Re: Trilinos packages

[Felix Salfelder]

On Thu, Mar 27, 2014 at 10:58:02PM +0100, Nico Schlömer wrote:
> As for the prefixing of the libraries with "trilinos_", I'd rather
> refrain from it for the moment. The arguments I can see for this

i see. perhaps it would be helpful to dig out the the referenced
'discussion with the ftpmaster' for the exact reasoning. anyway the
debian-policy [1] just states that

"""
If you have several shared libraries built from the same source tree,
you may lump them all together into a single shared library package
provided that all of their SONAMEs will always change together. Be aware
that this is not normally the case, and if the SONAMEs do not change
together, upgrading such a merged shared library package will be
unnecessarily difficult because of file conflicts with the old version
of the package. When in doubt, always split shared library packages so
that each binary package installs a single shared library.
""".

>   * The Debian package for Trilinos is meant for a researcher to get
> an application to compile and run with Trilinos to then deploy it on
> an HPC. If Debian follows a non-default library naming scheme, the
> user would have to maintain two separate build files for Debian and
> the cluster (which will typically host a customized Trilinos
> installation).
> 
>* The new Trilinos package includes many more subpackages than the
> old one did. Maintaining a Debian patch that changes all library names
> is possible, but would be a substantial effort.
> 
>* The old README brings up that prefixing avoids conflicts. While
> it it remains possible that another library by the same name appears
> in Debian, that has not been the case as long as Trilinos in Debian
> existed and isn't the case now.
> 
>* The old README brings up that it would be easier to identify
> trilinos libraries. While that is true, a user of Trilinos typically
> has a very good idea of what libraries he or she plans to use.
> 

i tend to agree. but lets have a look at the proposed "split library
packages" variant... the control file will will blow up, but only once.
the next hurdle will be installing the files into the right packages. it
should be rather possible to do this half-way automatically...

i'm starting to like the idea of splitting up the package. it will cause
a lot of packages, but no extra headaches.

> That said, I do see the benefit of prefixing the libraries with
> "trilinos_". I would suggest that I file a bug report upstream, talk
> to some of the developers, and see if we can incorporate that change
> in Trilinos itself. We would probably have to wait for a major
> release, but I think this coming fall they are bumping the major
> release number.

from the perspective of a trilinos developer, all library packages are
packages on their own, and the naming scheme looks fine to me. just
because we (may) want to lump them together into one binary package
doesnt justify a change, imo.

> > ideally those patches should be included in your package at alioth
> > (whether or not they have been accepted upstream).
> 
> Really? Why?

i was assuming that the patches make sense. some of them apparently are
build system related. so why not?

hth, regards
felix

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Re: Trilinos packages

[Nico Schlömer]

> yes. the old trilinos debian source package had a libname.patch and a
> soname.patch, these fix the names for a monolithic package. i suggest to
> import these (or just rebase your work on top of that).

I already incorporated a fix for proper so-naming upstream a while
ago, so that should be fixed.

As for the prefixing of the libraries with "trilinos_", I'd rather
refrain from it for the moment. The arguments I can see for this

  * The Debian package for Trilinos is meant for a researcher to get
an application to compile and run with Trilinos to then deploy it on
an HPC. If Debian follows a non-default library naming scheme, the
user would have to maintain two separate build files for Debian and
the cluster (which will typically host a customized Trilinos
installation).

   * The new Trilinos package includes many more subpackages than the
old one did. Maintaining a Debian patch that changes all library names
is possible, but would be a substantial effort.

   * The old README brings up that prefixing avoids conflicts. While
it it remains possible that another library by the same name appears
in Debian, that has not been the case as long as Trilinos in Debian
existed and isn't the case now.

   * The old README brings up that it would be easier to identify
trilinos libraries. While that is true, a user of Trilinos typically
has a very good idea of what libraries he or she plans to use.

That said, I do see the benefit of prefixing the libraries with
"trilinos_". I would suggest that I file a bug report upstream, talk
to some of the developers, and see if we can incorporate that change
in Trilinos itself. We would probably have to wait for a major
release, but I think this coming fall they are bumping the major
release number.


> ideally those patches should be included in your package at alioth
> (whether or not they have been accepted upstream).

Really? Why?

> is there a specific
> reason to maintain a second and different repository for ubuntu?

Not particularly. I just have Trilinos built on a nightly basis on
launchpad to make sure upcoming changes won't bite us; it also serves
me well as a test bed for changes in debian/.

Cheers,
Nico



On Wed, Mar 26, 2014 at 5:03 PM, Felix Salfelder  wrote:
> On Wed, Mar 26, 2014 at 10:22:23AM +0100, Nico Schlömer wrote:
>> I would suggest to first go with a monolithic
>> package and split it up at a later point.
>
> yes. the old trilinos debian source package had a libname.patch and a
> soname.patch, these fix the names for a monolithic package. i suggest to
> import these (or just rebase your work on top of that).
>
> also, theres a note on renaming in README.Debian. and a changelog that
> would be nice to have.
>
> README.Debian
> [..]
> Debian Trilinos libraries renaming
> ==
>
> Following a discussion with ftpmaster, the Trilinos libraries have
> been renamed to be less generic. They all use the same prefix now :
> libtrilinos_ . That should also help tremendously with
>  - avoiding conflicts with other libraries/packages
>  - identifying available trilinos libraries
> [..]
>
>> In the course of packaging Trilinos for Debian, I have identified
>> quite a number of bugs in Trilinos for which I maintain a little zoo
>> of patches, https://github.com/nschloe/trilinos-ubuntu/tree/master/patches.
>> Some of those have already made it upstream, and we'll have to see if
>> we can get in more of those before the next release freeze.
>
> ideally those patches should be included in your package at alioth
> (whether or not they have been accepted upstream). is there a specific
> reason to maintain a second and different repository for ubuntu?
>
> regards
> felix

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Re: Trilinos packages

[Felix Salfelder]

On Wed, Mar 26, 2014 at 10:22:23AM +0100, Nico Schlömer wrote:
> I would suggest to first go with a monolithic
> package and split it up at a later point.

yes. the old trilinos debian source package had a libname.patch and a
soname.patch, these fix the names for a monolithic package. i suggest to
import these (or just rebase your work on top of that).

also, theres a note on renaming in README.Debian. and a changelog that
would be nice to have.

README.Debian
[..]
Debian Trilinos libraries renaming
==

Following a discussion with ftpmaster, the Trilinos libraries have
been renamed to be less generic. They all use the same prefix now :
libtrilinos_ . That should also help tremendously with
 - avoiding conflicts with other libraries/packages
 - identifying available trilinos libraries
[..]

> In the course of packaging Trilinos for Debian, I have identified
> quite a number of bugs in Trilinos for which I maintain a little zoo
> of patches, https://github.com/nschloe/trilinos-ubuntu/tree/master/patches.
> Some of those have already made it upstream, and we'll have to see if
> we can get in more of those before the next release freeze.

ideally those patches should be included in your package at alioth
(whether or not they have been accepted upstream). is there a specific
reason to maintain a second and different repository for ubuntu?

regards
felix

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Re: Trilinos packages

[Nico Schlömer]

> i suspect that the clean way would be (binary) packages for each library
> the trilinos source package contains.

I fully agree. Trilinos is structurally similar to Boost which does
provide a sophisticated install structure. Unfortunately, the Trilinos
build system is flawed in certain places that make it difficult to
take an automated approach to that. One example is that the
interdependencies of the subpackages aren't presented in a
machine-readable form. Although, I'm submitting patches to Trilinos to
address these issues, I would suggest to first go with a monolithic
package and split it up at a later point.

In the course of packaging Trilinos for Debian, I have identified
quite a number of bugs in Trilinos for which I maintain a little zoo
of patches, https://github.com/nschloe/trilinos-ubuntu/tree/master/patches.
Some of those have already made it upstream, and we'll have to see if
we can get in more of those before the next release freeze.

I'll keep you all posted.

Cheers,
Nico



On Tue, Mar 18, 2014 at 12:56 PM, Felix Salfelder  wrote:
> On Tue, Mar 18, 2014 at 12:15:49PM +0100, Nico Schlömer wrote:
>> A quick poll on the Trilinos package naming:
>> Right now, we have "libtrilinos", which triggers a
>> package-name-doesnt-match-sonames warning since none of the Trilinos
>> libraries is called libtrilinos.* (rather libepetra.*, libbelos.*,
>> ...). This is similar to the libboost package which doesn't contain a
>> library by the name libboost.* either.
>
> i suspect that the clean way would be (binary) packages for each library
> the trilinos source package contains. and maybe have a trilinos-dev
> metapackage that depends on all the lib*-dev packages. this will add up
> to some copy and paste work, and end up with a lot of packages... i
> don't know if it's worth the effort.
>
> fwiw, theres another source package that creates a heap of libraries.
> it is the old trilinos package [1]. here, all sonames are prefixed by
> "libtrilinos_". looks like an alternative...
>
>> On the other hand, a software very similar to Trilinos, PETSc, goes by
>> the Debian name "petsc".
>
> i cannot find a (binary) package called "petsc". but there is (e.g.)
> libpetsc3.4.2, and it contains libpetsc.so.4.3.2. unkike trilinos, the
> petsc source package creates just one shared library. and afaics its
> soname matches the package name.
>
> hth
> felix
>
> [1] https://packages.debian.org/squeeze/amd64/libtrilinos/filelist

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Re: Trilinos packages

[Felix Salfelder]

On Tue, Mar 18, 2014 at 12:15:49PM +0100, Nico Schlömer wrote:
> A quick poll on the Trilinos package naming:
> Right now, we have "libtrilinos", which triggers a
> package-name-doesnt-match-sonames warning since none of the Trilinos
> libraries is called libtrilinos.* (rather libepetra.*, libbelos.*,
> ...). This is similar to the libboost package which doesn't contain a
> library by the name libboost.* either.

i suspect that the clean way would be (binary) packages for each library
the trilinos source package contains. and maybe have a trilinos-dev
metapackage that depends on all the lib*-dev packages. this will add up
to some copy and paste work, and end up with a lot of packages... i
don't know if it's worth the effort.

fwiw, theres another source package that creates a heap of libraries.
it is the old trilinos package [1]. here, all sonames are prefixed by
"libtrilinos_". looks like an alternative...

> On the other hand, a software very similar to Trilinos, PETSc, goes by
> the Debian name "petsc".

i cannot find a (binary) package called "petsc". but there is (e.g.)
libpetsc3.4.2, and it contains libpetsc.so.4.3.2. unkike trilinos, the
petsc source package creates just one shared library. and afaics its
soname matches the package name.

hth
felix

[1] https://packages.debian.org/squeeze/amd64/libtrilinos/filelist

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Re: Trilinos packages

[Nico Schlömer]

A quick poll on the Trilinos package naming:
Right now, we have "libtrilinos", which triggers a
package-name-doesnt-match-sonames warning since none of the Trilinos
libraries is called libtrilinos.* (rather libepetra.*, libbelos.*,
...). This is similar to the libboost package which doesn't contain a
library by the name libboost.* either.
On the other hand, a software very similar to Trilinos, PETSc, goes by
the Debian name "petsc".
What would you prefer for a package name: libtrilinos or trilinos
(with its -dev, -doc, -dbg variants, respectively)?

Cheers,
Nico

On Thu, Mar 13, 2014 at 11:12 PM, Anton Gladky  wrote:
> Hi Nico,
>
> I have built locally your package. But if you run lintian over
> .changes file, it gives a lot of errors and warnings. Please,
> deal with them.
>
> Thanks
>
>
> Anton
>
>
> 2014-03-10 16:35 GMT+01:00 Nico Schlömer :
>
>> > Did you repack it?
>>
>> Nope. For creating the printine-tar branch, I used the
>> --git-pristine-tar option as described on
>> https://wiki.debian.org/PackagingWithGit#pristine-tar.
>>
>> --Nico
>>
>>
>> On Mon, Mar 10, 2014 at 4:30 PM, Anton Gladky  wrote:
>> > 2014-03-10 16:25 GMT+01:00 Nico Schlömer :
>> >
>> >> > It seems, the checksum of tarball on the website and
>> >> > in pristine-tar branch is not the same.
>> >>
>> >> So what to do about this?
>> >
>> >
>> > Did you repack it?
>> >
>> > Anton
>> >
>> >
>> >
>
>

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Re: Trilinos packages

[Anton Gladky]

Hi Nico,

I have built locally your package. But if you run lintian over
.changes file, it gives a lot of errors and warnings. Please,
deal with them.

Thanks


Anton


2014-03-10 16:35 GMT+01:00 Nico Schlömer :

> > Did you repack it?
>
> Nope. For creating the printine-tar branch, I used the
> --git-pristine-tar option as described on
> https://wiki.debian.org/PackagingWithGit#pristine-tar.
>
> --Nico
>
>
> On Mon, Mar 10, 2014 at 4:30 PM, Anton Gladky  wrote:
> > 2014-03-10 16:25 GMT+01:00 Nico Schlömer :
> >
> >> > It seems, the checksum of tarball on the website and
> >> > in pristine-tar branch is not the same.
> >>
> >> So what to do about this?
> >
> >
> > Did you repack it?
> >
> > Anton
> >
> >
> >
>
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Re: Trilinos packages

[Anton Gladky]

 2014-03-10 16:35 GMT+01:00 Nico Schlömer :

> > Did you repack it?
>
> Nope. For creating the printine-tar branch, I used the
> --git-pristine-tar option as described on
> https://wiki.debian.org/PackagingWithGit#pristine-tar.
>

What tarball did you use for that? Downloaded from the website?

Anton
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Re: Trilinos packages

[Nico Schlömer]

> Did you repack it?

Nope. For creating the printine-tar branch, I used the
--git-pristine-tar option as described on
https://wiki.debian.org/PackagingWithGit#pristine-tar.

--Nico


On Mon, Mar 10, 2014 at 4:30 PM, Anton Gladky  wrote:
> 2014-03-10 16:25 GMT+01:00 Nico Schlömer :
>
>> > It seems, the checksum of tarball on the website and
>> > in pristine-tar branch is not the same.
>>
>> So what to do about this?
>
>
> Did you repack it?
>
> Anton
>
>
>

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Re: Trilinos packages

[Nico Schlömer]

> E: dh_python2:145: extension for python2.6 is missing. Build extensions for 
> all supported Python versions (`pyversions -vr`) or adjust X-Python-Version 
> field or pass --no-guessing-versions to dh_python2

I added

override_dh_python2:
dh_python2 --no-guessing-versions

to debian/rules. This should fix your error, please retry.

--Nico




On Mon, Mar 10, 2014 at 3:02 PM, Felix Salfelder  wrote:
> On Mon, Mar 10, 2014 at 01:51:24PM +0100, Nico Schlömer wrote:
>> I checked all other dependencies manually and found that
>> libparmetis-dev was the only thing from non-free. I removed it from
>> the list; please retry building.
>
> the build succeeded without the ENABLE_ParMETIS switch (takes
> forever..).
>
> there's something wrong with dh_python. this is possibly a problem on my side,
> but i don't have time to investigate right now.
>
> """
> [..]
> dh binary --with python2
>dh_python2
> W: dh_python2:437: public extension linked with libpython2.7: _Amesos.so
> W: dh_python2:437: public extension linked with libpython2.7: _Anasazi.so
> W: dh_python2:437: public extension linked with libpython2.7: _AztecOO.so
> W: dh_python2:437: public extension linked with libpython2.7: _Epetra.so
> W: dh_python2:437: public extension linked with libpython2.7: _EpetraExt.so
> W: dh_python2:437: public extension linked with libpython2.7: _Galeri.so
> W: dh_python2:437: public extension linked with libpython2.7: _IFPACK.so
> W: dh_python2:437: public extension linked with libpython2.7: _Komplex.so
> W: dh_python2:437: public extension linked with libpython2.7: _ML.so
> W: dh_python2:437: public extension linked with libpython2.7: _Pliris.so
> W: dh_python2:437: public extension linked with libpython2.7: _Teuchos.so
> W: dh_python2:437: public extension linked with libpython2.7: _TriUtils.so
> W: dh_python2:437: public extension linked with libpython2.7: _Abstract.so
> W: dh_python2:437: public extension linked with libpython2.7: _Solver.so
> W: dh_python2:437: public extension linked with libpython2.7: _StatusTest.so
> W: dh_python2:437: public extension linked with libpython2.7: ___init__.so
> W: dh_python2:437: public extension linked with libpython2.7: _Interface.so
> W: dh_python2:437: public extension linked with libpython2.7: ___init__.so
> W: dh_python2:437: public extension linked with libpython2.7: _NestedEpetra.so
> W: dh_python2:437: public extension linked with libpython2.7: ___init__.so
> E: dh_python2:145: extension for python2.6 is missing. Build extensions for 
> all supported Python versions (`pyversions -vr`) or adjust X-Python-Version 
> field or pass --no-guessing-versions to dh_python2
> """
>
> thanks
> felix

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Re: Trilinos packages

[Anton Gladky]

2014-03-10 16:25 GMT+01:00 Nico Schlömer :

> > It seems, the checksum of tarball on the website and
> > in pristine-tar branch is not the same.
>
> So what to do about this?
>

Did you repack it?

Anton
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Re: Trilinos packages

[Nico Schlömer]

> Hi Nico, is it possible to have working debian/watch?

Not right now. Sandia currently doesn't do public ftp reads. They are
in the process of switching to their new site trilinos.org right now,
and I already requested a public ftp list to be added alongside. Once
this is done, I'll adapt debian/watch.

> It seems, the checksum of tarball on the website and
> in pristine-tar branch is not the same.

So what to do about this?

--Nico


On Mon, Mar 10, 2014 at 2:20 PM, Anton Gladky  wrote:
>
> Hi Nico, is it possible to have working debian/watch?
> It seems, the checksum of tarball on the website and
> in pristine-tar branch is not the same.
>
>
> Anton
>
>
> 2014-03-10 13:51 GMT+01:00 Nico Schlömer :
>>
>> I checked all other dependencies manually and found that
>> libparmetis-dev was the only thing from non-free. I removed it from
>> the list; please retry building.
>>
>> --Nico
>>
>> On Mon, Mar 10, 2014 at 12:27 PM, Nico Schlömer
>>  wrote:
>> >> my recommendation is to disable parmetis in trilinos and defer the
>> >> problem until anybody actually requires it.
>> >
>> > Sure, why not.
>> >
>> >> how many (license) problems are left without parmetis?
>> >
>> > Not sure. If you build without parmetis (remove the dependency from
>> > debian/control and debian/rules), does the builder still complain?
>> >
>> > --Nico
>> >
>> >
>> > On Mon, Mar 10, 2014 at 11:59 AM, Felix Salfelder 
>> > wrote:
>> >> On Mon, Mar 10, 2014 at 11:33:26AM +0100, Nico Schlömer wrote:
>> >>> Are there general Debian guidelines for such situations?
>> >>
>> >> i'm sorry i don't know or care. i'm not even sure in which way non-free
>> >> is (not) a part of debian.
>> >>
>> >>> What's your opinion on this?
>> >>
>> >> imo it's best to avoid trouble (here: non-free packages).
>> >>
>> >> my recommendation is to disable parmetis in trilinos and defer the
>> >> problem until anybody actually requires it. if that is you, hopefully
>> >> somebody else will step in and help.
>> >>
>> >> how many (license) problems are left without parmetis?
>> >>
>> >> regards
>> >> felix
>>
>> --
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>>
>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
>
>

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Re: Trilinos packages

[Felix Salfelder]

On Mon, Mar 10, 2014 at 01:51:24PM +0100, Nico Schlömer wrote:
> I checked all other dependencies manually and found that
> libparmetis-dev was the only thing from non-free. I removed it from
> the list; please retry building.

the build succeeded without the ENABLE_ParMETIS switch (takes
forever..).

there's something wrong with dh_python. this is possibly a problem on my side,
but i don't have time to investigate right now.

"""
[..]
dh binary --with python2
   dh_python2
W: dh_python2:437: public extension linked with libpython2.7: _Amesos.so
W: dh_python2:437: public extension linked with libpython2.7: _Anasazi.so
W: dh_python2:437: public extension linked with libpython2.7: _AztecOO.so
W: dh_python2:437: public extension linked with libpython2.7: _Epetra.so
W: dh_python2:437: public extension linked with libpython2.7: _EpetraExt.so
W: dh_python2:437: public extension linked with libpython2.7: _Galeri.so
W: dh_python2:437: public extension linked with libpython2.7: _IFPACK.so
W: dh_python2:437: public extension linked with libpython2.7: _Komplex.so
W: dh_python2:437: public extension linked with libpython2.7: _ML.so
W: dh_python2:437: public extension linked with libpython2.7: _Pliris.so
W: dh_python2:437: public extension linked with libpython2.7: _Teuchos.so
W: dh_python2:437: public extension linked with libpython2.7: _TriUtils.so
W: dh_python2:437: public extension linked with libpython2.7: _Abstract.so
W: dh_python2:437: public extension linked with libpython2.7: _Solver.so
W: dh_python2:437: public extension linked with libpython2.7: _StatusTest.so
W: dh_python2:437: public extension linked with libpython2.7: ___init__.so
W: dh_python2:437: public extension linked with libpython2.7: _Interface.so
W: dh_python2:437: public extension linked with libpython2.7: ___init__.so
W: dh_python2:437: public extension linked with libpython2.7: _NestedEpetra.so
W: dh_python2:437: public extension linked with libpython2.7: ___init__.so
E: dh_python2:145: extension for python2.6 is missing. Build extensions for all 
supported Python versions (`pyversions -vr`) or adjust X-Python-Version field 
or pass --no-guessing-versions to dh_python2
"""

thanks
felix

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Re: Trilinos packages

[Anton Gladky]

Hi Nico, is it possible to have working debian/watch?
It seems, the checksum of tarball on the website and
in pristine-tar branch is not the same.


Anton


2014-03-10 13:51 GMT+01:00 Nico Schlömer :

> I checked all other dependencies manually and found that
> libparmetis-dev was the only thing from non-free. I removed it from
> the list; please retry building.
>
> --Nico
>
> On Mon, Mar 10, 2014 at 12:27 PM, Nico Schlömer
>  wrote:
> >> my recommendation is to disable parmetis in trilinos and defer the
> >> problem until anybody actually requires it.
> >
> > Sure, why not.
> >
> >> how many (license) problems are left without parmetis?
> >
> > Not sure. If you build without parmetis (remove the dependency from
> > debian/control and debian/rules), does the builder still complain?
> >
> > --Nico
> >
> >
> > On Mon, Mar 10, 2014 at 11:59 AM, Felix Salfelder 
> wrote:
> >> On Mon, Mar 10, 2014 at 11:33:26AM +0100, Nico Schlömer wrote:
> >>> Are there general Debian guidelines for such situations?
> >>
> >> i'm sorry i don't know or care. i'm not even sure in which way non-free
> >> is (not) a part of debian.
> >>
> >>> What's your opinion on this?
> >>
> >> imo it's best to avoid trouble (here: non-free packages).
> >>
> >> my recommendation is to disable parmetis in trilinos and defer the
> >> problem until anybody actually requires it. if that is you, hopefully
> >> somebody else will step in and help.
> >>
> >> how many (license) problems are left without parmetis?
> >>
> >> regards
> >> felix
>
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>
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>
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Re: Trilinos packages

[Nico Schlömer]

I checked all other dependencies manually and found that
libparmetis-dev was the only thing from non-free. I removed it from
the list; please retry building.

--Nico

On Mon, Mar 10, 2014 at 12:27 PM, Nico Schlömer
 wrote:
>> my recommendation is to disable parmetis in trilinos and defer the
>> problem until anybody actually requires it.
>
> Sure, why not.
>
>> how many (license) problems are left without parmetis?
>
> Not sure. If you build without parmetis (remove the dependency from
> debian/control and debian/rules), does the builder still complain?
>
> --Nico
>
>
> On Mon, Mar 10, 2014 at 11:59 AM, Felix Salfelder  wrote:
>> On Mon, Mar 10, 2014 at 11:33:26AM +0100, Nico Schlömer wrote:
>>> Are there general Debian guidelines for such situations?
>>
>> i'm sorry i don't know or care. i'm not even sure in which way non-free
>> is (not) a part of debian.
>>
>>> What's your opinion on this?
>>
>> imo it's best to avoid trouble (here: non-free packages).
>>
>> my recommendation is to disable parmetis in trilinos and defer the
>> problem until anybody actually requires it. if that is you, hopefully
>> somebody else will step in and help.
>>
>> how many (license) problems are left without parmetis?
>>
>> regards
>> felix

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Re: Trilinos packages

[Nico Schlömer]

> my recommendation is to disable parmetis in trilinos and defer the
> problem until anybody actually requires it.

Sure, why not.

> how many (license) problems are left without parmetis?

Not sure. If you build without parmetis (remove the dependency from
debian/control and debian/rules), does the builder still complain?

--Nico


On Mon, Mar 10, 2014 at 11:59 AM, Felix Salfelder  wrote:
> On Mon, Mar 10, 2014 at 11:33:26AM +0100, Nico Schlömer wrote:
>> Are there general Debian guidelines for such situations?
>
> i'm sorry i don't know or care. i'm not even sure in which way non-free
> is (not) a part of debian.
>
>> What's your opinion on this?
>
> imo it's best to avoid trouble (here: non-free packages).
>
> my recommendation is to disable parmetis in trilinos and defer the
> problem until anybody actually requires it. if that is you, hopefully
> somebody else will step in and help.
>
> how many (license) problems are left without parmetis?
>
> regards
> felix

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Re: Trilinos packages

[Felix Salfelder]

On Mon, Mar 10, 2014 at 11:33:26AM +0100, Nico Schlömer wrote:
> Are there general Debian guidelines for such situations?

i'm sorry i don't know or care. i'm not even sure in which way non-free
is (not) a part of debian.

> What's your opinion on this?

imo it's best to avoid trouble (here: non-free packages).

my recommendation is to disable parmetis in trilinos and defer the
problem until anybody actually requires it. if that is you, hopefully
somebody else will step in and help.

how many (license) problems are left without parmetis?

regards
felix

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Re: Trilinos packages

[Nico Schlömer]

I see that ParMETIS is free for educational purposes only
, so
requiring it as a dependency makes Trilinos installable for edu-only
as well. ParMETIS is optional to Trilinos so I might as well removed
it without major repercussions.
Are there general Debian guidelines for such situations? What's your
opinion on this?

--Nico

On Mon, Mar 10, 2014 at 11:23 AM, Felix Salfelder  wrote:
> On Mon, Mar 10, 2014 at 10:52:19AM +0100, Nico Schlömer wrote:
>> Strange, libparmetis-dev should be in jessie, cf.
>> .
>
> indeed it is, and i missed that. curiously, parmetis is non-free, and
> that is why i missed it.
>
> from my understanding (to some extent?) trilinos is free, so it might
> make sense to not use/link\ against libparmetis. doesn't the build
> dependency render your package non-free?
>
> particularly, there is gplv3 licensed software around (xyce) that build
> depends on trilinos. i'm no license or dfsg expert, anyhow, this doesn't
> look very clean to me..
>
> thanks
> felix

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Re: Trilinos packages

[Felix Salfelder]

On Mon, Mar 10, 2014 at 10:52:19AM +0100, Nico Schlömer wrote:
> Strange, libparmetis-dev should be in jessie, cf.
> .

indeed it is, and i missed that. curiously, parmetis is non-free, and
that is why i missed it.

from my understanding (to some extent?) trilinos is free, so it might
make sense to not use/link\ against libparmetis. doesn't the build
dependency render your package non-free?

particularly, there is gplv3 licensed software around (xyce) that build
depends on trilinos. i'm no license or dfsg expert, anyhow, this doesn't
look very clean to me..

thanks
felix

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Re: Trilinos packages

[Nico Schlömer]

Strange, libparmetis-dev should be in jessie, cf.
.

--Nico

On Mon, Mar 10, 2014 at 10:22 AM, Felix Salfelder  wrote:
> On Sat, Mar 08, 2014 at 12:39:57AM +0100, Nico Schlömer wrote:
>> > 1) Set VCS=fields
>> > 2) Standards-Version is 3.9.5 now
>> > 3) Use DEP-3 for patches (Description, Author, Last-Updates is enough)
>> > 4) Remove some unnecessary comments from debian/rules.
>> > It should be as short as possible. Leave only necessary notes.
>> > 5) Check 3rd-party files and add them to debian/copyright (if they are).
>>
>> Done and done; I pushed the changes to alioth.
>
> tried to build (dpkg-buildpackage -rfakeroot -b) on a machine close to 
> testing.
>
> [..]
> dpkg-checkbuilddeps: Unmet build dependencies: libparmetis-dev
> [..]
>
> apt-get install libparmetis-dev says
>
> """
> Package libparmetis-dev is not available, but is referred to by another 
> package.
> This may mean that the package is missing, has been obsoleted, or
> is only available from another source
> However the following packages replace it:
>   libscotchparmetis-dev:i386 libscotchparmetis-dev:armel libscotchparmetis-dev
>
> E: Package 'libparmetis-dev' has no installation candidate
> """
>
> installing libscotchparmetis-dev does not help.
> dpkg-buildpackage -rfakeroot -b -d yields
>
> [..]
>   Could not find the ParMETIS headers include directory! Please manually set
>   ParMETIS_INCLUDE_DIRS and/or ParMETIS_LIBRARY_DIRS or
> [..]
>
> i don't know what libscotchparmetis is, does it replaces libparmetis for
> trilinos? in that case it should be easy to fix...
>
> thanks
> felix

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Re: Trilinos packages

[Felix Salfelder]

On Sat, Mar 08, 2014 at 12:39:57AM +0100, Nico Schlömer wrote:
> > 1) Set VCS=fields
> > 2) Standards-Version is 3.9.5 now
> > 3) Use DEP-3 for patches (Description, Author, Last-Updates is enough)
> > 4) Remove some unnecessary comments from debian/rules.
> > It should be as short as possible. Leave only necessary notes.
> > 5) Check 3rd-party files and add them to debian/copyright (if they are).
> 
> Done and done; I pushed the changes to alioth.

tried to build (dpkg-buildpackage -rfakeroot -b) on a machine close to testing.

[..]
dpkg-checkbuilddeps: Unmet build dependencies: libparmetis-dev
[..]

apt-get install libparmetis-dev says

"""
Package libparmetis-dev is not available, but is referred to by another package.
This may mean that the package is missing, has been obsoleted, or
is only available from another source
However the following packages replace it:
  libscotchparmetis-dev:i386 libscotchparmetis-dev:armel libscotchparmetis-dev

E: Package 'libparmetis-dev' has no installation candidate
"""

installing libscotchparmetis-dev does not help.
dpkg-buildpackage -rfakeroot -b -d yields

[..]
  Could not find the ParMETIS headers include directory! Please manually set
  ParMETIS_INCLUDE_DIRS and/or ParMETIS_LIBRARY_DIRS or
[..]

i don't know what libscotchparmetis is, does it replaces libparmetis for
trilinos? in that case it should be easy to fix...

thanks
felix

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Re: Trilinos packages

[Nico Schlömer]

> 1) Set VCS=fields
> 2) Standards-Version is 3.9.5 now
> 3) Use DEP-3 for patches (Description, Author, Last-Updates is enough)
> 4) Remove some unnecessary comments from debian/rules.
> It should be as short as possible. Leave only necessary notes.
> 5) Check 3rd-party files and add them to debian/copyright (if they are).

Done and done; I pushed the changes to alioth.

--Nico


On Fri, Mar 7, 2014 at 10:38 PM, Anton Gladky  wrote:
> Please, do the following:
> 1) Set VCS=fields
> 2) Standards-Version is 3.9.5 now
> 3) Use DEP-3 for patches (Description, Author, Last-Updates is enough)
> 4) Remove some unnecessary comments from debian/rules.
> It should be as short as possible. Leave only necessary notes.
> 5) Check 3rd-party files and add them to debian/copyright (if they are).
>
> But the package looks fine! Though I did not build it yet. Please, check
> your .changes file with lintian.
>
> I will upload it shortly.
>
> Anton
>
>
> 2014-03-07 22:20 GMT+01:00 Nico Schlömer :
>
>> I hadn't, but I now found 
>> which I now followed. upstream and pristine-tar are now in place.
>>
>> --Nico
>>
>>
>> On Fri, Mar 7, 2014 at 6:40 PM, Anton Gladky  wrote:
>> > Did you push pristine-tar and upstream branches?
>> >
>> >
>> > Anton
>> >
>> >
>> > 2014-03-07 17:28 GMT+01:00 Nico Schlömer :
>> >
>> >> Alright.
>> >>
>> >> I've now pushed the contents of the ./debian/ folder to
>> >> alioth:/git/debian-science/packages//trilinos.git from where it can be
>> >> reviewed.
>> >> Will someone open a bug about the new package? Do I need to file na
>> >> official ITP?
>> >>
>> >> Cheers,
>> >> Nico
>> >>
>> >> On Fri, Mar 7, 2014 at 2:48 PM, Anton Gladky  wrote:
>> >> > Hi Nico,
>> >> >
>> >> > we need to update our Policy. Please, follow "new" rules.
>> >> >
>> >> > Anton
>> >> >
>> >> >
>> >> >
>> >
>> >
>
>

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Re: Trilinos packages

[Anton Gladky]

Please, do the following:
1) Set VCS=fields
2) Standards-Version is 3.9.5 now
3) Use DEP-3 for patches (Description, Author, Last-Updates is enough)
4) Remove some unnecessary comments from debian/rules.
It should be as short as possible. Leave only necessary notes.
5) Check 3rd-party files and add them to debian/copyright (if they are).

But the package looks fine! Though I did not build it yet. Please, check
your .changes file with lintian.

I will upload it shortly.

Anton


2014-03-07 22:20 GMT+01:00 Nico Schlömer :

> I hadn't, but I now found 
> which I now followed. upstream and pristine-tar are now in place.
>
> --Nico
>
>
> On Fri, Mar 7, 2014 at 6:40 PM, Anton Gladky  wrote:
> > Did you push pristine-tar and upstream branches?
> >
> >
> > Anton
> >
> >
> > 2014-03-07 17:28 GMT+01:00 Nico Schlömer :
> >
> >> Alright.
> >>
> >> I've now pushed the contents of the ./debian/ folder to
> >> alioth:/git/debian-science/packages//trilinos.git from where it can be
> >> reviewed.
> >> Will someone open a bug about the new package? Do I need to file na
> >> official ITP?
> >>
> >> Cheers,
> >> Nico
> >>
> >> On Fri, Mar 7, 2014 at 2:48 PM, Anton Gladky  wrote:
> >> > Hi Nico,
> >> >
> >> > we need to update our Policy. Please, follow "new" rules.
> >> >
> >> > Anton
> >> >
> >> >
> >> >
> >
> >
>
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Re: Trilinos packages

[Nico Schlömer]

I hadn't, but I now found 
which I now followed. upstream and pristine-tar are now in place.

--Nico


On Fri, Mar 7, 2014 at 6:40 PM, Anton Gladky  wrote:
> Did you push pristine-tar and upstream branches?
>
>
> Anton
>
>
> 2014-03-07 17:28 GMT+01:00 Nico Schlömer :
>
>> Alright.
>>
>> I've now pushed the contents of the ./debian/ folder to
>> alioth:/git/debian-science/packages//trilinos.git from where it can be
>> reviewed.
>> Will someone open a bug about the new package? Do I need to file na
>> official ITP?
>>
>> Cheers,
>> Nico
>>
>> On Fri, Mar 7, 2014 at 2:48 PM, Anton Gladky  wrote:
>> > Hi Nico,
>> >
>> > we need to update our Policy. Please, follow "new" rules.
>> >
>> > Anton
>> >
>> >
>> >
>
>

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Re: Trilinos packages

[Anton Gladky]

Did you push pristine-tar and upstream branches?


Anton


2014-03-07 17:28 GMT+01:00 Nico Schlömer :

> Alright.
>
> I've now pushed the contents of the ./debian/ folder to
> alioth:/git/debian-science/packages//trilinos.git from where it can be
> reviewed.
> Will someone open a bug about the new package? Do I need to file na
> official ITP?
>
> Cheers,
> Nico
>
> On Fri, Mar 7, 2014 at 2:48 PM, Anton Gladky  wrote:
> > Hi Nico,
> >
> > we need to update our Policy. Please, follow "new" rules.
> >
> > Anton
> >
> >
> >
>
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Re: Trilinos packages

[Nico Schlömer]

Alright.

I've now pushed the contents of the ./debian/ folder to
alioth:/git/debian-science/packages//trilinos.git from where it can be
reviewed.
Will someone open a bug about the new package? Do I need to file na
official ITP?

Cheers,
Nico

On Fri, Mar 7, 2014 at 2:48 PM, Anton Gladky  wrote:
> Hi Nico,
>
> we need to update our Policy. Please, follow "new" rules.
>
> Anton
>
>
>

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Re: Trilinos packages

[Anton Gladky]

Hi Nico,

we need to update our Policy. Please, follow "new" rules.

Anton
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Re: Trilinos packages

[Nico Schlömer]

Hi Anton,

thanks for the links. I've now signed up and go through the package
instructions.

Small hints/questions about
<http://debian-science.alioth.debian.org/debian-science-policy.html>:

  * The policy advises to use DM-Upload-Allowed,
<http://lintian.debian.org/tags/dm-upload-allowed-is-obsolete.html>
advises against. Which is the current policy?

  * The copyright format hint should point to
<http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/>
instead of the draft.

  * The Git link could be updated to <http://git-scm.com/>.

I've otherwise adapted the package accordingly and I'm now waiting for
debian-science membership approval I guess.

Cheers,
Nico

On Fri, Mar 7, 2014 at 11:42 AM, Anton Gladky  wrote:
> Hi Nico,
>
> we discussed it a year ago [1] and we keep our promise.
> Please, follow the procedure according Deb-Sci policy [2],
> create repo and ping me.
>
> [1]
> http://lists.alioth.debian.org/pipermail/debian-science-maintainers/2013-April/017553.html
> [2] http://debian-science.alioth.debian.org/debian-science-policy.html
>
> Regards
>
> Anton
>
>
> 2014-03-07 11:21 GMT+01:00 Nico Schlömer :
>>
>> Hi all,
>>
>> I've noticed that Trilinos for Debian is dead now for a while
>> <http://packages.qa.debian.org/t/trilinos.html>, and I'd like to help
>> reviving it. I already have stable
>> <https://launchpad.net/~nschloe/+archive/trilinos/+packages> and
>> nightly
>> <https://launchpad.net/~nschloe/+archive/trilinos-nightly/+packages>
>> builds for Ubuntu going which I actively maintain, so I guess it
>> wouldn't be too much of a leap.
>>
>> I'm not too familiar with the Debian community and infrastructure
>> though, so I'll need some assistance.
>>
>> Cheers,
>> Nico
>>
>> --
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>>
>> http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-science-maintainers
>
>

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Re: Trilinos packages

[Nico Schlömer]

> As mentionned in an earlier email latest trilinos FTBS
> with gcc 4.8 (sacado module is broken).

I've got all my work at <https://github.com/nschloe/trilinos-ubuntu>.
In the debian.trusty/rules, you'll find comments about the Sacado
issue with a link to the bug report on Trilinos.

> If you are more confortable with git we may move to Debian Science git
> repository.

Git would be great.

--Nico

On Fri, Mar 7, 2014 at 11:36 AM, trophime
 wrote:
> On Fri, 2014-03-07 at 11:21 +0100, Nico Schlömer wrote:
>> Hi all,
>>
>> I've noticed that Trilinos for Debian is dead now for a while
>> <http://packages.qa.debian.org/t/trilinos.html>, and I'd like to help
>> reviving it. I already have stable
>> <https://launchpad.net/~nschloe/+archive/trilinos/+packages> and
>> nightly <https://launchpad.net/~nschloe/+archive/trilinos-nightly/+packages>
>> builds for Ubuntu going which I actively maintain, so I guess it
>> wouldn't be too much of a leap.
>>
>> I'm not too familiar with the Debian community and infrastructure
>> though, so I'll need some assistance.
>
> I'm also trying to rebuild trilinos based on your changes in
> debian/rules. As mentionned in an earlier email latest trilinos FTBS
> with gcc 4.8 (sacado module is broken).
>
> What I suggest is to share our work using the vcs on Debian Science svn.
> If you are more confortable with git we may move to Debian Science git
> repository.
>
> Best
> C.
>
>>
>> Cheers,
>> Nico
>>
>
> --
>
>
> Christophe TROPHIME
> Research Engineer
>
> LNCMI
> CNRS - LNCMI
> 25, rue des Martyrs
> BP 166
> 38042 GRENOBLE Cedex 9
> FRANCE
> CNRS
>
> Tel : +33 (0)4 76 88 90 02
> Fax : +33 (0) 4 76 88 10 01
> Office U 19
> M@il : christophe.troph...@lncmi.cnrs.fr
> 
>

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Re: Trilinos packages

[Anton Gladky]

Hi Nico,

we discussed it a year ago [1] and we keep our promise.
Please, follow the procedure according Deb-Sci policy [2],
create repo and ping me.

[1]
http://lists.alioth.debian.org/pipermail/debian-science-maintainers/2013-April/017553.html
[2] http://debian-science.alioth.debian.org/debian-science-policy.html

Regards

Anton


2014-03-07 11:21 GMT+01:00 Nico Schlömer :

> Hi all,
>
> I've noticed that Trilinos for Debian is dead now for a while
> <http://packages.qa.debian.org/t/trilinos.html>, and I'd like to help
> reviving it. I already have stable
> <https://launchpad.net/~nschloe/+archive/trilinos/+packages> and
> nightly <
> https://launchpad.net/~nschloe/+archive/trilinos-nightly/+packages>
> builds for Ubuntu going which I actively maintain, so I guess it
> wouldn't be too much of a leap.
>
> I'm not too familiar with the Debian community and infrastructure
> though, so I'll need some assistance.
>
> Cheers,
> Nico
>
> --
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>
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>
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Re: Trilinos packages

[trophime]

On Fri, 2014-03-07 at 11:21 +0100, Nico Schlömer wrote:
> Hi all,
> 
> I've noticed that Trilinos for Debian is dead now for a while
> <http://packages.qa.debian.org/t/trilinos.html>, and I'd like to help
> reviving it. I already have stable
> <https://launchpad.net/~nschloe/+archive/trilinos/+packages> and
> nightly <https://launchpad.net/~nschloe/+archive/trilinos-nightly/+packages>
> builds for Ubuntu going which I actively maintain, so I guess it
> wouldn't be too much of a leap.
> 
> I'm not too familiar with the Debian community and infrastructure
> though, so I'll need some assistance.

I'm also trying to rebuild trilinos based on your changes in
debian/rules. As mentionned in an earlier email latest trilinos FTBS
with gcc 4.8 (sacado module is broken). 

What I suggest is to share our work using the vcs on Debian Science svn.
If you are more confortable with git we may move to Debian Science git
repository. 

Best
C.

> 
> Cheers,
> Nico
> 

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FRANCE
CNRS

Tel : +33 (0)4 76 88 90 02 
Fax : +33 (0) 4 76 88 10 01
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Trilinos packages

[Nico Schlömer]

Hi all,

I've noticed that Trilinos for Debian is dead now for a while
<http://packages.qa.debian.org/t/trilinos.html>, and I'd like to help
reviving it. I already have stable
<https://launchpad.net/~nschloe/+archive/trilinos/+packages> and
nightly <https://launchpad.net/~nschloe/+archive/trilinos-nightly/+packages>
builds for Ubuntu going which I actively maintain, so I guess it
wouldn't be too much of a leap.

I'm not too familiar with the Debian community and infrastructure
though, so I'll need some assistance.

Cheers,
Nico

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