plplot-devel

[Plplot-devel] Would you be willing to test PLplot against Octave-3.8.2 or later in the 3.8 series?

[Alan W. I. <ir...@be...>]

Hi Andrew:

In case you didn't have a chance to read it, the summary of the recent
part of my thread with Arjen is he now has a successful build on
Cygwin of our octave bindings against Octave-3.8.2.  However, he
discovered there were run-time errors when running our octave examples
for that version of Octave. I do not get those run-time errors for the
Octave-3.6.2 Linux case.

Would you be willing to test PLplot against Octave-3.8.2 or later
yourself to see if the issue Arjen is seeing is confined to
just Cygwin?

Alan
__________________________
Alan W. Irwin

Astronomical research affiliation with Department of Physics and Astronomy,
University of Victoria (astrowww.phys.uvic.ca).

Programming affiliations with the FreeEOS equation-of-state
implementation for stellar interiors (freeeos.sf.net); the Time
Ephemerides project (timeephem.sf.net); PLplot scientific plotting
software package (plplot.sf.net); the libLASi project
(unifont.org/lasi); the Loads of Linux Links project (loll.sf.net);
and the Linux Brochure Project (lbproject.sf.net).
__________________________

Linux-powered Science
__________________________

Re: [Plplot-devel] Would you be willing to test PLplot against Octave-3.8.2 or later in the 3.8 series?

[Andrew R. <and...@us...>]

Coincidentally I have just this week upgraded my Ubuntu install so I now
have octave 3.8.2. I will run some tests and see what happens.

Andre

On Thu, Jul 09, 2015 at 03:01:53AM -0700, Alan Irwin wrote:
> Hi Andrew:
> 
> In case you didn't have a chance to read it, the summary of the recent
> part of my thread with Arjen is he now has a successful build on
> Cygwin of our octave bindings against Octave-3.8.2.  However, he
> discovered there were run-time errors when running our octave examples
> for that version of Octave. I do not get those run-time errors for the
> Octave-3.6.2 Linux case.
> 
> Would you be willing to test PLplot against Octave-3.8.2 or later
> yourself to see if the issue Arjen is seeing is confined to
> just Cygwin?
> 
> Alan
> __________________________
> Alan W. Irwin
> 
> Astronomical research affiliation with Department of Physics and Astronomy,
> University of Victoria (astrowww.phys.uvic.ca).
> 
> Programming affiliations with the FreeEOS equation-of-state
> implementation for stellar interiors (freeeos.sf.net); the Time
> Ephemerides project (timeephem.sf.net); PLplot scientific plotting
> software package (plplot.sf.net); the libLASi project
> (unifont.org/lasi); the Loads of Linux Links project (loll.sf.net);
> and the Linux Brochure Project (lbproject.sf.net).
> __________________________
> 
> Linux-powered Science
> __________________________

Re: [Plplot-devel] Would you be willing to test PLplot against Octave-3.8.2 or later in the 3.8 series?

[Andrew R. <and...@us...>]

I've built and run the non-interactive octave tests and they complete with
no errors using octave-3.8.2 on Ubuntu 15.04 (vivid). I did have some
build errors, but that was just related to the hdf5.h header being in a
new location. 

Regards

Andrew

On Fri, Jul 10, 2015 at 09:48:54PM +0100, Andrew Ross wrote:
> 
> Coincidentally I have just this week upgraded my Ubuntu install so I now
> have octave 3.8.2. I will run some tests and see what happens.
> 
> Andre
> 
> On Thu, Jul 09, 2015 at 03:01:53AM -0700, Alan Irwin wrote:
> > Hi Andrew:
> > 
> > In case you didn't have a chance to read it, the summary of the recent
> > part of my thread with Arjen is he now has a successful build on
> > Cygwin of our octave bindings against Octave-3.8.2.  However, he
> > discovered there were run-time errors when running our octave examples
> > for that version of Octave. I do not get those run-time errors for the
> > Octave-3.6.2 Linux case.
> > 
> > Would you be willing to test PLplot against Octave-3.8.2 or later
> > yourself to see if the issue Arjen is seeing is confined to
> > just Cygwin?
> > 
> > Alan
> > __________________________
> > Alan W. Irwin
> > 
> > Astronomical research affiliation with Department of Physics and Astronomy,
> > University of Victoria (astrowww.phys.uvic.ca).
> > 
> > Programming affiliations with the FreeEOS equation-of-state
> > implementation for stellar interiors (freeeos.sf.net); the Time
> > Ephemerides project (timeephem.sf.net); PLplot scientific plotting
> > software package (plplot.sf.net); the libLASi project
> > (unifont.org/lasi); the Loads of Linux Links project (loll.sf.net);
> > and the Linux Brochure Project (lbproject.sf.net).
> > __________________________
> > 
> > Linux-powered Science
> > __________________________
> 
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Re: [Plplot-devel] Would you be willing to test PLplot against Octave-3.8.2 or later in the 3.8 series?

[Alan W. I. <ir...@be...>]

On 2015-07-10 23:27+0100 Andrew Ross wrote:

>
> I've built and run the non-interactive octave tests and they complete with
> no errors using octave-3.8.2 on Ubuntu 15.04 (vivid). I did have some
> build errors, but that was just related to the hdf5.h header being in a
> new location.

Hi Andrew:

The current status of the Cygwin octave-3.8.2 issue is
Arjen discovered the problem was an assumption in our scripts
concerning the location of the plplot_octave.oct dll for the Windows
case, and I am in the middle of fixing that assumption.

However, once I get that fix done, if Arjen runs into additional issues
it is good to know that PLplot basically works for octave-3.8.2
so many thanks for proving that.

With regard to the hdf5.h location issue you discovered on Ubuntu,
could you please make the required small adjustment to
cmake/modules/octave.cmake using PATH_SUFFIXES on the find_path
command so that it finds hdf5.h preferentially in the traditional
location (/usr/include/hdf5.h), but if it is not found there it looks
in the subdirectory of that location which is appropriate for Ubuntu
(and probably also later versions of Debian than I have at the
moment).

Thanks in advance for this small fix.

Alan
__________________________
Alan W. Irwin

Astronomical research affiliation with Department of Physics and Astronomy,
University of Victoria (astrowww.phys.uvic.ca).

Programming affiliations with the FreeEOS equation-of-state
implementation for stellar interiors (freeeos.sf.net); the Time
Ephemerides project (timeephem.sf.net); PLplot scientific plotting
software package (plplot.sf.net); the libLASi project
(unifont.org/lasi); the Loads of Linux Links project (loll.sf.net);
and the Linux Brochure Project (lbproject.sf.net).
__________________________

Linux-powered Science
__________________________

Re: [Plplot-devel] Would you be willing to test PLplot against Octave-3.8.2 or later in the 3.8 series?

[Alan W. I. <ir...@be...>]

On 2015-07-10 17:12-0700 Alan W. Irwin wrote:

> On 2015-07-10 23:27+0100 Andrew Ross wrote:
>
>>
>> I've built and run the non-interactive octave tests and they complete with
>> no errors using octave-3.8.2 on Ubuntu 15.04 (vivid). I did have some
>> build errors, but that was just related to the hdf5.h header being in a
>> new location.
>
> Hi Andrew:
>
> The current status of the Cygwin octave-3.8.2 issue is
> Arjen discovered the problem was an assumption in our scripts
> concerning the location of the plplot_octave.oct dll for the Windows
> case, and I am in the middle of fixing that assumption.
>
> However, once I get that fix done, if Arjen runs into additional issues
> it is good to know that PLplot basically works for octave-3.8.2
> so many thanks for proving that.
>
> With regard to the hdf5.h location issue you discovered on Ubuntu,
> could you please make the required small adjustment to
> cmake/modules/octave.cmake using PATH_SUFFIXES on the find_path
> command so that it finds hdf5.h preferentially in the traditional
> location (/usr/include/hdf5.h), but if it is not found there it looks
> in the subdirectory of that location which is appropriate for Ubuntu
> (and probably also later versions of Debian than I have at the
> moment).

To Andrew, Arjen and Greg:

@Andrew: You referred above to an hdf5.h issue on Ubuntu.  Please make the
suggested upstream build-system fix so no Ubuntu PLplot builder
runs into that issue.

Also, could you please run

scripts/comprehensive_test.sh --do_test_interactive no

on your Ubuntu platform and send me the resulting report tarball,
../comprehensive_test_disposeable/comprehensive_test.tar.gz ?

Running that script (with --do_test_interactive no) should be
essentially painless (except possibly if you are short of disk space),
and that test report on one of our most important platforms would be
most useful.

The current status of octave on Cygwin is Arjen can now build the
octave (3.8.2) binding of PLplot without issues, and all the "p"
octave examples work, and "x" examples 00 through 19 work as well.
However, he did encounter a segfault for the 20th example.
Greg's recent report for the same platform confirms that
segfault for octave example 20 issue.

Your above good Ubuntu results for octave 3.8.2, and some excellent
results I have just now (commit 338492f) achieved for the
test_noninteractive target of an epa_built plplot_lite that depends on
epa_built octave-3.8.2 supports the hypothesis that the segfault issue
Arjen has found and which Greg confirmed is likely nothing to do with
octave-3.8.2, and is instead some Windows or Cygwin issue with our
Octave-related code or with the octave-3.8.2 Cygwin build or
packaging.

@Arjen and Greg: since it appears to be impossible for Linux users to
replicate the segfault issue you guys are encountering, I think the
only way forward for you is to debug this issue on Cygwin.

To help simplify that debugging process you should locally modify
plplot_test/test_octave.sh.in to remove all examples other than x20.
After that, "make test_octave_psc" should just execute the 20th octave
example.  Once you have achieved that, then proceed with old-fashioned
debugging, i.e., locally modify examples/octave/x20c.m to output
additional results to localize which octave command is generating
the segfault, and then to dump all arguments of that command.

In off-list discussion with Arjen we have proved to our mutual
satisfication via md5sum, that the git checkout of the lena.pgm file
(used by example 20) is identical in the two cases.  In other words,
git is treating this file (as expected) as a binary file rather than a
text file (with accompanying bit flips due to line ending issues). We
have also looked at the octave fopen command that opens this file in
x20c.m. However, if your preliminary analysis to discover which octave
command in x20c.m segfaults indicates the problem could be in the lena
data that is read in, then it would be good to double check by dumping
some parts of that file from within the example.

In any case, I would be happy to run any x20c.m you guys have modified
to dump out results to give you a Linux versus Cygwin comparison of
those dumped results.

Good luck with the bug hunt, and let me know how it goes.

Alan
__________________________
Alan W. Irwin

Astronomical research affiliation with Department of Physics and Astronomy,
University of Victoria (astrowww.phys.uvic.ca).

Programming affiliations with the FreeEOS equation-of-state
implementation for stellar interiors (freeeos.sf.net); the Time
Ephemerides project (timeephem.sf.net); PLplot scientific plotting
software package (plplot.sf.net); the libLASi project
(unifont.org/lasi); the Loads of Linux Links project (loll.sf.net);
and the Linux Brochure Project (lbproject.sf.net).
__________________________

Linux-powered Science
__________________________

Re: [Plplot-devel] Would you be willing to test PLplot against Octave-3.8.2 or later in the 3.8 series?

[Arjen M. <Arj...@de...>]

Hi Alan,



>
> @Arjen and Greg: since it appears to be impossible for Linux users to replicate the
> segfault issue you guys are encountering, I think the only way forward for you is to
> debug this issue on Cygwin.
>
following your receipe I was able to determine that the crash happens in plimagefr2 - when it copies the yg array into the grid ygg. The values of nx and ny are 399 and 486 respectively, so that is quite correct. Why it should fail exactly at this point is something I cannot fathom. When I comment out the statement f2c( yg, ygg, ... ) in the SWIG source for plimagefr2, the failure simply occurs at f2c( a, aa, ... ).

It is quite possible that the failure occurs much earlier. That ought to be checked.

By the way, I noticed that the copies of these arrays are not freed, so that constitutes a memory leak, unless something is taking care of that that I have overlooked in the code.

Regards,

Arjen





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Re: [Plplot-devel] Would you be willing to test PLplot against Octave-3.8.2 or later in the 3.8 series?

[Arjen M. <Arj...@de...>]

Hi Alan, Greg,



Some more information - no solution though:

-        Commenting out all calls to pplimage and plimagefr to avoid the "calls" to f2c (that is a macro, not a function) so that only plimagefr2 was left made no difference to the segmentation fault.

-        Printing the allocated pointers in f2c revealed that the failure occurs at i = 122 for ygg, so in the middle of the procedure with no clue as to the cause.



Regards,



Arjen

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Re: [Plplot-devel] Would you be willing to test PLplot against Octave-3.8.2 or later in the 3.8 series?

[Alan W. I. <ir...@be...>]

On 2015-08-24 09:59-0000 Arjen Markus wrote:

> Hi Alan, Greg,
>
>
>
> Some more information - no solution though:
>
> -        Commenting out all calls to pplimage and plimagefr to avoid the "calls" to f2c (that is a macro, not a function) so that only plimagefr2 was left made no difference to the segmentation fault.
>
> -        Printing the allocated pointers in f2c revealed that the failure occurs at i = 122 for ygg, so in the middle of the procedure with no clue as to the cause.

Hi Arjen:

It sounds like you are trying to debug what happens in
bindings/octave/plplot_octaveOCTAVE_wrap.cxx.  Could you please send
that swig-generated file to me (without your edited changes) so I
could compare with what is generated by swig here?  I presume they
will be the same, but it would be good to double check that.

Since the error you have investigated at this detailed level seems to
occur right in the middle of an array, I think it would be worth your while to
try debugging at the higher (octave) level instead.  That is modify
examples/octave/x20c.m to

1. Find the exact octave command that is causing the issue, and
2. Dump out all arguments of that command including the detailed
contents of every vector and array into a file.
3. Send that file and your modified x20c.m here so I can
try the same experiment here to see if there are any differences.

Alan
__________________________
Alan W. Irwin

Astronomical research affiliation with Department of Physics and Astronomy,
University of Victoria (astrowww.phys.uvic.ca).

Programming affiliations with the FreeEOS equation-of-state
implementation for stellar interiors (freeeos.sf.net); the Time
Ephemerides project (timeephem.sf.net); PLplot scientific plotting
software package (plplot.sf.net); the libLASi project
(unifont.org/lasi); the Loads of Linux Links project (loll.sf.net);
and the Linux Brochure Project (lbproject.sf.net).
__________________________

Linux-powered Science
__________________________