gap on smc; whitelist gap-system.org

[Samuel Lelièvre]

Hi from GAP Days in Aachen!

Could the GAP version in smc's Sage be made to be
the complete GAP install? Or alternatively, would it be
possible to have a separate full GAP install?

Also, would it be possible to whitelist gap-system.org?
(IP addresses: 138.251.192.244 and 138.251.192.245).

Samuel

[William A Stein]

On Thu, Aug 28, 2014 at 2:58 PM, Samuel Lelièvre
<samuel....@gmail.com> wrote:
> Hi from GAP Days in Aachen!
>
> Could the GAP version in smc's Sage be made to be
> the complete GAP install?

What is a complete GAP install?

> Or alternatively, would it be
> possible to have a separate full GAP install?

What is a separate full GAP install? In particular, could you
clarify what is wrong with the Sage version of GAP?

Thanks,

William

>
> Also, would it be possible to whitelist gap-system.org?
> (IP addresses: 138.251.192.244 and 138.251.192.245).
>
> Samuel
>

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--
William Stein
Professor of Mathematics
University of Washington
http://wstein.org
wst...@uw.edu

[Samuel Lelièvre]

William wrote:

On Thu, Aug 28, 2014 at 2:58 PM, Samuel Lelièvre wrote:
> Hi from GAP Days in Aachen!
>
> Could the GAP version in smc's Sage be made to be
> the complete GAP install?

What is a complete GAP install?

>  Or alternatively, would it be
> possible to have a separate full GAP install?

What is a separate full GAP install?   In particular, could you
clarify what is wrong with the Sage version of GAP?

How complete the install is depends on
- Libs used (GAP compiled with/without gmp / readline)
- Components (databases etc)
- Packages

Below are the startup headers for launching GAP on
SageMathCloud and launching a "full" install on my
computer (although compiled without readline).

The one on SageMathCloud has both the gmp and
the readline libs, and all the "components", but less
packages than you get when installing a "full" GAP.

Samuel

---------- Launching SageMathCloud's GAP ----------
$ gap

 ┌───────┐   GAP, Version 4.7.5 of 24-May-2014 (free software, GPL)

 │  GAP  │   http://www.gap-system.org

 └───────┘   Architecture: x86_64-unknown-linux-gnu-gcc-default64

 Libs used:  gmp, readline

 Loading the library and packages ...

 Components: trans 1.0, prim 2.1, small* 1.0, id* 1.0

 Packages:   Alnuth 3.0.0, AtlasRep 1.5.0, AutPGrp 1.6, CTblLib 1.2.2, FactInt 1.5.3, GAPDoc 1.5.1, LAGUNA 3.6.4, Polycyclic 2.11, TomLib 1.2.4

 Try '?help' for help. See also  '?copyright' and  '?authors'

gap>

---------- Launching a "full" GAP install ----------
$ gap
 ┌───────┐   GAP, Version 4.7.5 of 24-May-2014 (free software, GPL)
 │  GAP  │   http://www.gap-system.org
 └───────┘   Architecture: x86_64-apple-darwin13.3.0-gcc-default64
 Libs used:  gmp
 Loading the library and packages ...
 Components: trans 1.0, prim 2.1, small* 1.0, id* 1.0
 Packages:   AClib 1.2, Alnuth 3.0.0, AtlasRep 1.5.0, AutPGrp 1.6, Browse 1.8.5, Carat 2.1.4, CRISP 1.3.8,
             Cryst 4.1.12, CrystCat 1.1.6, CTblLib 1.2.2, FactInt 1.5.3, FGA 1.2.0, GAPDoc 1.5.1, IO 4.3.1,
             IRREDSOL 1.2.4, LAGUNA 3.6.4, Polenta 1.3.2, Polycyclic 2.11, RadiRoot 2.7, ResClasses 3.3.2,
             Sophus 1.23, SpinSym 1.5, TomLib 1.2.4
 Try '?help' for help. See also  '?copyright' and  '?authors'
gap>
----------

[William A Stein]

On Thu, Aug 28, 2014 at 5:43 PM, Samuel Lelièvre
<samuel....@gmail.com> wrote:
>
>
> William wrote:
>>
>> On Thu, Aug 28, 2014 at 2:58 PM, Samuel Lelièvre wrote:
>> > Hi from GAP Days in Aachen!
>> >
>> > Could the GAP version in smc's Sage be made to be
>> > the complete GAP install?
>>
>> What is a complete GAP install?
>>
>> > Or alternatively, would it be
>> > possible to have a separate full GAP install?
>>
>> What is a separate full GAP install? In particular, could you
>> clarify what is wrong with the Sage version of GAP?
>
>
> How complete the install is depends on
> - Libs used (GAP compiled with/without gmp / readline)
> - Components (databases etc)
> - Packages
>
> Below are the startup headers for launching GAP on
> SageMathCloud and launching a "full" install on my
> computer (although compiled without readline).
>
> The one on SageMathCloud has both the gmp and
> the readline libs, and all the "components", but less
> packages than you get when installing a "full" GAP.

There are a large number of packages here.

http://www.gap-system.org/Packages/packages.html

Which ones should I install? All of them? Some of them?

Can you ask at the meeting?

William

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[William A Stein]

> There are a large number of packages here.
>
> http://www.gap-system.org/Packages/packages.html
>
> Which ones should I install? All of them? Some of them?
>
> Can you ask at the meeting?

Do you know if I could install *all* of them, or do some change
behavior of Gap and interfere with others? Or, like with Python,
possibly increase startup time.

William

[Dima Pasechnik]

On 2014-08-29, William A Stein <wst...@uw.edu> wrote:
>> There are a large number of packages here.
>>
>> http://www.gap-system.org/Packages/packages.html
>>
>> Which ones should I install? All of them? Some of them?
>>
>> Can you ask at the meeting?
>
> Do you know if I could install *all* of them, or do some change
> behavior of Gap and interfere with others? Or, like with Python,
> possibly increase startup time.

one can autoload a GAP package, then
be loaded at startup by default. Some packages are set
to autoload, some don't (but you can change this).
http://www.gap-system.org/Manuals/doc/ref/chap76.html

My understanding is that the default Unix installation of GAP
nowadays includes (almost) all packages; however, they might
need to be built explicitly to enable functionality implemented
in C.

I think for this (large) subset of packages, it's checked
that things work, but given that GAP has no namespaces,
problems do arise now and then with packages interfering with
one another.

Dima

[Samuel Lelièvre]

William Stein wrote:

You could install all of them, eg you can use Bob.
More detail on how follows (a bit lengthy maybe, sorry).

On the home page of the GAP website,

    http://www.gap-system.org/

one reads:

    Welcome to

        GAP - Groups, Algorithms, Programming -
        a System for Computational Discrete Algebra

    The current version is [GAP 4.7.5] released on 24 May 2014.

where [GAP 4.7.5] links to:

    http://www.gap-system.org/Releases/index.html

That page

   http://www.gap-system.org/Releases/index.html

gives the list of the packages that you get in the standard tarball.

At the top of that page you also read

    GAP 4.7.5 downloads

    [ You may also consider one of the [alternative installation methods] ]

where [alternative installation methods] links to:

    http://www.gap-system.org/Download/index.html#alternatives

The alternative installation methods discussed there include
Max Neunhöffer's 'Bob' tool.

      [BOB - a tool to download and build GAP and its packages from source]
      for Linux and Mac OS X. You only download BOB who does all the rest for you.
      You need a C-compiler and some libraries installed on your system but BOB
      will tell you exactly what is missing.

Place the Bob script in the directory where you want to install gap,
run the 'bob' script, and that will build GAP and all the packages.

To save space, you can then delete the gap tarball in 'bobdownloads/'.

[Alexander Konovalov]

Thank you for the BOB details, Samuel! And the direct link to BOB is

http://neunhoef.github.io/bob/

It will create several scripts to start GAP:

* gap64 to start 64-bit version of GAP
* gap64L to start the same using the workspace.
* similarly, gap32 and gap32L
* finally, gap and gapL which will (on 64-bit system) be same as gap64 and gap64L (could be symlinks, of course)

Perhaps one could just set that 'gap' will call 'gapL', since using the workspace will greatly speed up loading GAP.

[Alexander Konovalov]

On Friday, August 29, 2014 8:06:33 AM UTC+1, Stein William wrote:
> > There are a large number of packages here.
>
> >
>
> > http://www.gap-system.org/Packages/packages.html
>
> >
>
> > Which ones should I install? All of them? Some of them?
>
> >
>
> > Can you ask at the meeting?
>
>
>
> Do you know if I could install *all* of them, or do some change
>
> behavior of Gap and interfere with others? Or, like with Python,
>
> possibly increase startup time.
>

Installing all packages will not increase GAP startup time, since they are not loaded (it's not a good idea to load all packages simultaneously). It will only increase the disk space used by GAP. OTOH, the user will be able to use GAP help system to search across manuals of ALL packages installed on the system.

Then, since the same packages will be loaded after default GAP startup, the user will have the same experience in both cases.

Furthermore, testing the GAP distribution, we ensure that this particular set of packages is fitting together, so I'd not guarantee that tearing it apart will not cause any side effects.

Best regards,
Alexander

[William A Stein]

I'm cc'ing this to sage-devel. It is about GAPs long, long list of
packages, most of which we don't include or even package optionally
for Sage...

Can I use BOB to install all the "accepted GAP packages" into an
existing GAP install? It seems to me that BOB both builds GAP and
installs all packages into that GAP. I don't want that -- I instead
want to use the GAP I built as part of Sage.

Also, in general, my understanding is that installing a GAP package is
explained here

http://www.gap-system.org/Manuals/doc/ref/chap76.html#X7B6CD527825945CD

and basically that says to download the package, extract it, and
read/guess/etc. what to do next. In particular, what to do can be
anything from nothing, to really complicated, and there's no single
script to just run. I was expecting that I could just make a list of
packages and type something like

gap -i names of packages ...

and it would install all of them, like every other package system I've
ever used does (e.g., R, Pypi, Sage's, npm, and many others). If
BOB can basically do exactly this, then that's very, very cool and a
great contribution to GAP. If you could quickly summarize the
situation about what BOB can actually do with an existing GAP install,
it would be greatly appreciated. (I haven't just tried diving into
BOB due to lack of time.)

Thanks,

-- William



> Best regards,
> Alexander

>
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[William A Stein]

gap-system.org should now be whitelisted.

William

>
> Samuel

>
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[Alexander Konovalov]

Thank you for questions. At the moment, BOB performs a new install, so it's not suitable to update an existing GAP installation. That is a suggestion for the future perhaps, for BOB or for any other package manager for GAP that may appear. I was recommending BOB in response to Samuel saying "... alternatively, would it be possible to have a separate full GAP install?". If you prefer just to add some more packages to the GAP version that is built as part of Sage, and do not want all of them for some reasons, then it would be great at least to ensure that all packages listed under the 'PackagesToLoad' user preference in lib/package.gi are included:

  default:= [ "autpgrp", "alnuth", "crisp", "ctbllib", "factint", "fga",  
              "irredsol", "laguna", "polenta", "polycyclic", "resclasses",  
              "sophus", "tomlib" ],

But the actual list will be larger, since these default packages have some dependencies, as can be seen from the GAP startup information:

 ┌───────┐   GAP, Version 4.7.5 of 24-May-2014 (free software, GPL)
 │  GAP  │   http://www.gap-system.org
 └───────┘   Architecture: x86_64-unknown-linux-gnu-gcc-default64
 Libs used:  gmp, readline
 Loading the library and packages ...
 Components: trans 1.0, prim 2.1, small* 1.0, id* 1.0

 Packages:   AClib 1.2, Alnuth 3.0.0, AtlasRep 1.5.0, AutPGrp 1.6,
             Browse 1.8.5, Carat 2.1.4, CRISP 1.3.8, Cryst 4.1.12,
             CrystCat 1.1.6, CTblLib 1.2.2, FactInt 1.5.3, FGA 1.2.0,
             GAPDoc 1.5.1, IO 4.3.1, IRREDSOL 1.2.4, LAGUNA 3.6.4,
             Polenta 1.3.2, Polycyclic 2.11, RadiRoot 2.7, ResClasses 3.3.2,
             Sophus 1.23, SpinSym 1.5, TomLib 1.2.4
 Try '?help' for help. See also  '?copyright' and  '?authors'
gap>

Ideally, starting GAP from Sage, one should be able to see the same.

Best regards

Alexander

 

[William A Stein]

Hi Sage-devs,

Is there anybody out there whose interested in (greatly) increasing
the number of optional gap packages in the optional GAP spkg for Sage?

This thread has a lot of info about this. In particular, this would
be very beneficial to SageMathCloud...

-- William

On Tue, Sep 2, 2014 at 3:22 PM, Alexander Konovalov

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[Samuel Lelièvre]

William Stein wrote:

Is there anybody out there whose interested in (greatly) increasing
the number of optional gap packages in the optional GAP spkg for Sage?

This thread has a lot of info about this.    In particular, this would
be very beneficial to SageMathCloud...

 -- William

Ideally, the sagecell server(s) at sagecell.sagemath.org and
aleph.sagemath.org could also have a fuller GAP, so that it
would be a place to play with GAP online.

Samuel
 

[Dima Pasechnik]

On 2014-09-02, William A Stein <wst...@uw.edu> wrote:
> Hi Sage-devs,
>
> Is there anybody out there whose interested in (greatly) increasing
> the number of optional gap packages in the optional GAP spkg for Sage?

Probably it would be better to split the optional GAP spkg into parts, otherwise
it will be huge...
(the current gap_packages*.bz2 is already 27Mb)

There are also things like missing license info for a number of packages.
AFAIK GAP devs were not able to fix this.
I'm not sure whether it's OK to impose on such packages the GAP's
own license - probably not, as GAP is under GPL, and GPL needs
contributor's consent.

There also also few packges which provide interfaces to other systems,
like Singular, and they might be tricky to get right
within Sage.

If there are no other volunteers, I can look into this, but I can't
promise a fast completion, as papers+grants have priority in my
(publish&&grants)||perish case.

Dima

[Simon King]

Hi Dima,

On 2014-09-03, Dima Pasechnik <dim...@gmail.com> wrote:
> There also also few packges which provide interfaces to other systems,
> like Singular, and they might be tricky to get right
> within Sage.

If I recall correctly, at some GAP days, I managed to build he interface
to Singular with GAP in Sage. So, perhaps this would be doable via an
spkg. I don't recall what was needed to do, though.

Best regards,
Simon

[William A Stein]

Yes, that's exactly why I'm hoping we improve the Sage gap spkg,
rather than me just using BOB (say) on SageMathCloud. I want Sage and
all sage-related services to also have a better GAP install.

William

>
> Samuel

[William A Stein]

On Wed, Sep 3, 2014 at 1:44 AM, Dima Pasechnik <dim...@gmail.com> wrote:
> On 2014-09-02, William A Stein <wst...@uw.edu> wrote:
>> Hi Sage-devs,
>>
>> Is there anybody out there whose interested in (greatly) increasing
>> the number of optional gap packages in the optional GAP spkg for Sage?
>
> Probably it would be better to split the optional GAP spkg into parts, otherwise
> it will be huge...
> (the current gap_packages*.bz2 is already 27Mb)

Sure, that would be fine. E.g., we could have
gap_packages-recommended and gap_packages-more or something, i.e.,
name them in a way that divides them into two. Of course, for SMC
I'll just install both.

> There are also things like missing license info for a number of packages.
> AFAIK GAP devs were not able to fix this.
> I'm not sure whether it's OK to impose on such packages the GAP's
> own license - probably not, as GAP is under GPL, and GPL needs
> contributor's consent.

Yes, the licensing is a big problem, which is why this will only ever
be optional, and not something we distribute with Sage.

Of course, I don't want any packages that have licenses that mean I
can't install them in SMC...

> There also also few packges which provide interfaces to other systems,
> like Singular, and they might be tricky to get right
> within Sage.
>
> If there are no other volunteers, I can look into this, but I can't
> promise a fast completion, as papers+grants have priority in my
> (publish&&grants)||perish case.

Maybe you could provide some scratch directions, without doing everything...?

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[Dima Pasechnik]

OK, I have created  http://trac.sagemath.org/ticket/16928

The first task is to prepare a list of packages to be added...

Dima