fix conflict

RevathiJambunathan · Oct 16, 2020 · ca2a20c · ca2a20c
2 parents 8154234 + 1f8f4f7
commit ca2a20c
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diff --git a/.azure-pipelines.yml b/.azure-pipelines.yml
@@ -0,0 +1,61 @@
+# -*- mode: yaml -*-
+
+pool:
+  vmImage: 'ubuntu-latest'
+
+variables:
+  WARPX_CI_CCACHE: 'TRUE'
+  WARPX_CI_OPENPMD: 'TRUE'
+  FFTW_HOME: '/usr/'
+  BLASPP_HOME: '/usr/local/'
+  LAPACKPP_HOME: '/usr/local/'
+  OMP_NUM_THREADS: 1
+
+strategy:
+  matrix:
+    cartesian:
+      WARPX_CI_REGULAR_CARTESIAN: 'TRUE'
+    psatd:
+      WARPX_CI_PSATD: 'TRUE'
+    python:
+      WARPX_CI_PYTHON_MAIN: 'TRUE'
+    single_precision:
+      WARPX_CI_SINGLE_PRECISION: 'TRUE'
+    rz_or_nompi:
+      WARPX_CI_RZ_OR_NOMPI: 'TRUE'
+    qed:
+      WARPX_CI_QED: 'TRUE'
+
+steps:
+- script: |
+    cat /proc/cpuinfo | grep "model name" | sort -u
+    sudo apt-get update
+    sudo apt-get install -y ccache gcc gfortran g++ openmpi-bin libopenmpi-dev \
+      libfftw3-dev libfftw3-mpi-dev libhdf5-openmpi-dev pkg-config make \
+      python3 python3-pip python3-setuptools libblas-dev liblapack-dev
+    sudo update-alternatives --install /usr/bin/python python /usr/bin/python3 2
+    sudo update-alternatives --set python /usr/bin/python3
+    python -m pip install --upgrade pip
+    python -m pip install --upgrade wheel
+    python -m pip install --upgrade cmake matplotlib==3.2.2 mpi4py numpy scipy yt
+    export CEI_CMAKE="$HOME/.local/bin/cmake"
+    export CEI_SUDO="sudo"
+    sudo curl -L -o /usr/local/bin/cmake-easyinstall https://git.io/JvLxY
+    sudo chmod a+x /usr/local/bin/cmake-easyinstall
+    if [ "${WARPX_CI_OPENPMD:-FALSE}" == "TRUE" ]; then
+      cmake-easyinstall --prefix=/usr/local git+https://github.com/openPMD/openPMD-api.git \
+        -DopenPMD_USE_PYTHON=OFF -DBUILD_TESTING=OFF -DBUILD_EXAMPLES=OFF
+    fi
+    if [ "${WARPX_CI_RZ_OR_NOMPI:-FALSE}" == "TRUE" ]; then
+      cmake-easyinstall --prefix=/usr/local git+https://bitbucket.org/icl/blaspp.git \
+        -Duse_openmp=OFF -Dbuild_tests=OFF
+      cmake-easyinstall --prefix=/usr/local git+https://bitbucket.org/icl/lapackpp.git \
+        -DBUILD_LAPACKPP_TESTS=OFF
+    fi
+  displayName: 'Install dependencies'
+
+- script: |
+      export WARPX_TEST_COMMIT=$BUILD_SOURCEVERSION
+      ./run_test.sh
+  timeoutInMinutes: 360
+  displayName: 'Build & test'
diff --git a/.editorconfig b/.editorconfig
@@ -0,0 +1,32 @@
+# http://EditorConfig.org
+#
+# precedence of rules is bottom to top
+
+# this is the top-most EditorConfig file
+root = true
+
+
+[*]
+# 4 space indentation
+indent_style = space
+indent_size = 4
+
+# no end of line whitespaces
+trim_trailing_whitespace = true
+
+# unix-style newlines
+end_of_line = lf
+
+# newline ending in files
+insert_final_newline = true
+
+
+[*.md]
+# two end of line whitespaces are newlines without a paragraph
+trim_trailing_whitespace = false
+
+
+[Makefile]
+# TABs are part of its syntax
+indent_style = tab
+indent_size = unset
diff --git a/.github/workflows/ubuntu.yml b/.github/workflows/ubuntu.yml
@@ -20,7 +20,6 @@ jobs:
         sudo wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/7fa2af80.pub
         sudo apt-key add 7fa2af80.pub
         echo "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64 /" | sudo tee /etc/apt/sources.list.d/cuda.list
-        echo "deb https://developer.download.nvidia.com/compute/machine-learning/repos/ubuntu1804/x86_64 /" | sudo tee /etc/apt/sources.list.d/nvidia-ml.list
         sudo apt-get update
         sudo apt-get install -y cuda-command-line-tools-11-0 cuda-compiler-11-0 cuda-cupti-dev-11-0 cuda-minimal-build-11-0 cuda-nvml-dev-11-0 cuda-nvtx-11-0 libcurand-dev-11-0
         sudo ln -s cuda-11.0 /usr/local/cuda
@@ -54,7 +53,7 @@ jobs:
         sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
         echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
         sudo apt-get update
-        sudo apt-get install -y intel-oneapi-icc intel-oneapi-ifort
+        sudo apt-get install -y intel-oneapi-dpcpp-cpp-compiler-pro
         set +e
         source /opt/intel/oneapi/setvars.sh
         set -e
@@ -80,10 +79,7 @@ jobs:
         cmake .. -DCMAKE_VERBOSE_MAKEFILE=ON -DWarpX_MPI=OFF -DWarpX_OPENPMD=ON -DWarpX_openpmd_internal=OFF -DWarpX_PRECISION=single
         make -j 2
 
-  # broken in beta08
-  #   https://github.com/intel/llvm/issues/2187
   build_dpcc:
-    if: false
     name: oneAPI DPC++ SP [Linux]
     runs-on: ubuntu-latest
     steps:
@@ -101,9 +97,10 @@ jobs:
         sudo apt-key add GPG-PUB-KEY-INTEL-SW-PRODUCTS-2023.PUB
         echo "deb https://apt.repos.intel.com/oneapi all main" | sudo tee /etc/apt/sources.list.d/oneAPI.list
         sudo apt-get update
-        sudo apt-get install -y intel-oneapi-dpcpp-compiler intel-oneapi-mkl
+        sudo apt-get install -y intel-oneapi-dpcpp-cpp-compiler intel-oneapi-mkl-devel
         set +e
         source /opt/intel/oneapi/setvars.sh
+        source /opt/intel/oneapi/compiler/2021.1-beta08/env/vars.sh
         set -e
         git clone https://github.com/openPMD/openPMD-api.git
         mkdir openPMD-api/build
@@ -116,6 +113,7 @@ jobs:
       run: |
         set +e
         source /opt/intel/oneapi/setvars.sh
+        source /opt/intel/oneapi/compiler/2021.1-beta08/env/vars.sh
         set -e
         export CXX=$(which dpcpp)
         export CC=$(which clang)

diff --git a/.gitignore b/.gitignore
@@ -4,6 +4,7 @@ Python/pywarpx/libwarpx*.so
 d/
 f/
 o/
+build/
 tmp_build_dir/
 test_dir
 test_dir/
@@ -34,6 +35,14 @@ Docs/doxyhtml/
 Docs/doxyxml/
 Docs/source/_static/
 
+####################
+# Package Managers #
+####################
+# anonymous Spack environments
+# https://spack.readthedocs.io/en/latest/environments.html#anonymous-environments
+.spack-env/
+spack.lock
+
 #######
 # IDE #
 #######

diff --git a/.travis.yml b/.travis.yml
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -61,6 +61,13 @@ if(NOT WarpX_COMPUTE IN_LIST WarpX_COMPUTE_VALUES)
     message(FATAL_ERROR "WarpX_PRECISION (${WarpX_COMPUTE}) must be one of ${WarpX_COMPUTE_VALUES}")
 endif()
 
+option(WarpX_MPI_THREAD_MULTIPLE "MPI thread-multiple support, i.e. for async_io" ON)
+mark_as_advanced(WarpX_MPI_THREAD_MULTIPLE)
+
+set(WarpX_PARSER_DEPTH 24 CACHE STRING
+    "Maximum parser depth for input file functions")
+mark_as_advanced(WarpX_PARSER_DEPTH)
+
 option(WarpX_amrex_internal                    "Download & build AMReX" ON)
 
 # change the default build type to RelWithDebInfo (or Release) instead of Debug
@@ -222,6 +229,9 @@ if(WarpX_PSATD)
     target_compile_definitions(WarpX PRIVATE WARPX_USE_PSATD)
 endif()
 
+target_compile_definitions(WarpX PRIVATE
+    WARPX_PARSER_DEPTH=${WarpX_PARSER_DEPTH})
+
 
 # Warnings ####################################################################
 #

diff --git a/Docs/source/building/building.rst b/Docs/source/building/building.rst
@@ -54,6 +54,7 @@ options are:
     * ``USE_GPU=TRUE`` or ``FALSE``: Whether to compile for Nvidia GPUs (requires CUDA).
     * ``USE_OPENPMD=TRUE`` or ``FALSE``: Whether to support openPMD for I/O (requires openPMD-api).
     * ``MPI_THREAD_MULTIPLE=TRUE`` or ``FALSE``: Whether to initialize MPI with thread multiple support. Required to use asynchronous IO with more than ``amrex.async_out_nfiles`` (by default, 64) MPI tasks. Please see :doc:`../visualization/visualization` for more information.
+    * ``PRECISION=FLOAT USE_SINGLE_PRECISION_PARTICLES=TRUE``: Switch from default double precision to single precision (experimental).
 
 For a description of these different options, see the `corresponding page <https://amrex-codes.github.io/amrex/docs_html/BuildingAMReX.html>`__ in the AMReX documentation.
 
@@ -104,3 +105,5 @@ Building for specific platforms
    cori
    summit
    juwels
+   lassen
+   quartz
diff --git a/Docs/source/building/cmake.rst b/Docs/source/building/cmake.rst
@@ -8,6 +8,13 @@ Until we have transitioned our documentation and functionality completely, pleas
 
 Progress status: `see on GitHub <https://github.com/ECP-WarpX/WarpX/projects/10>`_
 
+Introduction to CMake
+=====================
+
+If you are new to CMake, `this short tutorial <https://hsf-training.github.io/hsf-training-cmake-webpage/>`_ from the HEP Software foundation is the perfect place to get started with it.
+
+If you just want to use CMake to build the project, jump into sections *1. Introduction*, *2. Building with CMake* and *9. Finding Packages*.
+
 Dependencies
 ============
 
@@ -25,7 +32,7 @@ Optional dependencies include:
 - `OpenMP 3.1+ <https://www.openmp.org>`_: for threaded CPU execution (currently not fully accelerated)
 - `FFTW3 <http://www.fftw.org>`_: for spectral solver (PSATD) support
 - `Boost 1.66.0+ <https://www.boost.org/>`_: for QED support
-- `openPMD-api 0.11.1+ <https://github.com/openPMD/openPMD-api>`_: we automatically download and compile a copy of openPMD-api for openPMD I/O support
+- `openPMD-api 0.12.0+ <https://github.com/openPMD/openPMD-api>`_: we automatically download and compile a copy of openPMD-api for openPMD I/O support
 
   - see `optional I/O backends <https://github.com/openPMD/openPMD-api#dependencies>`_
 - `CCache <https://ccache.dev>`_: to speed up rebuilds (needs 3.7.9+ for CUDA)
@@ -39,11 +46,12 @@ macOS/Linux:
 
    spack env create warpx-dev
    spack env activate warpx-dev
+   spack add adios2
    spack add ccache
    spack add cmake
    spack add fftw
+   spack add hdf5
    spack add mpi
-   spack add openpmd-api
    spack add pkgconfig  # for fftw
    # optional:
    # spack add cuda
@@ -56,13 +64,14 @@ or macOS/Linux:
 .. code-block:: bash
 
    brew update
+   brew install adios2
    brew install ccache
    brew install cmake
    brew install fftw
+   brew install hdf5-mpi
    brew install libomp
    brew install pkg-config  # for fftw
    brew install open-mpi
-   brew install openpmd-api
 
 Now, ``cmake --version`` should be at version 3.14.0 or newer.
 
@@ -109,23 +118,25 @@ You can inspect and modify build options after running ``cmake ..`` with either
 
 or by providing arguments to the CMake call: ``cmake .. -D<OPTION_A>=<VALUE_A> -D<OPTION_B>=<VALUE_B>``
 
-=========================== ============================================ =======================================================
-CMake Option                Default & Values                             Description
-=========================== ============================================ =======================================================
-``CMAKE_BUILD_TYPE``        **RelWithDebInfo**/Release/Debug             Type of build, symbols & optimizations
-``WarpX_ASCENT``            ON/**OFF**                                   Ascent in situ visualization
-``WarpX_COMPUTE``           NOACC/**OMP**/CUDA/DPCPP                     On-node, accelerated computing backend
-``WarpX_DIMS``              **3**/2/RZ                                   Simulation dimensionality
-``WarpX_MPI``               **ON**/OFF                                   Multi-node support (message-passing)
-``WarpX_OPENPMD``           ON/**OFF**                                   openPMD I/O (HDF5, ADIOS)
-``WarpX_PRECISION``         **double**/single                            Floating point precision (single/double)
-``WarpX_PSATD``             ON/**OFF**                                   Spectral solver
-``WarpX_QED``               ON/**OFF**                                   PICSAR QED (requires Boost and PICSAR)
-``WarpX_amrex_repo``        ``https://github.com/AMReX-Codes/amrex.git`` Repository URI to pull and build AMReX from
-``WarpX_amrex_branch``      ``development``                              Repository branch for ``WarpX_amrex_repo``
-``WarpX_amrex_internal``    **ON**/OFF                                   Needs a pre-installed AMReX library if set to ``OFF``
-``WarpX_openpmd_internal``  **ON**/OFF                                   Needs a pre-installed openPMD library if set to ``OFF``
-=========================== ============================================ =======================================================
+============================= ============================================ =======================================================
+CMake Option                  Default & Values                             Description
+============================= ============================================ =======================================================
+``CMAKE_BUILD_TYPE``          **RelWithDebInfo**/Release/Debug             Type of build, symbols & optimizations
+``WarpX_ASCENT``              ON/**OFF**                                   Ascent in situ visualization
+``WarpX_COMPUTE``             NOACC/**OMP**/CUDA/DPCPP                     On-node, accelerated computing backend
+``WarpX_DIMS``                **3**/2/RZ                                   Simulation dimensionality
+``WarpX_MPI``                 **ON**/OFF                                   Multi-node support (message-passing)
+``WarpX_MPI_THREAD_MULTIPLE`` **ON**/OFF                                   MPI thread-multiple support, i.e. for ``async_io``
+``WarpX_OPENPMD``             ON/**OFF**                                   openPMD I/O (HDF5, ADIOS)
+``WarpX_PARSER_DEPTH``        **24**                                       Maximum parser depth for input file functions
+``WarpX_PRECISION``           **double**/single                            Floating point precision (single/double)
+``WarpX_PSATD``               ON/**OFF**                                   Spectral solver
+``WarpX_QED``                 ON/**OFF**                                   PICSAR QED (requires Boost and PICSAR)
+``WarpX_amrex_repo``          ``https://github.com/AMReX-Codes/amrex.git`` Repository URI to pull and build AMReX from
+``WarpX_amrex_branch``        ``development``                              Repository branch for ``WarpX_amrex_repo``
+``WarpX_amrex_internal``      **ON**/OFF                                   Needs a pre-installed AMReX library if set to ``OFF``
+``WarpX_openpmd_internal``    **ON**/OFF                                   Needs a pre-installed openPMD library if set to ``OFF``
+============================= ============================================ =======================================================
 
 For example, one can also build against a local AMReX git repo.
 Assuming AMReX' source is located in ``$HOME/src/amrex`` and changes are committed into a branch such as ``my-amrex-branch`` then pass to ``cmake`` the arguments: ``-DWarpX_amrex_repo=file://$HOME/src/amrex -DWarpX_amrex_branch=my-amrex-branch``.

diff --git a/Docs/source/building/juwels.rst b/Docs/source/building/juwels.rst
@@ -25,7 +25,7 @@ Use the following commands to download the WarpX source code and switch to the c
    cd ~/src
 
    git clone https://github.com/ECP-WarpX/WarpX.git warpx
-   git clone --branch QED https://github.com/ECP-WarpX/picsar.git
+   git clone --branch development https://github.com/ECP-WarpX/picsar.git
    git clone --branch development https://github.com/AMReX-Codes/amrex.git
 
 We use the following modules and environments on the system.