Is archlinux good for scientists?

Snowman · 2006-03-07 19:51:06

The matpotlib in AUR was submitted as a zip file (not tar.gz). That's why it can't be accessed. I've posted a comment to notify the maintainer. You can get it here:
http://aur.archlinux.org/packages/matpl … lotlib.zip
BE AWARE THAT I HAVEN'T CHECKED IT AND HAVE REMOVED THE SAFE FLAG UNTIL IT GETS RESUBMITTED PROPERLY.

Here's an old PKGBUILD I had done a while ago.

pkgname=matplotlib
pkgver=0.84
pkgrel=1
pkgdesc=" matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms."
url="http://matplotlib.sourceforge.net/"
license=""
depends=('python')
makedepends=()
conflicts=()
replaces=()
backup=()
install=
source=(http://umn.dl.sourceforge.net/matplotlib/$pkgname-$pkgver.tar.gz)
md5sums=('9d7a9831f64a7c376b98333604e38cc1')

build() {
  cd $startdir/src/$pkgname-$pkgver
  python setup.py install --root=$startdir/pkg
}

Legout · 2006-03-07 20:14:32

Thanks,

but i already get a PKGBUILD for version 0.86.2 (btw 0.87 is out).

Now i´ve got another problem.
I started ipython and wanna import some moduls from scipy. that breaks with

In [1]: from scipy import special 
---------------------------------------------------------------------------
exceptions.ImportError                               Traceback (most recent call last)

/home/volker/<ipython console> 

/usr/lib/python2.4/site-packages/scipy/special/__init__.py 
      8 from basic import *
      9 import specfun
---> 10 import orthogonal
     11 from orthogonal import legendre, chebyt, chebyu, chebyc, chebys, 
     12      jacobi, laguerre, genlaguerre, hermite, hermitenorm, gegenbauer, 

/usr/lib/python2.4/site-packages/scipy/special/orthogonal.py 
     64 import _cephes as cephes
     65 _gam = cephes.gamma
---> 66 from scipy.linalg import eig
     67 
     68 def poch(z,m):

/usr/lib/python2.4/site-packages/scipy/linalg/__init__.py 
      6 from linalg_version import linalg_version as __version__
      7 
----> 8 from basic import *
      9 from decomp import *
     10 from matfuncs import *

/usr/lib/python2.4/site-packages/scipy/linalg/basic.py 
     15 #from blas import get_blas_funcs
     16 #from lapack import get_lapack_funcs
---> 17 from flinalg import get_flinalg_funcs
     18 from scipy.lib.lapack import get_lapack_funcs
     19 from numpy import asarray,zeros,sum,NewAxis,greater_equal,subtract,arange,

/usr/lib/python2.4/site-packages/scipy/linalg/flinalg.py 
     13     import _flinalg
     14 except ImportError:
---> 15     from numpy.distutils.misc_util import PostponedException
     16     _flinalg = PostponedException()
     17     print _flinalg.__doc__

ImportError: cannot import name PostponedException

and

In [9]: from scipy import optimize
---------------------------------------------------------------------------
exceptions.ImportError                               Traceback (most recent call last)

/home/volker/<ipython console> 

/usr/lib/python2.4/site-packages/scipy/optimize/__init__.py 
      9 from zeros import *
     10 from anneal import *
---> 11 from lbfgsb import fmin_l_bfgs_b
     12 from tnc import fmin_tnc
     13 from cobyla import fmin_cobyla

/usr/lib/python2.4/site-packages/scipy/optimize/lbfgsb.py 
     30 
     31 from numpy import zeros, float64, array, int32
---> 32 import _lbfgsb
     33 import optimize
     34 

ImportError: /usr/lib/libblas.so: undefined symbol: c_abs

I tried to reinstall libblas.so. But pacman -Qo libblas.so says it´s not owned by a package. So i don´t know how to reinstall.

Snowman · 2006-03-07 21:10:55

maybe it needs blas77:
http://aur.archlinux.org/packages.php?d … =1&ID=1809
Unfortunately, it seems to have problem with gfortran.

oliv · 2006-03-07 21:25:54

Good news (for those concerned ). I finally rebuild atlas-lapack (just .a files without parallel features), and scipy. Atlas-lapack provides lapack, atlas and blas (f77 and c interface). I can run the full test of scipy (test(level=10)) without errors.

It's done with gfortran and gcc 4.0.3, but I don't know how to test other functions than scipy. So if somebody can test it :
- atlas-lapack (updated, check the AUR)
- python-numpy (AUR)
- python-scipy (AUR added some fix as comments)

rafal · 2006-03-10 10:23:15

I'm trying to build atlas-lapack but it doen't build the package since after compiling everything it gets in an ininfinite loop and I must kill the process to.

any ideas what is wrong?

003
002
001
Enter number at top left of screen [0]: 
===============================================================================
                                  IMPORTANT
===============================================================================
Before going any further, check
   http://math-atlas.sourceforge.net/errata.html
This is the ATLAS errata file, which keeps a running count of all known
ATLAS bugs and system problems, with associated workarounds or fixes.
IF YOU DO NOT CHECK THIS FILE, YOU MAY BE COMPILING A LIBRARY WITH KNOWN BUGS.

Have you scoped the errata file? [y]: 
Configure will ask a series of questions, in one of two forms.  The first form
of question is a menu of choices.  One option in almost all menus is
'Other/UNKNOWN'.  If you are unsure of the answer, always choose this option.
The second form of question is a single line, with a default answer shown in
square braces.  If you hit return without typing anything, this default answer
will be used.  Again, if you are unsure of the answer, simply accept the
default.

ATLAS can detect almost everything it needs to know, so choosing the default
or 'Other/UNKNOWN' will at worst simply extend the install time (if you tell
config the answer to something ATLAS can skip some tests).

Configure makes no changes to the state of things until all questions have
been asked and answered.  Therefore, if you get confused and want to start
over, feel free to break out of this program (CTRL-C, CTRL-BREAK, etc)
and start again.  Alternatively, if you make a mistake you can finish the
configure process, and then edit the created make include file by hand to fix
the mistake manually (the name and location of this file will be printed
out at the end of configure).

If you have problems during configure or installation, consult the file
'ATLAS/doc/TroubleShoot.txt'.
---------- PRESS ENTER TO CONTINUE ---------- 
Are you ready to continue? [y]: Probing to make operating system determination:
Operating system configured as Linux

archinfo_x86.c: In function 'PrintUsage':
archinfo_x86.c:106: warning: incompatible implicit declaration of built-in function 'exit'
archinfo_x86.c: In function 'main':
archinfo_x86.c:211: warning: incompatible implicit declaration of built-in function 'exit'
Probing for architecture:
Enter your machine type:
   1. Other/UNKNOWN
   2. AMD Athlon
   3. 32 bit AMD Hammer
   4. 64 bit AMD Hammer
   5. Pentium PRO
   6. Pentium II
   7. Pentium III
   8. Pentium 4
   9. Pentium 4E (prescott)
  10. Transmeta Efficeon
Enter machine number [1]: Architecture is set to UNKNOWN

   GAS_x8632: DETECTED!
   GAS_x8664: NO.
   GAS_SPARC: NO.
   AS_OSX_PPC: NO.
   GAS_LINUX_PPC: NO.
   LINUX_PARISC: NO.
   HPUX_PARISC: NO.

Probing for supported ISA extensions:
   AltiVec: NO.
   AltiVec: NO.
   SSE3: NO.
   SSE2: DETECTED!
Number of CPUs: 1

Looking for compilers (this may take a while):
   /usr/bin/gcc  : v4.0.3
   g77 -O rejected
F77 = g77 (null)
CC = /usr/bin/gcc -fomit-frame-pointer -O3 -funroll-all-loops
MCC = /usr/bin/gcc -fomit-frame-pointer -O

FINDING tar, gzip, AND gunzip
   tar    : /bin/tar 
   gzip   : /bin/gzip 
   gunzip : /bin/gunzip 


Although your machine is not known, ATLAS has default parameters for OS='Linux'.
If you want to just trust these default values, you can use express setup,
drastically reducing the amount of questions you are required to answer

   use express setup? [y]: 



You need to choose a name which represents this architecture (eg. UltraSparc,
Dec21164, etc).  Do not use a generic name (eg. solaris, linux), which might
apply to different  hardware.  This architecture name will be appended to the
name of the created make include file, and appear in all subdirectories, so
don't make it longer than you like to type.  The name should follow the rules
for file names (so don't use punctuation and spaces, for instance).

   Enter Architecture name (ARCH) [Linux_UNKNOWNSSE2]: <arch> set to 'linuxspecific'



This next value is the size, in kilobytes, that ATLAS must read/write in order
to completely flush your largest cache.  ATLAS will flush this much memory
between timing calls, in order to ensure timings are not inflated by
cache preloading.  A safe maximum is usually twice the size of your actual
largest cache size.  If you do not know the size of your largest cache,
a maximum value is fine.  The only drawback to making this value large
is that it requires more memory to do timings, and may slow down
the install process (if you have only a small amount of memory, it can also
invalidate the timings by causing the timers to swap).  The default given
below is ATLAS's idea of either the maximum cache your system could have, or
the maximum ATLAS believes it is safe to flush.  If you are certain that
your largest cache is smaller than the default given below, expedite the
install by changing it.  If you are certain you have enough memory to
support the necessary memory demands without swapping, and the value
is not twice the size of your largest cache, increase it.  Otherwise, just
hit enter to continue.


0 smaller than min value of 64.  Try again.


1 smaller than min value of 64.  Try again.

   Enter Maximum cache size (KB) [4096]:    Enter Maximum cache size (KB) [4096]:    Enter Maximum cache size (KB) [4096]: 
The ATLAS install process is heavily file-based, and this can cause major
reliability problems when interacting with an overloaded or malfunctioning
remotely mounted filesystem.  ATLAS therefore has a mechanism in place to
allow for a delay before a file is declared to not be there, so that
slow NFS (i.e., waiting for amd timout) problems can be overcome, or for
handling slightly differing clocks between server/client.  This problem is
magnified if doing cross-compilation.  In the question below, we ask how
much of a delay, in seconds, ATLAS should tolerate between file creation
and appearance.  If you are installing on a local filesystem (eg. /tmp) or
a smooth-running NFS system, answer 0; for a moderately loaded NFS server, you
may want a value in the 10 second range, and for cross-compiling systems or
NFS servers experiencing errors, you may want to go as high as a couple
of minutes (120).
   Enter File creation delay in seconds [0]: 

I'm going to ask you for information about your Fortran 77 compiler.  ATLAS
does not need Fortran77 to build, so if you don't have a Fortran compiler,
the install can still be completed successfully.  However, ATLAS built without
a Fortran compiler will not be callable from Fortran (i.e., the user should
use the C interface), and we will not be able to do full testing, since some of
the tester code is written in Fortran77.



I'm going to ask you for information about your Fortran 77 compiler.  ATLAS
does not need Fortran77 to build, so if you don't have a Fortran compiler,
the install can still be completed successfully.  However, ATLAS built without
a Fortran compiler will not be callable from Fortran (i.e., the user should
use the C interface), and we will not be able to do full testing, since some of
the tester code is written in Fortran77.

F77 = 'g77 -O' doesn't seem to work for me.
   Enter 1 to enter a different F77, 0 to continue with none [1]: 

I'm going to ask you for information about your Fortran 77 compiler.  ATLAS
does not need Fortran77 to build, so if you don't have a Fortran compiler,
the install can still be completed successfully.  However, ATLAS built without
a Fortran compiler will not be callable from Fortran (i.e., the user should
use the C interface), and we will not be able to do full testing, since some of
the tester code is written in Fortran77.

   Enter f77 compiler [g77]:    Enter F77 Flags [-O]: 

I'm going to ask you for information about your Fortran 77 compiler.  ATLAS
does not need Fortran77 to build, so if you don't have a Fortran compiler,
the install can still be completed successfully.  However, ATLAS built without
a Fortran compiler will not be callable from Fortran (i.e., the user should
use the C interface), and we will not be able to do full testing, since some of
the tester code is written in Fortran77.

F77 = 'g77 -O' doesn't seem to work for me.
   Enter 1 to enter a different F77, 0 to continue with none [1]: 

I'm going to ask you for information about your Fortran 77 compiler.  ATLAS
does not need Fortran77 to build, so if you don't have a Fortran compiler,
the install can still be completed successfully.  However, ATLAS built without
a Fortran compiler will not be callable from Fortran (i.e., the user should
use the C interface), and we will not be able to do full testing, since some of
the tester code is written in Fortran77.

Legout · 2006-03-10 10:50:20

hi,

what´s your PC??

I´m using and AMD Sempron (Should work for all AMD 32bit). And i used this makecoms.

023
y

y
3
n
y
linuxspecific
0
1
gfortran
-0
n

If this won´t work, change the "3" into a number that matches your architecture.

Important. Delete your src befor u try to rebuild.

rafal · 2006-03-10 12:05:58

the problem is that I cannot insert anything as it is done automatically when I run makepkg. The architecture is set to UNKNOWN automatically too, a bug in Makefile? I have a Celeron 2400 processor.

Legout · 2006-03-10 12:22:51

The insert came from the "makecoms" file.
Delete the one in your build-directory and insert the one i´ve posted above.
Try changing the first 3 to some other architechtures.
And before you try to rebuild. delete src/

rafal · 2006-03-10 18:03:05

Legout wrote:

The insert came from the "makecoms" file.
Delete the one in your build-directory and insert the one i´ve posted above.
Try changing the first 3 to some other architechtures.
And before you try to rebuild. delete src/

thanks, I tried different options but none of them worked. Setting gfortran as a compiler failed every times.

At the end I removed "makecoms" from PKGBUILD and when done manually I got atlas-lapack package:)

Anybody is using PyX? or have an Arch package?
http://pyx.sourceforge.net/

Regards

oliv · 2006-03-12 18:51:24

You'll have to delete '< makecoms' from the PKGBUILD. When you will start makepkg, it will ask questions and you'll have to reply to it manually.

The important parts are :

Enter Architecture name (ARCH) => linuxspecific

Enter 1 to enter a different F77, 0 to continue with none => 1

Enter f77 compiler [g77] => gfortran

I still have to try to make automagically this configure part, but it's really a pain when the hardware isn't detected.

rafal · 2006-03-13 02:40:15

big_gie wrote:

I'm doing my master in physics, and using arch. It is great, but there could be more packages.
I<m using latex for any documents. I once used matlab, but switched to python for its opensourceness. With scipy, numpy and matplotlib, python can really make concurence to matlab. I tryed octave and scilab but I really don't like gnuplot for data display. Matplotlib is really great! (You can find scipy, numpy and matplotlib in aur). For big simulations, I use Intel's Fortran compiler witch works great and is free. I made an pkgbuild for Portland Group (PGI) set of compilers too, but it is really expensive.

Matplotlib is great except it gives only 2D plots and what about 3D surfaces? Any module for python?

Regards

Legout · 2006-03-23 13:36:31

I thought scipy.xplt could do 3d plotting.

So i installed scipy from aur. Compiling went fine. But it seems, that xplt (and all other plotting modules) aren´t available anymore.

Why??

Any ideas?

rafal · 2006-03-25 09:46:59

How to install matplotlib?

matlplotlib depends on wxwindows but when I'm trying to install wxwidgets from aur it is not possible because of the file conflicts wth wxgtk package which is already installed. If I try to uninstall wxgtk, pacman complaints that wxgtk is a dependency of wxpython.

How to solve these conflicts?
Which package do you have wxgtk or wxwidgets?
Or maybe there is another package wxwindows to install, from where?
Any idea?

iphitus · 2006-03-25 10:17:15

wxgtk provides wxwidgets,

wxwidgets is what wxwindows was renamed to.

Arch Linux

#26 2006-03-07 19:51:06

Re: Is archlinux good for scientists?

#27 2006-03-07 20:14:32

Re: Is archlinux good for scientists?

#28 2006-03-07 21:10:55

Re: Is archlinux good for scientists?

#29 2006-03-07 21:25:54

Re: Is archlinux good for scientists?

#30 2006-03-10 10:23:15

Re: Is archlinux good for scientists?

#31 2006-03-10 10:50:20

Re: Is archlinux good for scientists?

#32 2006-03-10 12:05:58

Re: Is archlinux good for scientists?

#33 2006-03-10 12:22:51

Re: Is archlinux good for scientists?

#34 2006-03-10 18:03:05

Re: Is archlinux good for scientists?

#35 2006-03-12 18:51:24

Re: Is archlinux good for scientists?

#36 2006-03-13 02:40:15

Re: Is archlinux good for scientists?

#37 2006-03-23 13:36:31

Re: Is archlinux good for scientists?

#38 2006-03-25 09:46:59

Re: Is archlinux good for scientists?

#39 2006-03-25 10:17:15

Re: Is archlinux good for scientists?

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