From ec3f5a021bc12d32bee8f33828f7daa20a9d24c6 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Tue, 4 Feb 2025 16:06:47 +0800
Subject: [PATCH 01/12] petsc: simplify configurePhase

---
 pkgs/by-name/pe/petsc/package.nix | 29 ++++++++++++-----------------
 1 file changed, 12 insertions(+), 17 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 3db7a522fff6..5645677df27d 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -47,7 +47,9 @@ stdenv.mkDerivation rec {
     lapack
   ] ++ lib.optional hdf5-support hdf5 ++ lib.optional petsc-withp4est p4est ++ lib.optionals withParmetis [ metis parmetis ];
 
-  prePatch = lib.optionalString stdenv.hostPlatform.isDarwin ''
+  postPatch = ''
+    patchShebangs ./lib/petsc/bin
+  '' + lib.optionalString stdenv.hostPlatform.isDarwin ''
     substituteInPlace config/install.py \
       --replace /usr/bin/install_name_tool ${cctools}/bin/install_name_tool
   '';
@@ -67,6 +69,15 @@ stdenv.mkDerivation rec {
     "--with-metis-dir=${metis}"
     "--with-parmetis=1"
     "--with-parmetis-dir=${parmetis}"
+  ] ++ lib.optionals petsc-withp4est [
+    "--with-p4est=1"
+    "--with-zlib-include=${zlib.dev}/include"
+    "--with-zlib-lib=[-L${zlib}/lib,-lz]"
+  ] ++ lib.optionals hdf5-support [
+    "--with-hdf5=1"
+    "--with-hdf5-fortran-bindings=1"
+    "--with-hdf5-include=${hdf5.dev}/include"
+    "--with-hdf5-lib=[-L${hdf5}/lib,-lhdf5]"
   ] ++ lib.optionals petsc-optimized [
     "--with-debugging=0"
     "COPTFLAGS=-O3"
@@ -74,22 +85,6 @@ stdenv.mkDerivation rec {
     "CXXOPTFLAGS=-O3"
     "CXXFLAGS=-O3"
   ];
-  preConfigure = ''
-    patchShebangs ./lib/petsc/bin
-  '' + lib.optionalString petsc-withp4est ''
-    configureFlagsArray+=(
-      "--with-p4est=1"
-      "--with-zlib-include=${zlib.dev}/include"
-      "--with-zlib-lib=-L${zlib}/lib -lz"
-    )
-  '' + lib.optionalString hdf5-support ''
-    configureFlagsArray+=(
-      "--with-hdf5=1"
-      "--with-hdf5-fortran-bindings=1"
-      "--with-hdf5-include=${hdf5.dev}/include"
-      "--with-hdf5-lib=-L${hdf5}/lib -lhdf5"
-    )
-  '';
 
   hardeningDisable = lib.optionals (!petsc-optimized) [
     "fortify"

From e6bda1731a4851ef920168fcc8e4e8f8cef8f441 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Tue, 4 Feb 2025 16:48:17 +0800
Subject: [PATCH 02/12] petsc: reformat with nixfmt-rfc-style

---
 pkgs/by-name/pe/petsc/package.nix | 97 ++++++++++++++++++-------------
 1 file changed, 56 insertions(+), 41 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 5645677df27d..c83df800ca11 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -42,49 +42,64 @@ stdenv.mkDerivation rec {
     gfortran
     pkg-config
   ] ++ lib.optional mpiSupport mpi;
-  buildInputs = [
-    blas
-    lapack
-  ] ++ lib.optional hdf5-support hdf5 ++ lib.optional petsc-withp4est p4est ++ lib.optionals withParmetis [ metis parmetis ];
+  buildInputs =
+    [
+      blas
+      lapack
+    ]
+    ++ lib.optional hdf5-support hdf5
+    ++ lib.optional petsc-withp4est p4est
+    ++ lib.optionals withParmetis [
+      metis
+      parmetis
+    ];
 
-  postPatch = ''
-    patchShebangs ./lib/petsc/bin
-  '' + lib.optionalString stdenv.hostPlatform.isDarwin ''
-    substituteInPlace config/install.py \
-      --replace /usr/bin/install_name_tool ${cctools}/bin/install_name_tool
-  '';
+  postPatch =
+    ''
+      patchShebangs ./lib/petsc/bin
+    ''
+    + lib.optionalString stdenv.hostPlatform.isDarwin ''
+      substituteInPlace config/install.py \
+        --replace /usr/bin/install_name_tool ${cctools}/bin/install_name_tool
+    '';
 
-  configureFlags = [
-    "--with-blas=1"
-    "--with-lapack=1"
-    "--with-scalar-type=${petsc-scalar-type}"
-    "--with-precision=${petsc-precision}"
-    "--with-mpi=${if mpiSupport then "1" else "0"}"
-  ] ++ lib.optionals mpiSupport [
-    "--CC=mpicc"
-    "--with-cxx=mpicxx"
-    "--with-fc=mpif90"
-  ] ++ lib.optionals (mpiSupport && withParmetis) [
-    "--with-metis=1"
-    "--with-metis-dir=${metis}"
-    "--with-parmetis=1"
-    "--with-parmetis-dir=${parmetis}"
-  ] ++ lib.optionals petsc-withp4est [
-    "--with-p4est=1"
-    "--with-zlib-include=${zlib.dev}/include"
-    "--with-zlib-lib=[-L${zlib}/lib,-lz]"
-  ] ++ lib.optionals hdf5-support [
-    "--with-hdf5=1"
-    "--with-hdf5-fortran-bindings=1"
-    "--with-hdf5-include=${hdf5.dev}/include"
-    "--with-hdf5-lib=[-L${hdf5}/lib,-lhdf5]"
-  ] ++ lib.optionals petsc-optimized [
-    "--with-debugging=0"
-    "COPTFLAGS=-O3"
-    "FOPTFLAGS=-O3"
-    "CXXOPTFLAGS=-O3"
-    "CXXFLAGS=-O3"
-  ];
+  configureFlags =
+    [
+      "--with-blas=1"
+      "--with-lapack=1"
+      "--with-scalar-type=${petsc-scalar-type}"
+      "--with-precision=${petsc-precision}"
+      "--with-mpi=${if mpiSupport then "1" else "0"}"
+    ]
+    ++ lib.optionals mpiSupport [
+      "--CC=mpicc"
+      "--with-cxx=mpicxx"
+      "--with-fc=mpif90"
+    ]
+    ++ lib.optionals (mpiSupport && withParmetis) [
+      "--with-metis=1"
+      "--with-metis-dir=${metis}"
+      "--with-parmetis=1"
+      "--with-parmetis-dir=${parmetis}"
+    ]
+    ++ lib.optionals petsc-withp4est [
+      "--with-p4est=1"
+      "--with-zlib-include=${zlib.dev}/include"
+      "--with-zlib-lib=[-L${zlib}/lib,-lz]"
+    ]
+    ++ lib.optionals hdf5-support [
+      "--with-hdf5=1"
+      "--with-hdf5-fortran-bindings=1"
+      "--with-hdf5-include=${hdf5.dev}/include"
+      "--with-hdf5-lib=[-L${hdf5}/lib,-lhdf5]"
+    ]
+    ++ lib.optionals petsc-optimized [
+      "--with-debugging=0"
+      "COPTFLAGS=-O3"
+      "FOPTFLAGS=-O3"
+      "CXXOPTFLAGS=-O3"
+      "CXXFLAGS=-O3"
+    ];
 
   hardeningDisable = lib.optionals (!petsc-optimized) [
     "fortify"

From 602e8d527b3277770acc30bcc6801f2889a1f07b Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Tue, 4 Feb 2025 19:53:26 +0800
Subject: [PATCH 03/12] petsc: add standalone metis support

---
 pkgs/by-name/pe/petsc/package.nix | 14 +++++++++-----
 1 file changed, 9 insertions(+), 5 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index c83df800ca11..6ad696a539cf 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -14,6 +14,7 @@
   hdf5-support ? false,
   hdf5,
   metis,
+  withMetis ? false,
   parmetis,
   withParmetis ? false,
   pkg-config,
@@ -27,6 +28,9 @@
 # This version of PETSc does not support a non-MPI p4est build
 assert petsc-withp4est -> p4est.mpiSupport;
 
+# Package parmetis depend on metis and mpi support
+assert withParmetis -> (withMetis && mpiSupport);
+
 stdenv.mkDerivation rec {
   pname = "petsc";
   version = "3.21.4";
@@ -49,10 +53,8 @@ stdenv.mkDerivation rec {
     ]
     ++ lib.optional hdf5-support hdf5
     ++ lib.optional petsc-withp4est p4est
-    ++ lib.optionals withParmetis [
-      metis
-      parmetis
-    ];
+    ++ lib.optional withMetis metis
+    ++ lib.optional withParmetis parmetis;
 
   postPatch =
     ''
@@ -76,9 +78,11 @@ stdenv.mkDerivation rec {
       "--with-cxx=mpicxx"
       "--with-fc=mpif90"
     ]
-    ++ lib.optionals (mpiSupport && withParmetis) [
+    ++ lib.optionals withMetis [
       "--with-metis=1"
       "--with-metis-dir=${metis}"
+    ]
+    ++ lib.optionals withParmetis [
       "--with-parmetis=1"
       "--with-parmetis-dir=${parmetis}"
     ]

From f4bba88df7414956e652134e198762d619d657cc Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Tue, 4 Feb 2025 20:10:36 +0800
Subject: [PATCH 04/12] petsc: add ptscotch support

---
 pkgs/by-name/pe/petsc/package.nix | 12 +++++++++++-
 1 file changed, 11 insertions(+), 1 deletion(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 6ad696a539cf..2c29bfd2129a 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -17,6 +17,8 @@
   withMetis ? false,
   parmetis,
   withParmetis ? false,
+  scotch,
+  withPtscotch ? false,
   pkg-config,
   p4est,
   zlib, # propagated by p4est but required by petsc
@@ -31,6 +33,8 @@ assert petsc-withp4est -> p4est.mpiSupport;
 # Package parmetis depend on metis and mpi support
 assert withParmetis -> (withMetis && mpiSupport);
 
+assert withPtscotch -> mpiSupport;
+
 stdenv.mkDerivation rec {
   pname = "petsc";
   version = "3.21.4";
@@ -54,7 +58,8 @@ stdenv.mkDerivation rec {
     ++ lib.optional hdf5-support hdf5
     ++ lib.optional petsc-withp4est p4est
     ++ lib.optional withMetis metis
-    ++ lib.optional withParmetis parmetis;
+    ++ lib.optional withParmetis parmetis
+    ++ lib.optional withPtscotch scotch;
 
   postPatch =
     ''
@@ -86,6 +91,11 @@ stdenv.mkDerivation rec {
       "--with-parmetis=1"
       "--with-parmetis-dir=${parmetis}"
     ]
+    ++ lib.optionals withPtscotch [
+      "--with-ptscotch=1"
+      "--with-ptscotch-include=${scotch.dev}/include"
+      "--with-ptscotch-lib=[-L${scotch}/lib,-lptscotch,-lptesmumps,-lptscotchparmetisv3,-lptscotcherr,-lesmumps,-lscotch,-lscotcherr]"
+    ]
     ++ lib.optionals petsc-withp4est [
       "--with-p4est=1"
       "--with-zlib-include=${zlib.dev}/include"

From 0b2160ea3cbdfa033401a5716ad094b9d76aeacf Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Tue, 4 Feb 2025 20:14:57 +0800
Subject: [PATCH 05/12] petsc: add scalapack and mumps support

---
 pkgs/by-name/pe/petsc/package.nix | 18 +++++++++++++++++-
 1 file changed, 17 insertions(+), 1 deletion(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 2c29bfd2129a..6a13227e4031 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -19,6 +19,10 @@
   withParmetis ? false,
   scotch,
   withPtscotch ? false,
+  scalapack,
+  withScalapack ? false,
+  mumps_par,
+  withMumps ? false,
   pkg-config,
   p4est,
   zlib, # propagated by p4est but required by petsc
@@ -34,6 +38,8 @@ assert petsc-withp4est -> p4est.mpiSupport;
 assert withParmetis -> (withMetis && mpiSupport);
 
 assert withPtscotch -> mpiSupport;
+assert withScalapack -> mpiSupport;
+assert withMumps -> withScalapack;
 
 stdenv.mkDerivation rec {
   pname = "petsc";
@@ -59,7 +65,9 @@ stdenv.mkDerivation rec {
     ++ lib.optional petsc-withp4est p4est
     ++ lib.optional withMetis metis
     ++ lib.optional withParmetis parmetis
-    ++ lib.optional withPtscotch scotch;
+    ++ lib.optional withPtscotch scotch
+    ++ lib.optional withScalapack scalapack
+    ++ lib.optional withMumps mumps_par;
 
   postPatch =
     ''
@@ -96,6 +104,14 @@ stdenv.mkDerivation rec {
       "--with-ptscotch-include=${scotch.dev}/include"
       "--with-ptscotch-lib=[-L${scotch}/lib,-lptscotch,-lptesmumps,-lptscotchparmetisv3,-lptscotcherr,-lesmumps,-lscotch,-lscotcherr]"
     ]
+    ++ lib.optionals withScalapack [
+      "--with-scalapack=1"
+      "--with-scalapack-dir=${scalapack}"
+    ]
+    ++ lib.optionals withMumps [
+      "--with-mumps=1"
+      "--with-mumps-dir=${mumps_par}"
+    ]
     ++ lib.optionals petsc-withp4est [
       "--with-p4est=1"
       "--with-zlib-include=${zlib.dev}/include"

From ad4db6e3abc06917e8dc171f401b2ece716ce757 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Tue, 4 Feb 2025 19:42:47 +0800
Subject: [PATCH 06/12] python312Packages.petsc4py: init at 3.22.3

---
 .../petsc/fix-petsc4py-install-prefix.patch   | 22 ++++++++++++++
 pkgs/by-name/pe/petsc/package.nix             | 30 +++++++++++++++----
 pkgs/top-level/python-packages.nix            |  6 ++++
 3 files changed, 53 insertions(+), 5 deletions(-)
 create mode 100644 pkgs/by-name/pe/petsc/fix-petsc4py-install-prefix.patch

diff --git a/pkgs/by-name/pe/petsc/fix-petsc4py-install-prefix.patch b/pkgs/by-name/pe/petsc/fix-petsc4py-install-prefix.patch
new file mode 100644
index 000000000000..dd3a50114f07
--- /dev/null
+++ b/pkgs/by-name/pe/petsc/fix-petsc4py-install-prefix.patch
@@ -0,0 +1,22 @@
+diff --git a/config/BuildSystem/config/packages/petsc4py.py b/config/BuildSystem/config/packages/petsc4py.py
+index 4a58243..831aa04 100644
+--- a/config/BuildSystem/config/packages/petsc4py.py
++++ b/config/BuildSystem/config/packages/petsc4py.py
+@@ -37,7 +37,7 @@ class Configure(config.package.Package):
+ 
+   def Install(self):
+     import os
+-    installLibPath = os.path.join(self.installDir, 'lib')
++    installLibPath = os.path.join(self.installDir, 'lib', '@PYTHON_SITEPACKAGES@')
+     if self.setCompilers.isDarwin(self.log):
+       apple = 'You may need to\n (csh/tcsh) setenv MACOSX_DEPLOYMENT_TARGET 10.X\n (sh/bash) MACOSX_DEPLOYMENT_TARGET=10.X; export MACOSX_DEPLOYMENT_TARGET\nbefore running make on PETSc'
+     else:
+@@ -70,7 +70,7 @@ class Configure(config.package.Package):
+       newdir += 'NUMPY_INCLUDE="'+numpy_include+'" '
+ 
+     self.addDefine('HAVE_PETSC4PY',1)
+-    self.addDefine('PETSC4PY_INSTALL_PATH','"'+os.path.join(self.installdir.dir,'lib')+'"')
++    self.addDefine('PETSC4PY_INSTALL_PATH','"'+installLibPath+'"')
+     self.addMakeMacro('PETSC4PY','yes')
+     self.addMakeRule('petsc4pybuild','', \
+                        ['@echo "*** Building petsc4py ***"',\
diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 6a13227e4031..87009b8a8f91 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -4,7 +4,10 @@
   fetchzip,
   cctools,
   gfortran,
+  replaceVars,
   python3,
+  python3Packages,
+  withPetsc4py ? false,
   blas,
   lapack,
   mpiSupport ? true,
@@ -51,11 +54,19 @@ stdenv.mkDerivation rec {
   };
 
   strictDeps = true;
-  nativeBuildInputs = [
-    python3
-    gfortran
-    pkg-config
-  ] ++ lib.optional mpiSupport mpi;
+
+  nativeBuildInputs =
+    [
+      python3
+      gfortran
+      pkg-config
+    ]
+    ++ lib.optional mpiSupport mpi
+    ++ lib.optionals withPetsc4py [
+      python3Packages.setuptools
+      python3Packages.cython
+    ];
+
   buildInputs =
     [
       blas
@@ -69,6 +80,14 @@ stdenv.mkDerivation rec {
     ++ lib.optional withScalapack scalapack
     ++ lib.optional withMumps mumps_par;
 
+  propagatedBuildInputs = lib.optional withPetsc4py python3Packages.numpy;
+
+  patches = [
+    (replaceVars ./fix-petsc4py-install-prefix.patch {
+      PYTHON_SITEPACKAGES = python3.sitePackages;
+    })
+  ];
+
   postPatch =
     ''
       patchShebangs ./lib/petsc/bin
@@ -86,6 +105,7 @@ stdenv.mkDerivation rec {
       "--with-precision=${petsc-precision}"
       "--with-mpi=${if mpiSupport then "1" else "0"}"
     ]
+    ++ lib.optional withPetsc4py "--with-petsc4py=1"
     ++ lib.optionals mpiSupport [
       "--CC=mpicc"
       "--with-cxx=mpicxx"
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index b98d245a8297..85ddafd5b6fe 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -10342,6 +10342,12 @@ self: super: with self; {
 
   pesq = callPackage ../development/python-modules/pesq { };
 
+  petsc4py = toPythonModule (pkgs.petsc.override {
+    python3 = python;
+    python3Packages = self;
+    withPetsc4py = true;
+  });
+
   pex = callPackage ../development/python-modules/pex { };
 
   pexif = callPackage ../development/python-modules/pexif { };

From 3389354ca5c3f51eca33025f73eaf36aaa23ab31 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Wed, 5 Feb 2025 15:32:48 +0800
Subject: [PATCH 07/12] petsc: add withFullDeps option

---
 pkgs/by-name/pe/petsc/package.nix  | 15 ++++++++-------
 pkgs/top-level/python-packages.nix |  2 ++
 2 files changed, 10 insertions(+), 7 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 87009b8a8f91..9c6e64d6e409 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -13,25 +13,26 @@
   mpiSupport ? true,
   mpi, # generic mpi dependency
   mpiCheckPhaseHook,
-  petsc-withp4est ? false,
-  hdf5-support ? false,
+  petsc-withp4est ? withFullDeps,
+  hdf5-support ? withFullDeps,
   hdf5,
   metis,
-  withMetis ? false,
+  withMetis ? withFullDeps,
   parmetis,
-  withParmetis ? false,
+  withParmetis ? false, # parmetis is unfree and should be enabled manualy
   scotch,
-  withPtscotch ? false,
+  withPtscotch ? withFullDeps,
   scalapack,
-  withScalapack ? false,
+  withScalapack ? withFullDeps,
   mumps_par,
-  withMumps ? false,
+  withMumps ? withFullDeps,
   pkg-config,
   p4est,
   zlib, # propagated by p4est but required by petsc
   petsc-optimized ? false,
   petsc-scalar-type ? "real",
   petsc-precision ? "double",
+  withFullDeps ? false
 }:
 
 # This version of PETSc does not support a non-MPI p4est build
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index 85ddafd5b6fe..dbabff224391 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -10346,6 +10346,8 @@ self: super: with self; {
     python3 = python;
     python3Packages = self;
     withPetsc4py = true;
+    withFullDeps = true;
+    petsc-optimized = true;
   });
 
   pex = callPackage ../development/python-modules/pex { };

From 291a201097ee67aafd3157149ab29d4e6a049e8a Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Wed, 5 Feb 2025 15:48:27 +0800
Subject: [PATCH 08/12] petsc: rename some optional dependency flags

---
 pkgs/by-name/pe/petsc/package.nix | 14 +++++++-------
 pkgs/top-level/all-packages.nix   |  2 +-
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 9c6e64d6e409..82b0f396a992 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -13,8 +13,8 @@
   mpiSupport ? true,
   mpi, # generic mpi dependency
   mpiCheckPhaseHook,
-  petsc-withp4est ? withFullDeps,
-  hdf5-support ? withFullDeps,
+  withP4est ? withFullDeps,
+  withHdf5 ? withFullDeps,
   hdf5,
   metis,
   withMetis ? withFullDeps,
@@ -36,7 +36,7 @@
 }:
 
 # This version of PETSc does not support a non-MPI p4est build
-assert petsc-withp4est -> p4est.mpiSupport;
+assert withP4est -> (p4est.mpiSupport && mpiSupport);
 
 # Package parmetis depend on metis and mpi support
 assert withParmetis -> (withMetis && mpiSupport);
@@ -73,8 +73,8 @@ stdenv.mkDerivation rec {
       blas
       lapack
     ]
-    ++ lib.optional hdf5-support hdf5
-    ++ lib.optional petsc-withp4est p4est
+    ++ lib.optional withHdf5 hdf5
+    ++ lib.optional withP4est p4est
     ++ lib.optional withMetis metis
     ++ lib.optional withParmetis parmetis
     ++ lib.optional withPtscotch scotch
@@ -133,12 +133,12 @@ stdenv.mkDerivation rec {
       "--with-mumps=1"
       "--with-mumps-dir=${mumps_par}"
     ]
-    ++ lib.optionals petsc-withp4est [
+    ++ lib.optionals withP4est [
       "--with-p4est=1"
       "--with-zlib-include=${zlib.dev}/include"
       "--with-zlib-lib=[-L${zlib}/lib,-lz]"
     ]
-    ++ lib.optionals hdf5-support [
+    ++ lib.optionals withHdf5 [
       "--with-hdf5=1"
       "--with-hdf5-fortran-bindings=1"
       "--with-hdf5-include=${hdf5.dev}/include"
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index fb3618d837a1..1144d59a2f83 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -17075,7 +17075,7 @@ with pkgs;
   ### SCIENCE/GEOLOGY
   pflotran = callPackage ../by-name/pf/pflotran/package.nix {
     petsc = petsc.override {
-      hdf5-support = true;
+      withHdf5 = true;
       hdf5 = hdf5-fortran-mpi;
       petsc-optimized = true;
     };

From d3b3d83b0fcd2d0e7fd7922a3da66e6a1c9491db Mon Sep 17 00:00:00 2001
From: qbisicwate <qbisicwate@gmail.com>
Date: Thu, 6 Feb 2025 17:46:19 +0800
Subject: [PATCH 09/12] petsc: use lib.{getDev,getLib} instead *.{dev,lib}

---
 pkgs/by-name/pe/petsc/package.nix | 12 ++++++------
 1 file changed, 6 insertions(+), 6 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 82b0f396a992..552416df8ec2 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -122,8 +122,8 @@ stdenv.mkDerivation rec {
     ]
     ++ lib.optionals withPtscotch [
       "--with-ptscotch=1"
-      "--with-ptscotch-include=${scotch.dev}/include"
-      "--with-ptscotch-lib=[-L${scotch}/lib,-lptscotch,-lptesmumps,-lptscotchparmetisv3,-lptscotcherr,-lesmumps,-lscotch,-lscotcherr]"
+      "--with-ptscotch-include=${lib.getDev scotch}/include"
+      "--with-ptscotch-lib=[-L${lib.getLib scotch}/lib,-lptscotch,-lptesmumps,-lptscotchparmetisv3,-lptscotcherr,-lesmumps,-lscotch,-lscotcherr]"
     ]
     ++ lib.optionals withScalapack [
       "--with-scalapack=1"
@@ -135,14 +135,14 @@ stdenv.mkDerivation rec {
     ]
     ++ lib.optionals withP4est [
       "--with-p4est=1"
-      "--with-zlib-include=${zlib.dev}/include"
-      "--with-zlib-lib=[-L${zlib}/lib,-lz]"
+      "--with-zlib-include=${lib.getDev zlib}/include"
+      "--with-zlib-lib=[-L${lib.getLib zlib}/lib,-lz]"
     ]
     ++ lib.optionals withHdf5 [
       "--with-hdf5=1"
       "--with-hdf5-fortran-bindings=1"
-      "--with-hdf5-include=${hdf5.dev}/include"
-      "--with-hdf5-lib=[-L${hdf5}/lib,-lhdf5]"
+      "--with-hdf5-include=${lib.getDev hdf5}/include"
+      "--with-hdf5-lib=[-L${lib.getLib hdf5}/lib,-lhdf5]"
     ]
     ++ lib.optionals petsc-optimized [
       "--with-debugging=0"

From 92dc787ceca4c86d4df79e1d53caaa4e32a882f0 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Fri, 14 Feb 2025 18:00:55 +0800
Subject: [PATCH 10/12] petsc: reorder build options and external dependency

---
 pkgs/by-name/pe/petsc/package.nix | 44 ++++++++++++++++++-------------
 1 file changed, 25 insertions(+), 19 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 552416df8ec2..9d5e412fad7b 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -7,32 +7,38 @@
   replaceVars,
   python3,
   python3Packages,
-  withPetsc4py ? false,
   blas,
   lapack,
-  mpiSupport ? true,
+  zlib, # propagated by p4est but required by petsc
   mpi, # generic mpi dependency
   mpiCheckPhaseHook,
-  withP4est ? withFullDeps,
-  withHdf5 ? withFullDeps,
-  hdf5,
-  metis,
-  withMetis ? withFullDeps,
-  parmetis,
-  withParmetis ? false, # parmetis is unfree and should be enabled manualy
-  scotch,
-  withPtscotch ? withFullDeps,
-  scalapack,
-  withScalapack ? withFullDeps,
-  mumps_par,
-  withMumps ? withFullDeps,
-  pkg-config,
-  p4est,
-  zlib, # propagated by p4est but required by petsc
+
+  # Build options
   petsc-optimized ? false,
   petsc-scalar-type ? "real",
   petsc-precision ? "double",
-  withFullDeps ? false
+  mpiSupport ? true,
+  withPetsc4py ? false, # petsc python binding
+  withFullDeps ? false, # full External libraries support
+
+  # External libraries options
+  withHdf5 ? withFullDeps,
+  withMetis ? withFullDeps,
+  withParmetis ? false, # parmetis is unfree and should be enabled manualy
+  withPtscotch ? withFullDeps,
+  withScalapack ? withFullDeps,
+  withMumps ? withFullDeps,
+  withP4est ? withFullDeps,
+
+  # External libraries
+  hdf5,
+  metis,
+  parmetis,
+  scotch,
+  scalapack,
+  mumps_par,
+  pkg-config,
+  p4est,
 }:
 
 # This version of PETSc does not support a non-MPI p4est build

From 3c01afec0a69da281268e5a921c087e08c6f7222 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Fri, 14 Feb 2025 19:05:03 +0800
Subject: [PATCH 11/12] petsc: add hdf5 fortran binding

---
 pkgs/by-name/pe/petsc/package.nix | 8 ++++----
 pkgs/top-level/all-packages.nix   | 1 -
 2 files changed, 4 insertions(+), 5 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 9d5e412fad7b..22735cacece5 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -31,7 +31,7 @@
   withP4est ? withFullDeps,
 
   # External libraries
-  hdf5,
+  hdf5-fortran-mpi,
   metis,
   parmetis,
   scotch,
@@ -79,7 +79,7 @@ stdenv.mkDerivation rec {
       blas
       lapack
     ]
-    ++ lib.optional withHdf5 hdf5
+    ++ lib.optional withHdf5 hdf5-fortran-mpi
     ++ lib.optional withP4est p4est
     ++ lib.optional withMetis metis
     ++ lib.optional withParmetis parmetis
@@ -147,8 +147,8 @@ stdenv.mkDerivation rec {
     ++ lib.optionals withHdf5 [
       "--with-hdf5=1"
       "--with-hdf5-fortran-bindings=1"
-      "--with-hdf5-include=${lib.getDev hdf5}/include"
-      "--with-hdf5-lib=[-L${lib.getLib hdf5}/lib,-lhdf5]"
+      "--with-hdf5-include=${lib.getDev hdf5-fortran-mpi}/include"
+      "--with-hdf5-lib=[-L${lib.getLib hdf5-fortran-mpi}/lib,-lhdf5]"
     ]
     ++ lib.optionals petsc-optimized [
       "--with-debugging=0"
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index 1144d59a2f83..f18c29a4280e 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -17076,7 +17076,6 @@ with pkgs;
   pflotran = callPackage ../by-name/pf/pflotran/package.nix {
     petsc = petsc.override {
       withHdf5 = true;
-      hdf5 = hdf5-fortran-mpi;
       petsc-optimized = true;
     };
   };

From 120cb83d3bd82c0ade523344e6fe0e7edf2e156d Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Fri, 14 Feb 2025 19:06:55 +0800
Subject: [PATCH 12/12] petsc: set optimized and withHdf5 default to true

Petsc is commonly optimized built with hdf5 support to be used
as a component of other software and project.
See
    1. https://sources.debian.org/src/petsc/3.22.2%2Bdfsg1-1/debian/rules/#L154
    2. https://aur.archlinux.org/cgit/aur.git/tree/PKGBUILD?h=petsc
---
 pkgs/by-name/pe/petsc/package.nix  | 4 ++--
 pkgs/top-level/all-packages.nix    | 8 --------
 pkgs/top-level/python-packages.nix | 1 -
 3 files changed, 2 insertions(+), 11 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index 22735cacece5..cec3dda54341 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -14,7 +14,7 @@
   mpiCheckPhaseHook,
 
   # Build options
-  petsc-optimized ? false,
+  petsc-optimized ? true,
   petsc-scalar-type ? "real",
   petsc-precision ? "double",
   mpiSupport ? true,
@@ -22,7 +22,7 @@
   withFullDeps ? false, # full External libraries support
 
   # External libraries options
-  withHdf5 ? withFullDeps,
+  withHdf5 ? true,
   withMetis ? withFullDeps,
   withParmetis ? false, # parmetis is unfree and should be enabled manualy
   withPtscotch ? withFullDeps,
diff --git a/pkgs/top-level/all-packages.nix b/pkgs/top-level/all-packages.nix
index f18c29a4280e..77e4a06b3c69 100644
--- a/pkgs/top-level/all-packages.nix
+++ b/pkgs/top-level/all-packages.nix
@@ -17072,14 +17072,6 @@ with pkgs;
 
   ### SCIENCE/PROGRAMMING
 
-  ### SCIENCE/GEOLOGY
-  pflotran = callPackage ../by-name/pf/pflotran/package.nix {
-    petsc = petsc.override {
-      withHdf5 = true;
-      petsc-optimized = true;
-    };
-  };
-
   ### SCIENCE/LOGIC
 
   abella = callPackage ../applications/science/logic/abella {
diff --git a/pkgs/top-level/python-packages.nix b/pkgs/top-level/python-packages.nix
index dbabff224391..f1e9cc7f6a70 100644
--- a/pkgs/top-level/python-packages.nix
+++ b/pkgs/top-level/python-packages.nix
@@ -10347,7 +10347,6 @@ self: super: with self; {
     python3Packages = self;
     withPetsc4py = true;
     withFullDeps = true;
-    petsc-optimized = true;
   });
 
   pex = callPackage ../development/python-modules/pex { };