bugGNU Octave - Bugs: bug #52475, ode15 is not compatible with...

 
 

bug #52475: ode15 is not compatible with SUNDIALS >= 3.0.0

Submitted by:  Sebastian <sschoeps>
Submitted on:  Tue 21 Nov 2017 09:48:12 PM UTC  
 
Category:  Libraries Severity:  3 - Normal
Priority:  5 - Normal Item Group:  Other
Status:  In Progress Assigned to:  None
Originator Name:  Open/Closed:  Open
Release:  dev Operating System:  Any

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( Jump to the original submission)

Wed 09 May 2018 08:29:56 AM UTC, comment #25:

thanks for uploading the configuration files.
From what I see:

1) I found an error in the configure tests that I will fix ASAP
2) I am surprised this worked ever before even for sundials2

Carlo de Falco <cdf>
Project Member
Wed 09 May 2018 05:28:21 AM UTC, comment #24:

Yes, the changeset is relative to the default branch.
Yes, you need to run bootstrat to get a new configure script when configure.ac is patched.

Carlo de Falco <cdf>
Project Member
Wed 09 May 2018 04:21:50 AM UTC, comment #23:

config.h (as fc28_config.h) and config.log (as fc28_config.log)
are attached.

Dmitri.

(file #44130, file #44131)

Dmitri A. Sergatskov <dasergatskov>
Wed 09 May 2018 04:06:21 AM UTC, comment #22:

I was messing with this stuff so I would need to recreate them.
Could you verify that
a) patach to be applied on default (dev) branch, not on stable.
b) since it patches configure.ac I need to re-run bootstrap
prior to configure.

Dmitri.
--

Dmitri A. Sergatskov <dasergatskov>
Wed 09 May 2018 03:49:50 AM UTC, comment #21:

Dmitri,

Thanks again for testing, I'm still not sure whether KLU for sparse Jacobian should be enabled or disabled for you ...

Can you please upload config.log and config.h?

Carlo de Falco <cdf>
Project Member
Tue 08 May 2018 10:54:16 PM UTC, comment #20:

configure step looked better, but compile failed:

Dmitri.
--

Dmitri A. Sergatskov <dasergatskov>
Tue 08 May 2018 09:23:22 PM UTC, comment #19:

here's a new try at the changeset.

(file #44127)

Carlo de Falco <cdf>
Project Member
Tue 08 May 2018 09:17:28 PM UTC, comment #18:

sorry, I actually meant this one:

Carlo de Falco <cdf>
Project Member
Tue 08 May 2018 09:16:16 PM UTC, comment #17:

do you have the following in config.h?

Carlo de Falco <cdf>
Project Member
Tue 08 May 2018 08:59:33 PM UTC, comment #16:

it is in sunlisol sub-directory:

Dmitri.
--

Dmitri A. Sergatskov <dasergatskov>
Tue 08 May 2018 08:53:51 PM UTC, comment #15:

Dmitri,

Thanks for testing.

Indeed there seems to be something wrong, either
SUNLINSOL_KLU is installed but is not detected
or it is not installed, in which case its header
should not be included.

Which one is the case for you? Does "locate sunlinsol_klu.h"
return something for you?

Carlo de Falco <cdf>
Project Member
Tue 08 May 2018 08:48:25 PM UTC, comment #14:

comment #13 was truncated:

(which, I think, is wrong)

and during compile:

Carlo de Falco <cdf>
Project Member
Tue 08 May 2018 07:44:14 PM UTC, comment #13:

With current dev snapshot (bc5f225bc578+ tip @) on Fedora 28
(Sundials 3.1.0):

during configure:

Dmitri A. Sergatskov <dasergatskov>
Tue 08 May 2018 05:58:04 PM UTC, comment #12:

here is an updated patch, this works for me on macos 10.13 with a self built sudials 3.1.0

can someone else test the patch and/or look at it (especially the configure tests)?

(file #44125)

Carlo de Falco <cdf>
Project Member
Tue 08 May 2018 03:20:26 PM UTC, comment #11:

Hi,
can you please be more specific about the compiler/linker flags you used to build _ode15_.oct from _ode15_.cc?

Carlo de Falco <cdf>
Project Member
Mon 07 May 2018 05:06:34 PM UTC, comment #10:

I built _ode15_.oct using this version of mingw:

c:\temp\Projects\ode15_ming64>where g++
c:\Program Files\mingw-w64\x86_64-7.2.0-win32-seh-rt_v5-rev1\mingw64\bin\g++.exe

Then, I ran these tests:

>> which ode15s

'ode15s' is a function from the file C:\Octave\OCTAVE~3.0\share\octave\4.4.0\m\ode\ode15s.m

>> test ode15s

PASSES 39 out of 39 tests

>> test ode15i

PASSES 48 out of 48 tests

I could do more testing, if needed.

Bill Greene <billgreene>
Mon 07 May 2018 04:20:17 PM UTC, comment #9:

The attached patch also changes configure tests.

(file #44113)

Carlo de Falco <cdf>
Project Member
Mon 07 May 2018 03:43:23 PM UTC, comment #8:

Hi,

I turned your patch into a proper changeset that applies on the current development branch and made a few style fixes.

How did you build and test the code?

If I apply the changeset and run "configure" the tests for IDADENSE and IDAKLU fail and ode15{i,s} get disabled ...

c.

(file #44112)

Carlo de Falco <cdf>
Project Member
Mon 07 May 2018 12:14:43 PM UTC, comment #7:

I think I patched revision 25054 of _ode15_.cc.

I can see that these patch files are rather problematic with
respect to the version of the file they are created for.
So, as you suggested, I just uploaded the full, modified _ode15_.cc. This version has been built and tested with octave 4.4.0.

(file #44110)

Bill Greene <billgreene>
Mon 07 May 2018 11:07:01 AM UTC, comment #6:

Bill, Thanks for your patch and sorry for the late reply.

The patch does seem to have been greated correctly
but it does not apply to the current development branch,
what exact version of Octave did you start with for creating the patch?

If you don't feel like going through the trouble of creating
a well formed mercurial changeset you can just download the latest version of ode15.cc from the hgweb interface using the following link:

http://hg.savannah.gnu.org/hgweb/octave/raw-file/default/libinterp/dldfcn/__ode15__.cc

and upload the full modified file.

c.

Carlo de Falco <cdf>
Project Member
Mon 16 Apr 2018 12:13:35 PM UTC, comment #5:

I attached a patch file to this bug report to update _ode15_.cc to build with sundials 3.1.

Bill Greene <billgreene>
Tue 03 Apr 2018 12:59:03 AM UTC, comment #4:

I added more tests to configure on the stable branch as a stopgap for this bug for the Octave 4.4 release

https://hg.savannah.gnu.org/hgweb/octave/rev/5dce8aa80652

This will automatically disable building against SUNDIALS 3.0.0 and later. Octave 4.4 will build against version 2.7.0 only. This is no longer a build failure error, so recategorizing and retitling.

Please do comment if there are still build errors that the new configure changes don't take care of automatically.

Leaving this bug open until after the release when someone has time to fix it on the development branch by rewriting the interface to the new IDA API.

Mike Miller <mtmiller>
Project Administrator
Fri 30 Mar 2018 07:05:15 PM UTC, comment #3:

I've built a copy of sundials 3.1.0 and I confirm the error and that the API has changed significantly.

I think we're probably short on time to get a true fix in for 4.4, so it might make sense to add tests to configure for the ida_dense API and conditionally compile out those parts of the code. I can take a look at doing that in the short term.

Mike Miller <mtmiller>
Project Administrator
Fri 30 Mar 2018 06:11:17 AM UTC, comment #2:

FYI -- Fedora 28 (beta is out, final is expected to be released on May 1) comes with sundials 3.1.0

Dmitri.
--

Dmitri A. Sergatskov <dasergatskov>
Wed 21 Mar 2018 11:23:11 PM UTC, comment #1:

It would be really nice if someone familiar with the SUNDIALS interface could take a look at this for Octave 4.4, since distributions will probably start moving to SUNDIALS 3 very soon.

Mike Miller <mtmiller>
Project Administrator
Tue 21 Nov 2017 09:48:12 PM UTC, original submission:

As initially reported in [1]: Sundials has changed the treatment of dense matrices [1], such that "ida_dense.h" which is included by "__ode15__.cc" is gone.

From the manual:

> Added generic SUNMATRIX module with three provided implementations:
> dense, banded and sparse.
> These replicate previous SUNDIALS Dls and Sls matrix structures in a
> single object-oriented API.


[1] http://octave.1599824.n4.nabble.com/Sundials-issues-with-ode15-tt4685656.html
[2] https://computation.llnl.gov/sites/default/files/public/idas_guide.pdf

Sebastian <sschoeps>

 

(Note: upload size limit is set to 16384 kB, after insertion of the required escape characters.)

Attach Files:
   
   
Comment:
   

Attached Files
file #44130:  fc28_config.log added by dasergatskov (2MiB - text/x-log)
file #44131:  fc28_config.h added by dasergatskov (114KiB - text/x-chdr)
file #44127:  open_bXICA7Gt.txt added by cdf (18KiB - text/plain)
file #44125:  open_TK6CSjvd.txt added by cdf (18KiB - text/plain)
file #44113:  open_K7lryXre.txt added by cdf (13KiB - text/plain)
file #44112:  open_tkJXJDPU.txt added by cdf (9KiB - text/plain - changes for default branch)
file #44110:  __ode15__.cc added by billgreene (33KiB - text/plain - modified file to support sundials 3.1)
file #43949:  __ode15__.cc.patch added by None (11KiB - application/octet-stream - Patch file for _ode15_.cc with the required, minimal changes to build with sundials 3.)

 

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Items that depend on this one: None found

 

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    Follow 19 latest changes.

    Date Changed by Updated Field Previous Value => Replaced by
    2018-05-09 dasergatskov Attached File- => Added fc28_config.log, #44130
        Attached File- => Added fc28_config.h, #44131
    2018-05-08 cdf Attached File- => Added open_bXICA7Gt.txt, #44127
    2018-05-08 cdf Attached File- => Added open_TK6CSjvd.txt, #44125
    2018-05-07 cdf Attached File- => Added open_K7lryXre.txt, #44113
    2018-05-07 cdf Attached File- => Added open_tkJXJDPU.txt, #44112
        Priority1 - Later => 5 - Normal
        StatusPostponed => In Progress
    2018-05-07 billgreene Attached File- => Added _ode15_.cc, #44110
    2018-04-16 None Attached File- => Added _ode15_.cc.patch, #43949
    2018-04-03 mtmiller CategoryConfiguration and Build System => Libraries
    2018-04-03 mtmiller Severity4 - Important => 3 - Normal
        Priority5 - Normal => 1 - Later
        Item GroupBuild Failure => Other
        StatusConfirmed => Postponed
        Summaryode15 does not compile with Sundials >=3.0 => ode15 is not compatible with SUNDIALS >= 3.0.0
    2018-03-30 mtmiller CategoryOctave Function => Configuration and Build System
    2018-03-21 mtmiller Severity3 - Normal => 4 - Important
    2017-11-29 siko1056 StatusNone => Confirmed

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