Merge remote-tracking branch 'upstream/development' into add_thread_s…

…anitizer

.github/workflows/cuda.yml

@@ -115,7 +115,7 @@ jobs:
         which nvcc || echo "nvcc not in PATH!"
 
         git clone https://github.com/AMReX-Codes/amrex.git ../amrex
-        cd ../amrex && git checkout --detach 24.07 && cd -
+        cd ../amrex && git checkout --detach dcb9cc0383dcc71e38dee9070574e325a812f8bf && 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

CMakeLists.txt

@@ -146,10 +146,19 @@ set_default_build_type("Release")
 
 # Option to enable interprocedural optimization
 # (also know as "link-time optimization" or "whole program optimization")
-option(WarpX_IPO                                "Compile WarpX with interprocedural optimization (will take more time)" OFF)
+set(_WarpX_IPO_DEFAULT OFF)
+set(_WarpX_PYTHON_IPO_DEFAULT ON)
+if(DEFINED CMAKE_INTERPROCEDURAL_OPTIMIZATION)
+    set(_WarpX_IPO_DEFAULT ${CMAKE_INTERPROCEDURAL_OPTIMIZATION})
+    set(_WarpX_PYTHON_IPO_DEFAULT ${CMAKE_INTERPROCEDURAL_OPTIMIZATION})
+endif()
+option(WarpX_IPO
+    "Compile WarpX with interprocedural optimization (will take more time)"
+    ${_WarpX_IPO_DEFAULT}
+)
 option(WarpX_PYTHON_IPO
     "Compile Python bindings with interprocedural optimization (IPO) / link-time optimization (LTO)"
-    ON
+    ${_WarpX_PYTHON_IPO_DEFAULT}
 )
 
 set(pyWarpX_VERSION_INFO "" CACHE STRING
@@ -455,7 +464,7 @@ endif()
 
 # Interprocedural optimization (IPO) / Link-Time Optimization (LTO)
 if(WarpX_IPO)
-    enable_IPO("${_ALL_TARGETS}")
+    warpx_enable_IPO("${_ALL_TARGETS}")
 endif()
 
 # link dependencies
@@ -488,7 +497,13 @@ foreach(D IN LISTS WarpX_DIMS)
     if(WarpX_PYTHON)
         target_link_libraries(pyWarpX_${SD} PRIVATE pybind11::module pybind11::windows_extras)
         if(WarpX_PYTHON_IPO)
-            target_link_libraries(pyWarpX_${SD} PRIVATE pybind11::lto)
+            if(DEFINED CMAKE_INTERPROCEDURAL_OPTIMIZATION)
+                warpx_enable_IPO(pyWarpX_${SD})
+            else()
+                # conditionally defined target in pybind11
+                # https://github.com/pybind/pybind11/blob/v2.12.0/tools/pybind11Common.cmake#L397-L403
+                target_link_libraries(pyWarpX_${SD} PRIVATE pybind11::lto)
+            endif()
         endif()
     endif()
 

Docs/requirements.txt

@@ -13,7 +13,7 @@ openpmd-viewer  # for checksumAPI
 
 # PICMI API docs
 # note: keep in sync with version in ../requirements.txt
-picmistandard==0.28.0
+picmistandard==0.29.0
 # for development against an unreleased PICMI version, use:
 # picmistandard @ git+https://github.com/picmi-standard/picmi.git#subdirectory=PICMI_Python
 

Docs/source/usage/parameters.rst

@@ -500,7 +500,7 @@ Domain Boundary Conditions
     * ``open``: For the electrostatic Poisson solver based on a Integrated Green Function method.
 
 * ``boundary.potential_lo_x/y/z`` and ``boundary.potential_hi_x/y/z`` (default `0`)
-    Gives the value of the electric potential at the boundaries, for ``pec`` boundaries. With electrostatic solvers
+    Gives the value of the electric potential, in Volts, at the boundaries, for ``pec`` boundaries. With electrostatic solvers
     (i.e., with ``warpx.do_electrostatic = ...``), this is used in order to compute the potential
     in the simulation volume at each timestep. When using other solvers (e.g. Maxwell solver),
     setting these variables will trigger an electrostatic solve at ``t=0``, to compute the initial
@@ -603,7 +603,7 @@ Whether the embedded boundary is defined with an analytical function or an STL f
 additionally define the electric potential at the embedded boundary with an analytical function:
 
 * ``warpx.eb_potential(x,y,z,t)`` (`string`)
-    Gives the value of the electric potential at the surface of the embedded boundary,
+    Gives the value of the electric potential, in Volts, at the surface of the embedded boundary,
     as a function of  `x`, `y`, `z` and `t`. With electrostatic solvers (i.e., with
     ``warpx.do_electrostatic = ...``), this is used in order to compute the potential
     in the simulation volume at each timestep. When using other solvers (e.g. Maxwell solver),
@@ -1156,8 +1156,8 @@ Particle initialization
     * ``gaussian_parse_momentum_function``: Gaussian momentum distribution where the mean and the standard deviation are given by functions of position in the input file.
       Both are assumed to be non-relativistic.
       The mean is the normalized momentum, :math:`u_m = \gamma v_m/c`.
-      The standard deviation is normalized, :math:`u_th = v_th/c`.
-      For example, this might be `u_th = sqrt(T*q_e/mass)/clight` given the temperature (in eV) and mass.
+      The standard deviation is normalized, :math:`u_{th} = v_{th}/c`.
+      For example, this might be ``u_th = sqrt(T*q_e/mass)/clight`` given the temperature (in eV) and mass.
       It requires the following arguments:
 
       * ``<species_name>.momentum_function_ux_m(x,y,z)``: mean :math:`u_{x}`

Examples/Tests/collision/analysis_collision_3d.py

@@ -111,4 +111,4 @@
                                           dim, species_name)
 
 test_name = os.path.split(os.getcwd())[1]
-checksumAPI.evaluate_checksum(test_name, fn, do_particles=False)
+checksumAPI.evaluate_checksum(test_name, fn)

Examples/Tests/nuclear_fusion/analysis_deuterium_deuterium_3d_intraspecies.py

@@ -47,7 +47,9 @@
 
 sigma_th = 2.603e-18
 error = np.abs(sigma-sigma_th)/sigma_th
-tolerance = 1e-2
+tolerance = 2e-2
+print('error = ', error)
+print('tolerance = ', tolerance)
 assert error < tolerance
 
 # Compare checksums with benchmark

Examples/Tests/nuclear_fusion/inputs_deuterium_deuterium_3d_intraspecies

@@ -8,6 +8,8 @@
 #     plasma simulations. Journal of Computational Physics, 388, pp.439-453.
 #     DOI: https://doi.org/10.1016/j.jcp.2019.03.020
 
+warpx.random_seed = 1034958209
+
 # algo
 algo.particle_shape = 3
 

Python/setup.py

@@ -59,7 +59,7 @@
       package_dir = {'pywarpx': 'pywarpx'},
       description = """Wrapper of WarpX""",
       package_data = package_data,
-      install_requires = ['numpy', 'picmistandard==0.28.0', 'periodictable'],
+      install_requires = ['numpy', 'picmistandard==0.29.0', 'periodictable'],
       python_requires = '>=3.8',
       zip_safe=False
 )

Regression/Checksum/benchmarks_json/Deuterium_Deuterium_Fusion_3D_intraspecies.json

@@ -1,34 +1,34 @@
 {
   "lev=0": {
     "rho": 0.0,
-    "rho_deuterium": 8203144355.71195,
-    "rho_helium3": 10.368009592276463
+    "rho_deuterium": 8203144355.767546,
+    "rho_helium3": 10.312416024595505
   },
   "neutron": {
-    "particle_momentum_x": 2.2543499835759282e-15,
-    "particle_momentum_y": 2.2526527390783875e-15,
-    "particle_momentum_z": 2.2619641737859965e-15,
-    "particle_position_x": 61.961041864660686,
-    "particle_position_y": 61.78141653674165,
-    "particle_position_z": 61.741022731492514,
-    "particle_weight": 505562702.7678892
+    "particle_momentum_x": 2.260586487910896e-15,
+    "particle_momentum_y": 2.2564723094408887e-15,
+    "particle_momentum_z": 2.263164930227645e-15,
+    "particle_position_x": 62.03084683414219,
+    "particle_position_y": 61.95011296352698,
+    "particle_position_z": 62.02404756675538,
+    "particle_weight": 502851860.91505826
   },
   "deuterium": {
-    "particle_momentum_x": 1.3370046499332103e-14,
-    "particle_momentum_y": 1.3364310231320824e-14,
-    "particle_momentum_z": 1.3372728873714894e-14,
-    "particle_position_x": 2560.1613417364665,
-    "particle_position_y": 2560.082464065988,
-    "particle_position_z": 2560.0018477161034,
-    "particle_weight": 7.999999989888742e+17
+    "particle_momentum_x": 1.3380470537895298e-14,
+    "particle_momentum_y": 1.3367685546044215e-14,
+    "particle_momentum_z": 1.3372922616599391e-14,
+    "particle_position_x": 2559.782513518522,
+    "particle_position_y": 2559.8747993471684,
+    "particle_position_z": 2560.2864832238383,
+    "particle_weight": 7.999999989942968e+17
   },
   "helium3": {
-    "particle_momentum_x": 2.2749239620327265e-15,
-    "particle_momentum_y": 2.268697031603961e-15,
-    "particle_momentum_z": 2.278045756364995e-15,
-    "particle_position_x": 61.961041864660686,
-    "particle_position_y": 61.78141653674165,
-    "particle_position_z": 61.741022731492514,
-    "particle_weight": 505562702.7678892
+    "particle_momentum_x": 2.278275200450756e-15,
+    "particle_momentum_y": 2.2738610200497133e-15,
+    "particle_momentum_z": 2.2792408973056887e-15,
+    "particle_position_x": 62.03084683414219,
+    "particle_position_y": 61.95011296352698,
+    "particle_position_z": 62.02404756675538,
+    "particle_weight": 502851860.91505826
   }
-}
+}

Regression/Checksum/benchmarks_json/collisionISO.json

@@ -11,12 +11,12 @@
     "jz": 0.0
   },
   "electron": {
-    "particle_momentum_x": 3.579130200773753e-19,
-    "particle_momentum_y": 3.5788119408700804e-19,
-    "particle_momentum_z": 3.584163522201744e-19,
-    "particle_position_x": 1.024188253213835,
-    "particle_position_y": 1.0238795904737117,
-    "particle_position_z": 1.02399735048655,
+    "particle_momentum_x": 3.579989064013309e-19,
+    "particle_momentum_y": 3.5822945977746767e-19,
+    "particle_momentum_z": 3.579753452653627e-19,
+    "particle_position_x": 1.0241322532163375,
+    "particle_position_y": 1.0238995904625479,
+    "particle_position_z": 1.02402135051502,
     "particle_weight": 714240000000.0
   }
 }

Regression/Checksum/benchmarks_json/collisionXYZ.json

@@ -6,7 +6,25 @@
     "Ex": 0.0,
     "Ey": 0.0,
     "Ez": 0.0,
-    "T_electron": 353384.4616461907,
-    "T_ion": 348277.2774202612
+    "T_electron": 353604.6247926339,
+    "T_ion": 347976.6168136309
+  },
+  "electron": {
+    "particle_momentum_x": 8.370755929299189e-19,
+    "particle_momentum_y": 8.228112213603589e-19,
+    "particle_momentum_z": 8.204295817378347e-19,
+    "particle_position_x": 21284971.94721422,
+    "particle_position_y": 21212829.42991966,
+    "particle_position_z": 21214774.536558084,
+    "particle_weight": 7.168263344048695e+28
+  },
+  "ion": {
+    "particle_momentum_x": 2.0074097598289766e-18,
+    "particle_momentum_y": 1.8203553942782305e-18,
+    "particle_momentum_z": 1.823420185235695e-18,
+    "particle_position_x": 21227192.857240494,
+    "particle_position_y": 21286501.692027714,
+    "particle_position_z": 21245587.6706009,
+    "particle_weight": 7.168263344048695e+28
   }
 }

Regression/WarpX-GPU-tests.ini

@@ -60,7 +60,7 @@ emailBody = Check https://ccse.lbl.gov/pub/GpuRegressionTesting/WarpX/ for more
 
 [AMReX]
 dir = /home/regtester/git/amrex/
-branch = 24.07
+branch = dcb9cc0383dcc71e38dee9070574e325a812f8bf
 
 [source]
 dir = /home/regtester/git/WarpX