futurile/guix-play
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

gnu: arpack-ng: Update to 3.9.0.

Browse Source 
* gnu/packages/maths.scm (arpack-ng): Update to 3.9.0.
[source]: Add 'patches'.
[build-system]: Switch to CMAKE-BUILD-SYSTEM.
[native-inputs]: Remove AUTOCONF, AUTOMAKE, and LIBTOOL.
(arpack-ng-openmpi)[inputs]: Use 'modify-inputs'.
[arguments]: Use gexps.
* gnu/packages/patches/arpack-ng-propagate-rng-state.patch: New file.
* gnu/local.mk (dist_patch_DATA): Add it.
This commit is contained in:
Ludovic Courtès 2023-06-16 15:26:04 +02:00 committed by Ludovic Courtès
parent 5594f4c999
commit ff208b4b62
No known key found for this signature in database
GPG Key ID: 090B11993D9AEBB5
3 changed files with 537 additions and 12 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

1
gnu/local.mk
View File

@ -905,6 +905,7 @@ dist_patch_DATA = \
%D%/packages/patches/aoflagger-use-system-provided-pybind11.patch \
%D%/packages/patches/apr-skip-getservbyname-test.patch \
%D%/packages/patches/ark-skip-xar-test.patch \
%D%/packages/patches/arpack-ng-propagate-rng-state.patch \
%D%/packages/patches/aspell-CVE-2019-25051.patch \
%D%/packages/patches/aspell-default-dict-dir.patch \
%D%/packages/patches/ath9k-htc-firmware-binutils.patch \

25
gnu/packages/maths.scm
View File

@ -973,7 +973,7 @@ halfspaces) or by their double description with both representations.")
(define-public arpack-ng
(package
(name "arpack-ng")
(version "3.8.0")
(version "3.9.0")
(home-page "https://github.com/opencollab/arpack-ng")
(source (origin
(method git-fetch)
@ -981,10 +981,11 @@ halfspaces) or by their double description with both representations.")
(file-name (git-file-name name version))
(sha256
(base32
"0l7as5z6xvbxly8alam9s4kws70952qq35a6vkljzayi4b9gbklx"))))
(build-system gnu-build-system)
"09smxilyn8v9xs3kpx3nlj2s7ql3v8z40mpc09kccbb6smyd35iv"))
(patches (search-patches "arpack-ng-propagate-rng-state.patch"))))
(build-system cmake-build-system)
(native-inputs
(list autoconf automake libtool pkg-config))
(list pkg-config))
(inputs
(list eigen lapack gfortran))
(synopsis "Fortran subroutines for solving eigenvalue problems")
@ -998,16 +999,16 @@ large scale eigenvalue problems.")
(package (inherit arpack-ng)
(name "arpack-ng-openmpi")
(inputs
`(("mpi" ,openmpi)
,@(package-inputs arpack-ng)))
(modify-inputs (package-inputs arpack-ng)
(prepend openmpi)))
(arguments
(substitute-keyword-arguments (package-arguments arpack-ng)
((#:configure-flags _ '())
''("--enable-mpi"))
((#:phases phases '%standard-phases)
`(modify-phases ,phases
(add-before 'check 'mpi-setup
,%openmpi-setup)))))
((#:configure-flags _ #~())
#~'("-DMPI=ON"))
((#:phases phases #~%standard-phases)
#~(modify-phases #$phases
(add-before 'check 'mpi-setup
#$%openmpi-setup)))))
(synopsis "Fortran subroutines for solving eigenvalue problems with MPI")))
(define-public lapack

523
gnu/packages/patches/arpack-ng-propagate-rng-state.patch Normal file
View File

@ -0,0 +1,523 @@
Fix a bug that manifests while running the test suite of 'python-igraph':
https://github.com/opencollab/arpack-ng/issues/401
https://github.com/opencollab/arpack-ng/pull/414
From d885b7be4ecdc9c1496f2d6f256f6c0d34962459 Mon Sep 17 00:00:00 2001
From: =?UTF-8?q?Szabolcs=20Horva=CC=81t?= <szhorvat@gmail.com>
Date: Sun, 9 Apr 2023 16:36:35 +0200
Subject: [PATCH] fix: ensure that LAPACK RNG state is propagated
- fixes #401, #410, #411
- restores 'inits' variable removed in ce2e69a849da1d10dad5d6d3ec4db6120b3ecf50, ensuring that the RNG state is propagated
- reverts e0d67054f573da351f12a226f7c7cc65a690ef3d to ensure that seed is different on each parallel thread
- updates seed initialization of parallel pdgetv0/psgetv0 so that they match that of pzgetv0/pcgetv0
---
PARPACK/SRC/MPI/pcgetv0.f | 48 +++++++++++++++++++++++----------------
PARPACK/SRC/MPI/pdgetv0.f | 40 ++++++++++++++++++++++++++------
PARPACK/SRC/MPI/psgetv0.f | 43 ++++++++++++++++++++++++++---------
PARPACK/SRC/MPI/pzgetv0.f | 48 +++++++++++++++++++++++----------------
SRC/cgetv0.f | 21 ++++++++++++-----
SRC/dgetv0.f | 21 ++++++++++++-----
SRC/sgetv0.f | 21 ++++++++++++-----
SRC/zgetv0.f | 21 ++++++++++++-----
8 files changed, 183 insertions(+), 80 deletions(-)
diff --git a/PARPACK/SRC/MPI/pcgetv0.f b/PARPACK/SRC/MPI/pcgetv0.f
index 59e3d1658..24fe8a0f1 100644
--- a/PARPACK/SRC/MPI/pcgetv0.f
+++ b/PARPACK/SRC/MPI/pcgetv0.f
@@ -176,13 +176,13 @@ subroutine pcgetv0
c | Local Scalars & Arrays |
c %------------------------%
c
- logical first, orth
+ logical first, inits, orth
integer idist, iseed(4), iter, msglvl, jj, myid, igen
Real
& rnorm0
Complex
& cnorm, cnorm2
- save first, iseed, iter, msglvl, orth, rnorm0
+ save first, iseed, inits, iter, msglvl, orth, rnorm0
c
Complex
& cnorm_buf, buf2(1)
@@ -203,6 +203,12 @@ subroutine pcgetv0
& ccdotc
external ccdotc, pscnorm2, slapy2
c
+c %-----------------%
+c | Data Statements |
+c %-----------------%
+c
+ data inits /.true./
+c
c %-----------------------%
c | Executable Statements |
c %-----------------------%
@@ -213,26 +219,30 @@ subroutine pcgetv0
c | random number generator |
c %-----------------------------------%
c
+ if (inits) then
c
-c %-----------------------------------%
-c | Generate a seed on each processor |
-c | using process id (myid). |
-c | Note: the seed must be between 1 |
-c | and 4095. iseed(4) must be odd. |
-c %-----------------------------------%
+c %-----------------------------------%
+c | Generate a seed on each processor |
+c | using process id (myid). |
+c | Note: the seed must be between 1 |
+c | and 4095. iseed(4) must be odd. |
+c %-----------------------------------%
c
- call MPI_COMM_RANK(comm, myid, ierr)
- igen = 1000 + 2*myid + 1
- if (igen .gt. 4095) then
- write(0,*) 'Error in p_getv0: seed exceeds 4095!'
- end if
+ call MPI_COMM_RANK(comm, myid, ierr)
+ igen = 1000 + 2*myid + 1
+ if (igen .gt. 4095) then
+ write(0,*) 'Error in p_getv0: seed exceeds 4095!'
+ end if
+c
+ iseed(1) = igen/1000
+ igen = mod(igen,1000)
+ iseed(2) = igen/100
+ igen = mod(igen,100)
+ iseed(3) = igen/10
+ iseed(4) = mod(igen,10)
c
- iseed(1) = igen/1000
- igen = mod(igen,1000)
- iseed(2) = igen/100
- igen = mod(igen,100)
- iseed(3) = igen/10
- iseed(4) = 7
+ inits = .false.
+ end if
c
if (ido .eq. 0) then
c
diff --git a/PARPACK/SRC/MPI/pdgetv0.f b/PARPACK/SRC/MPI/pdgetv0.f
index 0f348b820..5a1956997 100644
--- a/PARPACK/SRC/MPI/pdgetv0.f
+++ b/PARPACK/SRC/MPI/pdgetv0.f
@@ -177,11 +177,11 @@ subroutine pdgetv0
c | Local Scalars & Arrays |
c %------------------------%
c
- logical first, orth
- integer idist, iseed(4), iter, msglvl, jj
+ logical first, inits, orth
+ integer idist, iseed(4), iter, msglvl, jj, myid, igen
Double precision
& rnorm0, buf2(1)
- save first, iseed, iter, msglvl, orth, rnorm0
+ save first, iseed, inits, iter, msglvl, orth, rnorm0
c
Double precision
& rnorm_buf
@@ -206,6 +206,12 @@ subroutine pdgetv0
c
intrinsic abs, sqrt
c
+c %-----------------%
+c | Data Statements |
+c %-----------------%
+c
+ data inits /.true./
+c
c %-----------------------%
c | Executable Statements |
c %-----------------------%
@@ -216,10 +222,30 @@ subroutine pdgetv0
c | random number generator |
c %-----------------------------------%
c
- iseed(1) = 1
- iseed(2) = 3
- iseed(3) = 5
- iseed(4) = 7
+ if (inits) then
+c
+c %-----------------------------------%
+c | Generate a seed on each processor |
+c | using process id (myid). |
+c | Note: the seed must be between 1 |
+c | and 4095. iseed(4) must be odd. |
+c %-----------------------------------%
+c
+ call MPI_COMM_RANK(comm, myid, ierr)
+ igen = 1000 + 2*myid + 1
+ if (igen .gt. 4095) then
+ write(0,*) 'Error in p_getv0: seed exceeds 4095!'
+ end if
+c
+ iseed(1) = igen/1000
+ igen = mod(igen,1000)
+ iseed(2) = igen/100
+ igen = mod(igen,100)
+ iseed(3) = igen/10
+ iseed(4) = mod(igen,10)
+c
+ inits = .false.
+ end if
c
if (ido .eq. 0) then
c
diff --git a/PARPACK/SRC/MPI/psgetv0.f b/PARPACK/SRC/MPI/psgetv0.f
index d79a513b2..078e4fa8c 100644
--- a/PARPACK/SRC/MPI/psgetv0.f
+++ b/PARPACK/SRC/MPI/psgetv0.f
@@ -177,11 +177,11 @@ subroutine psgetv0
c | Local Scalars & Arrays |
c %------------------------%
c
- logical first, orth
- integer idist, iseed(4), iter, msglvl, jj
+ logical first, inits, orth
+ integer idist, iseed(4), iter, msglvl, jj, myid, igen
Real
& rnorm0
- save first, iseed, iter, msglvl, orth, rnorm0
+ save first, iseed, inits, iter, msglvl, orth, rnorm0
c
Real
& rnorm_buf
@@ -206,20 +206,41 @@ subroutine psgetv0
c
intrinsic abs, sqrt
c
+c %-----------------%
+c | Data Statements |
+c %-----------------%
+c
+ data inits /.true./
+c
c %-----------------------%
c | Executable Statements |
c %-----------------------%
c
c
-c %-----------------------------------%
-c | Initialize the seed of the LAPACK |
-c | random number generator |
-c %-----------------------------------%
+ if (inits) then
c
- iseed(1) = 1
- iseed(2) = 3
- iseed(3) = 5
- iseed(4) = 7
+c %-----------------------------------%
+c | Generate a seed on each processor |
+c | using process id (myid). |
+c | Note: the seed must be between 1 |
+c | and 4095. iseed(4) must be odd. |
+c %-----------------------------------%
+c
+ call MPI_COMM_RANK(comm, myid, ierr)
+ igen = 1000 + 2*myid + 1
+ if (igen .gt. 4095) then
+ write(0,*) 'Error in p_getv0: seed exceeds 4095!'
+ end if
+c
+ iseed(1) = igen/1000
+ igen = mod(igen,1000)
+ iseed(2) = igen/100
+ igen = mod(igen,100)
+ iseed(3) = igen/10
+ iseed(4) = mod(igen,10)
+c
+ inits = .false.
+ end if
c
if (ido .eq. 0) then
c
diff --git a/PARPACK/SRC/MPI/pzgetv0.f b/PARPACK/SRC/MPI/pzgetv0.f
index 731fb319f..94fb705f3 100644
--- a/PARPACK/SRC/MPI/pzgetv0.f
+++ b/PARPACK/SRC/MPI/pzgetv0.f
@@ -176,13 +176,13 @@ subroutine pzgetv0
c | Local Scalars & Arrays |
c %------------------------%
c
- logical first, orth
+ logical first, inits, orth
integer idist, iseed(4), iter, msglvl, jj, myid, igen
Double precision
& rnorm0
Complex*16
& cnorm, cnorm2
- save first, iseed, iter, msglvl, orth, rnorm0
+ save first, iseed, inits, iter, msglvl, orth, rnorm0
c
Complex*16
& cnorm_buf, buf2(1)
@@ -203,6 +203,12 @@ subroutine pzgetv0
& zzdotc
external zzdotc , pdznorm2 , dlapy2
c
+c %-----------------%
+c | Data Statements |
+c %-----------------%
+c
+ data inits /.true./
+c
c %-----------------------%
c | Executable Statements |
c %-----------------------%
@@ -213,26 +219,30 @@ subroutine pzgetv0
c | random number generator |
c %-----------------------------------%
c
+ if (inits) then
c
-c %-----------------------------------%
-c | Generate a seed on each processor |
-c | using process id (myid). |
-c | Note: the seed must be between 1 |
-c | and 4095. iseed(4) must be odd. |
-c %-----------------------------------%
+c %-----------------------------------%
+c | Generate a seed on each processor |
+c | using process id (myid). |
+c | Note: the seed must be between 1 |
+c | and 4095. iseed(4) must be odd. |
+c %-----------------------------------%
c
- call MPI_COMM_RANK(comm, myid, ierr)
- igen = 1000 + 2*myid + 1
- if (igen .gt. 4095) then
- write(0,*) 'Error in p_getv0: seed exceeds 4095!'
- end if
+ call MPI_COMM_RANK(comm, myid, ierr)
+ igen = 1000 + 2*myid + 1
+ if (igen .gt. 4095) then
+ write(0,*) 'Error in p_getv0: seed exceeds 4095!'
+ end if
+c
+ iseed(1) = igen/1000
+ igen = mod(igen,1000)
+ iseed(2) = igen/100
+ igen = mod(igen,100)
+ iseed(3) = igen/10
+ iseed(4) = mod(igen,10)
c
- iseed(1) = igen/1000
- igen = mod(igen,1000)
- iseed(2) = igen/100
- igen = mod(igen,100)
- iseed(3) = igen/10
- iseed(4) = 7
+ inits = .false.
+ end if
c
if (ido .eq. 0) then
c
diff --git a/SRC/cgetv0.f b/SRC/cgetv0.f
index b49e66708..c231eadcb 100644
--- a/SRC/cgetv0.f
+++ b/SRC/cgetv0.f
@@ -156,13 +156,13 @@ subroutine cgetv0
c | Local Scalars & Arrays |
c %------------------------%
c
- logical first, orth
+ logical first, inits, orth
integer idist, iseed(4), iter, msglvl, jj
Real
& rnorm0
Complex
& cnorm
- save first, iseed, iter, msglvl, orth, rnorm0
+ save first, iseed, inits, iter, msglvl, orth, rnorm0
c
c %----------------------%
c | External Subroutines |
@@ -180,6 +180,12 @@ subroutine cgetv0
& ccdotc
external ccdotc, scnrm2, slapy2
c
+c %-----------------%
+c | Data Statements |
+c %-----------------%
+c
+ data inits /.true./
+c
c %-----------------------%
c | Executable Statements |
c %-----------------------%
@@ -190,10 +196,13 @@ subroutine cgetv0
c | random number generator |
c %-----------------------------------%
c
- iseed(1) = 1
- iseed(2) = 3
- iseed(3) = 5
- iseed(4) = 7
+ if (inits) then
+ iseed(1) = 1
+ iseed(2) = 3
+ iseed(3) = 5
+ iseed(4) = 7
+ inits = .false.
+ end if
c
if (ido .eq. 0) then
c
diff --git a/SRC/dgetv0.f b/SRC/dgetv0.f
index 8be4fa26d..1d6dc01bd 100644
--- a/SRC/dgetv0.f
+++ b/SRC/dgetv0.f
@@ -157,11 +157,11 @@ subroutine dgetv0
c | Local Scalars & Arrays |
c %------------------------%
c
- logical first, orth
+ logical first, inits, orth
integer idist, iseed(4), iter, msglvl, jj
Double precision
& rnorm0
- save first, iseed, iter, msglvl, orth, rnorm0
+ save first, iseed, inits, iter, msglvl, orth, rnorm0
c
c %----------------------%
c | External Subroutines |
@@ -183,6 +183,12 @@ subroutine dgetv0
c
intrinsic abs, sqrt
c
+c %-----------------%
+c | Data Statements |
+c %-----------------%
+c
+ data inits /.true./
+c
c %-----------------------%
c | Executable Statements |
c %-----------------------%
@@ -193,10 +199,13 @@ subroutine dgetv0
c | random number generator |
c %-----------------------------------%
c
- iseed(1) = 1
- iseed(2) = 3
- iseed(3) = 5
- iseed(4) = 7
+ if (inits) then
+ iseed(1) = 1
+ iseed(2) = 3
+ iseed(3) = 5
+ iseed(4) = 7
+ inits = .false.
+ end if
c
if (ido .eq. 0) then
c
diff --git a/SRC/sgetv0.f b/SRC/sgetv0.f
index 26130a014..d861b2d6d 100644
--- a/SRC/sgetv0.f
+++ b/SRC/sgetv0.f
@@ -157,11 +157,11 @@ subroutine sgetv0
c | Local Scalars & Arrays |
c %------------------------%
c
- logical first, orth
+ logical first, inits, orth
integer idist, iseed(4), iter, msglvl, jj
Real
& rnorm0
- save first, iseed, iter, msglvl, orth, rnorm0
+ save first, iseed, inits, iter, msglvl, orth, rnorm0
c
c %----------------------%
c | External Subroutines |
@@ -183,6 +183,12 @@ subroutine sgetv0
c
intrinsic abs, sqrt
c
+c %-----------------%
+c | Data Statements |
+c %-----------------%
+c
+ data inits /.true./
+c
c %-----------------------%
c | Executable Statements |
c %-----------------------%
@@ -193,10 +199,13 @@ subroutine sgetv0
c | random number generator |
c %-----------------------------------%
c
- iseed(1) = 1
- iseed(2) = 3
- iseed(3) = 5
- iseed(4) = 7
+ if (inits) then
+ iseed(1) = 1
+ iseed(2) = 3
+ iseed(3) = 5
+ iseed(4) = 7
+ inits = .false.
+ end if
c
if (ido .eq. 0) then
c
diff --git a/SRC/zgetv0.f b/SRC/zgetv0.f
index cc13c3cfb..1fbd50851 100644
--- a/SRC/zgetv0.f
+++ b/SRC/zgetv0.f
@@ -156,13 +156,13 @@ subroutine zgetv0
c | Local Scalars & Arrays |
c %------------------------%
c
- logical first, orth
+ logical first, inits, orth
integer idist, iseed(4), iter, msglvl, jj
Double precision
& rnorm0
Complex*16
& cnorm
- save first, iseed, iter, msglvl, orth, rnorm0
+ save first, iseed, inits, iter, msglvl, orth, rnorm0
c
c %----------------------%
c | External Subroutines |
@@ -180,6 +180,12 @@ subroutine zgetv0
& zzdotc
external zzdotc, dznrm2, dlapy2
c
+c %-----------------%
+c | Data Statements |
+c %-----------------%
+c
+ data inits /.true./
+c
c %-----------------------%
c | Executable Statements |
c %-----------------------%
@@ -190,10 +196,13 @@ subroutine zgetv0
c | random number generator |
c %-----------------------------------%
c
- iseed(1) = 1
- iseed(2) = 3
- iseed(3) = 5
- iseed(4) = 7
+ if (inits) then
+ iseed(1) = 1
+ iseed(2) = 3
+ iseed(3) = 5
+ iseed(4) = 7
+ inits = .false.
+ end if
c
if (ido .eq. 0) then
c