Remove ATLAS

[mkoeppe]

(from #19719)

Our version of ATLAS is outdated and has not been tested in a long time. Latest upstream version as of 2021-09-21 is 3.11.40, released 2018-10-02, see ​https://github.com/math-atlas/math-atlas/releases

We remove this package.

However, we keep the makefile variable BLAS (used in packages' dependencies files), rather than hardcoding openblas in dependencies. It will make it easier to plug in another BLAS implementation if one comes along in the future, and it is also needed for #29387.

CC: @jhpalmieri @dimpase @kiwifb @jpflori

Component: packages: standard

Author: John Palmieri

Branch/Commit: 272424a

Reviewer: Matthias Koeppe

Issue created by migration from https://trac.sagemath.org/ticket/30350

[jhpalmieri]

Branch: u/jhpalmieri/remove-atlas

[jhpalmieri]

comment:4

Here is an attempt. I have questions:

• what to do with openblas/spkg-configure.m4? Any changes necessary?
• what about the spkg-install.in scripts for scipy and numpy? They refer to an ATLAS environment variable. Leave as is or change?
• I don't know anything about cygwin, so I don't know what to do about the installation instructions referring to ATLAS in src/doc/en/installation/source.rst.
  Anyway, this is a start.

---

New commits:

3c3022c

trac 30350: remove the ATLAS package

[jhpalmieri]

Commit: 3c3022c

[sagetrac-git]

Changed commit from 3c3022c to 0afdab5

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

0afdab5

trac 30350: remove the ATLAS package

[mkoeppe]

Author: John Palmieri

[mkoeppe]

comment:7

Sage development has entered the release candidate phase for 9.3. Setting a new milestone for this ticket based on a cursory review of ticket status, priority, and last modification date.

[mkoeppe]

comment:9

I support removing this package in 9.5. The branch needs rebasing

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. This was a forced push. New commits:

8ba1d79

trac 30350: remove the ATLAS package

[sagetrac-git]

Changed commit from 0afdab5 to 8ba1d79

[jhpalmieri]

comment:11

Rebased. I deleted the reference to ATLAS in the cygwin instructions in src/doc/en/installation/source.rst, but the other questions in comment:4 remain.

[mkoeppe]

comment:12

Replying to @jhpalmieri:

• what to do with openblas/spkg-configure.m4? Any changes necessary?

We could either keep the --with-blas=... option but make it an error if anything other than openblas is passed, or remove it.

[mkoeppe]

comment:13

Replying to @jhpalmieri:

• what about the spkg-install.in scripts for scipy and numpy? They refer to an ATLAS environment variable. Leave as is or change?

No change needed. The scripts just set the environment variable to a safe value so the installation does not pick up random things that may be in the user's environment. (Not sure why the default is different for macOS and for other systems.)

[mkoeppe]

comment:14

The changes to the documentation look fine.

[jhpalmieri]

comment:15

Is this the way to remove the --with-blas option?

diff --git a/build/pkgs/openblas/spkg-configure.m4 b/build/pkgs/openblas/spkg-configure.m4
index 177bbb1d4f..c81533ba71 100644
--- a/build/pkgs/openblas/spkg-configure.m4
+++ b/build/pkgs/openblas/spkg-configure.m4
@@ -110,26 +110,5 @@ SAGE_SPKG_CONFIGURE([openblas], [
   LIBS="$SAVE_LIBS"
   CFLAGS="$SAVE_CFLAGS"
  ])
- ], [
-  dnl REQUIRED-CHECK
-  AS_IF([test "x$with_blas" = xopenblas], [
-     sage_require_openblas=yes
-     sage_require_atlas=no])
-  ], [
-  dnl PRE
-  AC_MSG_CHECKING([BLAS library])
-  AC_ARG_WITH([blas],
-  [AS_HELP_STRING([--with-blas=openblas],
-    [use OpenBLAS as BLAS library (default)])]
-  [AS_HELP_STRING([--with-blas=atlas],
-    [use ATLAS as BLAS library])],,
-    [with_blas=openblas]  # default
-  )
-  AS_CASE(["$with_blas"],
-    [openblas], [],
-    [atlas],    [sage_spkg_install_openblas=no],
-                [AC_MSG_ERROR([allowed values for --with-blas are 'atlas' and 'openblas'])])
-  AC_MSG_RESULT([$with_blas])
-  AC_SUBST([SAGE_BLAS], [$with_blas])
-  ]
+ ]
 )

[mkoeppe]

comment:16

Yes, that looks right

[mkoeppe]

comment:17

After removing, this line:

build/make/Makefile.in:BLAS = @SAGE_BLAS@

needs changing

[jhpalmieri]

comment:18

Can I just change it to BLAS = openblas?

[mkoeppe]

comment:19

Yes

[sagetrac-git]

Changed commit from 8ba1d79 to 69db839

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

69db839

trac 30350: remove "--with-blas=" option to ./configure

[jhpalmieri]

comment:21

Okay, here are those changes.

[mkoeppe]

comment:22

build/pkgs/atlas/distros/ still contains some stuff

[sagetrac-git]

Changed commit from 69db839 to 272424a

[sagetrac-git]

Branch pushed to git repo; I updated commit sha1. New commits:

272424a

trac 30350: remove remaining bits in build/pkgs/atlas/distros

[jhpalmieri]

comment:24

Fixed, thanks.

[mkoeppe]

Reviewer: Matthias Koeppe

[mkoeppe]

comment:27

This seems to work well.

[jhpalmieri]

comment:28

Thank you!

[vbraun]

Changed branch from u/jhpalmieri/remove-atlas to 272424a