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[Pkg-octave-devel] Bug#708191: marked as done (octave-openmpi-ext will sometimes run successfully, error out or crash)

Your message dated Thu, 23 May 2013 21:02:57 +0200
with message-id <1369335777.8586.4.camel@rama.villemot.name>
and subject line Re: [Pkg-octave-devel] Bug#708191: octave-openmpi-ext will sometimes run successfully, error out or crash
has caused the Debian Bug report #708191,
regarding octave-openmpi-ext will sometimes run successfully, error out or crash
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.

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-- 
708191: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=708191
Debian Bug Tracking System
Contact owner@bugs.debian.org with problems
--- Begin Message --- 
Package: octave-openmpi-ext
Version: 1.0.2-2
Severity: normal

Dear Maintainer,

   I was running the provided hellocell.m, and hellostruct.m scripts and sometimes it would either run successfully, mpi would error out or it would just crash.

command:  mpirun -x LD_PRELOAD=libmpi.so.0 -np  4 octave -q --eval hellocell

error out
==============
==============
warning: X11 DISPLAY environment variable not set
warning: X11 DISPLAY environment variable not set
warning: X11 DISPLAY environment variable not set
warning: X11 DISPLAY environment variable not set
warning: dispatch is obsolete and will be removed from a future version of Octave; please use classes instead
warning: dispatch is obsolete and will be removed from a future version of Octave; please use classes instead
warning: dispatch is obsolete and will be removed from a future version of Octave; please use classes instead
warning: dispatch is obsolete and will be removed from a future version of Octave; please use classes instead
We are at rank 0 that is master etc..
[aurora:29333] *** An error occurred in MPI_Send
[aurora:29333] *** on communicator MPI_COMM_WORLD
[aurora:29333] *** MPI_ERR_RANK: invalid rank
[aurora:29333] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
warning: octave_chunk_buffer::clear: 1 active allocations remain!
--------------------------------------------------------------------------
mpirun has exited due to process rank 2 with PID 29333 on
node aurora exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[aurora:29330] 2 more processes have sent help message help-mpi-errors.txt / mpi_errors_are_fatal
[aurora:29330] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
================
================

when it crashes
================
================
*** glibc detected *** octave: double free or corruption (!prev): 0x0000000001040590 ***
======= Backtrace: =========
/lib/x86_64-linux-gnu/libc.so.6(+0x76d76)[0x7fc06b968d76]
/lib/x86_64-linux-gnu/libc.so.6(cfree+0x6c)[0x7fc06b96daac]
/usr/lib/x86_64-linux-gnu/liboctinterp.so.1(_ZNSt8_Rb_treeISsSt4pairIKSsN12symbol_table8fcn_infoEESt10_Select1stI
S4_ESt4lessISsESaIS4_EE8_M_eraseEPSt13_Rb_tree_nodeIS4_E+0x62)[0x7fc06de49262]
/usr/lib/x86_64-linux-gnu/liboctinterp.so.1(_ZNSt8_Rb_treeISsSt4pairIKSsN12symbol_table8fcn_infoEESt10_Select1stI
S4_ESt4lessISsESaIS4_EE8_M_eraseEPSt13_Rb_tree_nodeIS4_E+0x24)[0x7fc06de49224]
======= Memory map: ========
00400000-00401000 r-xp 00000000 08:06 135826                             /usr/bin/octave
00600000-00601000 r--p 00000000 08:06 135826                             /usr/bin/octave
00601000-00602000 rw-p 00001000 08:06 135826                             /usr/bin/octave
00fc7000-01cd5000 rw-p 00000000 00:00 0                                  [heap]
7fc050000000-7fc050021000 rw-p 00000000 00:00 0 
7fc050021000-7fc054000000 ---p 00000000 00:00 0 
7fc0561f2000-7fc056223000 r-xp 00000000 08:06 136540                     /usr/lib/x86_64-linux-gnu/octave/package
s/openmpi_ext-1.0.2/x86_64-pc-linux-gnu-api-v48+/MPI_Send.oct
7fc056223000-7fc056422000 ---p 00031000 08:06 136540                     /usr/lib/x86_64-linux-gnu/octave/package
s/openmpi_ext-1.0.2/x86_64-pc-linux-gnu-api-v48+/MPI_Send.oct
7fc056422000-7fc056425000 r--p 00030000 08:06 136540                     /usr/lib/x86_64-linux-gnu/octave/package
s/openmpi_ext-1.0.2/x86_64-pc-linux-gnu-api-v48+/MPI_Send.oct
7fc056425000-7fc056426000 rw-p 00033000 08:06 136540                     /usr/lib/x86_64-linux-gnu/octave/package
s/openmpi_ext-1.0.2/x86_64-pc-linux-gnu-api-v48+/MPI_Send.oct
7fc056426000-7fc05a428000 rw-s 00000000 00:12 55549                      /tmp/openmpi-sessions-larks@aurora_0/659
2/1/shared_mem_pool.aurora (deleted)
7fc05a428000-7fc05a435000 r-xp 00000000 08:06 135698                     /usr/lib/openmpi/lib/openmpi/mca_osc_rdm
a.so
7fc05a435000-7fc05a635000 ---p 0000d000 08:06 135698                     /usr/lib/openmpi/lib/openmpi/mca_osc_rdm
a.so
7fc05a635000-7fc05a636000 rw-p 0000d000 08:06 135698                     /usr/lib/openmpi/lib/openmpi/mca_osc_rdm
a.so
7fc05a636000-7fc05a640000 r-xp 00000000 08:06 135697                     /usr/lib/openmpi/lib/openmpi/mca_osc_pt2
pt.so
7fc05a640000-7fc05a83f000 ---p 0000a000 08:06 135697                     /usr/lib/openmpi/lib/openmpi/mca_osc_pt2
pt.so
7fc05a83f000-7fc05a841000 rw-p 00009000 08:06 135697                     /usr/lib/openmpi/lib/openmpi/mca_osc_pt2
pt.so
7fc05a841000-7fc05a85a000 r-xp 00000000 08:06 135671                     /usr/lib/openmpi/lib/openmpi/mca_coll_tu
ned.so
7fc05a85a000-7fc05aa5a000 ---p 00019000 08:06 135671                     /usr/lib/openmpi/lib/openmpi/mca_coll_tu
ned.so
7fc05aa5a000-7fc05aa5b000 rw-p 00019000 08:06 135671                     /usr/lib/openmpi/lib/openmpi/mca_coll_tu
ned.so
7fc05aa5b000-7fc05aa5e000 r-xp 00000000 08:06 135670                     /usr/lib/openmpi/lib/openmpi/mca_coll_sy
nc.so
7fc05aa5e000-7fc05ac5d000 ---p 00003000 08:06 135670                     /usr/lib/openmpi/lib/openmpi/mca_coll_sy
nc.so
7fc05ac5d000-7fc05ac5e000 rw-p 00002000 08:06 135670                     /usr/lib/openmpi/lib/openmpi/mca_coll_sy
nc.so
==============
==============
it keeps on going but I though I'd end it there.  If you want I can send you the complete output.  It would sometimes work, then error, then work, then crash, then work, etc

When I did that fixed it was to uninstall the the octave-openmpi-ext package and then use octave to install the 1.1.0 version from sourceforge. While I haven't test it a lot, it seems to work without erring out or crashing, out of the 10 or so times I tested it.

If you need any more information please let me know and I'll be happy to provide you anything I can. 

Brian

-- System Information:
Debian Release: jessie/sid
  APT prefers testing
  APT policy: (500, 'testing')
Architecture: amd64 (x86_64)

Kernel: Linux 3.2.0-4-amd64 (SMP w/8 CPU cores)
Locale: LANG=en_US.UTF-8, LC_CTYPE=en_US.UTF-8 (charmap=UTF-8) (ignored: LC_ALL set to en_US.UTF-8)
Shell: /bin/sh linked to /bin/dash

Versions of packages octave-openmpi-ext depends on:
ii  libc6          2.13-38
ii  libgcc1        1:4.7.2-5
ii  liboctave1     3.6.2-5
ii  libopenmpi1.3  1.4.5-1
ii  libstdc++6     4.7.2-5
ii  octave         3.6.2-5

Versions of packages octave-openmpi-ext recommends:
ii  openmpi-bin  1.4.5-1

octave-openmpi-ext suggests no packages.

-- no debconf information

--- End Message ---
--- Begin Message --- 
Version: 1.1.0-1

Le jeudi 23 mai 2013 à 12:29 -0400, Brian Woods a écrit :

> I installed the version of octave-openmpi-ext from unstable (which
> also forced octave to upgrade).  After that, it works consistently.
> The problems seems to be gone.  

Great, I’m therefore closing this bug.

> Thank you for your time.  Is there anything I can do?

Thanks for your feedback. I think we’re done, unless you find another
problem!

Best,

-- 
 .''`.    Sébastien Villemot
: :' :    Debian Developer
`. `'     http://www.dynare.org/sebastien
  `-      GPG Key: 4096R/381A7594

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