From dd6e89f2ecad21d1cf147c845451bba49bafdb92 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Mon, 3 Mar 2025 21:32:05 +0800
Subject: [PATCH 1/3] pflotran: replace hdf5 with hdf5-fortran-mpi

---
 pkgs/by-name/pf/pflotran/package.nix | 8 ++++----
 1 file changed, 4 insertions(+), 4 deletions(-)

diff --git a/pkgs/by-name/pf/pflotran/package.nix b/pkgs/by-name/pf/pflotran/package.nix
index ec0fdf2d92e5..3d5303aca8d9 100644
--- a/pkgs/by-name/pf/pflotran/package.nix
+++ b/pkgs/by-name/pf/pflotran/package.nix
@@ -8,7 +8,7 @@
   blas,
   lapack,
   parmetis,
-  hdf5,
+  hdf5-fortran-mpi,
   mpiCheckPhaseHook,
   python3,
 }:
@@ -32,7 +32,7 @@ stdenv.mkDerivation (finalAttrs: {
     petsc
     blas
     lapack
-    hdf5
+    hdf5-fortran-mpi
     parmetis
   ];
 
@@ -50,8 +50,8 @@ stdenv.mkDerivation (finalAttrs: {
   */
   preConfigure = ''
     substituteInPlace src/pflotran/makefile \
-      --subst-var-by "HDF5_FORTRAN_LIBS" "${lib.getLib hdf5}/lib" \
-      --subst-var-by "HDF5_FORTRAN_INCLUDE" "${lib.getDev hdf5}/include"
+      --subst-var-by "HDF5_FORTRAN_LIBS" "${lib.getLib hdf5-fortran-mpi}/lib" \
+      --subst-var-by "HDF5_FORTRAN_INCLUDE" "${lib.getDev hdf5-fortran-mpi}/include"
   '';
 
   configureFlags = [

From 77345dd2d50607de1f92fe5b78356932890866c5 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Mon, 3 Mar 2025 21:32:59 +0800
Subject: [PATCH 2/3] petsc: add setupHook to set PETSC_DIR env

---
 pkgs/by-name/pe/petsc/package.nix    | 2 ++
 pkgs/by-name/pe/petsc/setup-hook.sh  | 1 +
 pkgs/by-name/pf/pflotran/package.nix | 5 -----
 3 files changed, 3 insertions(+), 5 deletions(-)
 create mode 100644 pkgs/by-name/pe/petsc/setup-hook.sh

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index cec3dda54341..c8e7cf5fb780 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -179,6 +179,8 @@ stdenv.mkDerivation rec {
     inherit mpiSupport;
   };
 
+  setupHook = ./setup-hook.sh;
+
   meta = with lib; {
     description = "Portable Extensible Toolkit for Scientific computation";
     homepage = "https://petsc.org/release/";
diff --git a/pkgs/by-name/pe/petsc/setup-hook.sh b/pkgs/by-name/pe/petsc/setup-hook.sh
new file mode 100644
index 000000000000..4728b6cae777
--- /dev/null
+++ b/pkgs/by-name/pe/petsc/setup-hook.sh
@@ -0,0 +1 @@
+export PETSC_DIR=@out@
diff --git a/pkgs/by-name/pf/pflotran/package.nix b/pkgs/by-name/pf/pflotran/package.nix
index 3d5303aca8d9..b0005ec52d50 100644
--- a/pkgs/by-name/pf/pflotran/package.nix
+++ b/pkgs/by-name/pf/pflotran/package.nix
@@ -54,11 +54,6 @@ stdenv.mkDerivation (finalAttrs: {
       --subst-var-by "HDF5_FORTRAN_INCLUDE" "${lib.getDev hdf5-fortran-mpi}/include"
   '';
 
-  configureFlags = [
-    "--with-petsc-dir=${petsc}"
-    "--with-petsc-arch=linux-gnu-c-release"
-  ];
-
   meta = with lib; {
     description = "Parallel, multi-physics simulation code for subsurface flow and transport";
     homepage = "https://pflotran.org/";

From bb479b3fe9471100877d644a0ba5cf1ad9a62fa0 Mon Sep 17 00:00:00 2001
From: qbisi <qbisicwate@gmail.com>
Date: Mon, 3 Mar 2025 21:41:14 +0800
Subject: [PATCH 3/3] petsc: 3.21.4 -> 3.22.4

---
 pkgs/by-name/pe/petsc/package.nix    |  4 ++--
 pkgs/by-name/pf/pflotran/package.nix | 11 ++++++++++-
 2 files changed, 12 insertions(+), 3 deletions(-)

diff --git a/pkgs/by-name/pe/petsc/package.nix b/pkgs/by-name/pe/petsc/package.nix
index c8e7cf5fb780..7ef8de6b4674 100644
--- a/pkgs/by-name/pe/petsc/package.nix
+++ b/pkgs/by-name/pe/petsc/package.nix
@@ -53,11 +53,11 @@ assert withMumps -> withScalapack;
 
 stdenv.mkDerivation rec {
   pname = "petsc";
-  version = "3.21.4";
+  version = "3.22.4";
 
   src = fetchzip {
     url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${version}.tar.gz";
-    hash = "sha256-l7v+ASBL9FLbBmBGTRWDwBihjwLe3uLz+GwXtn8u7e0=";
+    hash = "sha256-8WV1ylXytkhiNa7YpWSOIpSvzLCCjdVVe5SiGfhicas=";
   };
 
   strictDeps = true;
diff --git a/pkgs/by-name/pf/pflotran/package.nix b/pkgs/by-name/pf/pflotran/package.nix
index b0005ec52d50..4feabaa3b2cc 100644
--- a/pkgs/by-name/pf/pflotran/package.nix
+++ b/pkgs/by-name/pf/pflotran/package.nix
@@ -2,6 +2,7 @@
   stdenv,
   lib,
   fetchFromBitbucket,
+  fetchzip,
   gfortran,
   mpi,
   petsc,
@@ -29,7 +30,15 @@ stdenv.mkDerivation (finalAttrs: {
   nativeBuildInputs = [ gfortran ];
 
   buildInputs = [
-    petsc
+    # upstream petsc has lots of fortran api change since 3.22.*
+    # will keep using old petsc-3.21.4 until pflotran support latest petsc
+    (petsc.overrideAttrs rec {
+      version = "3.21.4";
+      src = fetchzip {
+        url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${version}.tar.gz";
+        hash = "sha256-l7v+ASBL9FLbBmBGTRWDwBihjwLe3uLz+GwXtn8u7e0=";
+      };
+    })
     blas
     lapack
     hdf5-fortran-mpi