Release 3.0.2 (#42)

* Enable remap in RZ geometry.
* Add analysis application for particle remap.
* Improve numeric tolerances consistency between Tangram and Portage.
* Propagate recent fixes from R3D.
* Fix CI issues.
* Fix for IBM XL compiler.
* Fix slope limiter in multi-material cells.

CMakeLists.txt

@@ -62,6 +62,14 @@ endif()
 #------------------------------------------------------------------------------#
 option(ENABLE_APP_TIMINGS "Enable timings" OFF)
 
+#------------------------------------------------------------------------------#
+# Enable PORTAGE_DEBUG flag
+#------------------------------------------------------------------------------#
+option(PORTAGE_DEBUG "Additional checks will be performed and info printed" OFF)
+if (PORTAGE_DEBUG)
+  add_definitions(-DPORTAGE_DEBUG)
+endif()
+
 #----------------------------------------------------------------------------
 # Find packages here and set CMake variables. Set link dependencies
 # and compile definitions for portage_support target in

README.md

@@ -213,8 +213,8 @@ Thrust and TCMalloc in your build.  The cmake command for this is:
 
 INTEL_VERSION=18.0.5
 MPI_VERSION=2.1.2
-WONTON_VERSION=1.2.8
-TANGRAM_VERSION=1.0.4
+WONTON_VERSION="dev"
+TANGRAM_VERSION="dev"
 
 TPL_PREFIX=/usr/projects/ngc/private
 
@@ -249,8 +249,8 @@ export MODULEPATH=""
 
 INTEL_VERSION=18.0.1
 MPI_VERSION=2.1.2
-WONTON_VERSION=1.2.8
-TANGRAM_VERSION=1.0.4
+WONTON_VERSION="dev"
+TANGRAM_VERSION="dev"
 
 TPL_PREFIX=/usr/local/codes/ngc/private
 

app/CMakeLists.txt

@@ -14,6 +14,7 @@ add_subdirectory(simple_mesh_app)
 add_subdirectory(swarmapp)
 add_subdirectory(msmapp)
 add_subdirectory(momentumapp)
+add_subdirectory(particle-analysis)
 
 option(ENABLE_APP_TIMINGS "Enable timing in apps" OFF)
 

app/momentumapp/MomentumRemap_mm.h

@@ -131,10 +131,11 @@ void MomentumRemap_mm<D, Mesh_Wrapper, State_Wrapper>::InitMaterials(
   double dst_tol = 100 * std::numeric_limits<double>::epsilon();
   double vol_tol = 100 * std::numeric_limits<double>::epsilon();
 
-  get_material_moments<Mesh_Wrapper>(mesh, material_IDs, 
-    circle_cen, circle_rad, nquadrant_samples,
-    cell_num_mats, cell_mat_ids, cell_mat_volfracs, cell_mat_centroids, 
-    vol_tol, dst_tol, false);  
+  get_material_moments<Mesh_Wrapper, Wonton::CartesianCoordinates>(
+      mesh,material_IDs, 
+      circle_cen, circle_rad, nquadrant_samples,
+      cell_num_mats, cell_mat_ids, cell_mat_volfracs, cell_mat_centroids, 
+      vol_tol, dst_tol, false);  
 
   // Count the number of local materials and gather their IDs
   std::set<int> mat_ids;

app/momentumapp/test/CMakeLists.txt

@@ -7,11 +7,11 @@ message(STATUS "Adding momentum remap test")
 
 # this app can be run in serial or mpi mode - set an environment
 # variable so that either will work
-if(ENABLE_MPI)
+if(WONTON_ENABLE_MPI)
   set(RUN_COMMAND "mpirun -np 1")
 else()
   set(RUN_COMMAND "")
-endif(ENABLE_MPI)
+endif(WONTON_ENABLE_MPI)
 
 macro(ADD_MOMENTUM_TEST DIM TEST_NUM)
   file(COPY momentumapp${DIM}_test${TEST_NUM}.sh

app/momentumapp/test/errorsMM_gold0.txt

@@ -1,6 +1,6 @@
-0 1.11022e-15
-1 6.66134e-16
-2 0.0156782
+0 6.66134e-16
+1 1.48952e-15
+2 0.0154166
 3 1.62945
 4 0.124934
-5 0.112769
+5 0.113188

app/msmapp/CMakeLists.txt

@@ -29,9 +29,9 @@ if (WONTON_ENABLE_MPI AND WONTON_ENABLE_Jali)
     target_link_libraries(msmapp PRIVATE ${VTUNE_LIB})
   endif(ENABLE_PROFILE)
 
-
-  #if (ENABLE_APP_TESTS)
-  #  add_subdirectory(test)
-  #endif (ENABLE_APP_TESTS)
+  # add app tests if needed
+  if (ENABLE_APP_TESTS)
+    add_subdirectory(test)
+  endif (ENABLE_APP_TESTS)
 
 endif ()

app/msmapp/msmapp.cc

@@ -319,6 +319,10 @@ class runMSM {
     //Check the answer
     double totmerr=0., totserr=0., totint=0.;
 
+    //Create a diagnostics vector solely for the purpose of outputing to
+    //a file so we can run an app test
+    std::vector<double> diagnostics(6);
+
     auto& cellvecout = std::static_pointer_cast<Wonton::StateVectorUni<>>(targetStateWrapper.get("celldata"))->get_data();
     auto& cellvecout2 = std::static_pointer_cast<Wonton::StateVectorUni<>>(targetStateWrapper2.get("celldata"))->get_data();
     auto& nodevecout = std::static_pointer_cast<Wonton::StateVectorUni<>>(targetStateWrapper.get("nodedata"))->get_data();
@@ -354,10 +358,14 @@ class runMSM {
         totmerr = std::max(totmerr, std::fabs(merror));
         totserr = std::max(totserr, std::fabs(serror));
       }
-
+      
       std::printf("\n\nLinf NORM OF MM CELL ERROR: %le\n\n", totmerr);
       std::printf("\n\nLinf NORM OF MSM CELL ERROR: %le\n\n", totserr);
 
+      //Update diagnostics
+      diagnostics[0]=totmerr;
+      diagnostics[1]=totserr;
+
       if (controls_.print_detail == 1) {
         if (Dimension==2) {
           std::printf("Node Node-coord-1-2 Exact Mesh-Mesh Error Mesh-Swarm-Mesh Error\n");
@@ -391,6 +399,10 @@ class runMSM {
 
       std::printf("\n\nLinf NORM OF MM NODE ERROR: %lf\n\n", totmerr);
       std::printf("\n\nLinf NORM OF MSM NODE ERROR: %lf\n\n", totserr);
+
+      //Update diagnostics
+      diagnostics[2]=totmerr;
+      diagnostics[3]=totserr;
     }
 
     if (controls_.print_detail == 1) {
@@ -443,6 +455,12 @@ class runMSM {
     }        
 
     std::printf("\n\nLinf NORM OF MSM CELL ERROR: %le\n\n", totserr);
+    if (oper8tor == Portage::Meshfree::oper::VolumeIntegral)
+      std::printf("\n\nTOTAL INTEGRAL: %le\n\n", totint);
+
+    //Update diagnostics
+    diagnostics[4]=totserr;
+
     if (oper8tor == Portage::Meshfree::oper::VolumeIntegral)
       std::printf("\n\nTOTAL INTEGRAL: %le\n\n", totint);
 
@@ -474,7 +492,19 @@ class runMSM {
     }
 
     std::printf("\n\nLinf NORM OF MSM NODE ERROR: %lf\n\n", totserr);
+
+    //Update diagnostics
+    diagnostics[5]=totserr;
 
+
+    //Print diagnostics to a file
+    std::ofstream file("diagnostics.dat");
+    file << std::scientific;
+    file.precision(13);
+    for (auto&& value : diagnostics) {
+	      file << "-1 " << value <<std::endl;
+    }
+    file.close();
   }
 
   //Constructor
@@ -757,6 +787,9 @@ class runMSMJali {
     if (oper8tor == Portage::Meshfree::oper::VolumeIntegral)
       std::printf("\n\nTOTAL INTEGRAL: %le\n\n", totint);
 
+    if (oper8tor == Portage::Meshfree::oper::VolumeIntegral)
+      std::printf("\n\nTOTAL INTEGRAL: %le\n\n", totint);
+
     if (controls_.print_detail == 1) {
       if (Dimension==2) {
         std::printf("Node Node-coord-1-2 Exact Mesh-Swarm-Mesh Error\n");
@@ -817,10 +850,10 @@ void print_usage() {
     number source cells, int:        28 32 20\n\
     number target cells, int:        26 30 23\n\
     order, int, choice of 1 or 2:           2\n\
-    example, int, choice of -1...3:         3\n\
+    example, int, choice of -2...3:         3\n\
     double, smoothing factor:             1.5\n\
     double, boundary factor:              0.5\n\
-    string, part id field:             a_name\n\
+    string, part id field:   a_name (or NONE)\n\
     double, part id tolerance:          0.125\n\
     print detail, choice of 0 or 1:         1\n\
     geometry:                        tensor  \n\
@@ -1011,4 +1044,8 @@ int main(int argc, char** argv) {
   } else {
     runjob<3>(ctl, filename);
   }
+
+#ifdef WONTON_ENABLE_MPI
+  MPI_Finalize();
+#endif
 }

app/msmapp/test/CMakeLists.txt

@@ -0,0 +1,27 @@
+#
+# This file is part of the Ristra portage project.
+# Please see the license file at the root of this repository, or at:
+#     https://github.com/laristra/portage/blob/master/LICENSE
+#
+
+if (WONTON_ENABLE_MPI)
+
+  message(STATUS "Adding msmapp test")
+
+  # copy run script, input parameters, and gold files
+  file(GLOB data
+       "run.sh"
+       "example_input"
+       "gold/gold_diagnostics.dat")
+
+  file(COPY ${data} DESTINATION ${CMAKE_CURRENT_BINARY_DIR})
+
+  # add tests
+  add_test(NAME "test_msmapp" COMMAND ./run.sh)
+
+  set_property(TEST "test_msmapp"
+	       PROPERTY ENVIRONMENT
+               ROOT_DIR=${CMAKE_BINARY_DIR}/app/msmapp
+               COMPARE=${CMAKE_BINARY_DIR}/app/apptest_cmp/apptest_cmp)
+
+endif()

app/msmapp/test/gold/gold_diagnostics.dat

@@ -0,0 +1,6 @@
+-1 4.3291634482639e+00
+-1 2.7228090924636e-03
+-1 7.3670204276142e+00
+-1 2.5319967415767e-03
+-1 2.7228090924636e-03
+-1 2.5319967415767e-03

app/msmapp/test/run.sh

@@ -0,0 +1,14 @@
+#!/bin/bash
+
+# This file is part of the Ristra portage project.
+# Please see the license file at the root of this repository, or at:
+# https://github.com/laristra/portage/blob/master/LICENSE
+
+set -e
+set -x
+
+epsilon=1.e-10
+
+mpirun -np 1 ${ROOT_DIR}/msmapp "${ROOT_DIR}/test/example_input"
+
+${COMPARE} "gold_diagnostics.dat" "diagnostics.dat" ${epsilon}

app/part-by-part/CMakeLists.txt

@@ -5,7 +5,7 @@
 # ------------------------------------------------------------------------------
 
 # cannot build jali apps without MPI.
-if (WONTON_ENABLE_MPI AND WONTON_ENABLE_MPI)
+if (WONTON_ENABLE_Jali AND WONTON_ENABLE_MPI)
 
     # create binary
     add_executable(part-remap part-remap.cc)

app/particle-analysis/CMakeLists.txt

@@ -0,0 +1,18 @@
+# ------------------------------------------------------------------------------
+# This file is part of the Ristra portage project.
+# Please see the license file at the root of this repository, or at:
+#    https://github.com/laristra/portage/blob/master/LICENSE
+# ------------------------------------------------------------------------------
+
+if (WONTON_ENABLE_MPI)
+  # create binary
+  add_executable(particle-analysis remap.cc)
+
+  # link to portage and its dependencies
+  target_link_libraries(particle-analysis PRIVATE portage)
+
+  # build tests as well
+  if (ENABLE_APP_TESTS)
+    add_subdirectory(test)
+  endif()
+endif()