Merge pull request #64 from issp-center-dev/develop

ver. 1.3.0

.gitmodules

@@ -1,7 +1,3 @@
-[submodule "src/pfaffine"]
-	path = src/pfaffine
-	url = https://github.com/xrq-phys/Pfaffine
-	branch = blis
 [submodule "src/blis"]
 	path = src/blis
 	url = https://github.com/xrq-phys/blis

CMakeLists.txt

@@ -1,8 +1,9 @@
-cmake_minimum_required(VERSION 2.8.0 FATAL_ERROR)
+cmake_minimum_required(VERSION 3.5 FATAL_ERROR)
 project(mVMC NONE)
 
 option(USE_SCALAPACK "Use Scalapack" OFF)
 option(PFAFFIAN_BLOCKED "Use blocked-update Pfaffian to speed up." OFF)
+option(USE_GEMMT "Use GEMMT. Recommended regardless blocked-Pfaffian-update." ON)
 
 add_definitions(-D_mVMC)
 if(CONFIG)
@@ -17,18 +18,18 @@ message(STATUS "Build type: " ${CMAKE_BUILD_TYPE})
 option(BUILD_SHARED_LIBS "Build shared libraries" ON)
 
 option(GIT_SUBMODULE_UPDATE "execute `git submodule update` automatically" ON)
-enable_language(C Fortran)
-if(PFAFFIAN_BLOCKED)
-  enable_language(CXX)
-  set(CMAKE_CXX_STANDARD 11)
-endif(PFAFFIAN_BLOCKED)
+
+# First, enables C language only.
+# External packages only use their C API.
+enable_language(C)
 
 set(CMAKE_INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib")
 set(CMAKE_SKIP_BUILD_RPATH FALSE)
 set(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) 
 set(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE)
 set(CMAKE_MACOSX_RPATH 1)
 
+# TODO: Is this really needed?
 if("${CMAKE_BUILD_TYPE}" MATCHES "Debug")
   set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${CMAKE_C_FLAGS_DEBUG}")
 else()
@@ -37,16 +38,19 @@ else()
 endif()
 
 if(CMAKE_C_COMPILER_ID STREQUAL "Intel")
+  # TODO: Really needs separation?
   if("${CMAKE_C_COMPILER_VERSION}" VERSION_LESS "15.0.0.20140528")
      set(OMP_FLAG_Intel "-openmp")
   else()
     set(OMP_FLAG_Intel "-qopenmp")
   endif()
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OMP_FLAG_Intel}")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OMP_FLAG_Intel}")
 else()
   find_package(OpenMP)
   if(OPENMP_FOUND)
     set(CMAKE_C_FLAGS "${CMAKE_C_FLAGS} ${OpenMP_C_FLAGS}")
+    set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${OpenMP_C_FLAGS} ${OpenMP_EXE_LINKER_FLAGS}")
   endif(OPENMP_FOUND)	
 endif()
 
@@ -57,13 +61,44 @@ if(MPI_C_FOUND)
   set(CMAKE_EXE_LINKER_FLAGS "${CMAKE_EXE_LINKER_FLAGS} ${MPI_C_LINK_FLAGS}")
 endif(MPI_C_FOUND)
 
+# BLAS/LAPACK/Pfapack77 needs Fortran interface.
+enable_language(Fortran)
+
 find_package(LAPACK)
 if(USE_SCALAPACK MATCHES OFF)
   if(LAPACK_FOUND)
     add_definitions(-D_lapack)
   endif(LAPACK_FOUND)
 endif()
 
+if(PFAFFIAN_BLOCKED
+    OR USE_GEMMT)
+  set(Require_BLIS ON)
+endif()
+
+if(BLA_VENDOR MATCHES "Intel10*"
+    OR BLAS_LIBRARIES MATCHES "/*mkl*")
+  # Don't require BLIS when MKL is used.
+  add_definitions(-DMKL)
+  add_definitions(-DBLAS_EXTERNAL)
+  add_definitions(-DF77_COMPLEX_RET_INTEL)
+  set(Require_BLIS OFF)
+elseif(BLA_VENDOR MATCHES "FLA*"
+    OR BLAS_LIBRARIES MATCHES "/*blis*")
+  # Skip extra BLIS if it's already the BLAS vendor.
+  list(GET BLAS_LIBRARIES 0 BLIS_FIRST_LIB)
+  get_filename_component(BLIS_LIB_DIR ${BLIS_FIRST_LIB} DIRECTORY)
+  include_directories(${BLIS_LIB_DIR}/../include)
+  include_directories(${BLIS_LIB_DIR}/../include/blis)
+  set(Require_BLIS OFF)
+else()
+  # BLAS vendor preference:
+  # External > BLIS > Reference
+  if(DEFINED BLA_VENDOR)
+    add_definitions(-DBLAS_EXTERNAL)
+  endif()
+endif()
+
 # Build and enable tests
 # testing setup
 # enable_testing() must be called in the top-level CMakeLists.txt before any add_subdirectory() is called.
@@ -76,33 +111,54 @@ endif()
 
 # git submodule update
 # ref: https://cliutils.gitlab.io/modern-cmake/chapters/projects/submodule.html
-set(MVMC ON) # Option for upstream StdFace.
+option(MVMC "build mvmc" ON) # Option for upstream StdFace.
+option(TestStdFace "run test for StdFace" OFF)
 find_package(Git QUIET)
-set(STDFACE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/src/StdFace")
-if(GIT_FOUND AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
-  # Update submodules as needed
-  if(GIT_SUBMODULE_UPDATE)
-    message(STATUS "Submodule update")
-    execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive
-      WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
-      RESULT_VARIABLE GIT_SUBMOD_RESULT)
-    if(NOT GIT_SUBMOD_RESULT EQUAL "0")
-      message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
+
+if(NOT STDFACE_DIR)
+  set(STDFACE_DIR "${CMAKE_CURRENT_SOURCE_DIR}/src/StdFace")
+  if(GIT_FOUND AND EXISTS "${CMAKE_CURRENT_SOURCE_DIR}/.git")
+    # Update submodules as needed
+    if(GIT_SUBMODULE_UPDATE)
+      message(STATUS "Submodule update")
+      execute_process(COMMAND ${GIT_EXECUTABLE} submodule update --init --recursive
+        WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}
+        RESULT_VARIABLE GIT_SUBMOD_RESULT)
+      if(NOT GIT_SUBMOD_RESULT EQUAL "0")
+        message(FATAL_ERROR "git submodule update --init failed with ${GIT_SUBMOD_RESULT}, please checkout submodules")
+      endif()
     endif()
-  endif()
 
+    if(NOT EXISTS "${STDFACE_DIR}/CMakeLists.txt")
+      message(FATAL_ERROR "The submodule StdFace were not downloaded! GIT_SUBMODULE_UPDATE was turned off or failed. Please update submodules and try again.")
+    endif()
+  endif()
+else()
   if(NOT EXISTS "${STDFACE_DIR}/CMakeLists.txt")
-    message(FATAL_ERROR "The submodule StdFace were not downloaded! GIT_SUBMODULE_UPDATE was turned off or failed. Please update submodules and try again.")
+    message(FATAL_ERROR "STDFACE_DIR is manually set to ${STDFACE_DIR}, but ${STDFACE_DIR}/CMakeLists.txt does not exists")
+  else()
+    message(STATUS "STDFACE_DIR is manually set to ${STDFACE_DIR}.")
   endif()
 endif()
 add_subdirectory("${STDFACE_DIR}")
 
+# C++ support for pfupdates & ltl2inv.
+enable_language(CXX)
+set(CMAKE_CXX_STANDARD 11)
+
+if(Require_BLIS)
+  include("download_blis_artifact.cmake")
+else(Require_BLIS)
+  # Use bundled blis.h
+  include_directories(src/common/deps)
+endif(Require_BLIS)
+
 if(PFAFFIAN_BLOCKED)
   add_definitions(-D_pf_block_update)
-  include("download_blis_artifact.cmake")
-  # Must set BLIS artifact BEFORE adding pfupdates target.
   add_subdirectory(src/pfupdates)
-  add_dependencies(pfupdates blis_include)
+  if(Require_BLIS)
+    add_dependencies(pfupdates blis_include)
+  endif(Require_BLIS)
 endif(PFAFFIAN_BLOCKED)
 
 if (Document)
@@ -111,5 +167,9 @@ endif(Document)
 
 add_subdirectory(src/ComplexUHF)
 add_subdirectory(src/pfapack/fortran)
+add_subdirectory(src/ltl2inv)
+  if(Require_BLIS)
+    add_dependencies(ltl2inv blis_include)
+  endif(Require_BLIS)
 add_subdirectory(src/mVMC)
 add_subdirectory(tool)

README.md

@@ -62,4 +62,4 @@ are available at [mVMC-tutorial](https://github.com/issp-center-dev/mVMC-tutoria
 
 ## Authors
 
-Takahiro Misawa, Satoshi Morita, Takahiro Ohgoe, Kota Ido, Yuichi Motoyama, Mitsuaki Kawamura, Kazuyoshi Yoshimi, Takeo Kato, Masatoshi Imada.
+Takahiro Misawa, Satoshi Morita, Takahiro Ohgoe, Kota Ido, RuQing G. Xu, Yuichi Motoyama, Mitsuaki Kawamura, Kazuyoshi Yoshimi, Takeo Kato, Masatoshi Imada.

config/aocc.cmake

@@ -9,6 +9,9 @@ set(CMAKE_C_FLAGS_RELEASE "-Wno-unknown-pragmas -O3 -DNDEBUG -DHAVE_SSE2" CACHE
 set(CMAKE_Fortran_COMPILER "flang" CACHE STRING "" FORCE)
 set(CMAKE_Fortran_FLAGS_RELEASE "-O3 -DNDEBUG -DHAVE_SSE2" CACHE STRING "" FORCE)
 
+# OpenMP, libatomic
+set(CMAKE_EXE_LINKER_FLAGS "-fopenmp -latomic") 
+
 # for AOCL
 set(BLA_VENDOR "FLAME" CACHE STRING "" FORCE)
 

config/apple.cmake

@@ -2,15 +2,14 @@
 # additional libomp and gfortran installation required
 # mac computers are suggested to use this configuration for better performance
 
-if(NOT $ENV{HOMEBREW_PREFIX})
+if(NOT DEFINED ENV{HOMEBREW_PREFIX})
   message(FATAL "Homebrew is not installed. Please install Homebrew first.")
 endif()
 
 set(CMAKE_C_COMPILER "clang" CACHE STRING "" FORCE)
 set(CMAKE_CXX_COMPILER "clang++" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_DEBUG "-g -O0 -Wall  -Wformat -Werror=format-security")
 set(CMAKE_C_FLAGS_RELEASE "-O3 -Wno-unknown-pragmas -Wno-logical-not-parentheses")
-# set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)
 
 # OpenMP with libomp
 set(CMAKE_EXE_LINKER_FLAGS "-L$ENV{HOMEBREW_PREFIX}/opt/libomp/lib -lomp") 

config/gcc.cmake

@@ -3,4 +3,5 @@ set(CMAKE_C_COMPILER "gcc" CACHE STRING "" FORCE)
 set(CMAKE_CXX_COMPILER "g++" CACHE STRING "" FORCE)
 set(CMAKE_C_FLAGS_DEBUG "-g -O0 -Wall  -Wformat -Werror=format-security")
 set(CMAKE_C_FLAGS_RELEASE "-O3 -Wno-unknown-pragmas ")
+set(CMAKE_CXX_FLAGS_RELEASE "-O3 -Wno-unknown-pragmas ")
 set(CMAKE_Fortran_COMPILER "gfortran" CACHE STRING "" FORCE)

doc/CMakeLists.txt

@@ -1,4 +1,6 @@
 add_subdirectory(en/source)
 add_subdirectory(ja/source)
+add_subdirectory(tutorial/ja/source)
 
 add_custom_target(doc DEPENDS doc-ja doc-en)
+add_custom_target(tutorial DEPENDS tutorial-ja)

doc/en/source/algorithm.rst

@@ -92,7 +92,7 @@ Properties of the Pfaffian-Slater determinant
 In this section, we explain some properties of the Pfaffian-Slater
 determinant. We derive the general relation between a Pfaffian-Slater
 determinant and a single Slater determinant in :ref:`Antiparallel Pfaffian <PfaffianAP>`
-and :ref:`General Pfaffian <PfaffianP>` . We also discuss the meaning of the singular value
+and :ref:`General Pfaffian <PfaffianP>` . We also discuss meaning of the singular value
 decomposition of coefficients :math:`f_{ij}` in
 :ref:`SVD <PfaffianSingular>`.
 
@@ -190,7 +190,7 @@ redundancy.
 Relation between :math:`F_{IJ}` and :math:`\Phi_{In}` (the case of the general pairing)
 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
 
-We extend the relationship between the Pfaffian-Slater wave function and the
+We extend the relation between the Pfaffian-Slater wave function and the
 single Slater wave function into the general pairing case including the
 spin-parallel pairing. We define the Pfaffian-Slater wave function and
 the single Slater wave function as