ORNL-Fusion · tyounkin · Dec 12, 2023 · Dec 15, 2023 · Dec 15, 2023 · Jan 8, 2024
diff --git a/CMake/compile_time_options.cmake b/CMake/compile_time_options.cmake
@@ -6,7 +6,7 @@ set( CMAKE_BUILD_TYPE "Release" )
 
 # preprocessor definitions in source code are defined below:
 set( description "(no description added yet)" )
-set( GITR_USE_CUDA 0 CACHE STRING "${description}" FORCE )
+set( GITR_USE_CUDA 1 CACHE STRING "${description}" FORCE )
 set( GITR_USE_OPENMP 0 CACHE STRING "${description}" FORCE )
 set( GITR_USE_MPI 0 CACHE STRING "${description}" FORCE )
 set( GITR_USE_DOUBLE 1 CACHE STRING "${description}" FORCE )

diff --git a/CMake/crosslink_components.cmake b/CMake/crosslink_components.cmake
@@ -76,6 +76,7 @@ target_link_libraries( GITR
                        spectroscopy
                        libconfig_cxx
                        libconfig_c
+                       particle_diagnostics
                        utils
                        boris
                        surface_model
@@ -158,15 +159,15 @@ target_link_libraries( coulomb_tests
                        Catch2::Catch2WithMain
                        )
 
-target_link_libraries( file_io_tests
-                       libconfig_cxx
-                       libconfig_c
-                       flags
-                       utils
-                       boris
-                       geometry_check
-                       Catch2::Catch2WithMain
-                       )
+#target_link_libraries( file_io_tests
+#                       libconfig_cxx
+#                       libconfig_c
+#                       flags
+#                       utils
+#                       boris
+#                       geometry_check
+#                       Catch2::Catch2WithMain
+#                       )
 
 target_link_libraries( interpolator_tests Catch2::Catch2WithMain )
 

diff --git a/CMake/define_source_components.cmake b/CMake/define_source_components.cmake
@@ -31,6 +31,7 @@ set( non_gpu_targets
 
 # conditionally compile as GPU targets
 set( gpu_targets
+     particle_diagnostics
      surface_model
      interp2d
      interpRateCoeff

diff --git a/CMake/define_test_components.cmake b/CMake/define_test_components.cmake
@@ -15,8 +15,8 @@ set( gpu_test_targets
      cross_field_diffusion_tests
      atomic_tests
      coulomb_tests
-     file_io_tests
      )
+     #file_io_tests
 
 foreach( component IN LISTS cpu_test_targets )
 

diff --git a/CMake/enforce_build_order.cmake b/CMake/enforce_build_order.cmake
@@ -12,6 +12,7 @@ if( dependencies )
 
 endif()
 
+add_dependencies( boris particle_diagnostics )
 # ensure that all source targets are built before GITR
 add_dependencies( GITR ${non_gpu_targets} ${gpu_targets} )
 

diff --git a/build.sh b/build.sh
@@ -1,12 +1,12 @@
-cmake -S $1 -B $2 -G Ninja \
--DNETCDF_C_HEADERS_DIR="/home/5n4/build_right/external/netcdf-c-install/include" \
--DNETCDF_CXX_HEADERS_DIR="/home/5n4/build_right/external/netcdf-cxx4-install/include" \
--DNETCDF_C_SHARED_LIB_DIR="/home/5n4/build_right/external/netcdf-c-install/lib" \
--DNETCDF_CXX_SHARED_LIB_DIR="/home/5n4/build_right/external/netcdf-cxx4-install/lib" \
--DLIBCONFIG_C_HEADERS_DIR="/home/5n4/build_right/external/libconfig_install/include" \
--DLIBCONFIG_CXX_HEADERS_DIR="/home/5n4/build_right/external/libconfig_install/include" \
--DLIBCONFIG_C_LIB_DIR="/home/5n4/build_right/external/libconfig_install/lib" \
--DLIBCONFIG_CXX_LIB_DIR="/home/5n4/build_right/external/libconfig_install/lib" \
+cmake -S $1 -B $2 \
+-DNETCDF_C_HEADERS_DIR="/opt/cray/pe/netcdf/4.9.0.9/nvidia/23.3/include" \
+-DNETCDF_CXX_HEADERS_DIR="/opt/cray/pe/netcdf/4.9.0.9/nvidia/23.3/include" \
+-DNETCDF_C_SHARED_LIB_DIR="/opt/cray/pe/netcdf/4.9.0.9/nvidia/23.3/lib" \
+-DNETCDF_CXX_SHARED_LIB_DIR="/opt/cray/pe/netcdf/4.9.0.9/nvidia/23.3/lib" \
+-DLIBCONFIG_C_HEADERS_DIR="/global/homes/t/tyounkin/code/libconfigBuild/gnu/include" \
+-DLIBCONFIG_CXX_HEADERS_DIR="/global/homes/t/tyounkin/code/libconfigBuild/gnu/include" \
+-DLIBCONFIG_C_LIB_DIR="/global/homes/t/tyounkin/code/libconfigBuild/gnu/lib" \
+-DLIBCONFIG_CXX_LIB_DIR="/global/homes/t/tyounkin/code/libconfigBuild/gnu/lib" \
 &> $2/cmake_output.txt ;
 
-cmake --build $2 -- -j 0 &> $2/build_output.txt
+cmake --build $2 -- -j &> $2/build_output.txt
diff --git a/build/make_gitr.sh b/build/make_gitr.sh
@@ -0,0 +1,29 @@
+#!/bin/bash
+source ../env.default.sh
+
+cmake -DTHRUST_INCLUDE_DIR=$THRUST_DIR \
+  -DNETCDF_CXX_INCLUDE_DIR=$NETCDFCXX4INCLUDE \
+  -DNETCDF_CXX_LIBRARY=$NETCDFCXX4LIB \
+  -DLIBCONFIG_INCLUDE_DIR=$LIBCONFIG_INCLUDE_DIR \
+  -DLIBCONFIGPP_LIBRARY=$LIBCONFIGLIB \
+  -DLIBCONFIGPP_INCLUDE_DIR=$LIBCONFIG_INCLUDE_DIR \
+  -DNETCDF_DIR=$NETCDFDIR \
+  -DNETCDF_INCLUDE_DIR=$NETCDFINCLUDE \
+  -DNETCDF_LIBRARY=$NETCDFLIB \
+  -DUSE_CUDA=1 \
+  -DUSE_MPI=0 \
+  -DUSE_DOUBLE=1 \
+    ..
+#    -DNETCDF_CXX_INCLUDE_DIR=$NETCDFCXX4INCLUDE \
+#    -DNETCDF_CXX_LIBRARY=$NETCDFLIB_CPP \
+#    -DNETCDF_DIR=$NETCDFDIR \
+#    -DNETCDF_INCLUDE_DIR=$NETCDFINCLUDE \
+#    -DNETCDF_LIBRARY=$NETCDFLIB \
+#    -DLIBCONFIGPP_LIBRARY=$LIBCONFIGLIB \
+#    -DLIBCONFIGPP_INCLUDE_DIR=$LIBCONFIG_INCLUDE_DIR \
+#    -DCPPFLAGS=-I${H5DIR}/include \
+#    -DLDFLAGS=${H5DIR}/lib/libhdf5.dylib \
+#    -DHDF5_LIBRARIES=${H5DIR}/lib/libhdf5.a \
+#    -DHDF5_INCLUDE_DIRS=${H5DIR}/include \
+#    -DHDF5_C_COMPILER_EXECUTABLE=${H5DIR}/bin/h5pcc \
+#    -DHDF5_HL_LIBRARIES=${H5DIR}/lib/libhdf5_hl.dylib \
diff --git a/containers/run_podman_noninteractive.sh b/containers/run_podman_noninteractive.sh
@@ -0,0 +1,5 @@
+podman-hpc run -i -t --rm \
+--name gitr_container \
+--gpu \
+-v $(pwd):/host \
+docker.io/stonecoldhughes/gitr:noninteractive
diff --git a/dependencies/build_all_dependencies.sh b/dependencies/build_all_dependencies.sh
@@ -1,4 +1,4 @@
-export GITR_TOP_LEVEL=~/trash
+export GITR_TOP_LEVEL=$PWD
 ./build_zlib.sh
 ./build_m4.sh
 ./build_hdf5.sh

diff --git a/env.default.sh b/env.default.sh
diff --git a/examples/circle/input/gitrGeometry.cfg b/examples/circle/input/gitrGeometry.cfg
@@ -0,0 +1,56 @@
+geom =
+{
+    x1 =
+    [
+        -10000.0
+    ];
+    z1 =
+    [
+        0.0
+    ];
+    x2 =
+    [
+        10000.0
+    ];
+    z2 =
+    [
+        0.0
+    ];
+    slope =
+    [
+        0.0
+    ];
+    intercept =
+    [
+        0.0
+    ];
+    length =
+    [
+        20000.0
+    ];
+    Z =
+    [
+        1.0,
+        1.0
+    ];
+    surface =
+    [
+        1
+    ];
+    inDir =
+    [
+        -1
+    ];
+    potential =
+    [
+        25
+    ];
+    y1 = -10000.0;
+    y2 = 10000.0;
+    periodic = 0;
+    theta0 = 0.0;
+    theta1 = 0.0;
+    periodic_bc_x0 = -10000.0;
+    periodic_bc_x1 = 100000.0;
+    periodic_bc_x = 0;
+};
-Original file line number
+Diff line change
@@ Expand Up / @@ -12,6 +12,7 @@ if( dependencies ) @@
     endif()
+    add_dependencies( boris particle_diagnostics )
     # ensure that all source targets are built before GITR
     add_dependencies( GITR ${non_gpu_targets} ${gpu_targets} )
@@ Expand Down @@