Merge pull request #359 from Rombur/update_stack

Update software stack

README.md

@@ -20,7 +20,7 @@ Installing `adamantine` requires:
 * ArborX: 1.4.1 or later
 * Trilinos: 14.4.0 or later. If you want to *adamantine* to read an Exodus mesh,
   you need to enable SEACAS support.
-* deal.II: 9.5 or later. You need to compile deal.II with MPI, p4est, and ArborX support.
+* deal.II: 9.5 for the 1.0 release and 9.6 for the development version. You need to compile deal.II with MPI, p4est, and ArborX support.
 * Caliper: 2.10 or later. Optional dependency to profile `adamantine`.
 
 An example on how to install all the dependencies can be found in

ci/Dockerfile

@@ -1,4 +1,4 @@
-ARG BASE=nvidia/cuda:12.3.0-devel-ubuntu22.04
+ARG BASE=nvidia/cuda:12.6.2-devel-ubuntu24.04
 FROM $BASE
 
 ARG N_PROCS=8
@@ -39,8 +39,8 @@ RUN mkdir -p ${PREFIX} && \
     mkdir build
 
 # Install CMake
-RUN export CMAKE_VERSION=3.27.8 && \
-    export  CMAKE_SHA256=dfedc30abe69dcabe326a4de632210bb52004185bd2c0b096c21924f4510681f && \
+RUN export CMAKE_VERSION=3.30.5 && \
+    export CMAKE_SHA256=f747d9b23e1a252a8beafb4ed2bc2ddf78cff7f04a8e4de19f4ff88e9b51dc9d && \
     export CMAKE_URL=https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cmake-${CMAKE_VERSION}-linux-x86_64.tar.gz && \
     export CMAKE_ARCHIVE=${ARCHIVE_DIR}/cmake.tar.gz && \
     export CMAKE_BUILD_DIR=${BUILD_DIR}/cmake && \
@@ -54,9 +54,9 @@ RUN export CMAKE_VERSION=3.27.8 && \
 ENV PATH=${INSTALL_DIR}/cmake/bin:$PATH
 
 # Install OpenMPI
-RUN export OPENMPI_VERSION=5.0.0 && \
+RUN export OPENMPI_VERSION=5.0.5 && \
     export OPENMPI_VERSION_SHORT=5.0 && \
-    export OPENMPI_SHA256=9d845ca94bc1aeb445f83d98d238cd08f6ec7ad0f73b0f79ec1668dbfdacd613 && \
+    export OPENMPI_SHA256=6588d57c0a4bd299a24103f4e196051b29e8b55fbda49e11d5b3d32030a32776 && \
     export OPENMPI_URL=https://www.open-mpi.org/software/ompi/v${OPENMPI_VERSION_SHORT}/downloads/openmpi-${OPENMPI_VERSION}.tar.bz2 && \
     export OPENMPI_ARCHIVE=${ARCHIVE_DIR}/openmpi.tar.bz2 && \
     export OPENMPI_SOURCE_DIR=${SOURCE_DIR}/openmpi && \
@@ -87,10 +87,10 @@ ENV OMPI_CXX=c++
 ENV PATH=${INSTALL_DIR}/openmpi/bin:$PATH
 
 # Install Boost
-RUN export BOOST_VERSION=1.83.0 && \
-    export BOOST_VERSION_U=1_83_0 && \
-    export BOOST_URL=https://boostorg.jfrog.io/artifactory/main/release/${BOOST_VERSION}/source/boost_${BOOST_VERSION_U}.tar.bz2 && \
-    export BOOST_SHA256=6478edfe2f3305127cffe8caf73ea0176c53769f4bf1585be237eb30798c3b8e && \
+RUN export BOOST_VERSION=1.86.0 && \
+    export BOOST_VERSION_U=1_86_0 && \
+    export BOOST_URL=https://archives.boost.io/release/${BOOST_VERSION}/source/boost_${BOOST_VERSION_U}.tar.bz2 && \
+    export BOOST_SHA256=1bed88e40401b2cb7a1f76d4bab499e352fa4d0c5f31c0dbae64e24d34d7513b && \
     export BOOST_ARCHIVE=${ARCHIVE_DIR}/boost_${BOOST_VERSION_U}.tar.bz2 && \
     export BOOST_SOURCE_DIR=${SOURCE_DIR}/boost && \
     export BOOST_BUILD_DIR=${BUILD_DIR}/boost && \
@@ -220,6 +220,7 @@ RUN export TRILINOS_HASH=975307431d60d0859ebaa27c9169cbb1d4287513 && \
         -DTrilinos_ENABLE_SEACAS=ON \
         -DTrilinos_ENABLE_EXPLICIT_INSTANTIATION=ON \
         -DKokkos_ENABLE_CUDA=$CUDA \
+        -DKokkos_ENABLE_CUDA_CONSTEXPR=ON \
         -DKokkos_ARCH_AMPERE80=ON \
         -DBLAS_LIBRARY_NAMES="openblas" \
         -DBLAS_LIBRARY_DIRS=${OPENBLAS_DIR}/lib \
@@ -261,9 +262,9 @@ RUN export ADIAK_VERSION=0.4.0 && \
     rm -rf ${ADIAK_SOURCE_DIR}
 ENV ADIAK_DIR=${INSTALL_DIR}/adiak
 
-# Install Caliper 2.10.0
-RUN export CALIPER_HASH=9b5b5efe9096e3f2b306fcca91ae739ae5d00716 && \
-    export CALIPER_URL=https://github.com/LLNL/caliper/archive/${CALIPER_HASH}.tar.gz && \
+# Install Caliper 2.11.0
+RUN export CALIPER_VERSION=2.11.0 && \
+    export CALIPER_URL=https://github.com/LLNL/Caliper/archive/refs/tags/v${CALIPER_VERSION}.tar.gz && \
     export CALIPER_ARCHIVE=${ARCHIVE_DIR}/caliper.tar.gz && \
     export CALIPER_SOURCE_DIR=${SOURCE_DIR}/caliper && \
     export CALIPER_BUILD_DIR=${BUILD_DIR}/caliper && \
@@ -315,9 +316,9 @@ RUN export ARBORX_HASH=e026f8237dbd0aaf2ddf2e3bf0e492071db854a2 && \
     rm -rf ${ARBORX_SOURCE_DIR}
 ENV ARBORX_DIR=${INSTALL_DIR}/arborx
 
-# Install deal.II 9.5.1
-RUN export DEAL_II_HASH=9e847302b21355f355c87890477f4dd485da26b1 && \
-    export DEAL_II_URL=https://github.com/dealii/dealii/archive/${DEAL_II_HASH}.tar.gz && \
+# Install deal.II 9.6.2
+RUN export DEAL_II_VERSION=9.6.2 && \
+    export DEAL_II_URL=https://github.com/dealii/dealii/releases/download/v${DEAL_II_VERSION}/dealii-${DEAL_II_VERSION}.tar.gz && \
     export DEAL_II_ARCHIVE=${ARCHIVE_DIR}/dealii.tar.gz && \
     export DEAL_II_SOURCE_DIR=${SOURCE_DIR}/dealii && \
     export DEAL_II_BUILD_DIR=${BUILD_DIR}/dealii && \
@@ -330,6 +331,7 @@ RUN export DEAL_II_HASH=9e847302b21355f355c87890477f4dd485da26b1 && \
         -DCMAKE_CXX_COMPILER=${TRILINOS_DIR}/bin/nvcc_wrapper \
         -DCMAKE_CXX_STANDARD=17 \
         -DCMAKE_CXX_EXTENSIONS=OFF \
+        -DDEAL_II_EARLY_DEPRECATIONS=ON \
         -DDEAL_II_WITH_TBB=OFF \
         -DDEAL_II_WITH_64BIT_INDICES=ON \
         -DDEAL_II_WITH_COMPLEX_VALUES=OFF \

cmake/SetupDealII.cmake

@@ -1,5 +1,5 @@
 #### deal.II #################################################################
-find_package(deal.II 9.5 REQUIRED PATHS ${DEAL_II_DIR})
+find_package(deal.II 9.6 REQUIRED PATHS ${DEAL_II_DIR})
 
 deal_ii_initialize_cached_variables()
 

cmake/SetupTPLs.cmake

@@ -17,12 +17,12 @@ find_package(Boost 1.70.0 REQUIRED COMPONENTS ${Boost_COMPONENTS})
 if (ADAMANTINE_ENABLE_ADIAK)
   find_package(adiak REQUIRED PATHS ${ADIAK_DIR})
   add_compile_definitions(ADAMANTINE_WITH_ADIAK)
-  message(STATUS "Found Adiak: ${PACKAGE_PREFIX_DIR}")
+  message(STATUS "Found Adiak: ${adiak_DIR}")
 endif()
 
 #### Caliper #################################################################
 if (ADAMANTINE_ENABLE_CALIPER)
   find_package(caliper REQUIRED PATHS ${CALIPER_DIR})
   add_compile_definitions(ADAMANTINE_WITH_CALIPER)
-  message(STATUS "Found Caliper: ${caliper_INSTALL_PREFIX}")
+  message(STATUS "Found Caliper: ${caliper_DIR}")
 endif()

flake.nix

@@ -3,7 +3,7 @@
 {
   inputs = {
     nixpkgs = {
-      url = "github:nixos/nixpkgs/nixos-24.05";
+      url = "github:nixos/nixpkgs/nixos-24.11";
     };
     flake-utils = {
       url = "github:numtide/flake-utils";
@@ -13,7 +13,6 @@
     let
       pkgs = import nixpkgs {
         inherit system;
-        config.cudaSupport = true;
         config.allowUnfree = true;
       };
 
@@ -83,7 +82,6 @@
           cmake
           openmpi
           trilinos_override
-          cudatoolkit
         ];
 
         cmakeFlags = [
@@ -94,7 +92,7 @@
         ];
       });
 
-      deal_II = (with pkgs; stdenv.mkDerivation {
+      deal_II_952 = (with pkgs; stdenv.mkDerivation {
         pname = "deal_II";
         version = "9.5.2";
         src = fetchgit {
@@ -108,7 +106,6 @@
           cmake
           openmpi
           trilinos_override
-          cudatoolkit
           arborx
           p4est
           boost183
@@ -135,6 +132,14 @@
          ];
       });
 
+      deal_II_962 = deal_II_952.overrideAttrs ( with pkgs; previousAttrs : rec {
+        version = "9.6.2";
+        src = previousAttrs.src.override {
+          rev = "v9.6.2";
+          sha256 = "sha256-YVOQbvzWWSl9rmYd6LBx4w2S8wuxhVF8T2dKdOphta4=";
+        };
+      });
+
       trilinos_extra_args = ''
         -DTrilinos_ENABLE_ML=ON
         -DBoost_INCLUDE_DIRS=${pkgs.boost183}/include
@@ -155,7 +160,7 @@
         }
       );
 
-      adamantine-release = (with pkgs; stdenv.mkDerivation rec {
+      adamantine-base = (with pkgs; stdenv.mkDerivation rec {
         pname = "adamantine";
         version = "1.0";
 
@@ -166,7 +171,6 @@
         };
 
         buildInputs = [
-          deal_II
           arborx
           adiak
           caliper
@@ -182,9 +186,6 @@
         ];
 
         cmakeFlags = [
-          "-DDEAL_II_DIR=${deal_II}"
-          "-DCMAKE_BUILD_TYPE=Release"
-          "-DCMAKE_CXX_FLAGS=-ffast-math"
           "-DADAMANTINE_ENABLE_ADIAK=ON"
           "-DADAMANTINE_ENABLE_CALIPER=ON"
           "-DBOOST_DIR=${boost183}"
@@ -200,23 +201,37 @@
           ctest -R integration_2d
         '';
       });
+
+      adamantine-release = adamantine-base.overrideAttrs ( with pkgs; previousAttrs : rec {
+        buildInputs = previousAttrs.buildInputs ++ [ deal_II_952 ];
+        cmakeFlags = previousAttrs.cmakeFlags ++ [
+          "-DDEAL_II_DIR=${deal_II_952}"
+          "-DCMAKE_BUILD_TYPE=Release"
+          "-DCMAKE_CXX_FLAGS=-ffast-math"
+        ];
+      });
 
-      adamantine-latest = adamantine-release.overrideAttrs ( previousAttrs : rec {
+      adamantine-latest = adamantine-base.overrideAttrs ( with pkgs; previousAttrs : rec {
         version = "latest";
         src = pkgs.lib.cleanSource ./.;
+        buildInputs = previousAttrs.buildInputs ++ [ deal_II_962 ];
+        cmakeFlags = previousAttrs.cmakeFlags ++ [
+          "-DDEAL_II_DIR=${deal_II_962}"
+          "-DCMAKE_BUILD_TYPE=Release"
+          "-DCMAKE_CXX_FLAGS=-ffast-math"
+        ];
       });
 
-      adamantine-debug = adamantine-latest.overrideAttrs ( with pkgs; previousAttrs : rec {
+      adamantine-debug = adamantine-base.overrideAttrs ( with pkgs; previousAttrs : rec {
         version = "debug";
         separateDebugInfo = true;
-        cmakeFlags = [
-          "-DDEAL_II_DIR=${deal_II}"
+        src = pkgs.lib.cleanSource ./.;
+        buildInputs = previousAttrs.buildInputs ++ [ deal_II_962 ];
+        cmakeFlags = previousAttrs.cmakeFlags ++ [
+          "-DDEAL_II_DIR=${deal_II_962}"
           "-DCMAKE_BUILD_TYPE=Debug"
           "-DCMAKE_CXX_FLAGS=-O0"
           "-DCMAKE_CXX_FLAGS_DEBUG=-g3"
-          "-DADAMANTINE_ENABLE_ADIAK=ON"
-          "-DADAMANTINE_ENABLE_CALIPER=ON"
-          "-DBOOST_DIR=${boost183}"
         ];
       });
 

source/DataAssimilator.cc

@@ -51,7 +51,7 @@ DataAssimilator::DataAssimilator(MPI_Comm const &global_communicator,
     if (boost::optional<unsigned int> max_num_temp_vectors =
             database.get_optional<unsigned int>(
                 "solver.max_number_of_temp_vectors"))
-      _additional_data.max_n_tmp_vectors = *max_num_temp_vectors;
+      _additional_data.max_basis_size = *max_num_temp_vectors;
 
     // PropertyTreeInput data_assimilation.solver.max_iterations
     if (boost::optional<unsigned int> max_iterations =

source/DataAssimilator.hh

@@ -11,7 +11,6 @@
 #include <deal.II/fe/mapping_q1_eulerian.h>
 #include <deal.II/lac/full_matrix.h>
 #include <deal.II/lac/la_parallel_block_vector.h>
-#include <deal.II/lac/la_vector.h>
 #include <deal.II/lac/solver_gmres.h>
 #include <deal.II/lac/sparse_matrix.h>
 #include <deal.II/lac/trilinos_sparse_matrix.h>

source/MaterialProperty.hh

@@ -19,7 +19,6 @@
 #include <deal.II/fe/fe_dgq.h>
 #include <deal.II/grid/filtered_iterator.h>
 #include <deal.II/lac/la_parallel_vector.h>
-#include <deal.II/lac/la_vector.h>
 
 #include <boost/property_tree/ptree.hpp>