Merge pull request #106586 from doronbehar/pkg/octave/misc

octave: Use latest jdk & Allow 64 bit indices

pkgs/development/interpreters/octave/default.nix

@@ -23,15 +23,17 @@
 , fftwSinglePrec
 , zlib
 , curl
-, qrupdate
 , blas, lapack
-, arpack
+# These two should use the same lapack and blas as the above
+, qrupdate, arpack, suitesparse ? null
+# If set to true, the above 5 deps are overriden to use the blas and lapack
+# with 64 bit indexes support. If all are not compatible, the build will fail.
+, use64BitIdx ? false
 , libwebp
 , gl2ps
 , ghostscript ? null
 , hdf5 ? null
 , glpk ? null
-, suitesparse ? null
 , gnuplot ? null
 # - Include support for GNU readline:
 , enableReadline ? true
@@ -41,7 +43,7 @@
 , jdk ? null
 , python ? null
 , overridePlatforms ? null
-, sundials_2 ? null
+, sundials ? null
 # - Build Octave Qt GUI:
 , enableQt ? false
 , qtbase ? null
@@ -56,9 +58,42 @@
 , darwin
 }:
 
-assert (!blas.isILP64) && (!lapack.isILP64);
+let
-
+  # Not always evaluated
-mkDerivation rec {
+  blas' = if use64BitIdx then
+    blas.override {
+      isILP64 = true;
+    }
+  else
+    blas
+  ;
+  lapack' = if use64BitIdx then
+    lapack.override {
+      isILP64 = true;
+    }
+  else
+    lapack
+  ;
+  qrupdate' = qrupdate.override {
+    # If use64BitIdx is false, this override doesn't evaluate to a new
+    # derivation, as blas and lapack are not overriden.
+    blas = blas';
+    lapack = lapack';
+  };
+  arpack' = arpack.override {
+    blas = blas';
+    lapack = lapack';
+  };
+  # Not always suitesparse is required at all
+  suitesparse' = if suitesparse != null then
+    suitesparse.override {
+      blas = blas';
+      lapack = lapack';
+    }
+  else
+    null
+  ;
+in mkDerivation rec {
   version = "6.1.0";
   pname = "octave";
 
@@ -78,34 +113,36 @@ mkDerivation rec {
     fltk
     zlib
     curl
-    blas
+    blas'
-    lapack
+    lapack'
     libsndfile
     fftw
     fftwSinglePrec
     portaudio
-    qrupdate
+    qrupdate'
-    arpack
+    arpack'
     libwebp
     gl2ps
   ]
-  ++ (stdenv.lib.optionals enableQt [
+  ++ stdenv.lib.optionals enableQt [
     qtbase
     qtsvg
     qscintilla
-  ])
+  ]
-  ++ (stdenv.lib.optional (ghostscript != null) ghostscript)
+  ++ stdenv.lib.optionals (ghostscript != null) [ ghostscript ]
-  ++ (stdenv.lib.optional (hdf5 != null) hdf5)
+  ++ stdenv.lib.optionals (hdf5 != null) [ hdf5 ]
-  ++ (stdenv.lib.optional (glpk != null) glpk)
+  ++ stdenv.lib.optionals (glpk != null) [ glpk ]
-  ++ (stdenv.lib.optional (suitesparse != null) suitesparse)
+  ++ stdenv.lib.optionals (suitesparse != null) [ suitesparse' ]
-  ++ (stdenv.lib.optional (enableJava) jdk)
+  ++ stdenv.lib.optionals (enableJava) [ jdk ]
-  ++ (stdenv.lib.optional (sundials_2 != null) sundials_2)
+  ++ stdenv.lib.optionals (sundials != null) [ sundials ]
-  ++ (stdenv.lib.optional (gnuplot != null) gnuplot)
+  ++ stdenv.lib.optionals (gnuplot != null) [ gnuplot ]
-  ++ (stdenv.lib.optional (python != null) python)
+  ++ stdenv.lib.optionals (python != null) [ python ]
-  ++ (stdenv.lib.optionals (!stdenv.isDarwin) [ libGL libGLU libX11 ])
+  ++ stdenv.lib.optionals (!stdenv.isDarwin) [ libGL libGLU libX11 ]
-  ++ (stdenv.lib.optionals (stdenv.isDarwin) [ libiconv
+  ++ stdenv.lib.optionals stdenv.isDarwin [
-                                               darwin.apple_sdk.frameworks.Accelerate
+    libiconv
-                                               darwin.apple_sdk.frameworks.Cocoa ])
+    darwin.apple_sdk.frameworks.Accelerate
+    darwin.apple_sdk.frameworks.Cocoa
+  ]
   ;
   nativeBuildInputs = [
     pkgconfig
@@ -115,12 +152,12 @@ mkDerivation rec {
     fftwSinglePrec
     texinfo
   ]
-  ++ (stdenv.lib.optional (sundials_2 != null) sundials_2)
+  ++ stdenv.lib.optionals (sundials != null) [ sundials ]
-  ++ (stdenv.lib.optional enableJIT llvm)
+  ++ stdenv.lib.optionals enableJIT [ llvm ]
-  ++ (stdenv.lib.optionals enableQt [
+  ++ stdenv.lib.optionals enableQt [
     qtscript
     qttools
-  ])
+  ]
   ;
 
   doCheck = !stdenv.isDarwin;
@@ -128,14 +165,14 @@ mkDerivation rec {
   enableParallelBuilding = true;
 
   # See https://savannah.gnu.org/bugs/?50339
-  F77_INTEGER_8_FLAG = if blas.isILP64 then "-fdefault-integer-8" else "";
+  F77_INTEGER_8_FLAG = if use64BitIdx then "-fdefault-integer-8" else "";
 
   configureFlags = [
     "--with-blas=blas"
     "--with-lapack=lapack"
-    (if blas.isILP64 then "--enable-64" else "--disable-64")
+    (if use64BitIdx then "--enable-64" else "--disable-64")
   ]
-    ++ (if stdenv.isDarwin then [ "--enable-link-all-dependencies" ] else [ ])
+    ++ stdenv.lib.optionals stdenv.isDarwin [ "--enable-link-all-dependencies" ]
     ++ stdenv.lib.optionals enableReadline [ "--enable-readline" ]
     ++ stdenv.lib.optionals stdenv.isDarwin [ "--with-x=no" ]
     ++ stdenv.lib.optionals enableQt [ "--with-qt=5" ]
@@ -149,14 +186,20 @@ mkDerivation rec {
   '';
 
   passthru = {
-    inherit version;
     sitePath = "share/octave/${version}/site";
+    blas = blas';
+    lapack = lapack';
+    qrupdate = qrupdate';
+    arpack = arpack';
+    suitesparse = suitesparse';
+    inherit python;
+    inherit enableQt enableJIT enableReadline enableJava;
   };
 
   meta = {
     homepage = "https://www.gnu.org/software/octave/";
     license = stdenv.lib.licenses.gpl3Plus;
-    maintainers = with stdenv.lib.maintainers; [raskin];
+    maintainers = with stdenv.lib.maintainers; [ raskin doronbehar ];
     description = "Scientific Pragramming Language";
     # https://savannah.gnu.org/bugs/?func=detailitem&item_id=56425 is the best attempt to fix JIT
     broken = enableJIT;

pkgs/development/libraries/qrupdate/default.nix

@@ -25,10 +25,10 @@ stdenv.mkDerivation rec {
       "BLAS=-L${blas}/lib -lblas"
       "PREFIX=${placeholder "out"}"
       ${stdenv.lib.optionalString blas.isILP64
-      # Use their FFLAGS along with `-fdefault-integer-8`. If another
+      # If another application intends to use qrupdate compiled with blas with
-      # application intends to use arpack, it should add this to it's FFLAGS as
+      # 64 bit support, it should add this to it's FFLAGS as well. See (e.g):
-      # well. Otherwise (e.g): https://savannah.gnu.org/bugs/?50339
+      # https://savannah.gnu.org/bugs/?50339
-      "FFLAGS=-fimplicit-none -O3 -funroll-loops -fdefault-integer-8"
+      "FFLAGS=-fdefault-integer-8"
       }
     )
   '';

pkgs/development/libraries/sundials/2.x.nix

@@ -1,59 +0,0 @@
-{ stdenv
-, cmake
-, fetchurl
-, python
-# GNU Octave needs KLU for ODE solvers
-, suitesparse
-, blas, lapack
-, gfortran
-, lapackSupport ? true }:
-
-assert (!blas.isILP64) && (!lapack.isILP64);
-
-stdenv.mkDerivation rec {
-  pname = "sundials";
-  version = "2.7.0";
-
-  buildInputs = [ python ] ++ stdenv.lib.optionals (lapackSupport) [
-    gfortran
-    suitesparse
-  ];
-  nativeBuildInputs = [ cmake ];
-
-  src = fetchurl {
-    url = "https://computation.llnl.gov/projects/${pname}/download/${pname}-${version}.tar.gz";
-    sha256 = "01513g0j7nr3rh7hqjld6mw0mcx5j9z9y87bwjc16w2x2z3wm7yk";
-  };
-
-  patches = [
-    (fetchurl {
-      # https://github.com/LLNL/sundials/pull/19
-      url = "https://github.com/LLNL/sundials/commit/1350421eab6c5ab479de5eccf6af2dcad1eddf30.patch";
-      sha256 = "0g67lixp9m85fqpb9rzz1hl1z8ibdg0ldwq5z6flj5zl8a7cw52l";
-    })
-  ];
-
-  cmakeFlags = [
-    "-DEXAMPLES_INSTALL_PATH=${placeholder "out"}/share/examples"
-  ] ++ stdenv.lib.optionals (lapackSupport) [
-    "-DSUNDIALS_INDEX_TYPE=int32_t"
-    # GNU Octave needs KLU for ODE solvers
-    "-DKLU_ENABLE=ON"
-    "-DKLU_INCLUDE_DIR=${suitesparse}/include"
-    "-DKLU_LIBRARY_DIR=${suitesparse}/lib"
-    "-DLAPACK_ENABLE=ON"
-    "-DLAPACK_LIBRARIES=${lapack}/lib/lapack${stdenv.hostPlatform.extensions.sharedLibrary};${blas}/lib/blas${stdenv.hostPlatform.extensions.sharedLibrary}"
-  ];
-
-  # flaky tests, and patch in https://github.com/LLNL/sundials/pull/21 doesn't apply cleanly for sundials_3
-  doCheck = false;
-  checkPhase = "make test";
-
-  meta = with stdenv.lib; {
-    description = "Suite of nonlinear differential/algebraic equation solvers";
-    homepage    = "https://computation.llnl.gov/projects/sundials";
-    platforms   = platforms.all;
-    maintainers = with maintainers; [ idontgetoutmuch ];
-    license     = licenses.bsd3;
-  };
-}

pkgs/top-level/all-packages.nix

@@ -10561,19 +10561,16 @@ in
   octave = callPackage ../development/interpreters/octave {
     python = python3;
     mkDerivation = stdenv.mkDerivation;
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
   };
   octave-jit = callPackage ../development/interpreters/octave {
     python = python3;
     enableJIT = true;
     mkDerivation = stdenv.mkDerivation;
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
   };
   octaveFull = libsForQt5.callPackage ../development/interpreters/octave {
     python = python3;
     enableQt = true;
     overridePlatforms = ["x86_64-linux" "x86_64-darwin"];
-    jdk = jdk8; # TODO: remove override https://github.com/NixOS/nixpkgs/pull/89731
   };
 
   ocropus = callPackage ../applications/misc/ocropus { };
@@ -16195,10 +16192,6 @@ in
     python = python3;
   };
 
-  sundials_2 = callPackage ../development/libraries/sundials/2.x.nix {
-    python = python3;
-  };
-
   sutils = callPackage ../tools/misc/sutils { };
 
   svrcore = callPackage ../development/libraries/svrcore { };

pkgs/top-level/release-alternatives.nix

@@ -9,7 +9,7 @@ let
   blasUsers = [
     # "julia_07" "julia_10" "julia_11" "julia_13" "octave" "octaveFull"
     "fflas-ffpack" "linbox" "R" "ipopt" "hpl" "rspamd" "octopus"
-    "sundials" "sundials_2" "superlu" "suitesparse_5_3" "suitesparse_4_4"
+    "sundials" "superlu" "suitesparse_5_3" "suitesparse_4_4"
     "suitesparse_4_2" "scs" "scalapack" "petsc" "cholmod-extra"
     "arpack" "qrupdate" "libcint" "iml" "globalarrays" "arrayfire" "armadillo"
     "xfitter" "lammps" "plink-ng" "quantum-espresso" "siesta"