mirror of
https://git.gfz-potsdam.de/naaice/poet.git
synced 2025-12-15 12:28:22 +01:00
Merge branch 'ml/iphreeqc-v0.3' into 'main'
Update IPhreeqc Submodule to v0.3 See merge request naaice/poet!40
This commit is contained in:
Max Lübke
commit
5c92a2156f
@ -1,61 +1,83 @@
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FROM gcc:11.2.0
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FROM gcc:11.2.0 AS builder
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ENV DEBIAN_FRONTEND=noninteractive
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RUN apt-get update \
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&& apt-get install -y \
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git \
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sudo \
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git \
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ninja-build \
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fzf \
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libblas-dev && \
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libmpfr-dev \
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python3-dev && \
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apt-get clean && \
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rm -rf /var/lib/apt/lists/*
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WORKDIR /tmp
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RUN curl -Ls https://download.open-mpi.org/release/open-mpi/v5.0/openmpi-5.0.5.tar.gz | tar xz && \
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cd openmpi-5.0.5 && \
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ARG OPENMPI_VERSION=4.1.1
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ADD https://download.open-mpi.org/release/open-mpi/v${OPENMPI_VERSION%.*}/openmpi-${OPENMPI_VERSION}.tar.gz /tmp/openmpi.tar.gz
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RUN mkdir openmpi && \
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tar xf openmpi.tar.gz -C openmpi --strip-components 1 && \
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cd openmpi && \
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./configure --prefix=/usr/local && \
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make -j $(nproc) && \
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make install && \
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rm -rf /tmp/openmpi-5.0.5
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rm -rf /tmp/openmpi tmp/openmpi.tar.gz
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RUN curl -Lo cmake.sh https://github.com/Kitware/CMake/releases/download/v3.30.5/cmake-3.30.5-linux-x86_64.sh \
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&& bash ./cmake.sh --skip-license --prefix=/usr/local \
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ARG CMAKE_VERSION=3.30.5
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ADD https://github.com/Kitware/CMake/releases/download/v${CMAKE_VERSION}/cmake-${CMAKE_VERSION}-linux-x86_64.sh /tmp/cmake.sh
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RUN bash ./cmake.sh --skip-license --prefix=/usr/local \
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&& rm cmake.sh
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RUN curl -Ls https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v3.12.0.tar.gz | tar xz && \
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cd lapack-3.12.0 && \
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ARG LAPACK_VERSION=3.12.0
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ADD https://github.com/Reference-LAPACK/lapack/archive/refs/tags/v${LAPACK_VERSION}.tar.gz /tmp/lapack.tar.gz
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RUN mkdir lapack && \
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tar xf lapack.tar.gz -C lapack --strip-components 1 && \
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cd lapack && \
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mkdir build && \
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cd build && \
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cmake .. -G Ninja -DBUILD_SHARED_LIBS=ON && \
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ninja install && \
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rm -rf /tmp/lapack-3.12.0
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rm -rf /tmp/lapack tmp/lapack.tar.gz
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RUN curl -Ls https://cran.r-project.org/src/base/R-4/R-4.4.2.tar.gz | tar xz && \
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cd R-4.4.2 && \
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ARG R_VERSION=4.4.2
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ADD https://cran.r-project.org/src/base/R-${R_VERSION%%.*}/R-${R_VERSION}.tar.gz /tmp/R.tar.gz
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RUN mkdir R && \
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tar xf R.tar.gz -C R --strip-components 1 && \
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cd R && \
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./configure --prefix=/usr/local --enable-R-shlib --with-blas --with-lapack && \
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make -j $(nproc) && \
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make install && \
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rm -rf /tmp/R-4.4.2
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rm -rf /tmp/R tmp/R.tar.gz
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RUN /usr/local/bin/R -q -e "install.packages(c('Rcpp', 'RInside', 'qs'), repos='https://cran.rstudio.com/')"
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RUN curl -Ls https://gitlab.com/libeigen/eigen/-/archive/3.4.0/eigen-3.4.0.tar.bz2 | tar xj \
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&& mkdir /tmp/eigen-3.4.0/build \
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&& cd /tmp/eigen-3.4.0/build \
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&& cmake .. -G Ninja \
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&& ninja install \
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&& rm -rf /tmp/eigen-3.4.0
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ARG EIGEN_VERSION=3.4.0
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ADD https://gitlab.com/libeigen/eigen/-/archive/${EIGEN_VERSION}/eigen-${EIGEN_VERSION}.tar.bz2 /tmp/eigen.tar.bz2
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RUN git clone https://github.com/doctest/doctest.git /doctest \
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&& cd /doctest \
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&& mkdir build \
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&& cd build \
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&& cmake .. \
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&& make install \
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&& rm -rf /doctest
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RUN mkdir eigen && \
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tar xf eigen.tar.bz2 -C eigen --strip-components 1 && \
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cd eigen && \
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mkdir build && \
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cd build && \
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cmake .. -G Ninja && \
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ninja install && \
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rm -rf /tmp/eigen tmp/eigen.tar.bz2
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ARG GDB_VERSION=15.2
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ADD https://ftp.gnu.org/gnu/gdb/gdb-${GDB_VERSION}.tar.xz /tmp/gdb.tar.xz
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RUN mkdir gdb && \
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tar xf gdb.tar.xz -C gdb --strip-components 1 && \
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cd gdb && \
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./configure --prefix=/usr/local && \
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make -j $(nproc) && \
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make install && \
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rm -rf /tmp/gdb tmp/gdb.tar.xz
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RUN useradd -m -s /bin/bash -G sudo vscode \
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&& echo "vscode ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
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@ -64,7 +86,23 @@ USER vscode
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ENV LD_LIBRARY_PATH=/usr/local/lib:$LD_LIBRARY_PATH
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RUN sudo apt-get update && \
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sudo apt-get install -y zsh && \
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sudo apt-get clean && \
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sudo rm -rf /var/lib/apt/lists/*
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RUN sh -c "$(wget -O- https://github.com/deluan/zsh-in-docker/releases/download/v1.2.1/zsh-in-docker.sh)" -- \
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-t agnoster
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-t agnoster \
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-p zsh-syntax-highlighting
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RUN zsh -c "git clone https://github.com/zsh-users/zsh-syntax-highlighting.git ${ZSH_CUSTOM:-~/.oh-my-zsh/custom}/plugins/zsh-syntax-highlighting"
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RUN zsh -c "git clone --depth 1 https://github.com/junegunn/fzf.git ~/.fzf && ~/.fzf/install"
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RUN mkdir -p /home/vscode/.config/gdb \
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&& echo "set auto-load safe-path /" > /home/vscode/.config/gdb/gdbinit
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ENV CMAKE_GENERATOR=Ninja
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ENV CMAKE_EXPORT_COMPILE_COMMANDS=ON
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WORKDIR /home/vscode
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@ -1 +1 @@
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Subproject commit 61214a01ad4cf99527f657e6a41c68282e4886c4
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Subproject commit 38268b4aad03e6ce4755315f4cd690f007fa2720
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@ -2,6 +2,7 @@
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#include "PhreeqcEngine.hpp"
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#include "PhreeqcMatrix.hpp"
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#include "PhreeqcRunner.hpp"
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#include "SurrogateModels/DHT_Wrapper.hpp"
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#include "SurrogateModels/Interpolation.hpp"
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@ -170,16 +171,9 @@ poet::ChemistryModule::ChemistryModule(
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if (!is_master) {
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PhreeqcMatrix pqc_mat =
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PhreeqcMatrix(chem_params.database, chem_params.pqc_script);
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for (const auto &cell_id : chem_params.pqc_ids) {
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this->phreeqc_instances[cell_id] =
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std::make_unique<PhreeqcEngine>(pqc_mat, cell_id);
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}
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// for (std::size_t i = 0; i < chem_params.pqc_ids.size(); i++) {
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// this->phreeqc_instances[chem_params.pqc_ids[i]] =
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// std::make_unique<PhreeqcWrapper>(
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// chem_params.database, chem_params.pqc_scripts[i],
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// chem_params.pqc_sol_order, chem_params.field_header, wp_size_);
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// }
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this->pqc_runner =
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std::make_unique<PhreeqcRunner>(pqc_mat.subset(chem_params.pqc_ids));
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}
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}
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@ -8,10 +8,11 @@
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#include "ChemistryDefs.hpp"
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#include "Init/InitialList.hpp"
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#include "NameDouble.h"
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#include "SurrogateModels/DHT_Wrapper.hpp"
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#include "SurrogateModels/Interpolation.hpp"
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#include "PhreeqcEngine.hpp"
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#include "PhreeqcRunner.hpp"
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#include <array>
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#include <cstdint>
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#include <map>
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@ -390,7 +391,7 @@ protected:
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const InitialList::ChemistryInit params;
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std::map<int, std::unique_ptr<PhreeqcEngine>> phreeqc_instances;
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std::unique_ptr<PhreeqcRunner> pqc_runner;
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};
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} // namespace poet
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@ -48,13 +48,15 @@ void poet::ChemistryModule::WorkerLoop() {
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case CHEM_FIELD_INIT: {
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ChemBCast(&this->prop_count, 1, MPI_UINT32_T);
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if (this->ai_surrogate_enabled) {
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this->ai_surrogate_validity_vector.resize(this->n_cells); // resize statt reserve?
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this->ai_surrogate_validity_vector.resize(
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this->n_cells); // resize statt reserve?
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}
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break;
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}
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case CHEM_AI_BCAST_VALIDITY: {
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// Receive the index vector of valid ai surrogate predictions
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MPI_Bcast(&this->ai_surrogate_validity_vector.front(), this->n_cells, MPI_INT, 0, this->group_comm);
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MPI_Bcast(&this->ai_surrogate_validity_vector.front(), this->n_cells,
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MPI_INT, 0, this->group_comm);
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break;
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}
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case CHEM_WORK_LOOP: {
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@ -187,7 +189,6 @@ void poet::ChemistryModule::WorkerDoWork(MPI_Status &probe_status,
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}
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}
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phreeqc_time_start = MPI_Wtime();
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WorkerRunWorkPackage(s_curr_wp, current_sim_time, dt);
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@ -300,28 +301,19 @@ void poet::ChemistryModule::WorkerRunWorkPackage(WorkPackage &work_package,
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double dSimTime,
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double dTimestep) {
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std::vector<std::vector<double>> inout_chem = work_package.input;
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std::vector<std::size_t> to_ignore;
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for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) {
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if (work_package.mapping[wp_id] != CHEM_PQC) {
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continue;
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to_ignore.push_back(wp_id);
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}
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}
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this->pqc_runner->run(inout_chem, dTimestep, to_ignore);
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auto curr_input = work_package.input[wp_id];
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const auto pqc_id = static_cast<int>(curr_input[0]);
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auto &phreeqc_instance = this->phreeqc_instances[pqc_id];
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work_package.output[wp_id] = work_package.input[wp_id];
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curr_input.erase(std::remove_if(curr_input.begin(), curr_input.end(),
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[](double d) { return std::isnan(d); }),
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curr_input.end());
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phreeqc_instance->runCell(curr_input, dTimestep);
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std::size_t output_index = 0;
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for (std::size_t i = 0; i < work_package.output[wp_id].size(); i++) {
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if (!std::isnan(work_package.output[wp_id][i])) {
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work_package.output[wp_id][i] = curr_input[output_index++];
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}
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for (std::size_t wp_id = 0; wp_id < work_package.size; wp_id++) {
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if (work_package.mapping[wp_id] == CHEM_PQC) {
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work_package.output[wp_id] = inout_chem[wp_id];
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}
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}
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}
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