Merge branch 'ml/iphreeqc-v0.3' into 'main'

Update IPhreeqc Submodule to v0.3

See merge request naaice/poet!40

.devcontainer/Dockerfile

@@ -1,61 +1,83 @@
-FROM gcc:11.2.0
+FROM gcc:11.2.0 AS builder
 
 ENV DEBIAN_FRONTEND=noninteractive
 
 RUN apt-get update \
     && apt-get install -y \
-    git \
     sudo \
+    git \
     ninja-build \
-    fzf \
+    libmpfr-dev \
-    libblas-dev && \
+    python3-dev && \
     apt-get clean && \
     rm -rf /var/lib/apt/lists/*
 
 WORKDIR /tmp
 
-RUN curl -Ls https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz | tar xz && \
+ARG OPENMPI_VERSION=4.1.1
-    cd openmpi-5.0.5 && \
+ADD https://download.open-mpi.org/release/open-mpi/v${OPENMPI_VERSION%.*}/openmpi-${OPENMPI_VERSION}.tar.gz /tmp/openmpi.tar.gz
+
+RUN mkdir openmpi && \ 
+    tar xf openmpi.tar.gz -C openmpi --strip-components 1 && \
+    cd openmpi && \
     ./configure --prefix=/usr/local && \
     make -j $(nproc) && \
     make install && \
-    rm -rf /tmp/openmpi-5.0.5
+    rm -rf /tmp/openmpi tmp/openmpi.tar.gz
 
-RUN curl -Lo cmake.sh https://github.com/Kitware/CMake/releases/download/v3.30.5/cmake-3.30.5-linux-x86_64.sh \
+ARG CMAKE_VERSION=3.30.5
-    && bash ./cmake.sh --skip-license --prefix=/usr/local \
+ADD https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cmake-${CMAKE_VERSION}-linux-x86_64.sh /tmp/cmake.sh
+
+RUN bash ./cmake.sh --skip-license --prefix=/usr/local \
     && rm cmake.sh
 
-RUN curl -Ls https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v3.12.0.tar.gz | tar xz && \
+ARG LAPACK_VERSION=3.12.0
-    cd lapack-3.12.0 && \
+ADD https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v${LAPACK_VERSION}.tar.gz /tmp/lapack.tar.gz
+
+RUN mkdir lapack && \
+    tar xf lapack.tar.gz -C lapack --strip-components 1 && \
+    cd lapack && \
     mkdir build && \
     cd build && \
     cmake .. -G Ninja -DBUILD_SHARED_LIBS=ON && \
     ninja install && \
-    rm -rf /tmp/lapack-3.12.0
+    rm -rf /tmp/lapack tmp/lapack.tar.gz
 
-RUN curl -Ls https://cran.r-project.org/src/base/R-4/R-4.4.2.tar.gz | tar xz && \
+ARG R_VERSION=4.4.2
-    cd R-4.4.2 && \
+ADD https://cran.r-project.org/src/base/R-${R_VERSION%%.*}/R-${R_VERSION}.tar.gz /tmp/R.tar.gz
+
+RUN mkdir R && \
+    tar xf R.tar.gz -C R --strip-components 1 && \
+    cd R && \
     ./configure --prefix=/usr/local --enable-R-shlib --with-blas --with-lapack && \
     make -j $(nproc) && \
     make install && \
-    rm -rf /tmp/R-4.4.2
+    rm -rf /tmp/R tmp/R.tar.gz
 
 RUN  /usr/local/bin/R -q -e "install.packages(c('Rcpp', 'RInside', 'qs'), repos='https://cran.rstudio.com/')"
 
-RUN curl -Ls https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.bz2 | tar xj \
+ARG EIGEN_VERSION=3.4.0
-    && mkdir /tmp/eigen-3.4.0/build \
+ADD https://gitlab.com/libeigen/eigen/-/archive/${EIGEN_VERSION}/eigen-${EIGEN_VERSION}.tar.bz2 /tmp/eigen.tar.bz2
-    && cd /tmp/eigen-3.4.0/build \
-    && cmake .. -G Ninja \
-    && ninja install \
-    && rm -rf /tmp/eigen-3.4.0
 
-RUN git clone https://github.com/doctest/doctest.git /doctest \
+RUN mkdir eigen && \
-    && cd /doctest \
+    tar xf eigen.tar.bz2 -C eigen --strip-components 1 && \
-    && mkdir build \
+    cd eigen && \
-    && cd build \
+    mkdir build && \
-    && cmake .. \
+    cd build && \
-    && make install \
+    cmake .. -G Ninja && \
-    && rm -rf /doctest
+    ninja install && \
+    rm -rf /tmp/eigen tmp/eigen.tar.bz2
+
+ARG GDB_VERSION=15.2
+ADD https://ftp.gnu.org/gnu/gdb/gdb-${GDB_VERSION}.tar.xz /tmp/gdb.tar.xz
+
+RUN mkdir gdb && \
+    tar xf gdb.tar.xz -C gdb --strip-components 1 && \
+    cd gdb && \
+    ./configure --prefix=/usr/local && \
+    make -j $(nproc) && \
+    make install && \
+    rm -rf /tmp/gdb tmp/gdb.tar.xz
 
 RUN useradd -m -s /bin/bash -G sudo vscode \
     && echo "vscode ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
@@ -64,7 +86,23 @@ USER vscode
 
 ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
 
+RUN sudo apt-get update && \
+    sudo apt-get install -y zsh && \
+    sudo apt-get clean && \
+    sudo rm -rf /var/lib/apt/lists/*
+
 RUN sh -c "$(wget -O- https://github.com/deluan/zsh-in-docker/releases/download/v1.2.1/zsh-in-docker.sh)" -- \ 
-    -t agnoster 
+    -t agnoster \
+    -p zsh-syntax-highlighting
+
+RUN zsh -c "git clone https://github.com/zsh-users/zsh-syntax-highlighting.git ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-syntax-highlighting"
+
+RUN zsh -c "git clone --depth 1 https://github.com/junegunn/fzf.git ~/.fzf && ~/.fzf/install"
+
+RUN mkdir -p /home/vscode/.config/gdb \
+    && echo "set auto-load safe-path /" > /home/vscode/.config/gdb/gdbinit
+
+ENV CMAKE_GENERATOR=Ninja
+ENV CMAKE_EXPORT_COMPILE_COMMANDS=ON
 
 WORKDIR /home/vscode

ext/iphreeqc

@@ -1 +1 @@
-Subproject commit 61214a01ad4cf99527f657e6a41c68282e4886c4
+Subproject commit 38268b4aad03e6ce4755315f4cd690f007fa2720

src/Chemistry/ChemistryModule.cpp

@@ -2,6 +2,7 @@
 
 #include "PhreeqcEngine.hpp"
 #include "PhreeqcMatrix.hpp"
+#include "PhreeqcRunner.hpp"
 #include "SurrogateModels/DHT_Wrapper.hpp"
 #include "SurrogateModels/Interpolation.hpp"
 
@@ -170,16 +171,9 @@ poet::ChemistryModule::ChemistryModule(
   if (!is_master) {
     PhreeqcMatrix pqc_mat =
         PhreeqcMatrix(chem_params.database, chem_params.pqc_script);
-    for (const auto &cell_id : chem_params.pqc_ids) {
+
-      this->phreeqc_instances[cell_id] =
+    this->pqc_runner =
-          std::make_unique<PhreeqcEngine>(pqc_mat, cell_id);
+        std::make_unique<PhreeqcRunner>(pqc_mat.subset(chem_params.pqc_ids));
-    }
-    // for (std::size_t i = 0; i < chem_params.pqc_ids.size(); i++) {
-    //   this->phreeqc_instances[chem_params.pqc_ids[i]] =
-    //       std::make_unique<PhreeqcWrapper>(
-    //           chem_params.database, chem_params.pqc_scripts[i],
-    //           chem_params.pqc_sol_order, chem_params.field_header, wp_size_);
-    // }
   }
 }
 

src/Chemistry/ChemistryModule.hpp

@@ -8,10 +8,11 @@
 #include "ChemistryDefs.hpp"
 
 #include "Init/InitialList.hpp"
+#include "NameDouble.h"
 #include "SurrogateModels/DHT_Wrapper.hpp"
 #include "SurrogateModels/Interpolation.hpp"
 
-#include "PhreeqcEngine.hpp"
+#include "PhreeqcRunner.hpp"
 #include <array>
 #include <cstdint>
 #include <map>
@@ -390,7 +391,7 @@ protected:
 
   const InitialList::ChemistryInit params;
 
-  std::map<int, std::unique_ptr<PhreeqcEngine>> phreeqc_instances;
+  std::unique_ptr<PhreeqcRunner> pqc_runner;
 };
 } // namespace poet
 

src/Chemistry/WorkerFunctions.cpp

@@ -48,13 +48,15 @@ void poet::ChemistryModule::WorkerLoop() {
     case CHEM_FIELD_INIT: {
       ChemBCast(&this->prop_count, 1, MPI_UINT32_T);
       if (this->ai_surrogate_enabled) {
-        this->ai_surrogate_validity_vector.resize(this->n_cells); // resize statt reserve?
+        this->ai_surrogate_validity_vector.resize(
+            this->n_cells); // resize statt reserve?
       }
       break;
     }
     case CHEM_AI_BCAST_VALIDITY: {
       // Receive the index vector of valid ai surrogate predictions
-      MPI_Bcast(&this->ai_surrogate_validity_vector.front(), this->n_cells, MPI_INT, 0, this->group_comm);
+      MPI_Bcast(&this->ai_surrogate_validity_vector.front(), this->n_cells,
+                MPI_INT, 0, this->group_comm);
       break;
     }
     case CHEM_WORK_LOOP: {
@@ -187,7 +189,6 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status,
     }
   }
 
-
   phreeqc_time_start = MPI_Wtime();
 
   WorkerRunWorkPackage(s_curr_wp, current_sim_time, dt);
@@ -300,28 +301,19 @@ void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package,
                                                  double dSimTime,
                                                  double dTimestep) {
 
+  std::vector<std::vector<double>> inout_chem = work_package.input;
+  std::vector<std::size_t> to_ignore;
+
   for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) {
     if (work_package.mapping[wp_id] != CHEM_PQC) {
-      continue;
+      to_ignore.push_back(wp_id);
     }
+  }
+  this->pqc_runner->run(inout_chem, dTimestep, to_ignore);
 
-    auto curr_input = work_package.input[wp_id];
+  for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) {
-    const auto pqc_id = static_cast<int>(curr_input[0]);
+    if (work_package.mapping[wp_id] == CHEM_PQC) {
-
+      work_package.output[wp_id] = inout_chem[wp_id];
-    auto &phreeqc_instance = this->phreeqc_instances[pqc_id];
-    work_package.output[wp_id] = work_package.input[wp_id];
-
-    curr_input.erase(std::remove_if(curr_input.begin(), curr_input.end(),
-                                    [](double d) { return std::isnan(d); }),
-                     curr_input.end());
-
-    phreeqc_instance->runCell(curr_input, dTimestep);
-
-    std::size_t output_index = 0;
-    for (std::size_t i = 0; i < work_package.output[wp_id].size(); i++) {
-      if (!std::isnan(work_package.output[wp_id][i])) {
-        work_package.output[wp_id][i] = curr_input[output_index++];
-      }
     }
   }
 }