Bug#981128: libgmsh4: SIGABRT in dolfinx demo from gmsh polynomialBasis via Eigen::compute_inverse

[Bernhard Übelacker]

Am 12.02.21 um 16:06 schrieb Drew Parsons:
> 
> That could be the mismatch, if gmsh used its own copy of eigen different 
> from 3.3.9.  Alternatively if libdolfinx-dev was built against an older 
> version of eigen then it might make a discrepancy.
> 
> Dolfinx has just been updated in unstable. Bernhard, you could check if 
> the rebuild for this new version fixes your problem.  But likely we'll 
> want to apply Christophe's flag to the gmsh build.
> 
> Drew



Hello Drew,
I updated just all dolfinx packages to 2019.2.0~git20210130.c14cb0a-3.
(That drew updates for libbasix0 and libpetsc.)

But the fault does appear there too.

Kind regards,
Bernhard




# dpkg -l | grep -E "dolfinx|eigen3|gmsh" | LANG=C sort -k3b,3b -k2b,2b
ii  dolfinx-doc                            2019.2.0~git20210130.c14cb0a-3 all          Documentation and demo programs for DOLFIN
ii  libdolfinx-dev                         2019.2.0~git20210130.c14cb0a-3 all          Shared links and header files for DOLFIN
ii  libeigen3-dev                          3.3.9-2                        all          lightweight C++ template library for linear algebra
ii  gmsh                                   4.7.1+ds1-2                    amd64        Three-dimensional finite element mesh generator


$ python3 /usr/share/dolfinx/demo-python/gmsh/demo_gmsh.py
double free or corruption (out)
[debian:89745] *** Process received signal ***

(rr) bt
#0  __GI_raise (sig=sig at entry=6) at ../sysdeps/unix/sysv/linux/raise.c:50
#1  0x00007f5a72be4537 in __GI_abort () at abort.c:79
#2  0x00007f5a72c3d768 in __libc_message (action=action at entry=do_abort, fmt=fmt at entry=0x7f5a72d4be31 "%s\n") at ../sysdeps/posix/libc_fatal.c:155
#3  0x00007f5a72c44a5a in malloc_printerr (str=str at entry=0x7f5a72d4e210 "double free or corruption (out)") at malloc.c:5347
#4  0x00007f5a72c46088 in _int_free (av=0x7f5a72d7db80 <main_arena>, p=0x1df8070, have_lock=<optimized out>) at malloc.c:4314
#5  0x00007f5a6304fad8 in Eigen::internal::aligned_free (ptr=<optimized out>) at ./contrib/eigen/Eigen/src/Core/util/Memory.h:177
#6  Eigen::internal::conditional_aligned_free<true> (ptr=<optimized out>) at ./contrib/eigen/Eigen/src/Core/util/Memory.h:230
#7  Eigen::internal::conditional_aligned_delete_auto<int, true> (size=<optimized out>, ptr=<optimized out>) at ./contrib/eigen/Eigen/src/Core/util/Memory.h:416
#8  Eigen::DenseStorage<int, -1, -1, 1, 0>::~DenseStorage (this=0x7ffc1434ab18, __in_chrg=<optimized out>) at ./contrib/eigen/Eigen/src/Core/DenseStorage.h:542