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 $SAGE_LOCAL/lib/r ?
Change History (8)
comment:1 Changed 12 years ago by
comment:2 Changed 12 years ago by
Somebody (was?) does the following in spkg-install:
# For some reason make install sucks -- it doesn't copy the libraries or R bin over ?? cp lib/* "$SAGE_LOCAL"/lib/ cp bin/R "$SAGE_LOCAL"/bin/
Very, very odd to say the least.
Cheers,
Michael
comment:3 Changed 12 years ago by
- Owner changed from was to mabshoff
- Status changed from new to assigned
comment:4 Changed 12 years ago by
- Milestone set to sage-2.10.1
comment:5 Changed 12 years ago by
- Component changed from algebraic geometry to packages
comment:6 Changed 12 years ago by
- Summary changed from Configure R to use Atlas / other improvements to R package to [with spkg] Configure R to use Atlas / other improvements to R package
The r.spkg was a total disaster to put it nicely. It took me about sic hours to sort it all out, but two official revisions later I have:
http://sage.math.washington.edu/home/mabshoff/release-cycles-2.10.1/alpha2/r-2.6.1.p10.spkg
The spkg builds on Linux and OSX, passes testall and now uses ATLAS if it is provided.
Cheers,
Michael
comment:7 Changed 12 years ago by
- Summary changed from [with spkg] Configure R to use Atlas / other improvements to R package to [with spkg; positive review] Configure R to use Atlas / other improvements to R package
I read the new spkg-install, built this package on all our test machines, and ran this test with success on all of them:
was@debian32:~$ 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
- Resolution set to fixed
- Status changed from assigned to closed
Merged in Sage 2.10.1.alpha2
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.No clue. I didn't know that. It is surprising.