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Matías Graña | 5 Feb 2008 17:57
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scilab compile error

hi!
Though scilab does not belong to science overlay, I thought someone here
could help me with this issue. I couldn't emerge scilab. Tried both 4.0
and 4.1.2.

As asked by the emerge failing:
GENTOO_VM=sun-jdk-1.6  CLASSPATH="" JAVA_HOME="/opt/sun-jdk-1.6.0.03"
JAVACFLAGS="-source 1.4 -target 1.4" COMPILER=""

result of emerge --info at the end

Here is the end of the log:

[....]
lpvmgen.c:(.text+0x9c1d): warning: `sys_errlist' is deprecated; use `strerror' or `strerror_r' instead
lpvmgen.c:(.text+0x9c14): warning: `sys_nerr' is deprecated; use `strerror' or `strerror_r' instead
cp pvmgroups ../../bin/LINUX
cp libgpvm3.a ../../lib/LINUX
case xt in xt ) echo ranlib; ranlib ../../lib/LINUX/libgpvm3.a ;; esac
ranlib
cp pvmgs ../../lib/LINUX
make[3]: Leaving directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/pvm3/pvmgs/LINUX'
done building group server and library
make[2]: Leaving directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/pvm3'
make[1]: Leaving directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/pvm3'
making all in routines/Javasci...
make[1]: Entering directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/routines/Javasci'
make[2]: Entering directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/routines/Javasci/classes'
make[2]: Leaving directory `/var/tmp/portage/sci-mathematics/scilab-4.1.2/work/scilab-4.1.2/routines/Javasci/classes'
gcc -march=i686 -O2 -pipe -mmmx -msse -m3dnow `pkg-config gtk+-2.0 --cflags` -fPIC -I/usr/include
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Denis Dupeyron | 6 Feb 2008 14:15
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Re: scilab compile error

On Feb 5, 2008 5:57 PM, Matías Graña <matiasg <at> dm.uba.ar> wrote:
> Though scilab does not belong to science overlay, I thought someone here
> could help me with this issue. I couldn't emerge scilab. Tried both 4.0
> and 4.1.2.

It would be better if you filed a bug in our bugzilla at
http://bugs.gentoo.org. You would probably get more attention there
and it would help us track it in a better way.

Denis.
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Justin Findlay | 7 Feb 2008 08:13
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RFC: modeling software

I'm doing some computational astrophysics research, specifically
modeling the effect of star novas on planetary motion and my problem is
that I don't know the best way to do this.

The nature of this research consists of my extending a model already
developed by my advisor, and the problem is that I want to translate
this model into a simulation and I don't know what software to use.  My
advisor has given me full discretion in using whatever tools I need, so
I thought I'd ask here since I don't know where else to ask.  Since he
hasn't stipulated the use of any software to model the research I want
to take this opportunity to get experience with some of the FLOSS
projects out there.

What software do you think would be most useful for this project?

Justin
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M. Edward (Ed) Borasky | 7 Feb 2008 16:07
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Re: RFC: modeling software

Justin Findlay wrote:
> I'm doing some computational astrophysics research, specifically
> modeling the effect of star novas on planetary motion and my problem is
> that I don't know the best way to do this.
> 
> The nature of this research consists of my extending a model already
> developed by my advisor, and the problem is that I want to translate
> this model into a simulation and I don't know what software to use.  My
> advisor has given me full discretion in using whatever tools I need, so
> I thought I'd ask here since I don't know where else to ask.  Since he
> hasn't stipulated the use of any software to model the research I want
> to take this opportunity to get experience with some of the FLOSS
> projects out there.
> 
> What software do you think would be most useful for this project?
> 
> 
> Justin

"Modeling" is too vague a word to get a meaningful response. However, 
I'll assume that, since it's astrophysics, that you're solving some 
equations. There are two ways to solve equations, numeric and symbolic. 
You can also mix these approaches, although that's more difficult.

So ... can you specify the nature of the model? Is it equation-based? 
Numerical? Symbolic? Algebraic? Integral? Differential? None of the above?
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Justin Findlay | 7 Feb 2008 18:52
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Re: RFC: modeling software

On AD 2008 February 07 Thursday 07:07:24 AM -0800, M. Edward (Ed) Borasky wrote:
> "Modeling" is too vague a word to get a meaningful response. However, I'll 
> assume that, since it's astrophysics, that you're solving some equations. 
> There are two ways to solve equations, numeric and symbolic. You can also 
> mix these approaches, although that's more difficult.

The equation solving is pretty easily done by hand so far.

> So ... can you specify the nature of the model? Is it equation-based? 
> Numerical? Symbolic? Algebraic? Integral? Differential? None of the above?

This is the part I don't quite understand.  Maybe I should ask my
advisor and then I can come back with a more specific question, but in the
movies modeling usually consists of a fancy full color 3D graphical
simulation with sound effects. :-)

Justin
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Redouane Boumghar | 7 Feb 2008 20:49
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Re: RFC: modeling software

Hello everyone,

Justing, what do you mean by RFC ?
Is that about Rational Function Camera or Rational Function Coefficient ?
So you may need to model what a camera would see and I assume this can
be part of an astrophysical project using a rational function model.
But it seems you have to simulation nova stars effect on planetary motion,
and is there a best way to do that ?

Every little thing interacts with any little thing.
In my opinion, what is usually done is that researchers code their model
themselves in C/C++ (or other) using computional libraries and output files
that can be visualized in 3D using tools as VTK and others.

If you need animations and that you are ready to code a bit in python
to interpret your data into an animation, then you may use blender (blender3d.org).

If you have resolved the equations by hand, I assume your problem is only
about multimedia generation ?

Red.

Justin Findlay wrote:
> I'm doing some computational astrophysics research, specifically
> modeling the effect of star novas on planetary motion and my problem is
> that I don't know the best way to do this.
> 
> The nature of this research consists of my extending a model already
> developed by my advisor, and the problem is that I want to translate
> this model into a simulation and I don't know what software to use.  My
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Jan Marten Simons | 12 Feb 2008 21:47
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Interval arithmetics with Python

Hi,

I'm interested in doing interval arithmetics with python. I stumbled 
upon PyDx which can use mpfi for this. (mpfi itself uses mpfr, which is 
in portage). Additionally PyDx is using GMPy, which is also in portage.

So has anyone here bothered to write ebuilds for mpfi and PyDx, yet?

With regards,
Jan
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Jan Marten Simons | 25 Feb 2008 20:41
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Re: Interval arithmetics with Python

Jan Marten Simons schrieb:
> I'm interested in doing interval arithmetics with python. I stumbled 
> upon PyDx which can use mpfi for this. (mpfi itself uses mpfr, which is 
> in portage). Additionally PyDx is using GMPy, which is also in portage.
> So has anyone here bothered to write ebuilds for mpfi and PyDx, yet?

I did an ebuild for mpfi by now ( http://phpfi.com/298847 ), but I need 
some help with the ebuild for PyDX ( http://phpfi.com/298845 ):

During install I get "access denied" errors and I don't know how I can 
tell setup.py to install into the sandboxed directory (image).

With regards,
Jan

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Justin Bronder | 26 Feb 2008 16:45
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Empi, should it be in the science overlay?

I've been spending the majority of my Gentoo-related time working on a
solution to bug 44132 [1], basically, trying to find a way to gracefully
handle multiple installs of various MPI implementations at the same time in
Gentoo.  Theres more information about the solution in my devspace [2], but
a quick summary is that there is a new package (empi) that is much like
crossdev, a new eselect module for empi, and a new eclass that handles both
mpi implementations and packages depending on mpi.

So, I think I have pushed this work far enough along for it to actually be
somewhat officially offered.  My question then, is where should this be
located?  There are several mpi packages in the science overlay already, so
should I push this work to there, or would it be more appropriate to make a
new overlay specifically for hp-cluster?

Future work related to this project will be getting all mpi implementations
and dependant packages converted in the same overlay before bringing it up on
-dev for discussion about inclusion into the main tree.

I have no real preference either way, but the science team does already have
an overlay :)  Let me know what you think.

[1] https://bugs.gentoo.org/show_bug.cgi?id=44132
[2] http://dev.gentoo.org/~jsbronder/README.empi.txt

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Alexey Shvetsov | 26 Feb 2008 16:57
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Re: Empi, should it be in the science overlay?

Thats Cool !

I'll test it on my cluster =)
it uses infiniband and mvpich2 but some people want to use ordinary
eth as interconnect so it will be very useful =)

2008/2/26, Justin Bronder <jsbronder <at> gentoo.org>:
> I've been spending the majority of my Gentoo-related time working on a
>  solution to bug 44132 [1], basically, trying to find a way to gracefully
>  handle multiple installs of various MPI implementations at the same time in
>  Gentoo.  Theres more information about the solution in my devspace [2], but
>  a quick summary is that there is a new package (empi) that is much like
>  crossdev, a new eselect module for empi, and a new eclass that handles both
>  mpi implementations and packages depending on mpi.
>
>  So, I think I have pushed this work far enough along for it to actually be
>  somewhat officially offered.  My question then, is where should this be
>  located?  There are several mpi packages in the science overlay already, so
>  should I push this work to there, or would it be more appropriate to make a
>  new overlay specifically for hp-cluster?
>
>  Future work related to this project will be getting all mpi implementations
>  and dependant packages converted in the same overlay before bringing it up on
>  -dev for discussion about inclusion into the main tree.
>
>  I have no real preference either way, but the science team does already have
>  an overlay :)  Let me know what you think.
>
>  [1] https://bugs.gentoo.org/show_bug.cgi?id=44132
>  [2] http://dev.gentoo.org/~jsbronder/README.empi.txt
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