LCM: Enabling Yaml input. (#74)

If Teuchos is compiled with Yaml support, Albany's solver factory and LCM's material database can optionally be read as Yaml files. This is determined by the file extension. If the extension is .xml, the XMl parser for Teuchos ParameterList is invoked. If the extension is .yaml, the Yaml parser is invoked. Add small example (test) specifying the same problem with XML and Yaml formats. The readability of the input using Yaml is significantly improved. Only LCM is tested for this. A cursory search finds that ATO and QCAD call the XML parser for their own purposes. Adding support for the Yaml parser is not difficult, following the example of the LCM material database. Enable Yaml support by default on Fedora.
sandialabs · Feb 25, 2017 · 0827968 · 0827968
1 parent 7e88762
commit 0827968
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Showing 14 changed files with 765 additions and 23 deletions.
diff --git a/CMakeLists.txt b/CMakeLists.txt
@@ -469,8 +469,6 @@ ELSE()
   SET(ALBANY_TEMPUS FALSE)
 ENDIF()
 
-# Check if Trilinos has ROL
-
 # Check if Trilinos has ROL
 LIST(FIND Trilinos_PACKAGE_LIST ROL ROL_List_ID)
 IF (ROL_List_ID GREATER -1)
@@ -495,12 +493,12 @@ IF (ENABLE_ATO)
     MESSAGE("-- ATO  requires LCM...  compiling with -DALBANY_LCM")
     SET(ALBANY_LCM TRUE)
   ENDIF()
-  IF (ENABLE_ALBANY_EPETRA_EXE) 
-    IF (ENABLE_ATO_SOLVER_EPETRA) 
+  IF (ENABLE_ALBANY_EPETRA_EXE)
+    IF (ENABLE_ATO_SOLVER_EPETRA)
       SET(ALBANY_ATO_SOLVER_EPETRA TRUE)
       ADD_DEFINITIONS(-DALBANY_ATO_SOLVER_EPETRA)
       MESSAGE("-- ATO_SOLVER_EPETRA       is Enabled.")
-    ELSE() 
+    ELSE()
       MESSAGE("-- ATO_SOLVER_EPETRA       is disabled.")
     ENDIF()
   ELSE()
@@ -575,22 +573,22 @@ ENDIF()
 OPTION(ENABLE_CISM_INTERFACE "Flag to turn on FELIX Interface to the CISM code" OFF)
 OPTION(ENABLE_CISM_REDUCED_COMM "Flag to turn on reduced communicator for CISM-Albany runs" ON)
 OPTION(ENABLE_CISM_EPETRA "Flag to turn on Epetra for CISM-Albany" OFF)
-OPTION(ENABLE_CISM_CHECK_COMPARISONS "Flag to turn on comparisons checking for CISM-Albany" OFF) 
+OPTION(ENABLE_CISM_CHECK_COMPARISONS "Flag to turn on comparisons checking for CISM-Albany" OFF)
 
 IF (ENABLE_CISM_INTERFACE AND ENABLE_FELIX)
-  IF (ENABLE_CISM_CHECK_COMPARISONS) 
-    ADD_DEFINITIONS(-DCISM_CHECK_COMPARISONS) 
+  IF (ENABLE_CISM_CHECK_COMPARISONS)
+    ADD_DEFINITIONS(-DCISM_CHECK_COMPARISONS)
     MESSAGE("---> CISM_CHECK_COMPARISONS is Enabled, compiling with -DCISM_CHECK_COMPARISONS.  Error will be thrown if comparisons fail for CISM-Albany run.")
-  ELSE()  
-    MESSAGE("---> CISM_CHECK_COMPARISONS is Disabled, NOT compiling with -DCISM_CHECK_COMPARISONS.  Error will NOT be thrown if comparisons fail for CISM-Albany run.  Please be cautious when running ctest from CISM!") 
-  ENDIF() 
-  IF (ENABLE_CISM_REDUCED_COMM) 
+  ELSE()
+    MESSAGE("---> CISM_CHECK_COMPARISONS is Disabled, NOT compiling with -DCISM_CHECK_COMPARISONS.  Error will NOT be thrown if comparisons fail for CISM-Albany run.  Please be cautious when running ctest from CISM!")
+  ENDIF()
+  IF (ENABLE_CISM_REDUCED_COMM)
     ADD_DEFINITIONS(-DREDUCED_COMM)
     MESSAGE("---> CISM_REDUCED_COMM     is Enabled, compiling with -DREDUCED_COMM.  CISM-Albany will use reduced communicator.")
   ENDIF()
-  IF (ENABLE_ALBANY_EPETRA_EXE) 
-    IF (ENABLE_CISM_EPETRA) 
-      ADD_DEFINITIONS(-DCISM_USE_EPETRA) 
+  IF (ENABLE_ALBANY_EPETRA_EXE)
+    IF (ENABLE_CISM_EPETRA)
+      ADD_DEFINITIONS(-DCISM_USE_EPETRA)
       MESSAGE("---> CISM_EPETRA     is Enabled, compiling with -DCISM_USE_EPETRA.  CISM-Albany will run with Epetra software stack.")
      ELSE()
       MESSAGE("---> CISM_EPETRA     is Disabled, NOT compiling with -DCISM_USE_EPETRA.  CISM-Albany will run with Tpetra software stack.")
@@ -828,16 +826,16 @@ ENDIF()
 # Set optional build of MOR (Model Order Reduction) defaults to OFF
 OPTION(ENABLE_MOR "Flag to turn on MOR Source code" OFF)
 IF (ENABLE_MOR)
-  #Check if RBGen library has been built as a part of Anasazi.  
-  #If it has not, turn MOR off despite what user requested and print message explaining that MOR requires RBGen library. 
+  #Check if RBGen library has been built as a part of Anasazi.
+  #If it has not, turn MOR off despite what user requested and print message explaining that MOR requires RBGen library.
   LIST(FIND Trilinos_LIBRARIES rbgen rbgen_List_ID)
   IF (rbgen_List_ID GREATER -1)
     MESSAGE("-- Looking for rbgen library: -- found!  Continuing.")
     ADD_DEFINITIONS(-DALBANY_MOR)
     MESSAGE("-- MOR       is Enabled, compiling with -DALBANY_MOR")
     SET(ALBANY_MOR TRUE)
   ELSE()
-    MESSAGE("---- Looking for rbgen library: -- NOT found!") 
+    MESSAGE("---- Looking for rbgen library: -- NOT found!")
     MESSAGE("-- MOR requires RBGen library.  To turn on, rebuild Trilinos with Anasazi_ENABLE_RBGen turned ON")
     MESSAGE("-- MOR       is NOT Enabled.")
     SET(ALBANY_MOR FALSE)
@@ -1128,8 +1126,8 @@ IF (ENABLE_KOKKOS_UNDER_DEVELOPMENT)
   ADD_DEFINITIONS(-DALBANY_KOKKOS_UNDER_DEVELOPMENT)
   MESSAGE("-- Kokkos development        is Enabled, compiling with -DALBANY_KOKKOS_UNDER_DEVELOPMENT")
   SET(ALBANY_KOKKOS_UNDER_DEVELOPMENT TRUE)
-  IF (ENABLE_CUDA_ERROR_CHECK) 
-    ADD_DEFINITIONS(-DALBANY_CUDA_ERROR_CHECK) 
+  IF (ENABLE_CUDA_ERROR_CHECK)
+    ADD_DEFINITIONS(-DALBANY_CUDA_ERROR_CHECK)
     MESSAGE("-- CUDA Error Check        is Enabled, compiling with -DALBANY_CUDA_ERROR_CHECK")
   ELSE()
     MESSAGE("-- CUDA Error Check        is NOT Enabled.")
@@ -1276,6 +1274,23 @@ COMMENT "Generating API documentation with Doxygen" VERBATIM
 )
 endif(DOXYGEN_FOUND)
 
+# Enable yaml parsing for reading parameters lists
+IF (EXISTS "${Trilinos_INCLUDE_DIRS}/TeuchosCore_config.h")
+  FILE(READ ${Trilinos_INCLUDE_DIRS}/TeuchosCore_config.h CURRENT_CONFIG)
+  STRING(REGEX MATCH "\#define HAVE_TEUCHOSCORE_YAML_CPP" TEUCHOS_YAML_IS_SET ${CURRENT_CONFIG})
+  IF ("#define HAVE_TEUCHOSCORE_YAML_CPP" STREQUAL "${TEUCHOS_YAML_IS_SET}")
+    MESSAGE("-- Looking for YAML in Teuchos: Found, compiling with -DALBANY_YAML")
+    SET(ALBANY_YAML TRUE)
+    ADD_DEFINITIONS(-DALBANY_YAML)
+  ELSE ("#define HAVE_TEUCHOSCORE_YAML_CPP" STREQUAL "${TEUCHOS_YAML_IS_SET}")
+    MESSAGE("-- Looking for YAML in Teuchos: NOT found.")
+    SET(ALBANY_YAML FALSE)
+  ENDIF ("#define HAVE_TEUCHOSCORE_YAML_CPP" STREQUAL "${TEUCHOS_YAML_IS_SET}")
+ELSE (EXISTS "${Trilinos_INCLUDE_DIRS}/TeuchosCore_config.h")
+    MESSAGE("-- Looking for YAML in Teuchos: NOT found.")
+    SET(ALBANY_YAML FALSE)
+ENDIF (EXISTS "${Trilinos_INCLUDE_DIRS}/TeuchosCore_config.h")
+
 ## End of CMake options to Albany
 
 add_subdirectory(src)
@@ -1323,15 +1338,15 @@ IF(ALBANY_MPI)
 ENDIF(ALBANY_MPI)
 
 #Add option to run any pretest executables in a specific environment (mpiexec.hydra, srun, or other)
-IF (DEFINED ALBANY_PRETEST_EXEC) 
+IF (DEFINED ALBANY_PRETEST_EXEC)
   MESSAGE("-- ALBANY_PRETEST_EXEC is ${ALBANY_PRETEST_EXEC}")
 ELSE()
   # Not set in configure - set it to be empty
   SET(ALBANY_PRETEST_EXEC "" CACHE STRING "Command to use to execute pretests")
 ENDIF()
 
 #Add option to specify path to desired SEACAS utils
-IF (DEFINED ALBANY_SEACAS_PATH) 
+IF (DEFINED ALBANY_SEACAS_PATH)
   MESSAGE("-- ALBANY_SEACAS_PATH is ${ALBANY_SEACAS_PATH}")
 ENDIF()
 

diff --git a/doc/LCM/build/trilinos-config.sh b/doc/LCM/build/trilinos-config.sh
@@ -52,7 +52,7 @@ cmake \
  \
  -D Teuchos_ENABLE_STACKTRACE:BOOL=OFF \
  -D Teuchos_ENABLE_DEFAULT_STACKTRACE:BOOL=OFF \
- -D HAVE_INTREPID_KOKKOSCORE:BOOL=ON \
+ -D TeuchosCore_ENABLE_yaml-cpp:BOOL=ON \
  -D Kokkos_ENABLE_CXX11:BOOL=ON \
  -D Kokkos_ENABLE_Cuda_UVM:BOOL=lcm_enable_uvm \
  -D Kokkos_ENABLE_EXAMPLES:BOOL=lcm_enable_kokkos_examples \

diff --git a/examples/LCM/CMakeLists.txt b/examples/LCM/CMakeLists.txt
@@ -49,6 +49,9 @@ IF(ALBANY_SEACAS)
   add_subdirectory(ThermoMechanicalContact)
   add_subdirectory(BoreDemo)
   add_subdirectory(RigidBody)
+  IF(ALBANY_YAML)
+    add_subdirectory(YamlInput)
+  ENDIF()
   IF(ALBANY_EPETRA)
     add_subdirectory(HMC)
   ENDIF()

diff --git a/examples/LCM/YamlInput/CMakeLists.txt b/examples/LCM/YamlInput/CMakeLists.txt
@@ -0,0 +1,26 @@
+##*****************************************************************//
+##    Albany 3.0:  Copyright 2016 Sandia Corporation               //
+##    This Software is released under the BSD license detailed     //
+##    in the file "license.txt" in the top-level Albany directory  //
+##*****************************************************************//
+
+# Copy Input file from source to binary dir
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cuboid.g
+               ${CMAKE_CURRENT_BINARY_DIR}/cuboid.g COPYONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cuboid.xml
+               ${CMAKE_CURRENT_BINARY_DIR}/cuboid.xml COPYONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/cuboid.yaml
+               ${CMAKE_CURRENT_BINARY_DIR}/cuboid.yaml COPYONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/materials.xml
+               ${CMAKE_CURRENT_BINARY_DIR}/materials.xml COPYONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/materials.yaml
+               ${CMAKE_CURRENT_BINARY_DIR}/materials.yaml COPYONLY)
+configure_file(${CMAKE_CURRENT_SOURCE_DIR}/runtest.py
+               ${CMAKE_CURRENT_BINARY_DIR}/runtest.py COPYONLY)
+
+# Create symlink to AlbanyT
+execute_process(COMMAND ${CMAKE_COMMAND} -E create_symlink
+  ${AlbanyTPath} ${CMAKE_CURRENT_BINARY_DIR}/AlbanyT)
+get_filename_component(testName ${CMAKE_CURRENT_SOURCE_DIR} NAME)
+# Create the test with this name and standard executable
+add_test(NAME ${testName} COMMAND "python" "runtest.py")
diff --git a/examples/LCM/YamlInput/cuboid.g b/examples/LCM/YamlInput/cuboid.g