Install ATLAS header files and cleanup IML spkg

[jhpalmieri]

With the new ATLAS spkg from #10508, iml fails its self tests. See [#10508 comment:518] and later comments.

Use spkgs at:

• http://boxen.math.washington.edu/home/vbraun/spkg/atlas-3.10.1.p1.spkg (spkg diff)
• http://boxen.math.washington.edu/home/jdemeyer/spkg/iml-1.0.1.p15.spkg (spkg diff without deletes)

Apply attachment: 14699_env_version_bump.patch to SAGE_ROOT

Depends on #10508

CC: @nexttime @jpflori @jdemeyer @vbraun

Component: packages: standard

Keywords: atlas IML testsuite check cblas.h

Author: Jean-Pierre Flori, Volker Braun, Jeroen Demeyer

Reviewer: Jean-Pierre Flori

Merged: sage-5.10.rc2

Issue created by migration from https://trac.sagemath.org/ticket/14699

[jpflori]

comment:1

Surely an ATLAS problem, see #10508 comment:526 for a solution.

I suggest we call at least install_inc and potentially install_lib from ATLAS build system to install headers and static libs.

[jpflori]

comment:2

Or just install which should call both of them.

[nexttime]

comment:3

John, U sure about sage.math?

128.208.160.191	sage.math.washington.edu sage sage.math

[nexttime]

comment:4

Replying to @nexttime:

John, U sure about sage.math?

128.208.160.191	sage.math.washington.edu sage sage.math

(As opposed to

;; ANSWER SECTION:
sage.math.washington.edu. 600	IN	A	128.208.160.197

which is boxen.)

[jpflori]

comment:5

It would be nice to fix that on top of #14605 which I've tested quite extensively and is finished since some time.

[nexttime]

comment:6

+1 to also again install static libs.

[jpflori]

Changed keywords from none to atlas

[jpflori]

comment:7

In fact disregard my comment about #14605.
We should fix the issue here quickly, hopefully before 5.10 official release if it's not too late.
Although as it does not seem to prevent anything from working except for IML testsuite, 5.11 should be ok as well.

[nexttime]

Changed keywords from atlas to atlas IML testsuite check cblas.h

[sagetrac-Koen]

comment:9

A side-effect of this ticket is probably that numpy gets built without ATLAS acceleration.

[nexttime]

comment:10

For the record, I did get

ATLAS_CFLAGS=''
ATLAS_LIBS='-lcblas -latlas'

-L${SAGE_LOCAL}/lib "incidentally" came from / for GMP, although after -lcblas -latlas, but we meanwhile add ${SAGE_LOCAL}/lib to LIBRARY_PATH (in sage-env), so that it worked.

[nexttime]

comment:11

P.S.: Although IIRC according to POSIX, -Ldir1 -lfoo -Ldir2 -lbar is the same as -Ldir1 -Ldir2 -lfoo -lbar.

[jpflori]

Author: Jean-Pierre Flori

[nexttime]

comment:13

Replying to @nexttime:

P.S.: Although IIRC according to POSIX, -Ldir1 -lfoo -Ldir2 -lbar is the same as -Ldir1 -Ldir2 -lfoo -lbar.

At least GNU ld docs agree with this:

All -L options apply to all -l options, regardless of the order in which the options appear.

[sagetrac-Koen]

comment:14

You'd still need a line

    cmd += ' --incdir=' + os.path.join(conf['SAGE_LOCAL'],'include') 

in configure_atlas_library() for the header files to go the correct place?

And currently numpy is built without Atlas (it uses another blas): local/lib/python2.7/site-packages/numpy/core/dotblas.so normally contains ATL* symbols (for an old Atlas 3.8.3 version, at least).

[jpflori]

comment:15

Replying to @sagetrac-Koen:

You'd still need a line

    cmd += ' --incdir=' + os.path.join(conf['SAGE_LOCAL'],'include') 

in configure_atlas_library() for the header files to go the correct place?

I don't think so.
We use prefix and that should be enough from what I've seen in ATLAS configure script.

[jpflori]

comment:16

Replying to @sagetrac-Koen:

And currently numpy is built without Atlas (it uses another blas): local/lib/python2.7/site-packages/numpy/core/dotblas.so normally contains ATL* symbols (for an old Atlas 3.8.3 version, at least).

On my gcc110 install (where IML testsuite fails), numpy uses ATLAS correctly.
There is no ATLAS symbols in the file you pointed because we now use a shared version of ATLAS.
But if I run ldd on the file it points to the ATLAS libs.

And I seem to remember we had lots of troubles correctly biulding numpy and scipy with the new ATLAS so hopefully it was actually used.

[nexttime]

comment:17

s/inlcude/include/

and IMHO (=WTF?) also s/serial/single-threaded/g s/parallel/multi-threaded/g ...

(but the latter is not JP's invention I guess)

[jpflori]

comment:18

Replying to @nexttime:

s/inlcude/include/

Done.

and IMHO (=WTF?) also s/serial/single-threaded/g s/parallel/multi-threaded/g ...

(but the latter is not JP's invention I guess)

Not mine indeed.

[jpflori]

comment:69

In the IMl spkg, you don't reexport CFLAGS after checking for SAGE64 (both in spkg-check and spkg-install).

And when looking through trac there is a strange .patch part about renaming sage3_memleak, but that may just be a trac issue.

[jdemeyer]

comment:70

Replying to @jpflori:

In the IMl spkg, you don't reexport CFLAGS after checking for SAGE64 (both in spkg-check and spkg-install).

It's already exported before. No need to "reexport" it.

And when looking through trac there is a strange .patch part about renaming sage3_memleak, but that may just be a trac issue.

Indeed, that's a Trac bug.

[jdemeyer]

Changed work issues from SAGE64, to none

[jdemeyer]

comment:71

I should also note that the only new patch in IML is patches/remove_repl.patch, all the others were already (pre-patched) in the spkg.

[jpflori]

comment:72

Replying to @jdemeyer:

Replying to @jpflori:

In the IMl spkg, you don't reexport CFLAGS after checking for SAGE64 (both in spkg-check and spkg-install).

It's already exported before. No need to "reexport" it.

Damn, I was not aware of that!

And when looking through trac there is a strange .patch part about renaming sage3_memleak, but that may just be a trac issue.

Indeed, that's a Trac bug.

[jpflori]

comment:73

The spkg looks good, seems to work on my systems.

[jdemeyer]

Merged: sage-5.10.rc2

[jdemeyer]

comment:75

Thanks for the review, do you by chance feel like reviewing the IML upgrade at #748?

[jdemeyer]

Changed merged from sage-5.10.rc2 to none

[jdemeyer]

comment:76

Reverting the ATLAS package: #14753.

[jdemeyer]

Dependencies: #10508

[jdemeyer]

Merged: sage-5.10.rc2

[jdemeyer]

comment:79

Keeping "merged in" information for future reference, we should not change this ticket further.