Opened 12 years ago

Closed 12 years ago

#1852 closed defect (fixed)

[with spkg; positive review] Configure R to use Atlas / other improvements to R package

Reported by: pdenapo Owned by: mabshoff
Priority: major Milestone: sage-2.10.1
Component: packages: standard Keywords:
Cc: Merged in:
Authors: Reviewers:
Report Upstream: Work issues:
Branch: Commit:
Dependencies: Stopgaps:

Description

Currenty R in Sage is configured to use its own implementation of BLAS, it would be better to configure it to use ATLAS (wich has better performance, I think)

A parameter --with-blas can be pased to configure, to tell it wich BLAS we want to use.

A comenet: See also ticket #1721, we should avoid hardcoding the location of the BLAS library . If that thicket is implemented, perhaps an enviroment variable should be setto the BLAS library that we want to use (in sage-env?) (or a symlink from $SAGE_LOCAL/libblas.so to the system version)

Other questions:

  • why is R configured with --with-reccomended-packages=no ?

(perhaps it would be possible to offer the recommended packages as an optional package?)

  • why is the whoule source code of R installed in $SAGE_LOCAL/lib/r ?

Change History (8)

comment:1 Changed 12 years ago by was

Other questions: - why is R configured with --with-reccomended-packages=no ? (perhaps it would be possible to offer the recommended packages as an optional package?)

Because --with-recommended-packages=yes takes 5 times to build as no. Simple as that. And for the first few releases of R in Sage it makes sense to be conservative to keep breakage to a minimal. We will revisit this... say now.

  • why is the whoule source code of R installed in $SAGE_LOCAL/lib/r ?

No clue. I didn't know that. It is surprising.

comment:2 Changed 12 years ago by mabshoff

Somebody (was?) does the following in spkg-install:

# For some reason make install sucks -- it doesn't copy the libraries or R bin over ??

cp lib/* "$SAGE_LOCAL"/lib/
cp bin/R "$SAGE_LOCAL"/bin/

Very, very odd to say the least.

Cheers,

Michael

comment:3 Changed 12 years ago by mabshoff

  • Owner changed from was to mabshoff
  • Status changed from new to assigned

comment:4 Changed 12 years ago by mabshoff

  • Milestone set to sage-2.10.1

comment:5 Changed 12 years ago by AlexGhitza

  • Component changed from algebraic geometry to packages

comment:6 Changed 12 years ago by mabshoff

  • Summary changed from Configure R to use Atlas / other improvements to R package to [with spkg] Configure R to use Atlas / other improvements to R package

The r.spkg was a total disaster to put it nicely. It took me about sic hours to sort it all out, but two official revisions later I have:

http://sage.math.washington.edu/home/mabshoff/release-cycles-2.10.1/alpha2/r-2.6.1.p10.spkg

The spkg builds on Linux and OSX, passes testall and now uses ATLAS if it is provided.

Cheers,

Michael

comment:7 Changed 12 years ago by was

  • Summary changed from [with spkg] Configure R to use Atlas / other improvements to R package to [with spkg; positive review] Configure R to use Atlas / other improvements to R package

I read the new spkg-install, built this package on all our test machines, and ran this test with success on all of them:

was@debian32:~$ echo "import rpy; rpy.r('2+2')" | sage-2.10.1.alpha1/sage
----------------------------------------------------------------------
| SAGE Version 2.10.1.alpha1, Release Date: 2008-01-21               |
| Type notebook() for the GUI, and license() for information.        |
----------------------------------------------------------------------

sage: 4.0
sage: 

So thumbs up.

comment:8 Changed 12 years ago by mabshoff

  • Resolution set to fixed
  • Status changed from assigned to closed

Merged in Sage 2.10.1.alpha2

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