From the Trenches: MOTU Science

[LaserJock]

Hi everybody!!
I'm so glad we finally got our forum! \o/

I thought you might like a little update from the development world. Edgy (6.10) is pretty much frozen for new apps and new upstream (i.e. from the authors) versions but we still have a fair amount of time for bug fixing.

At the last Technical Board meeting the MOTU Science team gained another MOTU which is excellent news, welcome Fujitsu!

I keep a semi-regularly updated list of scientific software at http://tiber.tauware.de/~laserjock/motuscience/all.html so people can track Debian and Ubuntu versions. This is mostly for dev us but you might also find it interesting.

Starting to look towards the next release of Ubuntu (Edgy+1) I'd like to get a feel for what the scientific community sees most lacking in Ubuntu. What bugs are the biggest problem? What packages do you want added? etc.

Ground rules:

1. Keep it to scientific apps. MOTU Science isn't going to turn XGL on by default or anything like that.
2. If you have an app suggestion please try to also state the license of the program. Most of the time non-free licenses are what keeps things out of Ubuntu.
3. Just because something is mentioned here doesn't mean it's going to be done right away (if ever really). We have very limited resources (anybody want to help?) so we can only get so much done so it's helpful to prioritize work.

Thanks, rock on!

-LaserJock

[Miguel]

Hi LaserJock,

Do Multiverse apps qualify? Because scilab is still an old version (in dapper at least). I've also had some issues with the fonts. It would be nice to have scilab 4.0 in the repos, and it would be even nicer if it didn't have those weird fonts. Will fill a bug report in malone if needed.

Another issue I have is FORTRAN 95. The available f95 compiler in the official repos is gfortran. However, my codes (check www.pwscf.org) only compile with g95 (and IFC of course, which is also faster, but fglrx is enough taint in my system right now). I suppose this compiler thing should be thoroughly discussed. It might be interesting to note that Debian Etch doesn't either supply g95.

EDIT: Licences:

• g95 is GPL, being a fork of gfortran
• Scilab is non-free. The license is available here. According to the FSF:
  

  Scilab license: This is not a free software license because it does not allow commercial distribution of a modified version.

[akniss]

How about RKWard? It aims to be a user-friendly interface for R... which tends to be anything but user friendly when first starting.

http://rkward.sourceforge.net/

RKWard is GPL'd.

[LaserJock]

Hi LaserJock,

Do Multiverse apps qualify? Because scilab is still an old version (in dapper at least). I've also had some issues with the fonts. It would be nice to have scilab 4.0 in the repos, and it would be even nicer if it didn't have those weird fonts. Will fill a bug report in malone if needed.

Another issue I have is FORTRAN 95. The available f95 compiler in the official repos is gfortran. However, my codes (check www.pwscf.org) only compile with g95 (and IFC of course, which is also faster, but fglrx is enough taint in my system right now). I suppose this compiler thing should be thoroughly discussed. It might be interesting to note that Debian Etch doesn't either supply g95.

EDIT: Licences:

• g95 is GPL, being a fork of gfortran
• Scilab is non-free. The license is available here. According to the FSF:
  

Yes, scilab took a lot of effort but we and a new Debian maintainer were able to get scilab4.0 packaged and in for Edgy (6.10). It is enough of a change and difficult to package that I don't think we'll backport it or put it in -updates although if enough people want it I can look into it.

Regarding g95/gfortran, I've had good luck with g95 in OS X on my intel iMac. I hadn't thought of it much in Ubuntu since we have gfortran. Maybe I'll talk to the Debian science guys and see if anybody over there wants to package it. I doubt that MOTU Science really has the resources to maintain a compiler package but I can poke Debian at least

Thanks for the feedback, keep it coming.

-LaserJock

[LaserJock]

How about RKWard? It aims to be a user-friendly interface for R... which tends to be anything but user friendly when first starting.

http://rkward.sourceforge.net/

RKWard is GPL'd.

It was included in Ubuntu edgy (6.10) on June 20th.
Launchpad Page: https://launchpad.net/distros/ubuntu/+source/rkward

-LaserJock

[Miguel]

Yes, scilab took a lot of effort but we and a new Debian maintainer were able to get scilab4.0 packaged and in for Edgy (6.10). It is enough of a change and difficult to package that I don't think we'll backport it or put it in -updates although if enough people want it I can look into it.

Oh! I see, thank you very much for your efforts. Rest assured I appreciate it. If you had a little time, and it isn't too off-topic, I'd be interested in hearing the difficulties in packaging scilab. As compiling scilab from source (ver 3.1 at least) was straightforward, I wasn't expecting this.

Regarding g95/gfortran, I've had good luck with g95 in OS X on my intel iMac. I hadn't thought of it much in Ubuntu since we have gfortran. Maybe I'll talk to the Debian science guys and see if anybody over there wants to package it. I doubt that MOTU Science really has the resources to maintain a compiler package but I can poke Debian at least

OK, don't worry more than necessary, it's just a wishlist. The binary available in the web works pretty good. Untar somewhere and make some symbolic links in my $PATH. Compiling from source, however, is another problem. Basically because ./configure asks for a gcc file that I don't have.

I could ask for some DFT code, but it simply isn't practical. Because you need every optimization possible for your machine. It's one of the few cases when a few percent points make a difference... except in a small binary where you don't need -O2 or -O3 speed but -O precission.

[Miguel]

Hi LaserJock,

I have a little request regarding gnuplot, but this is probably a "wishlist bug report". The gnuplots of Mandrake 10.0 (my first distro) and Red Hat 3 (the distro in my computing cluster) are version 3.7. These do file autocompletion upon pressing tab. However, gnuplot 4.0 (at least compiled from source by myself, the ones in Ubuntu since 4.10 and the Debian Sarge and Etch ones) do not "tab-complete" names. I don't really know the reason for this. It would be nice to have this feature reactivated.

Thanks in advance,

Miguel

PS: I've recently migrated to Edgy and I just tested scilab 4.0. Great work!!!

[LaserJock]

Hi LaserJock,

I have a little request regarding gnuplot, but this is probably a "wishlist bug report". The gnuplots of Mandrake 10.0 (my first distro) and Red Hat 3 (the distro in my computing cluster) are version 3.7. These do file autocompletion upon pressing tab. However, gnuplot 4.0 (at least compiled from source by myself, the ones in Ubuntu since 4.10 and the Debian Sarge and Etch ones) do not "tab-complete" names. I don't really know the reason for this. It would be nice to have this feature reactivated.

Thanks in advance,

Miguel

PS: I've recently migrated to Edgy and I just tested scilab 4.0. Great work!!!

Miguel,
There is actually a reason for Gnuplot to act that way. Due to some licensing issues, Gnuplot can't be compiled with readline support by default. This is the case in Debian and consequently in Ubuntu. I'm not sure of all the reasoning and why virtually all other distros ship gnuplot with readline support enabled, but I don't think there is anything I can do about it as it is Debian policy. This exact problem was my first introduction to Debian packaging.

-LaserJock

[Steveire]

Can we get the latest version of k3dsurf into the repos?

[Miguel]

Hi again LaserJock,

I have to ask you a favour. Please open scilab, then go to Help->Apropos and browse, using scilab's browser, to any topic. Do you see very ugly fonts? This is not scilab related, though, because I've another program I compiled myself, XCrySDen, and also has these issues on small fonts. The only thing they have in common is use of Tcl-Tk.

I will fill a bug report, but there are so many currently opened it's like crazy.