Scientific Gentoo?

Message

yye00 · Post by **yye00** » Thu Feb 26, 2004 5:18 pm

Is it just me or are there others having difficulty emerging scientific apps in gentoo? Some things install nicely, others do not. Some apps install but segfault at startup. I am new to Gentoo but I so far I am really impressed. Impressed enough to start fixing some stuff that does not work!

Would anyone be interested in sending a list of top 10 sci-apps they use, and problems associated with them if any. The list can include items which are not in the sci-apps, but are science related.

gurke · Post by **gurke** » Thu Feb 26, 2004 9:55 pm

maybe those ebuilds are too old and no longer maintained. file a bugreport, if thats the case, to get them fixed. you may also post exact error messages, so we can help you.

qwkbrnfox · Post by **qwkbrnfox** » Thu Feb 26, 2004 10:55 pm

How about mayavi? I'd love to ditch tecplot.

yye00 · Post by **yye00** » Thu Feb 26, 2004 11:00 pm

Adding mayavi should not be difficult. I have a look at it tonight, see what needs to be done.
Data vizualizers are quite interesting, what else?
I have scigraphica which I am fixing now (it has hardcoded requests for python 1.5 and that is why it segfaults). Any other? Suggestions are welcome!

qwkbrnfox · Post by **qwkbrnfox** » Thu Feb 26, 2004 11:15 pm

yye00 wrote:Adding mayavi should not be difficult. I have a look at it tonight, see what needs to be done.
Data vizualizers are quite interesting, what else?
I have scigraphica which I am fixing now (it has hardcoded requests for python 1.5 and that is why it segfaults). Any other? Suggestions are welcome!

Hey, that would be great! Hopefully the vtk dependency won't be too bad. If I can push my luck a bit, would it be possible to include an ebuild for the cvs version? It seems that there is a long time between releases.

Thanks!

yye00 · Post by **yye00** » Thu Feb 26, 2004 11:19 pm

That is my intention. VTK do not seem to have released anything new so I guess the CVS will have to do. Same for mayavi, paraview and others. Do you do any parallel viz? If so what do you use for mpi? LAM or MPICH?

znmeb · Post by **znmeb** » Fri Feb 27, 2004 3:52 am

I'm slowly but surely migrating from Debian / Knoppix to Gentoo. In terms of "eyeball hours", I spend about 6 hours a day at work using Windows, both native and with CygWin. I managed to get CygWin KDE running yesterday, although it's slow. I haven't taken a shot at CygWin Portage yet, but will probably get to it next week.

At home, I spend evenings and weekends mostly in Linux. Most of that time is Gentoo, although there are still a few packages I can't live without that don't emerge right. I've filed bugs ... and I've found some of my bugs already filed ... but in a number of cases, I've ended up going directly to the original upstream sources.

My suspicion is that Gentoo ought to be evolving in that general direction. That is, the primary focus of "gentoo.org" should be a clearing house / test facility, as highly automated as is feasible, for keeping the latest open source contributions on users' desktops and servers.

For example, the most recent version of the R statistics package, which is a must-have for me, is 1.8.1 on the upstream (CRAN) archives. Yet Gentoo as of a day or so ago was still carrying 1.6.1. I have *never* had a source tarball from CRAN do anything remotely nasty on *any* Linux box. Indeed, there are CRAN folks who build RPMs and Debian packages and place them on the CRAN archive within *hours* of the release of the latest source tarballs. Why can't Gentoo?

TexMacs and LyX are two other must-haves for me. Gentoo is carrying TexMacs 1.0.2.4; 1.0.3.3 builds flawlessly and executes all of my stuff just fine on Gentoo. LyX is 1.3.2 in Gentoo; the upstream 1.3.4 builds and executes flawlessly as well.

Finally, another must-have is Maxima. I ran into a bug building it, checked the bug repository and determined that it was already filed. That was some time ago; it's still not fixed and Maxima still won't emerge. In that case, the problem appears to be upstream, although it isn't clear to me whether the bug is in Maxima or "clisp"; Maxima builds fine with "cmucl" as its LISP environment.

So what I'd like to see is:

1. A user finds a package upstream that satisfies Gentoo's freedom requirements.
2. Same user downloads the source and builds it on his/her *up to date* Gentoo box, making notes of any dependencies.
3. Same user fills out a form, preferably automated, on the Gentoo web site with enough details that someone from Gentoo.org can reproduce the build and test it.
4. Gentoo.org does whatever QA and license checking is necessary, then releases an e-build.
5. Same user tracks the upstream code and repeats steps 2 - 3 as necessary.

I'm willing to do that for R (and the ATLAS linear algebra package), since I hit the CRAN web site at least once a week and check the Debian unstable archives for R at roughly the same frequency. I'm essentially doing steps 1 and 2 for R, ATLAS, Maxima, TeXMacs and LyX now, although I don't track the release cycle and contents of the other 3 as faithfully as I track R and ATLAS. I probably don't have the time to do much more than that; I also do a fair amount of audio and network software acquistion. Does someone else want to volunteer to track some of the other common science packages?

Ed Borasky
http://algocompsynth.com/

znmeb · Post by **znmeb** » Fri Feb 27, 2004 3:58 am

yye00 wrote:Adding mayavi should not be difficult. I have a look at it tonight, see what needs to be done.
Data vizualizers are quite interesting, what else?
I have scigraphica which I am fixing now (it has hardcoded requests for python 1.5 and that is why it segfaults). Any other? Suggestions are welcome!

Have you looked at what's on Dirk Eddelbuettel's "Quantian Knoppix" distro?

http://dirk.eddelbuettel.com/quantian.html

I'm mostly a mathematician/computer scientist, so I'm not sure what the physicists, chemists and biologists would like on Quantian, but it has a *lot* more stuff than any other "science" distro. It's got math tools, data visualization tools, computational finance tools, etc.

Ed Borasky
http:/algocompsynth.com/

Zeddicus · Post by **Zeddicus** » Fri Feb 27, 2004 6:12 am

http://forums.gentoo.org/viewtopic.php? ... light=iraf

I can't vouch for the above software, but it's clear that a some Gentoo-ers want it. I'm at the very least curious, as I'm starting to do a lot of astronomical image analysis for my undergrad research.

furanku · Post by **furanku** » Fri Feb 27, 2004 8:03 am

I use gnuplot a lot, see the last postings in this thread, in short, since the beginning of february we have a new version in portage. The problem is, it crashes when the terminal window gets resized due to a combined bug in libreadline and gnuplot.

Some others in my workgroup use OpenDX (a mighty data visualisation package), for which an ebuild is in discussion, see this tread.

Another package I use is LAPACK (a (the?) linear algebra fortran library), which works, but could have some more gentoo related documentation, how to set it up with a machine optimised BLAS (Basic Linear Algebra System), namely ATLAS. If your numerical simulations run several days, you want to be sure you don't waste time in unoptimised libraries. Since gentoo is a source distribution, this would be a big advantage to other distributions!

Frank

[Edit] Just saw the link to Bug #30453 in the reply to your posting on gentoo-science, which answers my questions concerning LAPACK/BLAS/ATLAS. I love gentoo

Does anyone know about the quality of the implementation of GSL? How does it roughly compare to NAG in general and LAPACK in the LA part?

pranyi · Post by **pranyi** » Sat Feb 28, 2004 12:40 am

An ebuild of GAP (group algebra package) would be nice too.

It took me some hours to install it.

chocolate · Post by **chocolate** » Fri Mar 12, 2004 3:25 pm

yye00 wrote:Is it just me or are there others having difficulty emerging scientific apps in gentoo? Some things install nicely, others do not. Some apps install but segfault at startup. I am new to Gentoo but I so far I am really impressed. Impressed enough to start fixing some stuff that does not work!

Would anyone be interested in sending a list of top 10 sci-apps they use, and problems associated with them if any. The list can include items which are not in the sci-apps, but are science related.

I found myself in the same situation. I occur in some problems in installing and getting correct results from ifc packages in the gentoo site package database...luckily i've found the ebuild of ifc 8.0 in the discussion forum and it works! (even if some compilation options have not been implemented yet)

As far as other packages are concerned, I use the AVS (commercial ) packages and luckily it works properly under gentoo. I'm curious to try out OpenDx, I tested it some releases ago but it was quite unstable.

I am going to install mpich and lapack as well. I tryed (without success) to install the seplib seismic visualization libraries, and I'm currently wondering how can I succeed.

On the other hand, no problems in installing (and running) seismic unix and cubit, I am quite satisfied of the result

nngs · Post by **nngs** » Sat Mar 13, 2004 12:17 am

Never installed it successfully, I hope one day IRAF included in portage tree

http://iraf.noao.edu/

wam · Post by **wam** » Sat Mar 13, 2004 8:55 am

I use the following scientific products without any problems:-
Gnuplot for plotting.
Octave and Scilab
(all of them from portage)

oldefortran · Post by **oldefortran** » Sat Mar 13, 2004 5:07 pm

wam wrote:I use the following scientific products without any problems:-
Gnuplot for plotting.
Octave and Scilab
(all of them from portage)

Is scilab using the atlas libs?

wam · Post by **wam** » Sun Mar 14, 2004 9:04 am

scilab comes under two names...
scilab and scilab-atlas, the latter uses the atlas libraries.
I personally use the plain scilab

oldefortran · Post by **oldefortran** » Sun Mar 14, 2004 9:17 am

wam wrote:scilab comes under two names...
scilab and scilab-atlas, the latter uses the atlas libraries.
I personally use the plain scilab

Thanks!
I guess I have to start using "emerge -s package " more often instead of just "emerge package"

May I ask why you just use plain scilab? Shouldn't the atlas version improve speed very much?

oldefortran · Post by **oldefortran** » Sun Mar 14, 2004 9:29 am

Where did you find scilab-atlas?
I can't find it.

gwion · Post by **gwion** » Sun Mar 14, 2004 6:02 pm

i really enjoy using the emboss package (along with clustalw etc) as well as phylip. nice would be gentoo packages for clustalX (okok, it is just a frontend) and things like artemis.

what i would crave in linux is stuff like vector nti (we do our vector maps in this programme) but at the moment i prepare my stuff in linux and just draw the map in windows and vector nti...

however: the emboss stuff is great for molecular biology and sequence analysis.

cheers

chocolate · Post by **chocolate** » Tue Mar 16, 2004 11:46 am

I wonder if nice schedulers for cluster management like condor or some grid computing apps like the vdt package are going to be included in portage tree...

yye00 · Post by **yye00** » Wed Mar 17, 2004 3:34 pm

Greetings
I will soon make available ebuilds for the following :
->CactusCode: framework for high performance computing, and numerical relativity
->Globus 3.0 ebuild: for grid computing
->VTK: cvs version

I did not check OpenDX ebuild but I have been told it works.

Cheers!

chocolate · Post by **chocolate** » Wed Mar 17, 2004 3:57 pm

Simply great! Please let me know when you are releasing the ebuilds!

cottonmouth · Post by **cottonmouth** » Thu Mar 18, 2004 4:10 pm

Both Computer Algebra Software packages (maxima and yacas) I have tried to emerge (and compile from upstream tarball) unfortunately fail.

It seems like yacas at least has been dropped, as the lates upstream version, which has been around for a while, is not in the tree neither as stable or ~arch.

If I could get either to work from upstream tarballs I could give an .ebuild a go, but as of yet I'm not there. It's a pity cause CAS is a really nice tool.

All the best

Drewgrange · Post by **Drewgrange** » Thu Mar 18, 2004 7:57 pm

I was going to make a thread but I figure this would fit in with this thread.

Can anybody suggest some linux apps for Chemistry? Doesn't have to be for any specific purpose, I'd just like to check out some of the things that are out there.

yye00 · Post by **yye00** » Fri Mar 19, 2004 4:41 pm

I certainly will chocolate. Do you GRID?

As for chemistry apps, there is a wealth! All you have to do mate is emerge them.

You can go here and see the available science apps:
http://packages.gentoo.org/packages/?category=app-sci

I recommend chemtool as a starter, Kemistry too if you like, and you can go all the way to biopython if you like. But I am a physicist so I am not really an expert on these packages.

Cheers!

Scientific Gentoo?

Scientific Gentoo?

mayavi

Re: mayavi

Mayavi

Gentoo Science

Re: mayavi

Re: Scientific Gentoo?

scilab-atlas?

scientific gentoo - for clusters?