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CoolGenie
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PostPosted: Sun Dec 09, 2007 9:30 am    Post subject: SAGE mathematics software Reply with quote

Hello!
Why isn't SAGE (www.sagemath.org) included in the Portage tree? I will have to compile it by hand... :?
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phsdv
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PostPosted: Sun Dec 09, 2007 9:57 am    Post subject: Reply with quote

For new packages (or packages that are not in portage) you could look into bugzilla to see if there is an ebuild available. For sage there is one here, but as Francois wrote:
Quote:
The main problem is that it come with the sources for stuff that is already in portage and has a very bad building system in that you cannot use stuff that you already have installed at _all_. It is fully "integrated" with its own internal packaging system.
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platojones
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PostPosted: Sun Dec 09, 2007 5:33 pm    Post subject: Reply with quote

Yes, I just installed the source version on my system and this thing does not integrate well at all in a source based distro. I did some research, and it turns out that the reason they include and rebuild many packages you already have on your system (though they keep in all in a self-contained sandbox), is that they patch a lot of these dependent open-source packages to work with sage or are tied very tightly to one particular version. This means that to build it requires a very long compile time and consumes something like 800 mb of disk space. It's also a pretty hefty download, at 160 mb or somewhere around there. It was written by Mathematicians, not software engineers (not an insult, by any means, just helps explain why it's so different from most other open-source packages).

On the plus side, even though it includes and builds all of it's dependencies, it is completely self contained, so building it won't mess up your system, and on my system, it works really well. It's so easy to build (just untar it in it's own directory and type 'make'), that it's hard to go wrong. I think you can install just the binary portions in their own directory as well by setting an environment variable containing the target directory and typing 'make install'. Again, no big deal, just some extra compile time and disk space. Very interesting app. If it does become a gentoo package, a binary distribution would probably make the most sense.
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mark_alec
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PostPosted: Mon Dec 10, 2007 12:40 am    Post subject: Reply with quote

Moved from Other Things Gentoo to Unsupported Software.
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fb
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PostPosted: Tue Dec 11, 2007 12:42 am    Post subject: Reply with quote

I am the "Francois" quoted earlier. Reading all the comments in the bug is an education
in itself.
Several people cannot build it for various reason. I myself built it without problems on
an old (3-4 year) athlon but I was snubbed on a more recent intel dual processor machine.
I haven't tried on my ppc yet as I have OOo-2.3.1 to build but I don't remember it coming
in binary form for that arch and that is my main work machine where it would be most useful.
Note that not only is it self contained but according to the documentation it has its
own updating system 8O .
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platojones
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PostPosted: Tue Dec 11, 2007 1:06 am    Post subject: Reply with quote

Quote:

Note that not only is it self contained but according to the documentation it has its
own updating system 8O .


Indeed, almost like it's a totally self-contained Gentoo portage system. I just invoked it with ./sage -update and now it's recompiling itself with a bunch of patches.
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dtoo
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PostPosted: Tue Dec 11, 2007 7:30 am    Post subject: Reply with quote

very interesting, i will try it.
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ugus
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PostPosted: Sat Dec 29, 2007 11:33 am    Post subject: Reply with quote

I installed it. I can say, it is really very interesting and nice open source mathematic software. All of the most important mathematic programs are collected under one hood. You even do not need to install plot anymore :). And even more, it provides code-indent and auto-completion what original python interpreter does not do :D
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fb
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PostPosted: Sat Dec 29, 2007 11:51 am    Post subject: Reply with quote

For those who are compiling it from source and have some compilation problems
I discovered that having an intel compiler (fortran or C/C++) induce a wrong behavior
in one of the building components (scons). It will be fixed but it has snubbed me for
almost a month.
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fb
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PostPosted: Thu Jan 10, 2008 11:57 pm    Post subject: Reply with quote

I have been working more or less on pulling stuff out of the sage
build system and getting it to use portage provided one and then
making an ebuild using a minimum of internal packages.
This is taking quite a lot of time and of course there is the problem
that sage is moving quite fast. And also my build failed a number of
test because of a small patch not in portage on gmp :roll: (not even
a patch for a bug - no a patch for speed and "minimal" result).

To continue this stuff there will need to be an overlay to store the
packages that need a special patch or modification not yet integrated
upstream or in Gentoo, not to mention version not yet in portage.
I also cannot do it alone. I contacted the author of the sage bug
but so far I got no answer. I also know a few people have added themselve
on the bug.

You could say I am posting here to see if anyone would be interested
in working on this. Just contributing by testing would be fine too.
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Urban Cowboy
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PostPosted: Fri Jan 11, 2008 5:07 am    Post subject: Reply with quote

I've actually been looking for some good math software. Is it any good? How does it compare to derive?
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fb
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PostPosted: Fri Jan 11, 2008 7:00 am    Post subject: Reply with quote

I am not familiar with derive. And I am really just starting with sage.
It is python based and you can program it in python if you need to.
Depending on your need you may be satisfied with just maxima
(sage includes maxima).

You can try it online as it can be set as an application running on a
server and accessed by web-browser. Have a look there:
http://www.sagemath.org/ and here for example:
https://sage.math.washington.edu:8101/
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fb
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PostPosted: Mon Jan 21, 2008 6:55 am    Post subject: Reply with quote

OK, I did go ahead and posted an ebuild for the current version
of sage (2.10) in the sage bug.
It should solve a number of problems people had with 2.8.15.
It use some package from portage rather than the sage
provided one (atlas for example). Further gentoo-isation
should take place in an overlay - if there is enough interest.
Comments and feedback in the bug or this thread.
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ukavi
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PostPosted: Fri Feb 08, 2008 2:43 pm    Post subject: Reply with quote

First of all, good job so far. I would certainly be interested in gentooifying sage. I've already installed 2.10.1, it seems like this package certainly has a future, although thorough communication with upstream would not be bad idea. Yes, they are (genial) mathematicians, I have great respect for them and they should be helped making an open source project.

I kind of want to help, but I have no idea how. I can test, but my PC currently is extremely slow at building (i'm still using an athlon XP 1500+) (although I expect to buy something quad-coreish soonish). I can make ebuilds, but they will need checking. Please let sage live, it would be a perfect proof that open source software can indeed be better than proprietary software, even for smaller audiences (as opposed to big projects like OpenOffice.org, MySQL and of course the linux kernel).
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fb
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PostPosted: Fri Feb 08, 2008 6:04 pm    Post subject: Reply with quote

Thank you for your encouragements.

It would have been nice if you could have tested my 2.10.1 ebuild from bugzilla,
but that's definitely a bit slow. Note that once we have modularized the sage
install it may take less time (sage proper is still a long compile).
Progress may be slowed down by the fact that I am proud father since Tuesday.
But I'll try to a least update the ebuild as sage comes out.
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creidiki
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PostPosted: Fri Feb 08, 2008 6:12 pm    Post subject: Reply with quote

fb wrote:
Progress may be slowed down by the fact that I am proud father since Tuesday.


Congrats! I'll try to test the .1 ebuild from b.g.o. soon-ish :)
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fb
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PostPosted: Fri Feb 08, 2008 7:22 pm    Post subject: Reply with quote

It should build OK but report any problems.
Once installed it would be nice to run the test suite
(actually I should make that part of the ebuild).
As root run
Code:
sage -testall

and report if it pass, if there are any failure
try to post the relevant part of the test.log file.

I am also on the sage-devel mailing list and I have
good relations with the devs there. They are very
responsive to any issue I report.
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serial_penguin
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PostPosted: Fri Feb 08, 2008 9:12 pm    Post subject: Reply with quote

This is definitely a worthwhile effort! The 2.10.1 ebuild from bugzilla wouldn't build for me. I have an amd64 machine and encountered the config error
Code:

configure: error: ABI=amd64 is not among the following valid choices: 64 32 Failed to configure.

associated with installing the gmp package as noted at the sage bug. As noted there the portage ebuild for gmp has such a patch. I'm not exactly sure where in the sage hierarchy the patch needs to be applied. It would be nice if the portage stuff could be used in such situations, although the sage gmp may be unusually patched. The 2.10.1 tarball did build but took between 6 and 12 hours on a two - Dual-Core AMD Opteron(tm) Processor 2216 - machine. There was considerable overlap between what sage had to build and what was already installed on my machine.
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creidiki
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PostPosted: Fri Feb 08, 2008 9:35 pm    Post subject: Reply with quote

serial_penguin wrote:
The 2.10.1 tarball did build but took between 6 and 12 hours on a two - Dual-Core AMD Opteron(tm) Processor 2216 - machine. There was considerable overlap between what sage had to build and what was already installed on my machine.


Which is why I've been using the binaries on my Athlon-XP 2500+ :D
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ukavi
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PostPosted: Fri Feb 08, 2008 11:18 pm    Post subject: Reply with quote

fb wrote:
It should build OK but report any problems.
Once installed it would be nice to run the test suite
(actually I should make that part of the ebuild).
As root run
Code:
sage -testall

and report if it pass, if there are any failure
try to post the relevant part of the test.log file.

I am also on the sage-devel mailing list and I have
good relations with the devs there. They are very
responsive to any issue I report.

major parts passed on x86. somewhere near the documentation tests there were some failures. strangely, the whole testing process hang at "sage -t devel/sage-main/sage/calculus/calculus.py" and i don't have any further results. the gui performs fine afaik.
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fb
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PostPosted: Sat Feb 09, 2008 12:07 am    Post subject: Reply with quote

Batch answers to everybody:

@serial_penguin
OK, I thought the 64 bit abi thing was fixed upstream. I may organize a patch.
We are talking of a pure 64bit machine or 64bit kernel/ 32 bit user land?

@tulcod
I had the calculus.py hang on me before, but it didn't happen with 2.10
I will have to look at some of the changes. What is your version of maxima
and with which lisp was it build?

@serial_penguin again
The long build time of the original sage tarball is probably down to the tuning of atlas.
It takes a long time if there is no profile for your processor. However 12 hour seems
long for that kind of machine. Were you doing something at the same time?
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serial_penguin
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PostPosted: Sat Feb 09, 2008 12:50 am    Post subject: Reply with quote

fb wrote:
Batch answers to everybody:

@serial_penguin
OK, I thought the 64 bit abi thing was fixed upstream. I may organize a patch.
We are talking of a pure 64bit machine or 64bit kernel/ 32 bit user land?


I have a pure 64bit machine, kernel + userland.

fb wrote:

@serial_penguin again
The long build time of the original sage tarball is probably down to the tuning of atlas.
It takes a long time if there is no profile for your processor. However 12 hour seems
long for that kind of machine. Were you doing something at the same time?


The 6 - 12 hours is only my estimate. It may be closer to 6 hours. It had run for approximately 4 hours when I left the machine for the day. Yes, atlas does take a lot of time. Nothing else was running during the build.

A patch would be great.
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fb
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PostPosted: Sat Feb 09, 2008 1:31 am    Post subject: Reply with quote

serial_penguin wrote:
fb wrote:
Batch answers to everybody:

@serial_penguin
OK, I thought the 64 bit abi thing was fixed upstream. I may organize a patch.
We are talking of a pure 64bit machine or 64bit kernel/ 32 bit user land?


I have a pure 64bit machine, kernel + userland.

I guess I could blindly apply the gentoo patching for 4.2.1-r1 but I'd really
like to know why it works outside portage but not inside. Can you tell me
the output of
Code:
uname -m
and
Code:
uname -a
?
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serial_penguin
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PostPosted: Sat Feb 09, 2008 1:44 am    Post subject: Reply with quote

fb wrote:
serial_penguin wrote:
fb wrote:
Batch answers to everybody:

@serial_penguin
OK, I thought the 64 bit abi thing was fixed upstream. I may organize a patch.
We are talking of a pure 64bit machine or 64bit kernel/ 32 bit user land?


I have a pure 64bit machine, kernel + userland.

I guess I could blindly apply the gentoo patching for 4.2.1-r1 but I'd really
like to know why it works outside portage but not inside. Can you tell me
the output of
Code:
uname -m
and
Code:
uname -a
?

Code:

uname -a
Linux ledaig 2.6.23-gentoo-r3 #1 SMP Mon Dec 3 15:29:12 CST 2007 x86_64 Dual-Core AMD Opteron(tm) Processor 2216 AuthenticAMD GNU/Linux

Code:

uname -m
x86_64
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fb
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PostPosted: Sat Feb 09, 2008 2:24 am    Post subject: Reply with quote

Try inserting this in the src_unpack section after all the other patches:
Code:

   tar xjf gmp-4.2.1.p12.spkg
   rm gmp-4.2.1.p12.spkg
   epatch $FILESDIR/gmp-4.2.1.p12.patch
        cd gmp-4.2.1.p12/src
        sed -i -e 's:ABI = @ABI@:GMPABI = @GMPABI@:' \
      Makefile.in */Makefile.in */*/Makefile.in
        cd ../..
   tar cjf gmp-4.2.1.p12.spkg gmp-4.2.1.p12
   rm -rf gmp-4.2.1.p12

Copy /usr/portage/dev-libs/gmp/files/gmp-4.1.2-ABI-multilib.patch to
$YOUR_OVERLAY/sci-mathematics/sage/files/gmp-4.1.2.p12.patch
Edit gmp-4.1.2.p12.patch so that the 4 first lines are changed from:
Code:
Gentoo uses ABI env var already

--- gmp-4.2.1/configure
+++ gmp-4.2.1/configure
to
Code:
Gentoo uses ABI env var already

--- gmp-4.2.1.p12/src/configure
+++ gmp-4.2.1.p12/src/configure
And hopefully I didn't make any mistake there.
Try that and tell me if you have any problems.
And also give "emerge --info" nobody with this problem gave an emerge --info!
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