Merge pull request #350 from PrincetonUniversity/issue-309-meshfem3d

Issue 309 meshfem3d

CMakeLists.txt

@@ -17,6 +17,12 @@ set(NUM_CHUNKS 1)
 set(NUM_THREADS 160)
 set(NUM_VECTOR_LANES 1)
 
+# Set binary output directories.
+set(CMAKE_LIBRARY_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/lib)
+set(CMAKE_ARCHIVE_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/archive)
+set(CMAKE_RUNTIME_OUTPUT_DIRECTORY ${CMAKE_BINARY_DIR}/bin)
+
+
 if (SPECFEMPP_ENABLE_PYTHON)
     message("-- Adding -fPIC flag for Python binding.")
     if(CMAKE_CXX_COMPILER_ID STREQUAL "IntelLLVM")
@@ -121,7 +127,8 @@ configure_file(constants.hpp.in constants.hpp)
 include_directories(include)
 include_directories(${CMAKE_BINARY_DIR})
 
-add_subdirectory(meshfem2d)
+add_subdirectory(fortran/meshfem2d)
+add_subdirectory(fortran/meshfem3d)
 
 if (ENABLE_SIMD)
         message("-- Enabling SIMD")

docs/cookbooks/example_01.rst

@@ -25,11 +25,11 @@ If the above command returns a path to the ``specfem2d`` executable, then the bu
 
 .. code:: bash
 
-    export PATH=$PATH:<PATH TO SPECFEM++ BUILD DIRECTORY>
+    export PATH=$PATH:<PATH TO SPECFEM++ BUILD DIRECTORY/bin>
 
 .. note::
 
-    Make sure to replace ``<PATH TO SPECFEM++ BUILD DIRECTORY>`` with the actual path to the SPECFEM++ build directory on your system.
+    Make sure to replace ``<PATH TO SPECFEM++ BUILD DIRECTORY/bin>`` with the actual path to the SPECFEM++ build directory on your system.
 
 Now let's create the necessary directories to store the input files and output artifacts.
 

docs/cookbooks/example_02.rst

@@ -23,11 +23,11 @@ If the above command returns a path to the ``specfem2d`` executable, then the bu
 
 .. code:: bash
 
-    export PATH=$PATH:<PATH TO SPECFEM++ BUILD DIRECTORY>
+    export PATH=$PATH:<PATH TO SPECFEM++ BUILD DIRECTORY/bin>
 
 .. note::
 
-    Make sure to replace ``<PATH TO SPECFEM++ BUILD DIRECTORY>`` with the actual path to the SPECFEM++ build directory on your system.
+    Make sure to replace ``<PATH TO SPECFEM++ BUILD DIRECTORY/bin>`` with the actual path to the SPECFEM++ build directory on your system.
 
 Now let's create the necessary directories to store the input files and output artifacts.
 

docs/cookbooks/example_03.rst

@@ -25,11 +25,11 @@ If the above command returns a path to the ``specfem2d`` executable, then the bu
 
 .. code:: bash
 
-    export PATH=$PATH:<PATH TO SPECFEM++ BUILD DIRECTORY>
+    export PATH=$PATH:<PATH TO SPECFEM++ BUILD DIRECTORY/bin>
 
 .. note::
 
-    Make sure to replace ``<PATH TO SPECFEM++ BUILD DIRECTORY>`` with the actual path to the SPECFEM++ build directory on your system.
+    Make sure to replace ``<PATH TO SPECFEM++ BUILD DIRECTORY/bin>`` with the actual path to the SPECFEM++ build directory on your system.
 
 Now let's create the necessary directories to store the input files and output artifacts.
 

docs/getting_started/installation.rst

@@ -54,7 +54,7 @@ Finally, once compiled you could run SPECFEM++ from inside the build directory,
 
 .. code-block:: bash
 
-    export PATH=${PATH}:<location to build directory>
+    export PATH=${PATH}:<location to SPECFEM++ build directory/bin>
 
 Testing Installation
 =====================

examples/fluid-solid-interface/Snakefile

@@ -54,8 +54,8 @@ rule run_solver:
         runtime=10,
     shell:
         """
-            module purge
-            module load boost/1.73.0
+            # module purge
+            # module load boost/1.73.0
             mkdir -p OUTPUT_FILES/results
             echo "Hostname: $(hostname)" > output.log
             {SPECFEM_BIN} -p {input.config} >> output.log

meshfem2d/CMakeLists.txt → fortran/meshfem2d/CMakeLists.txt

@@ -233,7 +233,7 @@ set( MESHFEM_OBJECTS
 
 add_custom_command(
 	OUTPUT meshfem2D
-	COMMAND ${CMAKE_Fortran_COMPILER} ${FCFLAGS_f90} -o ${CMAKE_BINARY_DIR}/xmeshfem2D ${MESHFEM_OBJECTS} ${MESHFEM_SHARED_OBJECTS}
+	COMMAND ${CMAKE_Fortran_COMPILER} ${FCFLAGS_f90} -o ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/xmeshfem2D ${MESHFEM_OBJECTS} ${MESHFEM_SHARED_OBJECTS}
 	DEPENDS ${MESHFEM_OBJECTS} ${MESHFEM_SHARED_OBJECTS}
 )
 
@@ -242,6 +242,6 @@ add_custom_target(meshfem2D_exec ALL
 )
 
 add_custom_target(xadj_seismogram ALL
-    COMMAND ${CMAKE_Fortran_COMPILER} ${FCFLAGS_f90} -o ${CMAKE_BINARY_DIR}/xadj_seismogram ${CMAKE_CURRENT_SOURCE_DIR}/adj_seismogram.f90
+    COMMAND ${CMAKE_Fortran_COMPILER} ${FCFLAGS_f90} -o ${CMAKE_RUNTIME_OUTPUT_DIRECTORY}/xadj_seismogram ${CMAKE_CURRENT_SOURCE_DIR}/adj_seismogram.f90
     DEPENDS ${CMAKE_CURRENT_SOURCE_DIR}/adj_seismogram.f90
 )

fortran/meshfem3d/.gitignore

@@ -0,0 +1 @@
+*build*

fortran/meshfem3d/CMakeLists.txt

@@ -0,0 +1,25 @@
+# Minimum CMake version required
+cmake_minimum_required(VERSION 3.10)
+
+# Project name and language
+project(MESHFEM3D LANGUAGES Fortran C)
+
+# Set the Fortran standard to 95
+set(CMAKE_Fortran_STANDARD 95)
+set(CMAKE_Fortran_STANDARD_REQUIRED ON)
+
+set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/fortran/meshfem3d/modules)
+include_directories("${CMAKE_BINARY_DIR}/fortran/meshfem3d/modules")
+
+set(ADIOS "OFF" CACHE BOOL "Use ADIOS for I/O")
+
+if (ADIOS)
+  message(STATUS "ADIOS enabled for Meshfem3D Compilation")
+else(ADIOS)
+  message(STATUS "ADIOS disabled for Meshfem3D Compilation")
+endif(ADIOS)
+
+add_subdirectory(setup)
+add_subdirectory(shared)
+add_subdirectory(meshfem3D)
+add_subdirectory(generate_databases)

fortran/meshfem3d/generate_databases/CMakeLists.txt

@@ -0,0 +1,121 @@
+# Minimum CMake version required
+cmake_minimum_required(VERSION 3.10)
+
+# Project name and language
+project(MESHFEM3D_MESHFEM3D LANGUAGES Fortran C)
+
+# Set the Fortran standard to 95
+set(CMAKE_Fortran_STANDARD 95)
+set(CMAKE_Fortran_STANDARD_REQUIRED ON)
+
+set(CMAKE_Fortran_MODULE_DIRECTORY ${CMAKE_BINARY_DIR}/fortran/meshfem3d/modules)
+include_directories("${CMAKE_BINARY_DIR}/fortran/meshfem3d/modules")
+
+set(MESHFEM3D_GENERATE_DATABASES_MODULE
+  calc_jacobian.f90
+  create_mass_matrices.f90
+  create_regions_mesh.f90
+  fault_generate_databases.f90
+  finalize_databases.f90
+  generate_databases_par.F90
+  generate_databases.f90
+  get_absorbing_boundary.F90
+  get_coupling_surfaces.f90
+  get_model.F90
+  get_MPI.f90
+  get_perm_color.f90
+  lts_generate_databases.F90
+  memory_eval.f90
+  model_1d_cascadia.f90
+  model_1d_prem.f90
+  model_1d_socal.f90
+  model_aniso.f90
+  model_coupled.f90
+  model_default.f90
+  model_external_values.F90
+  model_ipati.f90
+  model_gll.f90
+  model_salton_trough.f90
+  model_tomography.f90
+  parse_sep.c
+  pml_set_local_dampingcoeff.f90
+  read_parameters.f90
+  read_partition_files.f90
+  save_arrays_solver.F90
+  setup_color_perm.f90
+  setup_mesh_adjacency.f90
+  setup_mesh.f90
+  wavefield_discontinuity_generate_databases.f90
+)
+
+set(MESHFEM3D_GEN_DB_HDF5_MODULE
+  read_partition_files_hdf5.F90
+  save_arrays_solver_hdf5.F90
+)
+
+if (ADIOS)
+  message(STATUS "ADIOS enabled")
+  list(APPEND MESHFEM3D_GENERATE_DATABASES_MODULE
+          model_gll_adios.F90
+          model_ipati_adios.F90
+          read_partition_files_adios.F90
+          save_arrays_solver_adios.F90
+          save_moho_adios.F90
+  )
+endif(ADIOS)
+
+# Add MPI dependency
+if (MPI_PARALLEL)
+  list(APPEND MESHFEM3D_GENERATE_DATABASES_MODULE model_sep)
+else(MPI_PARALLEL)
+  list(APPEND MESHFEM3D_GENERATE_DATABASES_MODULE model_sep_nompi)
+endif(MPI_PARALLEL)
+
+# Create parameter library module
+add_library(meshfem3D_generate_databases_module generate_databases_par.F90)
+add_library(meshfem3D::generate_databases_module ALIAS meshfem3D_generate_databases_module)
+target_link_libraries(meshfem3D_generate_databases_module PRIVATE meshfem3D::constants meshfem3D::shared_module meshfem3D::shared)
+
+# Create HDF5 module
+message(STATUS "Creating HDF5 module using: ${MESHFEM3D_GEN_DB_HDF5_MODULE}")
+add_library(meshfem3D_generate_databases_hdf5_module
+  ${MESHFEM3D_GEN_DB_HDF5_MODULE}
+)
+add_library(meshfem3D::generate_databases_hdf5_module ALIAS meshfem3D_generate_databases_hdf5_module)
+target_link_libraries(meshfem3D_generate_databases_hdf5_module PRIVATE
+  meshfem3D::shared_hdf5_module
+  meshfem3D::shared_module
+  meshfem3D::generate_databases_module
+)
+
+# Compile library
+add_library(meshfem3D_generate_databases
+  ${MESHFEM3D_GENERATE_DATABASES_MODULE}
+)
+
+add_library(meshfem3D::generate_databases ALIAS meshfem3D_generate_databases)
+target_link_libraries(meshfem3D_generate_databases PRIVATE
+  meshfem3D::generate_databases_module
+  meshfem3D::generate_databases_hdf5_module
+  meshfem3D::shared_module
+  meshfem3D::constants
+  meshfem3D::version
+  meshfem3D::shared_hdf5_module
+  meshfem3D::config
+)
+
+# Create executable
+add_executable(xgenerate_databases generate_databases.f90)
+target_link_libraries(xgenerate_databases PRIVATE
+  meshfem3D::generate_databases_module
+  meshfem3D::generate_databases_hdf5_module
+  meshfem3D::shared
+  meshfem3D::shared_module
+  meshfem3D::mesh_hdf5_module
+  meshfem3D::shared_hdf5_module
+  meshfem3D::shared_adios_module
+  meshfem3D::adios_methods_stubs
+  meshfem3D::param_reader
+  meshfem3D::version
+  meshfem3D::generate_databases
+)

fortran/meshfem3d/generate_databases/Makefile

@@ -0,0 +1,55 @@
+#=====================================================================
+#
+#                         S p e c f e m 3 D
+#                         -----------------
+#
+#     Main historical authors: Dimitri Komatitsch and Jeroen Tromp
+#                              CNRS, France
+#                       and Princeton University, USA
+#                 (there are currently many more authors!)
+#                           (c) October 2017
+#
+# This program is free software; you can redistribute it and/or modify
+# it under the terms of the GNU General Public License as published by
+# the Free Software Foundation; either version 3 of the License, or
+# (at your option) any later version.
+#
+# This program is distributed in the hope that it will be useful,
+# but WITHOUT ANY WARRANTY; without even the implied warranty of
+# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+# GNU General Public License for more details.
+#
+# You should have received a copy of the GNU General Public License along
+# with this program; if not, write to the Free Software Foundation, Inc.,
+# 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+#
+#=====================================================================
+
+DIR = generate_databases
+
+# The rest of this file is generic
+#######################################
+
+####
+#### targets
+####
+
+default:
+	$(MAKE) -C ../.. $(DIR)
+
+all:
+	$(MAKE) -C ../.. all
+
+clean:
+	$(MAKE) -C ../.. CLEAN=$(DIR) clean
+
+cleanall:
+	$(MAKE) -C ../.. clean
+
+backup:
+	mkdir -p bak
+	cp *f90 *h Makefile bak
+
+bak: backup
+
+.PHONY: default all clean cleanall backup bak