[PR PATCH] openblas: fix bug that affects numpy/scipy/octave/sagemath

[PR PATCH] openblas: fix bug that affects numpy/scipy/octave/sagemath

[tornaria]

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There is a new pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages openblas
https://github.com/void-linux/void-packages/pull/43153

openblas: fix bug that affects numpy/scipy/octave/sagemath
See: https://github.com/xianyi/OpenBLAS/issues/3976

Include patches from upstream:
 - https://github.com/xianyi/OpenBLAS/pull/3978/
 - https://github.com/xianyi/OpenBLAS/pull/3980/
 - https://github.com/xianyi/OpenBLAS/pull/3984/

<!-- Uncomment relevant sections and delete options which are not applicable -->

#### Testing the changes
- I tested the changes in this PR: **briefly**

I had >100 test failures in sagemath with 0.3.22_1 that are all fixed with these patches.

@ahesford 

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A patch file from https://github.com/void-linux/void-packages/pull/43153.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-openblas-43153.patch --]
[-- Type: text/x-diff, Size: 7327 bytes --]

From 3c3e5860446deedcf3a293997aa7657598f1e094 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Fri, 31 Mar 2023 23:38:23 -0300
Subject: [PATCH] openblas: fix bug that affects numpy/scipy/octave/sagemath

See: https://github.com/xianyi/OpenBLAS/issues/3976

Include patches from upstream:
 - https://github.com/xianyi/OpenBLAS/pull/3978/
 - https://github.com/xianyi/OpenBLAS/pull/3980/
 - https://github.com/xianyi/OpenBLAS/pull/3984/
---
 srcpkgs/openblas/patches/3978.patch |  22 ++++++
 srcpkgs/openblas/patches/3980.patch | 107 ++++++++++++++++++++++++++++
 srcpkgs/openblas/patches/3984.patch |  32 +++++++++
 srcpkgs/openblas/template           |   3 +-
 4 files changed, 162 insertions(+), 2 deletions(-)
 create mode 100644 srcpkgs/openblas/patches/3978.patch
 create mode 100644 srcpkgs/openblas/patches/3980.patch
 create mode 100644 srcpkgs/openblas/patches/3984.patch

diff --git a/srcpkgs/openblas/patches/3978.patch b/srcpkgs/openblas/patches/3978.patch
new file mode 100644
index 000000000000..097d841bd70b
--- /dev/null
+++ b/srcpkgs/openblas/patches/3978.patch
@@ -0,0 +1,22 @@
+From 12aabb9f9ba57a74a3feedfafd97b7aeecbac450 Mon Sep 17 00:00:00 2001
+From: Martin Kroeker <martin@ruby.chemie.uni-freiburg.de>
+Date: Wed, 29 Mar 2023 09:44:33 +0200
+Subject: [PATCH] fix conditional
+
+---
+ lapack/getf2/zgetf2_k.c | 2 +-
+ 1 file changed, 1 insertion(+), 1 deletion(-)
+
+diff --git a/lapack/getf2/zgetf2_k.c b/lapack/getf2/zgetf2_k.c
+index f3412f52ff..dbc78abc60 100644
+--- a/lapack/getf2/zgetf2_k.c
++++ b/lapack/getf2/zgetf2_k.c
+@@ -107,7 +107,7 @@ blasint CNAME(blas_arg_t *args, BLASLONG *range_m, BLASLONG *range_n, FLOAT *sa,
+       temp2 = *(b + jp * 2 + 1);
+ 
+   //    if ((temp1 != ZERO) || (temp2 != ZERO)) {
+-	if ((fabs(temp1) >= DBL_MIN) && (fabs(temp2) >= DBL_MIN)) {
++	if ((fabs(temp1) >= DBL_MIN) || (fabs(temp2) >= DBL_MIN)) {
+ 		
+ 	if (jp != j) {
+ 	  SWAP_K(j + 1, 0, 0, ZERO, ZERO, a + j * 2, lda,
diff --git a/srcpkgs/openblas/patches/3980.patch b/srcpkgs/openblas/patches/3980.patch
new file mode 100644
index 000000000000..fb45c33325e2
--- /dev/null
+++ b/srcpkgs/openblas/patches/3980.patch
@@ -0,0 +1,107 @@
+From 6c431239da3e4480651480f91b3438d7ad1903e5 Mon Sep 17 00:00:00 2001
+From: Martin Kroeker <martin@ruby.chemie.uni-freiburg.de>
+Date: Wed, 29 Mar 2023 22:14:21 +0200
+Subject: [PATCH] Split test condition in LU computation - non-denormal for
+ computation, exact zero for reporting singularity
+
+---
+ lapack/getf2/getf2_k.c  | 23 ++++++++++++--------
+ lapack/getf2/zgetf2_k.c | 48 ++++++++++++++++++++++-------------------
+ 2 files changed, 40 insertions(+), 31 deletions(-)
+
+diff --git a/lapack/getf2/getf2_k.c b/lapack/getf2/getf2_k.c
+index d29ed588e9..80c66dd7a6 100644
+--- a/lapack/getf2/getf2_k.c
++++ b/lapack/getf2/getf2_k.c
+@@ -100,16 +100,21 @@ blasint CNAME(blas_arg_t *args, BLASLONG *range_m, BLASLONG *range_n, FLOAT *sa,
+       jp--;
+       temp1 = *(b + jp);
+ 
+-      //if (temp1 != ZERO) {
++      if (temp1 != ZERO) {
++#if defined(DOUBLE)
+ 	if (fabs(temp1) >= DBL_MIN ) {
+-	temp1 = dp1 / temp1;
+-
+-	if (jp != j) {
+-	  SWAP_K(j + 1, 0, 0, ZERO, a + j, lda, a + jp, lda, NULL, 0);
+-	}
+-	if (j + 1 < m) {
+-	  SCAL_K(m - j - 1, 0, 0, temp1, b + j + 1, 1, NULL, 0, NULL, 0);
+-	}
++#else
++	if (fabs(temp1) >= FLT_MIN ) {
++#endif
++  	  temp1 = dp1 / temp1;
++
++	  if (jp != j) {
++	    SWAP_K(j + 1, 0, 0, ZERO, a + j, lda, a + jp, lda, NULL, 0);
++	  }
++	  if (j + 1 < m) {
++	    SCAL_K(m - j - 1, 0, 0, temp1, b + j + 1, 1, NULL, 0, NULL, 0);
++	  }
++        }
+       } else {
+ 	if (!info) info = j + 1;
+       }
+diff --git a/lapack/getf2/zgetf2_k.c b/lapack/getf2/zgetf2_k.c
+index dbc78abc60..e3d53c96f2 100644
+--- a/lapack/getf2/zgetf2_k.c
++++ b/lapack/getf2/zgetf2_k.c
+@@ -106,30 +106,34 @@ blasint CNAME(blas_arg_t *args, BLASLONG *range_m, BLASLONG *range_n, FLOAT *sa,
+       temp1 = *(b + jp * 2 + 0);
+       temp2 = *(b + jp * 2 + 1);
+ 
+-  //    if ((temp1 != ZERO) || (temp2 != ZERO)) {
++      if ((temp1 != ZERO) || (temp2 != ZERO)) {
++#if defined(DOUBLE)
+ 	if ((fabs(temp1) >= DBL_MIN) || (fabs(temp2) >= DBL_MIN)) {
+-		
+-	if (jp != j) {
+-	  SWAP_K(j + 1, 0, 0, ZERO, ZERO, a + j * 2, lda,
++#else
++	if ((fabs(temp1) >= FLT_MIN) || (fabs(temp2) >= FLT_MIN)) {
++#endif		
++	  if (jp != j) {
++	    SWAP_K(j + 1, 0, 0, ZERO, ZERO, a + j * 2, lda,
+ 		 a + jp * 2, lda, NULL, 0);
+-	}
+-
+-	if (fabs(temp1) >= fabs(temp2)){
+-	  ratio = temp2 / temp1;
+-	  den = dp1 /(temp1 * ( 1 + ratio * ratio));
+-	  temp3 =  den;
+-	  temp4 = -ratio * den;
+-	} else {
+-	  ratio = temp1 / temp2;
+-	  den = dp1 /(temp2 * ( 1 + ratio * ratio));
+-	  temp3 =  ratio * den;
+-	  temp4 = -den;
+-	}
+-
+-	if (j + 1 < m) {
+-	  SCAL_K(m - j - 1, 0, 0, temp3, temp4,
+-		 b + (j + 1) * 2, 1, NULL, 0, NULL, 0);
+-	}
++	  }
++
++	  if (fabs(temp1) >= fabs(temp2)){
++	    ratio = temp2 / temp1;
++	    den = dp1 /(temp1 * ( 1 + ratio * ratio));
++	    temp3 =  den;
++	    temp4 = -ratio * den;
++	  } else {
++	    ratio = temp1 / temp2;
++	    den = dp1 /(temp2 * ( 1 + ratio * ratio));
++	    temp3 =  ratio * den;
++	    temp4 = -den;
++	  }
++
++	  if (j + 1 < m) {
++	    SCAL_K(m - j - 1, 0, 0, temp3, temp4,
++	  	 b + (j + 1) * 2, 1, NULL, 0, NULL, 0);
++	  }
++        }
+       } else {
+ 	if (!info) info = j + 1;
+       }
diff --git a/srcpkgs/openblas/patches/3984.patch b/srcpkgs/openblas/patches/3984.patch
new file mode 100644
index 000000000000..0448d396ad58
--- /dev/null
+++ b/srcpkgs/openblas/patches/3984.patch
@@ -0,0 +1,32 @@
+From 36fcb52094c4c99eec651a61311204c466b7f054 Mon Sep 17 00:00:00 2001
+From: Martin Kroeker <martin@ruby.chemie.uni-freiburg.de>
+Date: Sat, 1 Apr 2023 00:02:54 +0200
+Subject: [PATCH] Fix logic - we want real OR imaginary part of X to be nonzero
+ here
+
+---
+ driver/level2/zspr_k.c | 4 ++--
+ 1 file changed, 2 insertions(+), 2 deletions(-)
+
+diff --git a/driver/level2/zspr_k.c b/driver/level2/zspr_k.c
+index d888a81ee2..7f0eefd6b3 100644
+--- a/driver/level2/zspr_k.c
++++ b/driver/level2/zspr_k.c
+@@ -53,7 +53,7 @@ int CNAME(BLASLONG m, FLOAT alpha_r, FLOAT alpha_i,
+ 
+   for (i = 0; i < m; i++){
+ #ifndef LOWER
+-    if ((X[i * 2 + 0] != ZERO) && (X[i * 2 + 1] != ZERO)) {
++    if ((X[i * 2 + 0] != ZERO) || (X[i * 2 + 1] != ZERO)) {
+       AXPYU_K(i + 1, 0, 0,
+ 	      alpha_r * X[i * 2 + 0] - alpha_i * X[i * 2 + 1],
+ 	      alpha_i * X[i * 2 + 0] + alpha_r * X[i * 2 + 1],
+@@ -61,7 +61,7 @@ int CNAME(BLASLONG m, FLOAT alpha_r, FLOAT alpha_i,
+     }
+     a += (i + 1) * 2;
+ #else
+-    if ((X[i * 2 + 0] != ZERO) && (X[i * 2 + 1] != ZERO)) {
++    if ((X[i * 2 + 0] != ZERO) || (X[i * 2 + 1] != ZERO)) {
+       AXPYU_K(m - i, 0, 0,
+ 	      alpha_r * X[i * 2 + 0] - alpha_i * X[i * 2 + 1],
+ 	      alpha_i * X[i * 2 + 0] + alpha_r * X[i * 2 + 1],
diff --git a/srcpkgs/openblas/template b/srcpkgs/openblas/template
index 6310d955f537..6f78974f49dc 100644
--- a/srcpkgs/openblas/template
+++ b/srcpkgs/openblas/template
@@ -1,8 +1,7 @@
 # Template file for 'openblas'
 pkgname=openblas
-reverts="0.3.19_1"
 version=0.3.22
-revision=1
+revision=2
 build_style=gnu-makefile
 make_build_args="HOSTCC=gcc USE_OPENMP=1"
 make_install_args="OPENBLAS_INCLUDE_DIR=\$(PREFIX)/include/openblas"

Re: openblas: fix bug that affects numpy/scipy/octave/sagemath

[ahesford]

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New comment by ahesford on void-packages repository

https://github.com/void-linux/void-packages/pull/43153#issuecomment-1492804320

Comment:
Let's wait on these patches and revert instead. Upstream hasn't yet accepted the most recent one and, given the extent of these issues, I'd rather let the fixes settle into a new release rather than trying to squash these bugs with patches. 

Re: openblas: fix bug that affects numpy/scipy/octave/sagemath

[martin-frbg]

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New comment by martin-frbg on void-packages repository

https://github.com/void-linux/void-packages/pull/43153#issuecomment-1492895352

Comment:
0.2.23  is to be released this weekend, you can bet I'll run the _latest_ versions of the numpy/scipy testsuites this time in addition to OpenBLAS' own. (And thanks for confirming that this fixes all of sagemath's testsuite errors too)

Re: openblas: fix bug that affects numpy/scipy/octave/sagemath

[ahesford]

[-- Attachment #1: Type: text/plain, Size: 314 bytes --]

New comment by ahesford on void-packages repository

https://github.com/void-linux/void-packages/pull/43153#issuecomment-1492944165

Comment:
@tornaria I reverted Void's package pending final upstream testing and a new release. If you want to use this PR to manage the update to 0.3.23, feel free to keep it open.

Re: openblas: fix bug that affects numpy/scipy/octave/sagemath

[martin-frbg]

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New comment by martin-frbg on void-packages repository

https://github.com/void-linux/void-packages/pull/43153#issuecomment-1493115558

Comment:
released 0.3.23 just now

Re: [PR PATCH] [Updated] openblas: fix bug that affects numpy/scipy/octave/sagemath

[tornaria]

[-- Attachment #1: Type: text/plain, Size: 1628 bytes --]

There is an updated pull request by tornaria against master on the void-packages repository

https://github.com/tornaria/void-packages openblas
https://github.com/void-linux/void-packages/pull/43153

openblas: fix bug that affects numpy/scipy/octave/sagemath
See: https://github.com/xianyi/OpenBLAS/issues/3976

Include patches from upstream:
 - https://github.com/xianyi/OpenBLAS/pull/3978/
 - https://github.com/xianyi/OpenBLAS/pull/3980/
 - https://github.com/xianyi/OpenBLAS/pull/3984/

<!-- Uncomment relevant sections and delete options which are not applicable -->

#### Testing the changes
- I tested the changes in this PR: **briefly**

I had >100 test failures in sagemath with 0.3.22_1 that are all fixed with these patches.

@ahesford 

<!--
#### New package
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A patch file from https://github.com/void-linux/void-packages/pull/43153.patch is attached

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: github-pr-openblas-43153.patch --]
[-- Type: text/x-diff, Size: 1424 bytes --]

From bbf8abd113d5b48f09ac671f4ea5d8c347cbd529 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Gonzalo=20Tornar=C3=ADa?= <tornaria@cmat.edu.uy>
Date: Sun, 2 Apr 2023 16:34:23 -0300
Subject: [PATCH] openblas: update to 0.3.23.

---
 srcpkgs/openblas/template | 9 ++++-----
 1 file changed, 4 insertions(+), 5 deletions(-)

diff --git a/srcpkgs/openblas/template b/srcpkgs/openblas/template
index c51bd98e2963..61a891a86a30 100644
--- a/srcpkgs/openblas/template
+++ b/srcpkgs/openblas/template
@@ -1,8 +1,7 @@
 # Template file for 'openblas'
 pkgname=openblas
-reverts="0.3.22_1"
-version=0.3.21
-revision=2
+version=0.3.23
+revision=1
 build_style=gnu-makefile
 make_build_args="HOSTCC=gcc USE_OPENMP=1"
 make_install_args="OPENBLAS_INCLUDE_DIR=\$(PREFIX)/include/openblas"
@@ -12,9 +11,9 @@ short_desc="Optimized BLAS (Basic Linear Algebra Subprograms) based on GotoBLAS2
 maintainer="Andrew J. Hesford <ajh@sideband.org>"
 license="BSD-3-Clause"
 homepage="https://www.openblas.net/"
-changelog="https://raw.githubusercontent.com/xianyi/OpenBLAS/v${version}/Changelog.txt"
+changelog="https://raw.githubusercontent.com/xianyi/OpenBLAS/develop/Changelog.txt"
 distfiles="https://github.com/xianyi/OpenBLAS/archive/v${version}.tar.gz"
-checksum=f36ba3d7a60e7c8bcc54cd9aaa9b1223dd42eaf02c811791c37e8ca707c241ca
+checksum=5d9491d07168a5d00116cdc068a40022c3455bf9293c7cb86a65b1054d7e5114
 
 case "$XBPS_TARGET_MACHINE" in
 	ppc64*) ;;

Re: openblas: update to 0.3.23.

[tornaria]

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New comment by tornaria on void-packages repository

https://github.com/void-linux/void-packages/pull/43153#issuecomment-1493422873

Comment:
I will run sagemath testsuite and report back when I'm done.

Re: openblas: update to 0.3.23.

[tornaria]

[-- Attachment #1: Type: text/plain, Size: 232 bytes --]

New comment by tornaria on void-packages repository

https://github.com/void-linux/void-packages/pull/43153#issuecomment-1493596050

Comment:
@ahesford everything looks ok now. I've tested sagemath with this, locally and in #43225.

Re: [PR PATCH] [Closed]: openblas: update to 0.3.23.

[ahesford]

[-- Attachment #1: Type: text/plain, Size: 1308 bytes --]

There's a closed pull request on the void-packages repository

openblas: update to 0.3.23.
https://github.com/void-linux/void-packages/pull/43153

Description:
Fixes a  bug that affects numpy/scipy/octave/sagemath

See: https://github.com/xianyi/OpenBLAS/issues/3976

<!-- Uncomment relevant sections and delete options which are not applicable -->

#### Testing the changes
- I tested the changes in this PR: **briefly**

I had >100 test failures in sagemath with 0.3.22_1 that should all be fixed in 0.3.23.

@ahesford 

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