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Scientific Applications on Linux

The site lists both free and commerical applications.

For a drafting program, I would recommend QCad which is a nice GPL 2D drafting package. Unfortunatly I am not aware of any GPL 3D drafting programs which are either robust or mature enough for industrial use. Periodically I attempt to get TurboCad running under Wine, but while it seems to be getting closer to working, still no success yet.

Don't overlook the Python Programming Language which has a variety of extensions which make it very suitable for number crunching applications. Its is fairly easy to learn how to make GUI-based applications for specialized purposes, and its speed of development combined with robust error-checking and interpreted execution mode makes it ideal for implementing small engineering solutions.

for projects like this is Scientific Applications on Linux. There are heaps of applications there, many of them GPL, but I don't have a very clear idea of exactly what you are trying to achieve...

From the SAL website:
F is a carefully crafted subset of the most recent version of Fortran, the world's most powerful numeric language. F retains the modern features of Fortran--modules and data abstraction, for example--but discards facilities such as EQUIVALENCE, which are difficult to teach, use, or debug.

Backwards compatibility is extremely important for the Fortran crowd (who tend to be a very conservative bunch). Having to rewrite source code is not going to make them happy.

check out Scientific Applications for Linux It is sure to have something you are looking for (plus more)

It's not 'hard numbers', but then, a lot of people have already pointed out that hard numbers may not REALLY be what you want. (After all, since when is "Everybody's doin' it" a persuasive argument for a good scientist?)

On the other hand, I see there are still lots of applications listed at the Scientific Applications on Linux site and the NCBI Toolbox of Bioinformatics code compiles and runs just fine on my linux box, and BioPerl, BioJava, and BioPython all run just fine on Linux (there are even a couple of fledgling BioPHP projects out just getting started out there, which will obviously also work.

Disclaimer - both of the semi-active "BioPHP" type projects that I know of - Here and here - were started independently by individual amateurs...and one of them is me. Both projects are still in the early stages (Genephp has more code available at the moment) and have different development approaches, but are slowly working on trying to combine development towards a 'formal' set of "BioPHP" modules. Blatant plug - if you are interested in helping with friendly advice or actual development or testing, please join the mailing list which both projects use)

Against my better judgement, I'll bite. You really do seem like you're trolling, but I have a few minutes to kill this morning. In fact, because I'm in such a good mood, I'll even explain why so many people are giving you flack in this thread, just in case you don't already know. Then I'll include a few reasons to consider a linux platform.

First, the flack: You're asking a robust community a very simple question to which you could easily get a plethora of answers. This is akin to asking every professor in the math department of a university what 2+2 is.

This is actually one of the more annoying characteristics of many (but not all) windows users, not to mention non-geeks in general: an overall lack of resourcefulness. You want the answers to all of life's questions handed to you. When something doesn't work, you steadfastly refuse to think beyond "I clicked here and it didn't work. I clicked here again, and it still didn't work. It must be broke!

For the record, the bullets that I'm copying and pasting from http://linux-newbie.sunsite.dk are from the first search result on a google search for "linux benefits". With that, here are a few reasons to consider a linux platform:

A modern, very stable, multi-user, multitasking environment on your inexpensive PC hardware, at no (or almost no) monetary cost for the software. Linux is a rich and powerful platform--don't think of it as a "poor people" operating system. Out-of-box Linux has as much capability as MS Windows NT with $5000 in software add-ons, is more stable, and requires less powerful hardware for comparable tasks.

Standard platform. Linux is VERY standard--it is essentially a POSIX compliant UNIX. (Yes, Linux is a best-of-the-breed UNIX. The word "UNIX" is not used in conjunction with Linux because "UNIX" is a registered trademark.) Linux includes all the UNIX standard tools and utilities.

Unsurpassed computing power, portability, and flexibility. A Linux cluster recently (April 1999) beat a Cray supercomputer in a standard benchmark. Linux is most popular on Intel-based PCs (price of the hardware), but it runs very well on numerous other hardware platforms, from toy-like to mainframes. One distribution (Debian) expresses the idea like this: "Linux, The Universal Operating System." Linux can be customized to perform almost any computing task.

Advanced graphical user interface. Linux uses a standard, network-transparent X-windowing system with a "window manager" (typically KDE or GNOME).

Dozens of excellent, free, general-interest desktop applications. This include a range of web browsers, email programs, word processors, spreadsheets, bitmap and vector graphics programs, file managers, audio players, CD writers, some games, etc.

Thousands of free applets, tools, and smaller programs. "Small is beautiful" goes well with Linux philosophy. The small Linux tools and applets often work in tandem to perform more complex tasks.

Hundreds of specialized applications built by researchers around the world (astronomy, information technology, chemistry, physics, engineering, linguistics, biology, ...). In many fields, Linux seems like "the only" operating system in existence (try to find out what your friend astronomer runs on her computer). The software in this category is typically not very easy to use, but if you want the power, it is the best software that humanity has in these areas. Doubtful? Have a look at: http://SAL.KachinaTech.COM/Z/2/index.shtml for examples.

Scores of top-of-the line commercial programs including all the big databases (e.g., Oracle, Sybase, but no Microsoft's). Many (most?) of these are offered free for developers and for personal

You should realize though that most of these companies purchase the hardware from companies like Sager (Linux forum) and Compal, and those companies also supply the big-name guys like Compaq, HP, Dell, and Toshiba. So when you find some no-name laptop, it is usually equivalent to some branded laptop that never touched the hands of HP/Compaq/Toshiba/Dell. (And figuring out exactly *which* brand-name laptop it is equivalent to can be extremely difficult) Some of the below claim to manufacture their own notebooks, but what this means is that they buy them from Saeger/Compal or someone else, and put in a hard drive/CPU/RAM, which is why you will find identical looking cases at several of these vendors.

If you find a HP/Compaq/Toshiba/Dell/IBM/Sony branded laptop that has linux preinstalled, it means that the vendor paid for windows and removed it. I do not list them below because I think this is a despicable and deceptive practice. These manufacturers do not (yet) sell no-os or linux laptops. (But please, call them and ask!! The squeaky wheel gets the grease!) Also if you order a no-OS laptop, please request linux to be installed anyway, and tell them you'll pay for it! Let them know there is demand!

1. Linux-preinstalled laptops
2. ASA Computers
3. ASLab (Linux Forum)
4. American Computer
5. Cyclox
6. Kachina Tech (positively ancient laptops -- K6 and PII)
7. QLI Tech
8. Workstation 2000

1. No-os laptops
2. ARM Computer
3. Chem USA
4. Mtech Laptops (these guys outright lied to me about what they could deliver, in order to get my order, were not able to deliver the laptop, and I had to cancel my order -- which took 3 months to process and they kept $5 for the priviledge -- do not do business with them)
5. PC Torque
6. Power Notebooks (very good customer service according to Reseller Ratings) (Linux forum)
7. Xtreme Notebooks

-- Bob

The Scientific Applications on Linux site has a few entries for spreadsheets and many more for data processing and visualization.

The Scientific Applications on Linux site has a few entries for spreadsheets and many more for data processing and visualization.

The Scientific Applications on Linux site has a few entries for spreadsheets and many more for data processing and visualization.

Also, finite element analysis comes to mind as a fertile realm for OO. In fact there's a book on it:
Object Oriented Methods and Finite Element Analysis

Scientific Applications on Linx (SAL)

• GCC for C/C++/FORTRAN coding. It's free, it's not the fastest in the world but it's competent.
• Octave is a great, free replacement for Matlab. For general data manipulation it seems fine, where it really lacks relative to Matlab is in the GUI.
• Gnuplot is a great all-round, all-purpose, scriptable plotting tool that can also do fitting. For general everyday tasks gnuplot gets used a lot in our lab.
• SciGraphica is a great 2d/3d/vector/polar/ plotting and analysis package. It is a little like an Origin clone so is pretty easy to pick up, and can be extended with Python plugins. I am one of the developers ;0) (although far too busy atm to contribute, anyone want to help?). More suitable for publication-quality plots and still heavily in development. A new release is imminent. Plug ;0).
• teTeX is the main (La)TeX distribution for Linux and you'll most probably have it in Debian anyway but for writing reports, articles, books, theses, even letters you shouldn't need to use anything else. Really.
• OpenOffice if you have to deal with mad, crazy, annoying .doc using people.

There's plenty more where they came from. Most distrbutions come with a lot of these things anyway. These are mainly analysis or document tools, there's plenty of other things for both these areas and any other which plenty of other posters have shown. I've written a little guide for my local group. Some of it's out of date (and some of it's wrong but I have better things to fix) but it does have a list of common tools we use. And, of course, SAL is a pretty comprehensive database of unix tools. HTH.

is Scientific Applications for Linux (SAL), the one i use is in greece http://sal.duth.gr, but there are mirrors around the world.
I think the official site is at http://sal.kachinatech.com/ .

many applications there , not all free though ..

I do quite a bit of number crunching. Here are
some of the resources I use:

Netlib (www.netlib.org) -- Yes, it's mostly Fortran, but that's a good thing! Just use f2c (easy to find) and translate to C if that's what you want. Don't underestimate the power of decades-old programs -- old == widely used and well-tested.

StatLib (lib.stat.cmu.edu) -- Collection of statistical software, in various languages, including C, Fortran, and S.

SAL, Scientific Applications on Linux (sal.kachinatech.com) -- a very large collection of links.

Freshmeat (www.freshmeat.net) -- Not scientifically oriented, but there is much scientific stuff there, along with all kinds of miscellany.

Octave (www.octave.org) -- A package for matrix manipulations, similar to Matlab, but free. Useful for all kinds of problems.

R (www.r-project.org) -- An implementation of the S language for statistics, but also useful for general problems, similar to Octave. S+ is a commercial implementation of S.

Well, that ought to be enough to get started. To echo something other posters have mentioned -- don't even bother with Windows software. If your budget is tight, save your money for hardware, don't waste it on the MS tax.

SAL is a good resource for finding science apps that run on Linux. Worldwide mirrors, many apps are free.

SAL has listings of a bunch of OODBs.

VTK has some nice wrappers for various languages.
I spent some time playing with the TCL/TK side of it, and it was great for quickly trying out ideas.
Another package that comes to mind is VIS5D.
See Somewhere here

Another one: Scientific Applications on Linux

I've taken SNMP data from radio network nodes, dropped it into Gnuplot, and placed on a web page a rotating GIF of a 3-D contour plot showing what the error rates are througout a building. There also are tools which can be interfaced to external data. I've used network configuration data to produce charts (although TkIned has tools to do this already).

I've taken SNMP data from radio network nodes, dropped it into Gnuplot, and placed on a web page a rotating GIF of a 3-D contour plot showing what the error rates are througout a building. There also are tools which can be interfaced to external data. I've used network configuration data to produce charts (although TkIned has tools to do this already).

Check out 'Scientific Applications on Linux' Here
A much-underrated directory of apps for linux.

I forgot to mention: a list of CAD programs is available at SAL (Scientific Applications on Linux): sal.kachinatech.com. They also list non-free programs.

I forgot to mention: a list of CAD programs is available at SAL (Scientific Applications on Linux): sal.kachinatech.com. They also list non-free programs.

Here are a couple of links to try:
(I can't comment on any of them except PCB, which, although very simple, works fairly well and is quite intuitive to use).
MUCS-PCB
PCB
SATCAD

Also try Scientific Applications on Linux

numerical computation stuff isn't exactly the hardest thing to code up

Should have said: in comparison to *symbolic* computational stuff. There are many numeric cruncher programs out there, but in the land of nontrivial symbolic math, you can practically count them on one hand. (I looked into this a while back, esp. in the SAL pages)

Not to belittle the work that has gone into MATLAB or Octave, only that writing a free replacement for Maple or Mathematica would be a much harder undertaking. Less algorithms, more heuristics, and a much hairier problem space.

...profile your code with iprobe

About page coloring, this is something I heard freebsd does and not linux. myth or reality? I don't know.

So far, to reduce bottlenecks all I've done was to try and use sparse solvers, as I can get quite a few 0s in my system (up to a ridiculous 97%) But yep, you still need some profiling to get your code just right, especially if you have several \emph{blocks} working together in your code.

if you're interested, the libraries I'm using for sparse solvers are meschach (great but sparse documentation) and since yesterday sparse QR (I can't tell yet if it's any better than some of the solvers in meschach, but it looks nice nonetheless...).

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At the Linux Metapage (http://stommel.tamu.edu/~baum/linux-meta.html) there's pointers to a lot of different types of software for Linux.

In particular, there's a pointers to to SAL (http://SAL.KachinaTech.COM/index.shtml) and LinuxApps (http://www.linuxapps.com/) and other software lists that might interest scientific Linux users.

Works for me.

There have been a lot of Ask Slashdot's about software for molecular munging, genetic gerrymandering and physical futzing. All your questions can be answered in one location.


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Sun/Linux however is a small niche, so it wouldn't have the HUGE support that Intel/Linux has. Solaris is heavily tested by Sun on their hardware platforms, and given that there hardware is sold in certain configurations with the OS, I trust that they have a great ability to debug and test their systems, and that bugs when reported are dealt with quickly. Does Sun/Linux have the same situation?

I see your point. Sun/Linux is IMO very well supported, and in the past I had really good experiences on that particular area. Granted, you are not likely to find a Sun/Linux guru in a 10 km radius (it is scary that you can find a pretty knowledgeable Linux user in that same area nowadays... or maybe I'm just lucky), but the number of people using Linux on Sun hardware is surprinsingly high. I wouldn't call debian-sparc a high traffic list, but it's not that low traffic either. This message regarding Debian GNU/Linux running on a e450 is amusing.

There are companies providing Linux preinstalled on Sun hardware (or at least Sun compatible hardware) like Kachina Technologies (no I don't work for them, but I admit I'm biased, I've got superb service from them in the past). I know there are more vendors offering Linux on Sun, but I don't have a list handy... sorry.

If GNUChess is multithreaded it will run fine on a MOSIX cluster as-is. Granted, MOSIX is a wee bit lossier than a native MPI program, but why sweat the port whan you can throw more power at the one you have.

As for software that runs on a Beowulf, Scientific Applications on Linux used to have a fair rundown of them.

Thanks for posting this. I agree that the biological side of things could be improved. There are quite a lot of important Open/Free bio-informatics sites and projects. I know that the EBI is pretty committed and there are links available through the Scientific Applications on Linux site. Perhaps it's such a large area that it would be a good thing to have an independent /.-like site that provided forums for these discussions - taking sci.molbio etc to a nicer medium, it could allow for sharing of graphics which would help some awkward discussions.

Thanks for posting this. I agree that the biological side of things could be improved. There are quite a lot of important Open/Free bio-informatics sites and projects. I know that the EBI is pretty committed and there are links available through

It's under the Linux Negitive side at the bottom of the page. Is there some exploit that screws up SMP Linux boxes running 2.2.0 or something? Or, is this his flowery way of saying that there aren't many things that really use SMP yet?

Believing it's the latter, isn't that totall BS because

• Since in general source is avaliable for almost every app, and compile time flags, and smp optimization can be done for just about any app? (Doesn't SAL have a pretty big section about compilers for specific needs like this?
  
• Even applications that are not SMP optimized benifit from good SMP implementation, since, this is suppose to be a server, and more than one job will be happening at a time, thus, there is more than one CPU to use?
  

Yes, not my subject, I could be totally wrong, but, I didn't think that that statement was totally true.