Merge branch 'development' into fix_insulator_BC_time

.github/workflows/clang_sanitizers.yml

@@ -15,8 +15,7 @@ concurrency:
 jobs:
   build_UB_sanitizer:
     name: Clang UB sanitizer
-    runs-on: ubuntu-22.04
-    container: ubuntu:23.10
+    runs-on: ubuntu-24.04
     if: github.event.pull_request.draft == false
     env:
       CC: clang
@@ -65,10 +64,6 @@ jobs:
     - name: run with UB sanitizer
       run: |
 
-        # We need these two lines because these tests run inside a docker container
-        export OMPI_ALLOW_RUN_AS_ROOT=1
-        export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-
         export OMP_NUM_THREADS=2
 
         #MPI implementations often leak memory
@@ -81,9 +76,9 @@ jobs:
 
   build_thread_sanitizer:
     name: Clang thread sanitizer
-    runs-on: ubuntu-22.04
-    container: ubuntu:23.10
-    if: github.event.pull_request.draft == false
+    runs-on: ubuntu-24.04
+    # TODO Fix data race conditions and re-enable job
+    if: 0 #github.event.pull_request.draft == false
     env:
       CC: clang
       CXX: clang++
@@ -149,10 +144,6 @@ jobs:
         export TSAN_OPTIONS='ignore_noninstrumented_modules=1'
         export ARCHER_OPTIONS="verbose=1"
 
-        # We need these two lines because these tests run inside a docker container
-        export OMPI_ALLOW_RUN_AS_ROOT=1
-        export OMPI_ALLOW_RUN_AS_ROOT_CONFIRM=1
-
         export OMP_NUM_THREADS=2
 
         mpirun -n 2 ./build/bin/warpx.rz Examples/Physics_applications/laser_acceleration/inputs_base_rz warpx.serialize_initial_conditions = 0

.github/workflows/cuda.yml

@@ -126,7 +126,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 456c93c7d9512f1cdffac0574973d7df41417898 && cd -
+        cd ../amrex && git checkout --detach 24.12 && cd -
         make COMP=gcc QED=FALSE USE_MPI=TRUE USE_GPU=TRUE USE_OMP=FALSE USE_FFT=TRUE USE_CCACHE=TRUE -j 4
 
         ccache -s

.github/workflows/dependencies/clang17.sh

@@ -7,11 +7,6 @@
 
 set -eu -o pipefail
 
-# This dependency file is currently used within a docker container,
-# which does not come with sudo.
-apt-get -qqq update
-apt-get -y install sudo
-
 # `man apt.conf`:
 #   Number of retries to perform. If this is non-zero APT will retry
 #   failed files the given number of times.

.pre-commit-config.yaml

@@ -69,7 +69,7 @@ repos:
 # Python: Ruff linter & formatter
 #   https://docs.astral.sh/ruff/
 - repo: https://github.com/astral-sh/ruff-pre-commit
-  rev: v0.7.4
+  rev: v0.8.1
   hooks:
     # Run the linter
     - id: ruff

CMakeLists.txt

@@ -1,7 +1,7 @@
 # Preamble ####################################################################
 #
 cmake_minimum_required(VERSION 3.24.0)
-project(WarpX VERSION 24.11)
+project(WarpX VERSION 24.12)
 
 include(${WarpX_SOURCE_DIR}/cmake/WarpXFunctions.cmake)
 

Docs/source/conf.py

@@ -107,9 +107,9 @@ def __init__(self, *args, **kwargs):
 # built documents.
 #
 # The short X.Y version.
-version = "24.11"
+version = "24.12"
 # The full version, including alpha/beta/rc tags.
-release = "24.11"
+release = "24.12"
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

Docs/source/usage/parameters.rst

@@ -3589,22 +3589,27 @@ This shifts analysis from post-processing to runtime calculation of reduction op
     * ``Timestep``
         This type outputs the simulation's physical timestep (in seconds) at each mesh refinement level.
 
-* ``<reduced_diags_name>.intervals`` (`string`)
+* ``reduced_diags.intervals`` (`string`)
     Using the `Intervals Parser`_ syntax, this string defines the timesteps at which reduced
-    diagnostics are written to file.
+    diagnostics are written to the file.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.intervals``.
 
-* ``<reduced_diags_name>.path`` (`string`) optional (default `./diags/reducedfiles/`)
-    The path that the output file will be stored.
+* ``reduced_diags.path`` (`string`) optional (default `./diags/reducedfiles/`)
+    The path where the output file will be stored.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.path``.
 
-* ``<reduced_diags_name>.extension`` (`string`) optional (default `txt`)
-    The extension of the output file.
+* ``reduced_diags.extension`` (`string`) optional (default `txt`)
+    The extension of the output file (the suffix).
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.extension``.
 
-* ``<reduced_diags_name>.separator`` (`string`) optional (default a `whitespace`)
+* ``reduced_diags.separator`` (`string`) optional (default a `whitespace`)
     The separator between row values in the output file.
     The default separator is a whitespace.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.separator``.
 
-* ``<reduced_diags_name>.precision`` (`integer`) optional (default `14`)
+* ``reduced_diags.precision`` (`integer`) optional (default `14`)
     The precision used when writing out the data to the text files.
+    This can also be specified for the specific diagnostic by setting ``<reduced_diags_name>.precision``.
 
 Lookup tables and other settings for QED modules
 ------------------------------------------------

Examples/Physics_applications/laser_ion/inputs_test_2d_laser_ion_acc_picmi.py

@@ -196,7 +196,6 @@
 histuH_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histuH",
-    period=100,
     species=hydrogen,
     bin_number=1000,
     bin_min=0.0,
@@ -208,7 +207,6 @@
 histue_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histue",
-    period=100,
     species=electrons,
     bin_number=1000,
     bin_min=0.0,
@@ -222,7 +220,6 @@
 histuzAll_rdiag = picmi.ReducedDiagnostic(
     diag_type="ParticleHistogram",
     name="histuzAll",
-    period=100,
     species=hydrogen,
     bin_number=1000,
     bin_min=-0.474,
@@ -233,7 +230,6 @@
 field_probe_z_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_Z",
-    period=100,
     integrate=0,
     probe_geometry="Line",
     x_probe=0.0,
@@ -246,7 +242,6 @@
 field_probe_scat_point_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_ScatPoint",
-    period=1,
     integrate=0,
     probe_geometry="Point",
     x_probe=0.0,
@@ -256,7 +251,6 @@
 field_probe_scat_line_rdiag = picmi.ReducedDiagnostic(
     diag_type="FieldProbe",
     name="FieldProbe_ScatLine",
-    period=100,
     integrate=1,
     probe_geometry="Line",
     x_probe=-2.5e-6,
@@ -267,7 +261,8 @@
 )
 
 load_balance_costs_rdiag = picmi.ReducedDiagnostic(
-    diag_type="LoadBalanceCosts", name="LBC", period=100
+    diag_type="LoadBalanceCosts",
+    name="LBC",
 )
 
 # Set up simulation
@@ -278,6 +273,7 @@
     particle_shape="cubic",
     warpx_numprocs=[1, 2],  # deactivate `numprocs` for dynamic load balancing
     warpx_use_filter=1,
+    warpx_reduced_diags_intervals=100,
     warpx_load_balance_intervals=100,
     warpx_load_balance_costs_update="heuristic",
 )

Examples/Tests/implicit/inputs_test_1d_semi_implicit_picard

@@ -85,7 +85,6 @@ diag1.electrons.variables = z w ux uy uz
 diag1.protons.variables = z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Examples/Tests/implicit/inputs_test_1d_theta_implicit_picard

@@ -85,7 +85,6 @@ diag1.electrons.variables = z w ux uy uz
 diag1.protons.variables = z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb

@@ -109,7 +109,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Examples/Tests/implicit/inputs_test_2d_theta_implicit_jfnk_vandb_filtered

@@ -109,7 +109,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Examples/Tests/implicit/inputs_test_2d_theta_implicit_strang_psatd

@@ -92,7 +92,6 @@ diag1.electrons.variables = x z w ux uy uz
 diag1.protons.variables = x z w ux uy uz
 
 warpx.reduced_diags_names = particle_energy field_energy
+reduced_diags.intervals = 1
 particle_energy.type = ParticleEnergy
-particle_energy.intervals = 1
 field_energy.type = FieldEnergy
-field_energy.intervals = 1

Python/pywarpx/picmi.py

@@ -2770,6 +2770,21 @@ class Simulation(picmistandard.PICMI_Simulation):
 
     warpx_used_inputs_file: string, optional
         The name of the text file that the used input parameters is written to,
+
+    warpx_reduced_diags_path: string, optional
+        Sets the default path for reduced diagnostic output files
+
+    warpx_reduced_diags_extension: string, optional
+        Sets the default extension for reduced diagnostic output files
+
+    warpx_reduced_diags_intervals: string, optional
+        Sets the default intervals for reduced diagnostic output files
+
+    warpx_reduced_diags_separator: string, optional
+        Sets the default separator for reduced diagnostic output files
+
+    warpx_reduced_diags_precision: integer, optional
+        Sets the default precision for reduced diagnostic output files
     """
 
     # Set the C++ WarpX interface (see _libwarpx.LibWarpX) as an extension to
@@ -2836,6 +2851,12 @@ def init(self, kw):
         self.checkpoint_signals = kw.pop("warpx_checkpoint_signals", None)
         self.numprocs = kw.pop("warpx_numprocs", None)
 
+        self.reduced_diags_path = kw.pop("warpx_reduced_diags_path", None)
+        self.reduced_diags_extension = kw.pop("warpx_reduced_diags_extension", None)
+        self.reduced_diags_intervals = kw.pop("warpx_reduced_diags_intervals", None)
+        self.reduced_diags_separator = kw.pop("warpx_reduced_diags_separator", None)
+        self.reduced_diags_precision = kw.pop("warpx_reduced_diags_precision", None)
+
         self.inputs_initialized = False
         self.warpx_initialized = False
 
@@ -2902,6 +2923,13 @@ def initialize_inputs(self):
 
         pywarpx.warpx.numprocs = self.numprocs
 
+        reduced_diags = pywarpx.warpx.get_bucket("reduced_diags")
+        reduced_diags.path = self.reduced_diags_path
+        reduced_diags.extension = self.reduced_diags_extension
+        reduced_diags.intervals = self.reduced_diags_intervals
+        reduced_diags.separator = self.reduced_diags_separator
+        reduced_diags.precision = self.reduced_diags_precision
+
         particle_shape = self.particle_shape
         for s in self.species:
             if s.particle_shape is not None:
@@ -3943,7 +3971,7 @@ def __init__(
         self,
         diag_type,
         name=None,
-        period=1,
+        period=None,
         path=None,
         extension=None,
         separator=None,

Python/setup.py

@@ -65,7 +65,7 @@
 
 setup(
     name="pywarpx",
-    version="24.11",
+    version="24.12",
     packages=["pywarpx"],
     package_dir={"pywarpx": "pywarpx"},
     description="""Wrapper of WarpX""",

Source/Diagnostics/ReducedDiags/ReducedDiags.cpp

@@ -28,12 +28,15 @@ m_rd_name{rd_name}
 {
     BackwardCompatibility();
 
+    const ParmParse pp_rd("reduced_diags");
     const ParmParse pp_rd_name(m_rd_name);
 
     // read path
+    pp_rd.query("path", m_path);
     pp_rd_name.query("path", m_path);
 
     // read extension
+    pp_rd.query("extension", m_extension);
     pp_rd_name.query("extension", m_extension);
 
     // check if it is a restart run
@@ -61,13 +64,16 @@ m_rd_name{rd_name}
 
     // read reduced diags intervals
     std::vector<std::string> intervals_string_vec = {"1"};
-    pp_rd_name.getarr("intervals", intervals_string_vec);
+    pp_rd.queryarr("intervals", intervals_string_vec);
+    pp_rd_name.queryarr("intervals", intervals_string_vec);
     m_intervals = utils::parser::IntervalsParser(intervals_string_vec);
 
     // read separator
+    pp_rd.query("separator", m_sep);
     pp_rd_name.query("separator", m_sep);
 
     // precision of data in the output file
+    utils::parser::queryWithParser(pp_rd, "precision", m_precision);
     utils::parser::queryWithParser(pp_rd_name, "precision", m_precision);
 }
 // end constructor

Source/WarpX.H

@@ -1597,8 +1597,6 @@ private:
      */
     void HandleParticlesAtBoundaries (int step, amrex::Real cur_time, int num_moved);
 
-    void ScrapeParticles ();
-
     /** Update the E and B fields in the explicit em PIC scheme.
      *
      * At the beginning, we have B^{n} and E^{n}.

Tools/PostProcessing/read_raw_data.py

@@ -202,7 +202,7 @@ def _read_field(raw_file, field_name):
             f.seek(offset)
             if header.version == 1:
                 f.readline()  # skip the first line
-            arr = np.fromfile(f, "float64", np.product(shape))
+            arr = np.fromfile(f, "float64", np.prod(shape))
             arr = arr.reshape(shape, order="F")
             box_shape = [slice(low, hig + 1) for low, hig in zip(lo, hi)]
             if header.ncomp > 1:
@@ -225,7 +225,7 @@ def _read_buffer(snapshot, header_fn, _component_names):
         lo = box[0] - dom_lo
         hi = box[1] - dom_lo
         shape = hi - lo + 1
-        size = np.product(shape)
+        size = np.prod(shape)
         with open(snapshot + "/Level_0/" + fn, "rb") as f:
             f.seek(offset)
             if header.version == 1:

Tools/machines/perlmutter-nersc/perlmutter_cpu_warpx.profile.example

@@ -11,7 +11,7 @@ module load cmake/3.24.3
 module load cray-fftw/3.3.10.6
 
 # optional: for QED support with detailed tables
-export BOOST_ROOT=/global/common/software/spackecp/perlmutter/e4s-23.05/default/spack/opt/spack/linux-sles15-zen3/gcc-11.2.0/boost-1.82.0-ow5r5qrgslcwu33grygouajmuluzuzv3
+export BOOST_ROOT=/global/common/software/spackecp/perlmutter/e4s-23.08/default/spack/opt/spack/linux-sles15-zen3/gcc-12.3.0/boost-1.83.0-nxqk3hnci5g3wqv75wvsmuke3w74mzxi
 
 # optional: for openPMD and PSATD+RZ support
 module load cray-hdf5-parallel/1.12.2.9

Tools/machines/perlmutter-nersc/perlmutter_gpu_warpx.profile.example

@@ -15,7 +15,7 @@ module load cudatoolkit
 module load cmake/3.24.3
 
 # optional: for QED support with detailed tables
-export BOOST_ROOT=/global/common/software/spackecp/perlmutter/e4s-23.05/default/spack/opt/spack/linux-sles15-zen3/gcc-11.2.0/boost-1.82.0-ow5r5qrgslcwu33grygouajmuluzuzv3
+export BOOST_ROOT=/global/common/software/spackecp/perlmutter/e4s-23.08/default/spack/opt/spack/linux-sles15-zen3/gcc-12.3.0/boost-1.83.0-nxqk3hnci5g3wqv75wvsmuke3w74mzxi
 
 # optional: for openPMD and PSATD+RZ support
 module load cray-hdf5-parallel/1.12.2.9