Merge pull request #272 from LLNL/update/update_TPLs

Update Spack to 0.22

.gitlab/os.yml

@@ -4,7 +4,7 @@
 .sys_config:
   variables:
     LLNL_SERVICE_USER: sphapp
-    UPSTREAM_DIR: /usr/WS2/wciuser/Spheral/spheral-spack-tpls
+    UPSTREAM_DIR: /usr/WS2/sduser/Spheral/spack_upstream/0.22
     DISPLAY: ':0.0'
 
 .on_toss_3_x86:

.gitlab/scripts.yml

@@ -12,7 +12,6 @@
     - cd $CI_BUILD_DIR
     - echo $SPEC
 
-    - ml load python/3
     - $BUILD_ALLOC ./$SCRIPT_DIR/gitlab/build_and_install.py --spec="$SPEC" --extra-cmake-args="$EXTRA_CMAKE_ARGS"
 
 .build_and_test:

.uberenv_config.json

@@ -3,7 +3,7 @@
   "package_version" : "develop",
   "package_source_dir" : "../../..",
   "spack_url" : "https://github.com/spack/spack",
-  "spack_commit" : "5e0d2107348eed6cbe6deca43a30f5b06c5e40af",
+  "spack_commit" : "5fe93fee1eec46a0750bd340198bffcb92ff9eec",
   "spack_configs_path" : "scripts/spack/configs",
   "spack_packages_path" : "scripts/spack/packages"
 }

Dockerfile

@@ -31,7 +31,7 @@ ARG HOST_CONFIG=docker-$SPEC
 ENV DEBIAN_FRONTEND=noninteractive
 RUN apt-get update -y
 RUN apt-get upgrade -y
-RUN apt-get install -y build-essential git gfortran mpich autotools-dev autoconf sqlite pkg-config uuid gettext cmake libncurses-dev libgdbm-dev libffi-dev libssl-dev libexpat-dev libreadline-dev liblapack-dev libbz2-dev locales python python3 unzip libtool wget curl tk-dev
+RUN apt-get install -y build-essential git gfortran mpich autotools-dev autoconf sqlite pkg-config uuid gettext cmake libncurses-dev libgdbm-dev libffi-dev libssl-dev libexpat-dev libreadline-dev libbz2-dev locales python python3 unzip libtool wget curl tk-dev
 
 # Setup system locale for pip package encoding/decoding 
 RUN locale-gen en_US.UTF-8

RELEASE_NOTES.md

@@ -14,6 +14,14 @@ Notable changes include:
       * Multiple Spheral Python modules / CMake targets can be specified for a single directory.
       * KernelIntegrator and FieldList directories are divided into 2 modules / targets.
     * tpl-manager.py will no longer use generic x86_64 configs for non LC systems. Users will be required to supply their own configs for pointing spack at external packages.
+    * Spack version is increased from 0.19 to 0.22.
+    * Spack upstream is updated.
+    * Removed the python 3 module load for the Gitlab CI to fix an issue with pkg-config changing.
+    * Zlib target and TPL cmake file is removed.
+    * PYB11Generator repo is updated.
+    * Spack config and package files inside Spheral are updated to accommodate Spack 0.22.
+      * Package recipes for py-numpy-stl, py-pillow, py-pipreqs, td, and tk are removed.
+      * Versions for python dependencies in the Spheral spack recipe are fixed and updated (in some cases).
 
   * Bug Fixes / improvements:
 

cmake/CMakeDefinitions.cmake

@@ -73,5 +73,5 @@ if (ENABLE_TIMER)
 endif()
 
 if (ENABLE_MPI)
-    add_definitions(-DUSE_MPI=1)
+  add_definitions(-DUSE_MPI=1)
 endif()

cmake/InstallTPLs.cmake

@@ -89,7 +89,7 @@ foreach(_comp ${AXOM_COMPONENTS_ENABLED})
 endforeach()
 
 # TPLs that must be imported
-list(APPEND SPHERAL_EXTERN_LIBS zlib boost eigen qhull silo hdf5 polytope)
+list(APPEND SPHERAL_EXTERN_LIBS boost eigen qhull silo hdf5 polytope)
 
 blt_list_append( TO SPHERAL_EXTERN_LIBS ELEMENTS aneos IF ENABLE_ANEOS)
 blt_list_append( TO SPHERAL_EXTERN_LIBS ELEMENTS opensubdiv IF ENABLE_OPENSUBDIV)
@@ -108,6 +108,7 @@ endforeach()
 if (EXISTS ${EXTERNAL_SPHERAL_TPL_CMAKE})
   include(${EXTERNAL_SPHERAL_TPL_CMAKE})
 endif()
+
 # Copied from serac, needed to bypass generator expression issue during export
 set(_props)
 if( ${CMAKE_VERSION} VERSION_GREATER_EQUAL "3.13.0" )

cmake/SetupSpheral.cmake

@@ -5,7 +5,6 @@ include(ExternalProject)
 #-------------------------------------------------------------------------------
 set(CMAKE_CXX_STANDARD 17)
 set(CMAKE_EXPORT_COMPILE_COMMANDS On)
-set(CMAKE_EXPORT_COMPILE_COMMANDS On)
 
 if (NOT SPHERAL_CMAKE_MODULE_PATH)
   set(SPHERAL_CMAKE_MODULE_PATH "${SPHERAL_ROOT_DIR}/cmake")
@@ -83,8 +82,6 @@ if(ENABLE_CUDA)
   list(APPEND SPHERAL_CXX_DEPENDS cuda)
 endif()
 
-option(BOOST_HEADER_ONLY "only use the header only components of Boost" OFF)
-
 #-------------------------------------------------------------------------------#
 # Set a default build type if none was specified
 #-------------------------------------------------------------------------------#

cmake/spheral/InstantiateCXX.cmake

@@ -40,7 +40,7 @@ function(instantiate _inst_var _source_var)
         # Uses BLT's python for instantiations to work when building CXX_ONLY as well as with python
         add_custom_command(OUTPUT  ${CMAKE_CURRENT_BINARY_DIR}/${_inst_file}
                            DEPENDS ${_inst_py}
-                           COMMAND ${PYTHON_EXECUTABLE} ${SPHERAL_ROOT_DIR}/src/helpers/InstantiationGenerator.py ${_inst_py} ${_inst_file} ${_dim}
+                           COMMAND ${Python3_EXECUTABLE} ${SPHERAL_ROOT_DIR}/src/helpers/InstantiationGenerator.py ${_inst_py} ${_inst_file} ${_dim}
                            BYPRODUCTS ${_inst_file}
                            COMMENT "Generating instantiation ${_inst_file}..."
                            )

cmake/spheral_cxx-config.cmake.in

@@ -1,37 +1,47 @@
 
 @PACKAGE_INIT@
 
-if(NOT axom_DIR)
-  set(axom_DIR "@axom_DIR@" CACHE PATH "")
-endif()
-set(SPHERAL_CXX_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
-set(SPHERAL_CXX_INCLUDE_DIRS "${SPHERAL_CXX_INSTALL_PREFIX}/include")
-if(NOT @ENABLE_CXXONLY@ AND NOT TARGET Python3)
-  set(python_DIR "@python_DIR@")
-  set(Python_EXECUTABLE ${python_DIR}/bin/python3)
-  set(Python3_EXECUTABLE ${python_DIR}/bin/python3)
-  find_package(Python3 COMPONENTS Interpreter Development)
-  set(PYTHON_EXE ${Python3_EXECUTABLE})
-endif()
+if(NOT SPHERAL_FOUND)
+  #----------------------------------------------------------------------------
+  # Set user configuration options and features
+  #----------------------------------------------------------------------------
 
-# Guard these assignments to not interfere with projects that use Spheral and SpheralC as TPLs
-if(SPHERALC_STANDALONE)
-  set(CMAKE_C_COMPILER "@CMAKE_C_COMPILER@" CACHE PATH "Spheral C compiler path")
-  set(CMAKE_CXX_COMPILER "@CMAKE_CXX_COMPILER@" CACHE PATH "Spheral C++ compiler path")
-  set(CMAKE_Fortran_COMPILER "@CMAKE_Fortran_COMPILER@" CACHE PATH "Spheral C++ compiler path")
-  set(ENABLE_MPI @ENABLE_MPI@ CACHE BOOL "")
-  if(SPHERAL_ENABLE_MPI)
-    set(MPI_C_COMPILER "@MPI_C_COMPILER@" CACHE PATH "")
-    set(MPI_CXX_COMPILER "@MPI_CXX_COMPILER@" CACHE PATH "")
-    set(MPI_Fortran_COMPILER "@MPI_Fortran_COMPILER@" CACHE PATH "")
+  # Language features
+  set(SPHERAL_ENABLE_MPI "@ENABLE_MPI@")
+  set(SPHERAL_ENABLE_OPENMP "@ENABLE_OPENMP@")
+  set(SPHERAL_ENABLE_CUDA "@ENABLE_CUDA@")
+  if(NOT axom_DIR)
+    set(axom_DIR "@axom_DIR@" CACHE PATH "")
   endif()
-endif()
 
-if(NOT TARGET axom)
-  find_package(axom REQUIRED QUIET NO_DEFAULT_PATH PATHS ${axom_DIR} ${axom_DIR}/lib ${axom_DIR}/lib/cmake)
-endif()
-include("${SPHERAL_CXX_INSTALL_PREFIX}/lib/cmake/spheral_cxx-targets.cmake")
+  set(SPHERAL_CXX_INSTALL_PREFIX "@CMAKE_INSTALL_PREFIX@")
+  set(SPHERAL_CXX_INCLUDE_DIRS "${SPHERAL_CXX_INSTALL_PREFIX}/include")
+  if(NOT @ENABLE_CXXONLY@ AND NOT TARGET Python3)
+    set(python_DIR "@python_DIR@")
+    set(Python_EXECUTABLE ${python_DIR}/bin/python3)
+    set(Python3_EXECUTABLE ${python_DIR}/bin/python3)
+    find_package(Python3 COMPONENTS Interpreter Development)
+    set(PYTHON_EXE ${Python3_EXECUTABLE})
+  endif()
 
-set_property(TARGET Spheral_CXX
-  APPEND PROPERTY
-  INTERFACE_INCLUDE_DIRECTORIES ${SPHERAL_CXX_INCLUDE_DIRS})
+  if(NOT TARGET axom)
+    find_package(axom REQUIRED QUIET NO_DEFAULT_PATH PATHS ${axom_DIR} ${axom_DIR}/lib ${axom_DIR}/lib/cmake)
+  endif()
+  if(SPHERALC_STANDALONE)
+    set(CMAKE_C_COMPILER "@CMAKE_C_COMPILER@" CACHE PATH "Spheral C compiler path")
+    set(CMAKE_CXX_COMPILER "@CMAKE_CXX_COMPILER@" CACHE PATH "Spheral C++ compiler path")
+    set(CMAKE_Fortran_COMPILER "@CMAKE_Fortran_COMPILER@" CACHE PATH "Spheral C++ compiler path")
+    set(ENABLE_MPI @ENABLE_MPI@ CACHE BOOL "")
+    if(SPHERAL_ENABLE_MPI)
+      set(MPI_C_COMPILER "@MPI_C_COMPILER@" CACHE PATH "")
+      set(MPI_CXX_COMPILER "@MPI_CXX_COMPILER@" CACHE PATH "")
+      set(MPI_Fortran_COMPILER "@MPI_Fortran_COMPILER@" CACHE PATH "")
+    endif()
+  endif()
+  include("${SPHERAL_CXX_INSTALL_PREFIX}/lib/cmake/spheral_cxx-targets.cmake")
+
+  set_property(TARGET Spheral_CXX
+    APPEND PROPERTY
+    INTERFACE_INCLUDE_DIRECTORIES ${SPHERAL_CXX_INCLUDE_DIRS})
+  set(SPHERAL_FOUND TRUE)
+endif()

scripts/devtools/tpl-manager.py

@@ -11,7 +11,7 @@
 project_dir=os.path.abspath(os.path.join(os.path.realpath(__file__), "../../../"))
 
 default_spheral_spack_dir=os.path.join(os.getcwd(), "../spheral-spack-tpls")
-default_upstream_dir="/usr/WS2/wciuser/Spheral/spheral-spack-tpls/spack/opt/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_p/"
+default_upstream_dir="/usr/WS2/sduser/Spheral/spack_upstream/0.22/spack/opt/spack/__spack_path_placeholder__/__spack_path_placeholder__/__spack_path_p"
 
 uberenv_path = os.path.join(project_dir, "scripts/devtools/uberenv/uberenv.py")
 uberenv_project_json = os.path.join(os.getcwd(), ".uberenv_config.json")
@@ -59,24 +59,24 @@ def parse_args():
   parser.add_argument('--no-spec', action='store_true',
       help='Skip output of the dependency graph.')
 
+  parser.add_argument('--skip-init', action='store_true',
+      help='Skip setting up and configuring Spack.')
+
   return parser.parse_args()
 
 
 # Helper function for executing commands stolen from uberenv
-def sexe(cmd,ret_output=False,echo=False):
+def sexe(cmd,ret_output=False,echo=True):
     """ Helper for executing shell commands. """
     if echo:
-        print("[exe: {0}]".format(cmd))
+      print("[exe: {0}]".format(cmd))
+    p = subprocess.run(cmd, shell=True,
+                       capture_output=ret_output,
+                       check=True, text=True)
     if ret_output:
-        p = subprocess.Popen(cmd,
-                             shell=True,
-                             stdout=subprocess.PIPE,
-                             stderr=subprocess.STDOUT)
-        out = p.communicate()[0]
-        out = out.decode('utf8')
-        return p.returncode,out
-    else:
-        return subprocess.call(cmd,shell=True)
+      if echo:
+        print(p.stdout)
+      return p.stdout
 
 
 # Parse the json formatted spec list...
@@ -89,26 +89,13 @@ def parse_spec_list(file_path):
 #------------------------------
 # Dependencies
 #------------------------------
-def build_deps(args):
+def build_spack(args):
   print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
-  print("~~~~~ Building Dependencies")
+  print("~~~~~ Configuring Spack")
   print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
   print("")
   print("{0}".format(project_dir))
 
-
-  # Figure out what specs this script is building TPLs for.
-  spec_list=[]
-  if args.spec_list:
-    spec_list = parse_spec_list(args.spec_list)
-  elif args.spec:
-    spec_list.append(args.spec)
-  else:
-    print("ERROR: Please define --spec or --spec-list, aborting...")
-    sys.exit(1) 
-  for s in spec_list:
-    print("** SPEC : {0}".format(s))
-
   spack_upstream_opt=""
   if os.path.isdir(args.upstream_dir) and not args.no_upstream:
     spack_upstream_opt="--upstream {0}".format(args.upstream_dir)
@@ -137,9 +124,9 @@ def build_deps(args):
     # We need to install spack without any configuration files so we can use
     # spack arch to determine the OS of the system and later to use spack find
     # for generating external package files on external systems.
-    if sexe("python3 {0} --setup-only {1} {2} {3} {4}".format(uberenv_path, prefix_opt, uberenv_project_json_opt, spack_upstream_opt, uberenv_spack_url_opt), echo=True): sys.exit(1)
+    sexe("python3 {0} --setup-only {1} {2} {3} {4}".format(uberenv_path, prefix_opt, uberenv_project_json_opt, spack_upstream_opt, uberenv_spack_url_opt))
 
-    spack_arch_os = sexe("{0} arch -o".format(spack_cmd), ret_output=True)[1].strip()
+    spack_arch_os = sexe("{0} arch -o".format(spack_cmd), ret_output=True, echo=False).strip()
     print("INFO : Detected Operating System :{0}".format(spack_arch_os))
 
     spheral_config_dir += spack_arch_os
@@ -150,12 +137,31 @@ def build_deps(args):
 
 
   # Setup spack w/ Uberenv and the appropriate external package/compiler configs.
-  if sexe("python3 {0} --setup-only {1} {2} {3} {4} {5}".format(uberenv_path, prefix_opt, uberenv_project_json_opt, spack_config_dir_opt, spack_upstream_opt, uberenv_spack_url_opt), echo=True): sys.exit(1)
+  sexe("python3 {0} --setup-only {1} {2} {3} {4} {5}".format(uberenv_path, prefix_opt, uberenv_project_json_opt, spack_config_dir_opt, spack_upstream_opt, uberenv_spack_url_opt))
 
   # Uberenv doesn't copy the concretizer.yaml options...
   if os.path.exists(spheral_config_dir+"/concretizer.yaml"):
-    sexe("cp {0}/concretizer.yaml {1}".format(spheral_config_dir, os.path.join(args.spheral_spack_dir, "spack/etc/spack/defaults")), echo=True)
+    sexe("cp {0}/concretizer.yaml {1}".format(spheral_config_dir, os.path.join(args.spheral_spack_dir, "spack/etc/spack/defaults")))
 
+def build_deps(args):
+  print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
+  print("~~~~~ Building Dependencies")
+  print("~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~")
+  print("")
+  print("{0}".format(project_dir))
+  # Figure out what specs this script is building TPLs for.
+  spec_list=[]
+  if args.spec_list:
+    spec_list = parse_spec_list(args.spec_list)
+  elif args.spec:
+    spec_list.append(args.spec)
+  else:
+    print("ERROR: Please define --spec or --spec-list, aborting...")
+    sys.exit(1)
+  for s in spec_list:
+    print("** SPEC : {0}".format(s))
+  spack_cmd=os.path.join(args.spheral_spack_dir, "spack/bin/spack")
+
   # Optionally add a parallel job number for spack builds
   if args.spack_jobs:
     spack_cmd += " --jobs={0}".format(args.spack_jobs)
@@ -170,27 +176,25 @@ def build_deps(args):
   # Loop through the specs we want TPLs for and build/install/get them as necessary.
   if not args.init_only:
       for s in spec_list:
-
         print("** Building TPL's and generating host-config for {0}%{1} ...".format(package_name,s))
         os.environ["SPEC"] = s
         os.environ["LC_ALL"] = "en_US.UTF-8"
 
         if not args.no_spec:
-            if sexe("{0} spec --fresh -I {1}@develop%{2}".format(spack_cmd, package_name, s), echo=True) : sys.exit(1)
-
-        # Install only the dependencies for Spheral
-        if sexe("{0} install --fail-fast --fresh --deprecated --only dependencies {2}@develop%{3} 2>&1 | tee -a \"dev-build-{3}-out.txt\"".format(spack_cmd, os.getcwd(), package_name, s), echo=True) : sys.exit(1)
+          sexe("{0} spec --fresh -IL {1}@develop%{2} 2>&1 | tee -a \"spec-info-{2}-out.txt\"".format(spack_cmd, package_name, s))
 
-        # Using dev-build we can have spack generate an init-config with the local source files for spheral.
-        if sexe("{0} dev-build --fresh --deprecated -u initconfig {2}@develop%{3} 2>&1 | tee -a \"dev-build-{3}-out.txt\"".format(spack_cmd, os.getcwd(), package_name, s), echo=True) : sys.exit(1)
+        # Install only the dependencies for Spheral and create CMake configure file
+        sexe("{0} dev-build -q --fresh -u initconfig {1}@develop%{2} 2>&1 | tee -a \"tpl-build-{2}-out.txt\"".format(spack_cmd, package_name, s))
 
       if not args.no_clean:
-        sexe("rm dev-build-* spack-build-* spack-configure-args.txt")
+        sexe("rm -f spec-info-* tpl-build-* spack-build-* spack-configure-args.txt")
 
 #------------------------------------------------------------------------------
 
 def main():
   args = parse_args()
+  if (not args.skip_init):
+    build_spack(args)
   build_deps(args)