bugGNU Octave - Bugs: bug #55028, plots executed from script...


bug #55028: plots executed from script containing many plots seg fault

Submitter:  Michael Godfrey <godfrey>
Submitted:  Thu 15 Nov 2018 01:15:22 PM UTC
Category:  Plotting with OpenGL Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Segfault, Bus Error, etc.
Status:  Fixed Assigned to:  None
Originator Name:  Godfrey Open/Closed:  * Closed
Release:  * dev Operating System:  * GNU/Linux
Fixed Release:  None Planned Release:  None
* Mandatory Fields

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Sat 12 Jan 2019 07:41:47 PM UTC, comment #11: 

closing report and mark as fixed on the wiki

Andreas Weber <andy1978>
Group Member
Sat 12 Jan 2019 06:10:48 PM UTC, comment #10: 

Yes, cd73f8e9235f

fixes the problem.

Unless there is other experience, closing report is OK.


Michael Godfrey <godfrey>
Group Member
Fri 11 Jan 2019 11:28:27 PM UTC, comment #9: 

@Michael, can you reproduce this now with Pantxo's fix in place?  Otherwise, I'm going to cross it of at https://wiki.octave.org/Bug_Fix_List_-_5.0_Release.

Rik <rik5>
Group administrator
Mon 07 Jan 2019 01:20:25 PM UTC, comment #8: 

@Michael: The fix for bug #48519 has been pushed to stable. Can you confirm that it also fixes this bug?

Pantxo Diribarne <pantxo>
Group Member
Sun 30 Dec 2018 08:43:12 PM UTC, comment #7: 

I think this could be a duplicate of #48519 where I get the same backtrace as in the first post.

Andreas Weber <andy1978>
Group Member
Fri 21 Dec 2018 03:23:02 PM UTC, comment #6: 

I have learned a bit more about this: It is the use of clf
instead of close("all") that causes the seg fault.

clf requires a pause(0.0001) following it to prevent
the seg fault. So, for example:

close ("all");
do_plot = 1;
%% the plot_.. commands below contain: clear -x do_plot -x inpt_file
%% This is to ensure that they do not "inherent" any variable data
close ("all")
close ("all")
%%close ("all")

seg faults with
Plot file is: airdata_1946-61_extr_1953/de_trend/plot_orig_norm.pdf
title_1 = 21-Dec-2018: airdata_1946-61_extr_1953
fatal: caught signal Segmentation fault -- stopping myself...
Segmentation fault (core dumped)

replacing the clf with close("all")

prevents the seg fault.

Note that there is in each case only one current figure so it is unclear
why clf and close("all") should produce different results.

Michael Godfrey <godfrey>
Group Member
Tue 11 Dec 2018 09:40:22 AM UTC, comment #5: 

Some background: this has been a problem for a long
time, but was fixed at some point. I had put pause(1)
calls in the code and then about a year ago I found
that the pause was not needed. Then recently the seg
fault returned. The plots require a quite large set of

I will try to isolate the problem, but I do not right
now have the time to work on it. bisecting may be useful...

One point: it seems odd that pause(0.00001) prevents
the seg fault. This pause is placed just after the previous
plot and there is considerable computing before the plot
that seg faults.

Anyhow, I will work on it more when I can.

Michael Godfrey <godfrey>
Group Member
Mon 10 Dec 2018 11:11:56 PM UTC, comment #4: 

Can you make a test script? I cannot reproduce it.


Dmitri A. Sergatskov <dasergatskov>
Mon 10 Dec 2018 10:29:25 PM UTC, comment #3: 

I should add that the "many" plots in the title is
inaccurate. The seg fault occurs on the second of the
plots. So, 2 plots a re sufficient to cause the fault.

Michael Godfrey <godfrey>
Group Member
Mon 10 Dec 2018 10:07:01 PM UTC, comment #2: 

I looked at this again using current dev.
Just running under gdb I get
essentially the same seg fault as below:

Thread 8 "QThread" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffcb7fe700 (LWP 27417)]
0x00007ffff5a37dd2 in QMetaObject::activate(QObject*, int, int, void**) ()
   from /lib64/libQt5Core.so.5

Also, the timing window seems to be pretty small.
pause(0.00001) prevents the seg fault.

Right now I have very limited time to debug this. Sorry.

Michael Godfrey <godfrey>
Group Member
Thu 15 Nov 2018 01:36:15 PM UTC, comment #1: 

Definitely timing. I placed pause(5) after each plot
and script completes normally.

I will open a new report for the fact that
pause with no argument hangs. ^C is required to continue.

Michael Godfrey <godfrey>
Group Member
Thu 15 Nov 2018 01:15:22 PM UTC, original submission:  

This problem has returned in the current dev.
HG 1861e2ea0a4b

When I run a script containing many plots Octave seg faults
after only a few plots. Running under gdb I get:
Thread 8 "QThread" received signal SIGSEGV, Segmentation fault.
[Switching to Thread 0x7fffcb7fe700 (LWP 30871)]
0x00007ffff5a45dd2 in QMetaObject::activate(QObject*, int, int, void**) ()
   from /lib64/libQt5Core.so.5

and bt:
#0  0x00007ffff5a45dd2 in QMetaObject::activate(QObject*, int, int, void**) ()
    at /lib64/libQt5Core.so.5
#1  0x00007fffe00ea8ea in QtHandles::Figure::updateBoundingBoxHelper(void*) (data=0xe54cd0)
    at libgui/graphics/Figure.cc:639
#2  0x00007ffff7785f90 in graphics_event::execute() (this=0x7fffcb7fae10)
    at libinterp/corefcn/graphics.h:12891
#3  0x00007ffff7785f90 in gh_manager::do_process_events(bool) (this=0x7fffbc19a340, force=false)
    at libinterp/corefcn/graphics.cc:11396
#4  0x00007ffff773a55b in gh_manager::process_events() () at libinterp/corefcn/graphics.h:12937
#5  0x00007ffff773a55b in Fdrawnow(octave_value_list const&, int) (args=...)
    at libinterp/corefcn/graphics.cc:12737
#6  0x00007ffff738bbd0 in octave_builtin::call(octave::tree_evaluator&, int, octave_value_list const&) (this=0x7fffbc0734a0, tw=..., nargout=0, args=...) at libinterp/octave-value/ov-builtin.cc:65
#7  0x00007ffff750ed6e in octave::tree_evaluator::visit_index_expression(octave::tree_index_expression&) (this=0x7fffbc003e08, idx_expr=...) at libinterp/parse-tree/pt-eval.cc:1913
#8  0x00007ffff73cc0be in octave::tree_evaluator::evaluate(octave::tree_expression*, int)
    (this=this@entry=0x7fffbc003e08, expr=expr@entry=0x7fffbcd1cdd0, nargout=<optimized out>,
    nargout@entry=0) at libinterp/parse-tree/pt-eval.h:302
#9  0x00007ffff750a679 in octave::tree_evaluator::visit_statement(octave::tree_statement&)
    (this=0x7fffbc003e08, stmt=...) at libinterp/parse-tree/pt-eval.cc:2680

This may be related to the fact that after each plot I adjust the size of the bounding box.
I will try a few experiments as time permits.
My system is: Current Linux FC29: 4.18.17-300.fc29.x86_64

Michael Godfrey <godfrey>
Group Member


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    Follow 4 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2019-01-12 andy1978 StatusReady For Test Fixed
        Open/ClosedOpen Closed
    2019-01-11 rik5 StatusNeed Info Ready For Test
    2019-01-07 pantxo StatusNone Need Info

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