Your message dated Tue, 10 Oct 2023 22:04:08 +0000
with message-id <[email protected]>
and subject line Bug#995599: fixed in fenics-dolfinx 1:0.7.0-1exp2
has caused the Debian Bug report #995599,
regarding 32-bit segfault: max_num_vertices_per_facet=-1 in
to be marked as done.
This means that you claim that the problem has been dealt with.
If this is not the case it is now your responsibility to reopen the
Bug report if necessary, and/or fix the problem forthwith.
(NB: If you are a system administrator and have no idea what this
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immediately.)
--
995599: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=995599
Debian Bug Tracking System
Contact [email protected] with problems
--- Begin Message ---
Package: libopenmpi3
Version: 4.1.2~rc1-4
Severity: important
Control: affects -1 src:fenics-dolfinx
fenics-dolfinx FTBFS on 32-bit arches, i386, armel, armhf, see
https://buildd.debian.org/status/package.php?p=fenics-dolfinx&suite=experimental
https://buildd.debian.org/status/fetch.php?pkg=fenics-dolfinx&arch=i386&ver=1%3A0.3.0-3&stamp=1633022115&raw=0
(ignore the 2021-10-02 failed builds using libhdf5-mpi-dev
1.10.7+repack-2, they need libcurl-dev, i.e. libcurl4-openssl-dev, see
Bug##995594 )
The symptom in dolfinx build logs is
signal number 11 SEGV: Segmentation Violation, probably memory access out of
range
when running demo_poisson_mpi_2
PETSc suggests running with -start_in_debugger. When I do that on i386
porterbox and run demo_poisson manually with 2 processes, it gives a
more detailed backtrace:
(experimental_i386-dchroot)barriere$ mpiexec -n 2 ./demo_poisson
-start_in_debugger
PETSC: Attaching gdb to ./demo_poisson of pid 5638 on display :0.0 on machine
barriere
PETSC: Attaching gdb to ./demo_poisson of pid 5639 on display :0.0 on machine
barriere
Unable to start debugger in xterm: No such file or directory
Unable to start debugger in xterm: No such file or directory
[0]PETSC ERROR:
------------------------------------------------------------------------
[0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably
memory access out of range
[0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[0]PETSC ERROR: or see
https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[0]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to
find memory corruption errors
[0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[0]PETSC ERROR: to get more information on the crash.
[0]PETSC ERROR: PetscAbortErrorHandler: User provided function() line 0 in
unknown file (null)
To prevent termination, change the error handler using PetscPushErrorHandler()
[barriere:05638] *** Process received signal ***
[barriere:05638] Signal: Aborted (6)
[barriere:05638] Signal code: (-6)
[barriere:05638] [ 0] linux-gate.so.1(__kernel_rt_sigreturn+0x0)[0xf7f32090]
[barriere:05638] [ 1] linux-gate.so.1(__kernel_vsyscall+0x9)[0xf7f32069]
[barriere:05638] [ 2] /lib/i386-linux-gnu/libc.so.6(gsignal+0xc6)[0xf5f00f36]
[barriere:05638] [ 3] /lib/i386-linux-gnu/libc.so.6(abort+0x125)[0xf5ee9312]
[barriere:05638] [ 4]
/usr/lib/petscdir/petsc3.14/i386-linux-gnu-real/lib/libpetsc_real.so.3.14(+0x153d26)[0xf653dd26]
[barriere:05638] [ 5]
/usr/lib/petscdir/petsc3.14/i386-linux-gnu-real/lib/libpetsc_real.so.3.14(PetscError+0xd0)[0xf653a3b0]
[barriere:05638] [ 6]
/usr/lib/petscdir/petsc3.14/i386-linux-gnu-real/lib/libpetsc_real.so.3.14(PetscSignalHandlerDefault+0x1a0)[0xf653e790]
[barriere:05638] [ 7]
/usr/lib/petscdir/petsc3.14/i386-linux-gnu-real/lib/libpetsc_real.so.3.14(+0x154979)[0xf653e979]
[barriere:05638] [ 8] linux-gate.so.1(__kernel_sigreturn+0x0)[0xf7f32080]
[barriere:05638] [ 9]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx4mesh16build_dual_graphEP19ompi_communicator_tRKNS_5graph13AdjacencyListIxEEi+0xd7f)[0xf7ead68f]
[barriere:05638] [10]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx4mesh21partition_cells_graphEP19ompi_communicator_tiiRKNS_5graph13AdjacencyListIxEENS0_9GhostModeERKSt8functionIFNS4_IiEES2_iS7_ibEE+0x21d)[0xf7ebeb9d]
[barriere:05638] [11]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx4mesh21partition_cells_graphEP19ompi_communicator_tiiRKNS_5graph13AdjacencyListIxEENS0_9GhostModeE+0x59)[0xf7ebece9]
[barriere:05638] [12]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZNSt17_Function_handlerIFKN7dolfinx5graph13AdjacencyListIiEEP19ompi_communicator_tiiRKNS2_IxEENS0_4mesh9GhostModeEEPFS3_S6_iiS9_SB_EE9_M_invokeERKSt9_Any_dataOS6_OiSK_S9_OSB_+0x35)[0xf7dff8b5]
[barriere:05638] [13]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx4mesh11create_meshEP19ompi_communicator_tRKNS_5graph13AdjacencyListIxEERKNS_3fem17CoordinateElementERKN2xt17xtensor_containerINSC_7uvectorIdSaIdEEELj2ELNSC_11layout_typeE1ENSC_22xtensor_expression_tagEEENS0_9GhostModeERKSt8functionIFKNS4_IiEES2_iiS7_SM_EE+0x163)[0xf7e96d63]
[barriere:05638] [14]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(+0x10fdab)[0xf7dfedab]
[barriere:05638] [15]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx10generation13RectangleMesh6createEP19ompi_communicator_tRKSt5arrayIS4_IdLj3EELj2EES4_IjLj2EENS_4mesh8CellTypeENSA_9GhostModeERKSt8functionIFKNS_5graph13AdjacencyListIiEES3_iiRKNSF_IxEESC_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xb8)[0xf7dff7c8]
[barriere:05638] [16]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx10generation13RectangleMesh6createEP19ompi_communicator_tRKSt5arrayIS4_IdLj3EELj2EES4_IjLj2EENS_4mesh8CellTypeENSA_9GhostModeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x5f)[0xf7dff83f]
[barriere:05638] [17] ./demo_poisson(+0x19953)[0x565ed953]
[barriere:05638] [18]
/lib/i386-linux-gnu/libc.so.6(__libc_start_main+0x106)[0xf5eeafd6]
[barriere:05638] [19] ./demo_poisson(+0x18451)[0x565ec451]
[barriere:05638] *** End of error message ***
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
[1]PETSC ERROR:
------------------------------------------------------------------------
[1]PETSC ERROR: Caught signal number 15 Terminate: Some process (or the batch
system) has told this process to end
[1]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger
[1]PETSC ERROR: or see
https://www.mcs.anl.gov/petsc/documentation/faq.html#valgrind
[1]PETSC ERROR: or try http://valgrind.org on GNU/linux and Apple Mac OS X to
find memory corruption errors
[1]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run
[1]PETSC ERROR: to get more information on the crash.
[1]PETSC ERROR: PetscAbortErrorHandler: User provided function() line 0 in
unknown file (null)
To prevent termination, change the error handler using PetscPushErrorHandler()
[barriere:05639] *** Process received signal ***
[barriere:05639] Signal: Aborted (6)
[barriere:05639] Signal code: (-6)
[barriere:05639] [ 0] linux-gate.so.1(__kernel_rt_sigreturn+0x0)[0xf7f66090]
[barriere:05639] [ 1] linux-gate.so.1(__kernel_vsyscall+0x9)[0xf7f66069]
[barriere:05639] [ 2] /lib/i386-linux-gnu/libc.so.6(gsignal+0xc6)[0xf5f34f36]
[barriere:05639] [ 3] /lib/i386-linux-gnu/libc.so.6(abort+0x125)[0xf5f1d312]
[barriere:05639] [ 4]
/usr/lib/petscdir/petsc3.14/i386-linux-gnu-real/lib/libpetsc_real.so.3.14(+0x153d26)[0xf6571d26]
[barriere:05639] [ 5]
/usr/lib/petscdir/petsc3.14/i386-linux-gnu-real/lib/libpetsc_real.so.3.14(PetscError+0xd0)[0xf656e3b0]
[barriere:05639] [ 6]
/usr/lib/petscdir/petsc3.14/i386-linux-gnu-real/lib/libpetsc_real.so.3.14(PetscSignalHandlerDefault+0x1a0)[0xf6572790]
[barriere:05639] [ 7]
/usr/lib/petscdir/petsc3.14/i386-linux-gnu-real/lib/libpetsc_real.so.3.14(+0x154979)[0xf6572979]
[barriere:05639] [ 8] linux-gate.so.1(__kernel_sigreturn+0x0)[0xf7f66080]
[barriere:05639] [ 9]
/usr/lib/i386-linux-gnu/openmpi/lib/openmpi3/mca_btl_vader.so(+0x4cd6)[0xf1354cd6]
[barriere:05639] [10]
/usr/lib/i386-linux-gnu/libopen-pal.so.40(opal_progress+0x30)[0xf4dcde70]
[barriere:05639] [11]
/usr/lib/i386-linux-gnu/libopen-pal.so.40(ompi_sync_wait_mt+0xbd)[0xf4dd4a5d]
[barriere:05639] [12]
/usr/lib/i386-linux-gnu/libmpi.so.40(ompi_request_default_wait+0x236)[0xf7a1b2c6]
[barriere:05639] [13]
/usr/lib/i386-linux-gnu/libmpi.so.40(ompi_coll_base_sendrecv_actual+0xbb)[0xf7a73b2b]
[barriere:05639] [14]
/usr/lib/i386-linux-gnu/libmpi.so.40(ompi_coll_base_alltoall_intra_pairwise+0xf7)[0xf7a77b67]
[barriere:05639] [15]
/usr/lib/i386-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_alltoall_intra_do_this+0x11d)[0xf11b28ed]
[barriere:05639] [16]
/usr/lib/i386-linux-gnu/openmpi/lib/openmpi3/mca_coll_tuned.so(ompi_coll_tuned_alltoall_intra_dec_fixed+0x99)[0xf11adca9]
[barriere:05639] [17]
/usr/lib/i386-linux-gnu/libmpi.so.40(MPI_Alltoall+0x182)[0xf7a2f6d2]
[barriere:05639] [18]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx3MPI10all_to_allIxEENS_5graph13AdjacencyListIT_EEP19ompi_communicator_tRKS5_+0x15d)[0xf7eb95ed]
[barriere:05639] [19]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx4mesh16build_dual_graphEP19ompi_communicator_tRKNS_5graph13AdjacencyListIxEEi+0xdd6)[0xf7ee16e6]
[barriere:05639] [20]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx4mesh21partition_cells_graphEP19ompi_communicator_tiiRKNS_5graph13AdjacencyListIxEENS0_9GhostModeERKSt8functionIFNS4_IiEES2_iS7_ibEE+0x21d)[0xf7ef2b9d]
[barriere:05639] [21]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx4mesh21partition_cells_graphEP19ompi_communicator_tiiRKNS_5graph13AdjacencyListIxEENS0_9GhostModeE+0x59)[0xf7ef2ce9]
[barriere:05639] [22]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZNSt17_Function_handlerIFKN7dolfinx5graph13AdjacencyListIiEEP19ompi_communicator_tiiRKNS2_IxEENS0_4mesh9GhostModeEEPFS3_S6_iiS9_SB_EE9_M_invokeERKSt9_Any_dataOS6_OiSK_S9_OSB_+0x35)[0xf7e338b5]
[barriere:05639] [23]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx4mesh11create_meshEP19ompi_communicator_tRKNS_5graph13AdjacencyListIxEERKNS_3fem17CoordinateElementERKN2xt17xtensor_containerINSC_7uvectorIdSaIdEEELj2ELNSC_11layout_typeE1ENSC_22xtensor_expression_tagEEENS0_9GhostModeERKSt8functionIFKNS4_IiEES2_iiS7_SM_EE+0x163)[0xf7ecad63]
[barriere:05639] [24]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(+0x10fbb2)[0xf7e32bb2]
[barriere:05639] [25]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx10generation13RectangleMesh6createEP19ompi_communicator_tRKSt5arrayIS4_IdLj3EELj2EES4_IjLj2EENS_4mesh8CellTypeENSA_9GhostModeERKSt8functionIFKNS_5graph13AdjacencyListIiEES3_iiRKNSF_IxEESC_EERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0xb8)[0xf7e337c8]
[barriere:05639] [26]
/fenics/fenics-dolfinx-0.3.0/debian/tmp-real/usr/lib/i386-linux-gnu/libdolfinx_real.so.0.3(_ZN7dolfinx10generation13RectangleMesh6createEP19ompi_communicator_tRKSt5arrayIS4_IdLj3EELj2EES4_IjLj2EENS_4mesh8CellTypeENSA_9GhostModeERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x5f)[0xf7e3383f]
[barriere:05639] [27] ./demo_poisson(+0x19953)[0x5658d953]
[barriere:05639] [28]
/lib/i386-linux-gnu/libc.so.6(__libc_start_main+0x106)[0xf5f1efd6]
[barriere:05639] [29] ./demo_poisson(+0x18451)[0x5658c451]
[barriere:05639] *** End of error message ***
Since there two processes, there are 2 backtraces here. The first is
in libdolfinx_real.so and reaches dolfinx::mesh::build_dual_graph
which seems to be using ompi_communicator to access dolfinx's
graph::AdjacencyList, before the segfault is reached.
The second process seems to be accessing MPI::all_to_all for the
graph::AdjacencyList and then goes from libdolfinx_real.so to
libmpi.so, then libopen-pal.so and finally reaches mca_btl_vader.so
before hitting the segfault.
So if I'm reading the trace correctly, the segfault is triggered
inside mca_btl_vader.so
This is kind of Severity:serious (FTBFS), except that fenics-dolfinx
is in experimental, and the old version of dolfinx in unstable doesn't
crash this way. I'm hoping to push the new version of dolfinx to
unstable soon though.
--- End Message ---
--- Begin Message ---
Source: fenics-dolfinx
Source-Version: 1:0.7.0-1exp2
Done: Drew Parsons <[email protected]>
We believe that the bug you reported is fixed in the latest version of
fenics-dolfinx, which is due to be installed in the Debian FTP archive.
A summary of the changes between this version and the previous one is
attached.
Thank you for reporting the bug, which will now be closed. If you
have further comments please address them to [email protected],
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Drew Parsons <[email protected]> (supplier of updated fenics-dolfinx package)
(This message was generated automatically at their request; if you
believe that there is a problem with it please contact the archive
administrators by mailing [email protected])
-----BEGIN PGP SIGNED MESSAGE-----
Hash: SHA512
Format: 1.8
Date: Tue, 10 Oct 2023 19:41:57 +0200
Source: fenics-dolfinx
Architecture: source
Version: 1:0.7.0-1exp2
Distribution: experimental
Urgency: medium
Maintainer: Debian Science Team
<[email protected]>
Changed-By: Drew Parsons <[email protected]>
Closes: 995599
Changes:
fenics-dolfinx (1:0.7.0-1exp2) experimental; urgency=medium
.
* reinstate build-time tests since catch2 v3 is now packaged.
Drop internet access for debian/tests.
* reinstate demo_poisson_mpi C++ tests and python unit tests
test_cffi_assembly test_compute_closest_entity_2d. Segfault on
32 bit systems seems to have cleared now. Closes: #995599.
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