@@ -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 \
@@ -973,7 +973,7 @@ (define-public vinci
(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 @@ (define-public arpack-ng
(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 @@ (define-public arpack-ng-openmpi
(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
new file mode 100644
@@ -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
From: Ludovic Courtès <ludovic.courtes@inria.fr> * 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. --- gnu/local.mk | 1 + gnu/packages/maths.scm | 25 +- .../arpack-ng-propagate-rng-state.patch | 523 ++++++++++++++++++ 3 files changed, 537 insertions(+), 12 deletions(-) create mode 100644 gnu/packages/patches/arpack-ng-propagate-rng-state.patch base-commit: 2426e51688d479042ea115a634c6be2d8b9f3b99