[Insight-developers] Linear algebra licensing and ITK 3.18 Release

Tue Mar 16 03:35:40 EDT 2010

what about OpenNL 3.0? BSd, supports all kind of plateform AND gpu.

http://gpgpu.org/2010/02/14/opennl-cuda-sparse-linear-solvers

On Tue, Mar 16, 2010 at 7:15 AM, Tom Vercauteren
<tom.vercauteren at m4x.org> wrote:
> Hi Luis,
>
> Thanks for getting back to me.
>
> It looks like lbfgs and lbfgsb is much more of a problem than lsqr...
>
> Indeed, the authors of lsqr chose to also license their software as BSD.
>  http://www.stanford.edu/group/SOL/software/BSDlicense.txt
> So while ACM might own the copyright of the code for some obscure
> reasons, at least we are not willingly infringing the authors will.
>
> L-BFGS L-BFGS-B seems more problematic, there is the same issue of
> copyright potentially held by ACM
>  http://portal.acm.org/citation.cfm?id=279236
> but the authors refer to their software as a GPL one:
>  http://www.eecs.northwestern.edu/~nocedal/lbfgsb.html
>  http://www.eecs.northwestern.edu/~nocedal/lbfgs.html
> even though this is not consistent with what is written on these pages
>  "This software is freely available for educational or commercial purposes."
>  "This software is freely available [...] all commercial products using it"
>
> We should think moving towards the elastix implementation of it:
>  http://elastix.isi.uu.nl/doxygen/a00204.html
> which is BSD
>  http://elastix.isi.uu.nl/legal.php
>
> Another option could be
>  http://www.chokkan.org/software/liblbfgs/
>
> I am adding this info to the bug entry.
>
> Hope this helps,
> Tom
>
> On Mon, Mar 15, 2010 at 23:14, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>> Hi Tom,
>>
>>
>> A)   Good point,
>>       We should have filed a bug entry on this issue.
>>
>>       I just did so:
>>       http://public.kitware.com/Bug/view.php?id=10422
>>
>>       and added an email trail of the discussions in the mailing list:
>>       http://public.kitware.com/Bug/view.php?id=10422#bugnotes
>>
>>
>> B)  At this point the main concern is     "lsqr".
>>
>>     but, during the weekend we heard (in the Slicer-dev mailing
>>     list) that the lbfgsb optimizer may have similar issues.
>>
>>
>> C)  The immediate things to try are:
>>
>>                    1) test       vnl_sparse_lu
>>                    2) test       itpack
>>
>>      These two, are pieces of code that already in the ITK
>>      repository and that could be replacements for "lsqr".
>>
>>
>> D)  My understanding about the "lsqr" problem is that the
>>      Fortran version of this routine(s) was published in ACM:
>>
>>           http://portal.acm.org/citation.cfm?id=355989
>>
>>       as Algorithm 583:
>>
>> http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.86.1305&rep=rep1&type=pdf
>>
>>     and it is listed in the Collection of ACM algorithtms
>>
>>                    http://calgo.acm.org/
>>
>>     as
>>
>>                    http://calgo.acm.org/583.gz
>>
>>      and that this code is the same as the FORTRAN one in
>>
>>                  http://www.netlib.org/linalg/lsqr
>>
>>      that then was put into VXL
>>
>> http://www.itk.org/cgi-bin/viewcvs.cgi/Utilities/vxl/v3p/netlib/linalg/lsqr.f?revision=1.2&root=Insight&view=markup
>>
>>      from which the VXL  C version was generated:
>>
>> http://www.itk.org/cgi-bin/viewcvs.cgi/Utilities/vxl/v3p/netlib/linalg/lsqr.c?root=Insight&view=markup
>>
>>
>> The software in ACM Algorithms is subject to this license
>> http://www.acm.org/publications/policies/softwarecrnotice
>>
>> <quote>
>> "Noncommercial Use
>> The ACM grants to you (hereafter, User) a royalty-free, nonexclusive
>> right to execute, copy, modify and distribute both the binary and
>> source code solely for academic, research and other similar
>> noncommercial uses, subject to the following conditions:"
>> </quote>
>>
>>
>>
>>      The key question at this point is
>>
>>          Who holds the copyright of  "lsqr.f"    ?
>>
>>       Is it
>>
>>      1) Association for Computing Machinery, Inc. ?
>>
>> or
>>
>>      2) Michael Saunders (http://www.stanford.edu/~saunders/)
>>          and Chris Page.
>>
>>      I'm sending emails to the three of them,
>>      and I'm anticipating an interesting set of responses....
>>
>>      Once we figure out who is the copyright holder,
>>      we can ask them about licensing....
>>
>>
>>
>>  Thanks for your persistence with this issue...
>>
>>
>>        Luis
>>
>>
>> ----------------------------------------------------------------------------------------
>> On Fri, Mar 5, 2010 at 12:09 PM, Tom Vercauteren
>> <tom.vercauteren at gmail.com> wrote:
>>> Hi Luis and Bill,
>>>
>>> Sorry to come back to it, but I have to admit I am a bit lost on the
>>> linear algebra problem that blocks the 3.18 release.
>>>
>>> Is there a bug tracker entry that lists the remaining issues that
>>> needs to be solved before getting 3.18 out? I am not sure to know what
>>> needs to be fixed exactly. Is it only lsqr as implied by your message
>>> here:
>>>  http://www.itk.org/pipermail/insight-users/2010-January/035063.html
>>> or are there other potential problems?
>>>
>>> If it's only lsqr, are you sure that we are not allowed to use it? If
>>> I look at the different lsqr packages here,
>>>  http://www.stanford.edu/group/SOL/software/lsqr.html
>>> I would be inclined to think that the lsqr code is licensed under the
>>> CPL which seems to be incompatible with BSD*.
>>> However, lsqr is only one part of the SOL package from Stanford:
>>>  http://www.stanford.edu/group/SOL/software.html
>>>
>>> And from this page, it is clearly stated that
>>>  "The software may alternatively be used under the terms of a  BSD License."
>>>
>>> Could that solve the 3.18 blocker?
>>>
>>> Anyhow, this raises some other related questions. What is the base
>>> plan for 3.18?
>>> 1) Find a decent set of patches that answers the licensing issues
>>> or
>>> 2) Try and get a suitable replacement for the linear algebra package as a whole
>>>
>>> Similarly is there a defined roadmap on this for ITK 4.0?
>>>
>>> In the meantime, I have updated the wiki page:
>>>  http://www.itk.org/Wiki/Proposals:Sparse_Linear_Solvers
>>>
>>> Unfortunately, I have not been able to find a decent linear algebra
>>> package that covers ITK's needs:
>>> - Support high-level dense matrix algorithms (e.g. Cholesky, LU and QR
>>> factorization, linear solvers, matrix exponential)
>>> - Support high-level sparse matrix algorithm (e.g. least squares
>>> solvers, linear solver)
>>> - BSD-style license
>>> - Maintained code
>>>
>>> Despites its headers-only LGPL awkwardnesses (see
>>> http://public.kitware.com/pipermail/insight-users/2010-February/035070.html
>>> ), the closest I can see is still Eigen.
>>>
>>> Regards,
>>> Tom
>>>
>>> * IANAL
>>>
>>> On Mon, Mar 1, 2010 at 23:59, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>>> Hi John,
>>>>
>>>> The ITK 3.18 release is stuck on finding a replacement
>>>> for the linear solvers that we use from VNL/VXL.
>>>>
>>>> The code that we are currently using for solving linear
>>>> equations is copyrighted by ACM and its license precludes
>>>> commercial use. (therefore it is not compatible with ITK's
>>>> license, and has to be removed).
>>>>
>>>> We have been looking at another linear solvers, but have
>>>> not got to the point where we have a suitable replacement.
>>>>
>>>> You will find a summary of our exploration in the following
>>>> Wiki page:
>>>>
>>>> http://www.itk.org/Wiki/Proposals:Sparse_Linear_Solvers
>>>>
>>>>
>>>> We will appreciate any suggestions,
>>>>
>>>>
>>>>       Thanks,
>>>>
>>>>
>>>>              Luis
>>>>
>>>>
>>>> ------------------------------------------------------------------------------------
>>>> On Mon, Mar 1, 2010 at 3:06 PM, John Drescher <drescherjm at gmail.com> wrote:
>>>>> On Thu, Dec 3, 2009 at 10:16 PM, Luis Ibanez <luis.ibanez at kitware.com> wrote:
>>>>>> The agenda for tomorrow's tcon has been posted at:
>>>>>>
>>>>>> http://www.itk.org/Wiki/Agenda%26Status_120309
>>>>>>
>>>>>> It includes a suggested list of items to work on
>>>>>> for the release of ITK 3.18 by January 2010.
>>>>>>
>>>>>
>>>>> BTW, What happened to this release?
>>>>>
>>>>> John
>>>>> _____________________________________
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>>>
>>
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