyright (C) 2013 Free Software Foundation, Inc.
License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law. Type "show copying"
and "show warranty" for details.
This GDB was configured as "x86_64-redhat-linux-gnu".
For bug reporting instructions, please see:
<http://www.gnu.org/software/gdb/bugs/>...
Reading symbols from /data/jarle/anaconda3/envs/mpdaf/bin/python3.11...Dwarf Error: wrong version in compilation unit header (is 5, should be 2, 3, or 4) [in module /data/jarle/anaconda3/envs/mpdaf/bin/python3.11]
(no debugging symbols found)...done.
(gdb) run /data/jarle/MUSE/Musered/UltraFaintDwarfs/HydraII/test_combine.py
Starting program: /data/jarle/anaconda3/envs/mpdaf/bin/python /data/jarle/MUSE/Musered/UltraFaintDwarfs/HydraII/test_combine.py
[Thread debugging using libthread_db enabled]
Using host libthread_db library "/lib64/libthread_db.so.1".
Dwarf Error: wrong version in compilation unit header (is 5, should be 2, 3, or 4) [in module /data/jarle/anaconda3/envs/mpdaf/lib/python3.11/lib-dynload/_ctypes.cpython-311-x86_64-linux-gnu.so]
<...many more such Dwarf Errors, but those are not fatal...>
<... some New Thread statements ...>
New Thread 0x7fffd8708700 (LWP 3123)]
WARNING: UnitsWarning: '1e-20 erg/s/cm 2/Angstrom' contains multiple slashes, which is discouraged by the FITS standard [astropy.units.format.generic]
WARNING: UnitsWarning: '1e-20 erg/s/cm 2/Angstrom' contains multiple slashes, which is discouraged by the FITS standard [astropy.units.format.generic]
Dwarf Error: wrong version in compilation unit header (is 5, should be 2, 3, or 4) [in module /data/jarle/anaconda3/envs/mpdaf/lib/libgomp.so.1]
1: scipost/2018-03-17T02:52:22.284/DATACUBE_FINAL.fits
2: scipost/2018-04-15T03:17:05.919/DATACUBE_FINAL.fits
nfiles: 2
num_nthreads: 460
[New Thread 0x7ff7032b4780 (LWP 3124)]
<... More New Thread statements ...>
omp_get_num_threads: 48
Using 48 threads
Read fits files
naxes 912 931 3722
04/04/23 - 02:18PM 0.0%
Program received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7ff69cff1800 (LWP 3157)]
0x00007fffd7d02cc6 in mpdaf_merging_median._omp_fn.1 ()
from /data/jarle/anaconda3/envs/mpdaf/lib/python3.11/site-packages/mpdaf/tools/_ctools.cpython-311-x86_64-linux-gnu.so
Missing separate debuginfos, use: debuginfo-install glibc-2.17-326.el7_9.x86_64
(gdb) gdb backtrace
Undefined command: "gdb". Try "help".
(gdb) backtrace
#0 0x00007fffd7d02cc6 in mpdaf_merging_median._omp_fn.1 ()
from /data/jarle/anaconda3/envs/mpdaf/lib/python3.11/site-packages/mpdaf/tools/_ctools.cpython-311-x86_64-linux-gnu.so
#1 0x00007ffff00bcffc in __kmp_GOMP_microtask_wrapper ()
from /data/jarle/anaconda3/envs/mpdaf/lib/python3.11/site-packages/mkl/../../../libiomp5.so
#2 0x00007ffff0158053 in __kmp_invoke_microtask ()
from /data/jarle/anaconda3/envs/mpdaf/lib/python3.11/site-packages/mkl/../../../libiomp5.so
#3 0x00007ffff00d4353 in __kmp_invoke_task_func ()
from /data/jarle/anaconda3/envs/mpdaf/lib/python3.11/site-packages/mkl/../../../libiomp5.so
#4 0x00007ffff00d3362 in __kmp_launch_thread ()
from /data/jarle/anaconda3/envs/mpdaf/lib/python3.11/site-packages/mkl/../../../libiomp5.so
#5 0x00007ffff0158cdc in _INTERNALdb99f3be::__kmp_launch_worker(void*) ()
from /data/jarle/anaconda3/envs/mpdaf/lib/python3.11/site-packages/mkl/../../../libiomp5.so
#6 0x00007ffff7bc6ea5 in start_thread () from /lib64/libpthread.so.0
#7 0x00007ffff71e6b0d in clone () from /lib64/libc.so.6
(gdb) q
A debugging session is active.
Any idea what is going on here?