pflotran: init at 6.0.1 (#377999)

pkgs/by-name/pe/petsc/package.nix

···
 
 stdenv.mkDerivation rec {
   pname = "petsc";
-  version = "3.21.3";
+  version = "3.21.4";
 
   src = fetchzip {
     url = "https://web.cels.anl.gov/projects/petsc/download/release-snapshots/petsc-${version}.tar.gz";
-    hash = "sha256-dxHa8JUJCN4zRIXMCx7gcvbzFH2SPtkJ377ssIevjgU=";
+    hash = "sha256-l7v+ASBL9FLbBmBGTRWDwBihjwLe3uLz+GwXtn8u7e0=";
   };
 
   strictDeps = true;

pkgs/by-name/pf/pflotran/make.patch

···
+diff --git a/src/pflotran/makefile b/src/pflotran/makefile
+index 17587c91d..7caf73e8c 100644
+--- a/src/pflotran/makefile
++++ b/src/pflotran/makefile
+@@ -51,7 +51,7 @@ PETSC_MAKE_STOP_ON_ERROR=
+ # so that PFLOTRAN will be built with the same options as 
+ # the petsc configured in $PETSC_DIR/$PETSC_ARCH
+ 
+-MYFLAGS = -I. 
++MYFLAGS = -I. -L@HDF5_FORTRAN_LIBS@ -I@HDF5_FORTRAN_INCLUDE@
+ 
+ ###############################################################################
+ # Preprocessor flags for special PFLOTRAN features/hacks
+@@ -183,7 +183,7 @@ ifdef ug_mpi_scatter_ghost
+ endif
+ 
+ ifdef have_hdf5
+-LIBS +=  -L${HDF5_LIB} -lhdf5_fortran -lhdf5 -lz 
++LIBS +=  -L${HDF5_LIB} -lhdf5 -lhdf5_fortran -lhdf5_hl_fortran -lhdf5_f90cstub -lz
+ endif
+ 
+ # Set this accordingly on your platform
+@@ -273,7 +273,7 @@ pflotran_rxn_obj = ${pflotran_src}pflotran_rxn.o
+ 
+ # PFLOTRAN executable
+ pflotran : $(pflotran_obj)
+-	${FLINKER} -o pflotran $(pflotran_obj) ${PETSC_LIB} ${LIBS} 
++	${FLINKER} -o pflotran $(pflotran_obj) ${PETSC_LIB} ${LIBS} -lhdf5 -lhdf5_fortran -lhdf5_hl_fortran -lhdf5_f90cstub
+ 
+ # PFLOTRAN as a library
+ libpflotran.a : $(pflotran_obj)
+@@ -286,11 +286,11 @@ libpflotranchem.a : $(chem_obj) $(shared_mode_aux_obj) $(util_obj)
+ # object files lists below.... This is a workaround.
+ pflotran_rxn : libpflotranchem.a $(pflotran_rxn_obj)
+ 	${FLINKER} -o $@ $(pflotran_rxn_obj) $(chem_obj) $(shared_mode_aux_obj) \
+-	$(util_obj) ${PETSC_LIB} ${LIBS} 
++	$(util_obj) ${PETSC_LIB} ${LIBS} -lhdf5 -lhdf5_fortran -lhdf5_hl_fortran -lhdf5_f90cstub
+ 
+ # PFLOTRAN derivative test
+ pflotran_derivative : $(pflotran_base_obj) pflotran_derivative.o
+-	${FLINKER} -o pflotran_derivative $(pflotran_base_obj) pflotran_derivative.o ${PETSC_LIB} ${LIBS} 
++	${FLINKER} -o pflotran_derivative $(pflotran_base_obj) pflotran_derivative.o ${PETSC_LIB} ${LIBS} -lhdf5 -lhdf5_fortran -lhdf5_hl_fortran -lhdf5_f90cstub
+ 
+ $(SRC_DIR)/pflotran_provenance.F90 : FORCE
+ ifeq ($(UPDATE_PROVENANCE),1)

pkgs/by-name/pf/pflotran/package.nix

···
+{
+  stdenv,
+  lib,
+  fetchFromBitbucket,
+  gfortran,
+  mpi,
+  petsc,
+  blas,
+  lapack,
+  parmetis,
+  hdf5,
+  mpiCheckPhaseHook,
+  python3,
+}:
+
+stdenv.mkDerivation (finalAttrs: {
+  pname = "PFLOTRAN";
+  version = "6.0.1";
+
+  src = fetchFromBitbucket {
+    owner = "pflotran";
+    repo = "pflotran";
+    rev = "v${finalAttrs.version}";
+    hash = "sha256-AZXzay6GWbnxONB8Slg8gV0KN1CxGCXbJ45ZeWL1034=";
+  };
+
+  patches = [ ./make.patch ];
+
+  nativeBuildInputs = [ gfortran ];
+
+  buildInputs = [
+    petsc
+    blas
+    lapack
+    hdf5
+    parmetis
+  ];
+
+  propagatedBuildInputs = [ mpi ];
+  propagatedUserEnvPkgs = [ mpi ];
+  passthru = { inherit mpi; };
+
+  enableParallelBuilding = true;
+
+  /*
+    Pflotran does not use a "real" autotools configure script, but a simple bash
+    script, that is merely named configure. Consequently, many common mechanism
+    don't work. Thus, we need to help make to figure out some include and library
+    paths.
+  */
+  preConfigure = ''
+    substituteInPlace src/pflotran/makefile \
+      --subst-var-by "HDF5_FORTRAN_LIBS" "${lib.getLib hdf5}/lib" \
+      --subst-var-by "HDF5_FORTRAN_INCLUDE" "${lib.getDev hdf5}/include"
+  '';
+
+  configureFlags = [
+    "--with-petsc-dir=${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/";
+    license = licenses.lgpl3Only;
+    maintainers = [ maintainers.sheepforce ];
+  };
+})

pkgs/top-level/all-packages.nix

···
 
   hdf5-fortran = hdf5.override { fortranSupport = true; };
 
+  hdf5-fortran-mpi = hdf5.override {
+    fortranSupport = true;
+    mpiSupport = true;
+    cppSupport = false;
+  };
+
   hdf5-threadsafe = hdf5.override { threadsafe = true; };
 
   heaptrack = libsForQt5.callPackage ../development/tools/profiling/heaptrack { };
···
   xflr5 = libsForQt5.callPackage ../applications/science/physics/xflr5 { };
 
   ### SCIENCE/PROGRAMMING
+
+  ### SCIENCE/GEOLOGY
+  pflotran = callPackage ../by-name/pf/pflotran/package.nix {
+    petsc = petsc.override {
+      hdf5-support = true;
+      hdf5 = hdf5-fortran-mpi;
+      petsc-optimized = true;
+    };
+  };
 
   ### SCIENCE/LOGIC