Public bug reported:
Whether it is under Python, or C++, vtkWindBladeReader fails to be
instanciated and crashes the process (full error below). The problem
seems to be related to MPI.
This is a user-face issue, and not only a developer issue, as it's
consequence is that mayavi2 and packages that depend on it (eg python-
surfer and python-mne) no longer run.
The simplest way to reproduce the problem is with 'python -c "import
vtk; vtk.vtkWindBladeReader()"'. I am attaching cmake and cxx files that
show that simply instanciating the object under C++ reproduces the
crash, and thus that it is related to vtk, and not only python-vtk.
The crash message is the following:
$ python -c "import vtk; vtk.vtkWindBladeReader()"
[gael:13146] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable
either could not be found or was not executable by this user in file
ess_singleton_module.c at line 231
[gael:13146] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable
either could not be found or was not executable by this user in file
ess_singleton_module.c at line 140
[gael:13146] [[INVALID],INVALID] ORTE_ERROR_LOG: A system-required executable
either could not be found or was not executable by this user in file
runtime/orte_init.c at line 128
--------------------------------------------------------------------------
It looks like orte_init failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during orte_init; some of which are due to configuration or
environment problems. This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):
orte_ess_set_name failed
--> Returned value A system-required executable either could not be found or
was not executable by this user (-127) instead of ORTE_SUCCESS
--------------------------------------------------------------------------
--------------------------------------------------------------------------
It looks like MPI_INIT failed for some reason; your parallel process is
likely to abort. There are many reasons that a parallel process can
fail during MPI_INIT; some of which are due to configuration or environment
problems. This failure appears to be an internal failure; here's some
additional information (which may only be relevant to an Open MPI
developer):
ompi_mpi_init: orte_init failed
--> Returned "A system-required executable either could not be found or was
not executable by this user" (-127) instead of "Success" (0)
--------------------------------------------------------------------------
[gael:13146] *** An error occurred in MPI_Init
[gael:13146] *** on a NULL communicator
[gael:13146] *** Unknown error
[gael:13146] *** MPI_ERRORS_ARE_FATAL: your MPI job will now abort
--------------------------------------------------------------------------
An MPI process is aborting at a time when it cannot guarantee that all
of its peer processes in the job will be killed properly. You should
double check that everything has shut down cleanly.
Reason: Before MPI_INIT completed
Local host: gael
PID: 13146
--------------------------------------------------------------------------
This crash message makes me strongly believe that it is due to a
misconfigured MPI or a missing dependency.
ProblemType: Bug
DistroRelease: Ubuntu 15.10
Package: libvtk5.10 5.10.1+dfsg-2
ProcVersionSignature: Ubuntu 4.2.0-18.22-generic 4.2.3
Uname: Linux 4.2.0-18-generic x86_64
ApportVersion: 2.19.1-0ubuntu5
Architecture: amd64
CurrentDesktop: Unity
Date: Thu Nov 26 17:23:11 2015
InstallationDate: Installed on 2015-03-19 (252 days ago)
InstallationMedia: Ubuntu 14.10 "Utopic Unicorn" - Release amd64 (20141022.1)
SourcePackage: vtk
UpgradeStatus: Upgraded to wily on 2015-11-21 (5 days ago)
** Affects: vtk (Ubuntu)
Importance: Undecided
Status: New
** Tags: amd64 apport-bug wily
** Attachment added: "Source files of a simple C++ project to reproduce the bug"
https://bugs.launchpad.net/bugs/1520306/+attachment/4525929/+files/bug_vtk.zip
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https://bugs.launchpad.net/bugs/1520306
Title:
vtk vtkWindBladeReader fails to be instanciated
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