diff options
| -rw-r--r-- | gnu/local.mk | 1 | ||||
| -rw-r--r-- | gnu/packages/maths.scm | 25 | ||||
| -rw-r--r-- | gnu/packages/patches/arpack-ng-propagate-rng-state.patch | 523 |
3 files changed, 537 insertions, 12 deletions
diff --git a/gnu/local.mk b/gnu/local.mk index c817c9c926..e9ce4ada54 100644 --- a/gnu/local.mk +++ b/gnu/local.mk @@ -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 \ diff --git a/gnu/packages/maths.scm b/gnu/packages/maths.scm index 0d59ff30f7..b0b3e382ae 100644 --- a/gnu/packages/maths.scm +++ b/gnu/packages/maths.scm @@ -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 diff --git a/gnu/packages/patches/arpack-ng-propagate-rng-state.patch b/gnu/packages/patches/arpack-ng-propagate-rng-state.patch new file mode 100644 index 0000000000..4466bb8e50 --- /dev/null +++ b/gnu/packages/patches/arpack-ng-propagate-rng-state.patch @@ -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 |