Merge pull request #200 from LLNL/feature/toss4

Patches for building on TOSS4 with spack v0.19.1.

.gitlab/machines.yml

@@ -18,7 +18,7 @@
     - shell
   variables:
     HOSTNAME: "lassen"
-    BUILD_ALLOC: lalloc 1
+    BUILD_ALLOC: lalloc 1 -W 90
     TEST_ALLOC: $BUILD_ALLOC
   extends: [.on_blueos]
 

.gitlab/scripts.yml

@@ -42,7 +42,7 @@
   script:
     - ml load mpifileutils
     - cd $SPHERAL_BUILDS_DIR
-    - source $CI_PROJECT_DIR/$SCRIPT_DIR/gitlab/clean_spheral_builds.sh 50
+    - source $CI_PROJECT_DIR/$SCRIPT_DIR/gitlab/clean_spheral_builds.sh 40
   extends: [.toss_resource_general]
   when: always
 

.uberenv_config.json

@@ -3,7 +3,7 @@
   "package_version" : "develop",
   "package_source_dir" : "../../..",
   "spack_url" : "https://github.com/spack/spack",
-  "spack_commit" : "457fe842f05edb5d17160b0ecf32aeca9d46113c",
+  "spack_commit" : "5e0d2107348eed6cbe6deca43a30f5b06c5e40af",
   "spack_configs_path" : "scripts/spack/configs",
   "spack_packages_path" : "scripts/spack/packages"
 }

RELEASE_NOTES.md

@@ -1,3 +1,22 @@
+Version vYYYY-MM-DD -- Release date YYYY-MM-DD
+==============================================
+
+This release contains ...
+
+  * Important Notes:
+
+Notable changes include:
+
+  * New features/ API changes:
+
+  * Build changes / improvements:
+    * toss_4_x86_64_ib system compatibility.
+    * Updated spack version to v0.19.1
+    * `--debug` and `--no-spec` options added to tpl-manager.py for outputing debug and skipping `spack spec` step.
+
+  * Bug Fixes / improvements:
+    * r-path for additional TPLs can be propogated to Spheral libraries with `SPHERAL_ADDITIONAL_RPATHS`.
+
 Version v2023.03.0 -- Release date 2023-03-29
 ==============================================
 

cmake/spheral/SpheralAddLibs.cmake

@@ -113,7 +113,7 @@ function(spheral_add_cxx_library
 
   # Set the r-path of the C++ lib such that it is independent of the build dir when installed
   set_target_properties(Spheral_${package_name} PROPERTIES
-                        INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${conduit_DIR}/lib;${axom_DIR}/lib;${boost_DIR}/lib;${hdf5_DIR}/lib"
+    INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${conduit_DIR}/lib;${axom_DIR}/lib;${boost_DIR}/lib;${hdf5_DIR}/lib;${SPHERAL_ADDITIONAL_RPATHS}"
                         )
 endfunction()
 
@@ -161,7 +161,7 @@ function(spheral_add_pybind11_library package_name)
 
   # Set the r-path of the C++ lib such that it is independent of the build dir when installed
   set_target_properties(${MODULE_NAME} PROPERTIES
-    INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${conduit_DIR}/lib;${axom_DIR}/lib;${boost_DIR}/lib;${python_DIR}/lib;${hdf5_DIR}/lib"
+    INSTALL_RPATH "${CMAKE_INSTALL_PREFIX}/lib;${conduit_DIR}/lib;${axom_DIR}/lib;${boost_DIR}/lib;${python_DIR}/lib;${hdf5_DIR}/lib;${SPHERAL_ADDITIONAL_RPATHS}"
                         )
 
 endfunction()

docs/build_guide/include/tpls.rst.inc

@@ -64,7 +64,7 @@ Above we are telling ``tpl-manager`` to build our TPLs with the ``gcc`` that is
    By default we have ``python`` bindings enabled (``+python``) and docs disabled (``~docs``). Therefore the spec ``gcc+mpi+python~docs`` will build the same TPL set as just ``gcc``.For more information on ``spec`` syntax please see the spack documentation on `specs-dependencies <https://spack.readthedocs.io/en/latest/basic_usage.html#specs-dependencies>`_.
 
 .. note::
-   Spheral minimally requires a C++11 compliant compiler.
+   Spheral minimally requires a C++14 compliant compiler.
 
 [ex_running_tpl_manager-end]
 
@@ -96,7 +96,7 @@ Above we are telling ``tpl-manager`` to build our TPLs with ``gcc`` at version `
    By default we have ``python`` bindings enabled (``+python``) and docs disabled (``~docs``). Therefore the spec ``gcc@8.3.1+mpi+python~docs`` will build the same TPL set as just ``gcc@8.3.1``.For more information on ``spec`` syntax please see the spack documentation on `specs-dependencies <https://spack.readthedocs.io/en/latest/basic_usage.html#specs-dependencies>`_.
 
 .. note::
-   ``gcc@8.3.1`` is the recommended compiler for building Spheral on LC (Livermore Computing). Spheral minimally requires a C++11 compliant compiler.
+   ``gcc@8.3.1`` is the recommended compiler for building Spheral on LC (Livermore Computing). Spheral minimally requires a C++14 compliant compiler.
 
 CUDA Support
 ------------

scripts/devtools/tpl-manager.py

@@ -41,9 +41,18 @@ def parse_args():
   parser.add_argument('--spack-url', type=str, default="",
       help='URL of spack to use.')
 
-  parser.add_argument('--no-clean', type=bool, default=False,
+  parser.add_argument('--no-clean', action='store_true',
       help='Do not clean spack generated log files.')
 
+  parser.add_argument('--debug', action='store_true',
+      help='Run spack commands with -d debug output.')
+
+  parser.add_argument('--verbose', action='store_true',
+      help='Run spack install with -v for tpl build output.')
+
+  parser.add_argument('--no-spec', action='store_true',
+      help='Skip output of the dependency graph.')
+
   return parser.parse_args()
 
 
@@ -120,6 +129,10 @@ def build_deps(args):
   os.environ["SPACK_DISABLE_LOCAL_CONFIG"] = "1"
   spack_cmd=os.path.join(args.spheral_spack_dir, "spack/bin/spack")
 
+  # Add -d to spack command when requesting debug output
+  if args.debug:
+    spack_cmd += " -d"
+
   with open(uberenv_project_json) as f:
     package_name=json.loads(f.read())["package_name"]
 
@@ -128,8 +141,9 @@ def build_deps(args):
     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 sexe("{0} spec -I {1}@develop%{2}".format(spack_cmd, package_name, s), echo=True) : sys.exit(1)
-    if sexe("{0} dev-build --deprecated --quiet -d {1} -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)
+    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)
+    if sexe("{0} dev-build --fresh --quiet --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)
 
   if not args.no_clean:
     sexe("rm dev-build-* spack-build-* spack-configure-args.txt")

scripts/spack/configs/blueos_3_ppc64le_ib/packages.yaml

@@ -137,8 +137,3 @@ packages:
     - spec: hwloc@5.7.5
       prefix: /usr
     buildable: false
-  netlib-lapack:
-    buildable: false
-    externals:
-    - spec: netlib-lapack@3.9.0
-      prefix: /usr/gapps/bdiv/blueos_3_ppc64le_ib_p9/gcc-8-cuda-10/lapack/3.9.0

scripts/spack/configs/toss_3_x86_64_ib/packages.yaml

@@ -137,8 +137,3 @@ packages:
     - spec: hwloc@5.7.5
       prefix: /usr
     buildable: false
-  netlib-lapack:
-    buildable: false
-    externals:
-    - spec: netlib-lapack@3.9.0
-      prefix: /usr/gapps/bdiv/toss_3_x86_64_ib/clang-10-mvapich2-2.3/lapack/3.9.0

scripts/spack/configs/toss_4_x86_64_ib/compilers.yaml

@@ -0,0 +1,27 @@
+compilers:
+- compiler:
+    spec: clang@14.0.6
+    paths:
+      cc: /usr/tce/packages/clang/clang-14.0.6/bin/clang
+      cxx: /usr/tce/packages/clang/clang-14.0.6/bin/clang++
+      f77: /usr/tce/packages/gcc/gcc-10.3.1/bin/gfortran
+      fc: /usr/tce/packages/gcc/gcc-10.3.1/bin/gfortran
+    flags: {}
+    operating_system: rhel8
+    target: x86_64
+    modules: []
+    environment: {}
+    extra_rpaths: []
+- compiler:
+    spec: gcc@10.3.1
+    paths:
+      cc: /usr/tce/packages/gcc/gcc-10.3.1/bin/gcc
+      cxx: /usr/tce/packages/gcc/gcc-10.3.1/bin/g++
+      f77: /usr/tce/packages/gcc/gcc-10.3.1/bin/gfortran
+      fc: /usr/tce/packages/gcc/gcc-10.3.1/bin/gfortran
+    flags: {}
+    operating_system: rhel8
+    target: x86_64
+    modules: []
+    environment: {}
+    extra_rpaths: []

scripts/spack/configs/toss_4_x86_64_ib/packages.yaml

@@ -0,0 +1,114 @@
+packages:
+  all:
+    # This defaults us to machine specific flags of ivybridge which allows
+    # us to run on broadwell as well
+    target: [ivybridge]
+    compiler: [gcc, clang]
+  cmake:
+    version: [3.23.1]
+    buildable: false
+    externals:
+    - spec: cmake@3.23.1
+      prefix: /usr/tce/packages/cmake/cmake-3.23.1
+
+  mvapich2:
+    externals:
+    - spec: mvapich2@2.3.6%gcc@10.3.1~cuda~debug~regcache~wrapperrpath ch3_rank_bits=32
+        file_systems=lustre,nfs,ufs process_managers=slurm
+      prefix: /usr/tce/packages/mvapich2/mvapich2-2.3.6-gcc-10.3.1
+    buildable: false
+
+# ------ SYSTEM LIBS -------
+  ncurses:
+    externals:
+    - spec: ncurses@5.9
+      prefix: /usr
+    buildable: false
+  readline:
+    externals:
+    - spec: readline@7.0
+      prefix: /usr
+    buildable: false
+  autoconf:
+    externals:
+    - spec: autoconf@2.69
+      prefix: /usr
+    buildable: false
+  automake:
+    externals:
+    - spec: automake@1.13.4
+      prefix: /usr
+    buildable: false
+  libtool:
+    externals:
+    - spec: libtool@2.4.2
+      prefix: /usr
+    buildable: false
+  bzip2:
+    externals:
+    - spec: bzip2@1.0.6
+      prefix: /usr
+    buildable: false
+  expat:
+    externals:
+    - spec: expat@2.4.1
+      prefix: /usr
+    buildable: false
+  gdbm:
+    externals:
+    - spec: gdbm@1.19
+      prefix: /usr
+    buildable: false
+  gettext:
+    externals:
+    - spec: gettext@0.19
+      prefix: /usr
+    buildable: false
+  libffi:
+    externals:
+    - spec: libffi@3.3
+      prefix: /usr
+    buildable: false
+  openssl:
+    externals:
+    - spec: openssl@1.1.1
+      prefix: /usr
+    buildable: false
+  ossp-uuid:
+    externals:
+    - spec: ossp-uuid@1.62
+      prefix: /usr
+    buildable: false
+  sqlite:
+    externals:
+    - spec: sqlite@3.36.0
+      prefix: /usr
+    buildable: false
+  pkg-config:
+    externals:
+    - spec: pkg-config@0.27.1
+      prefix: /usr
+    buildable: false
+  tar:
+    externals:
+    - spec: tar@1.26
+      prefix: /usr
+    buildable: false
+  elfutils:
+    externals:
+    - spec: elfutils@0.176
+      prefix: /usr
+    buildable: false
+
+#---- Extension Dependencies
+
+  hwloc:
+    externals:
+    - spec: hwloc@5.7.5
+      prefix: /usr
+    buildable: false
+  netlib-lapack:
+    buildable: false
+    externals:
+    - spec: netlib-lapack@3.9.0
+      prefix: /usr

scripts/spack/packages/py-numpy-stl/package.py

@@ -17,5 +17,6 @@ class PyNumpyStl(PythonPackage):
     version('2.11.2', sha256='192556df794b9ef0c1333fd5f034e4a3905d63f52345a0cc1e359045670e34b6')
 
     extends('python@2.7:2.8', type=['build', 'run'])
+    depends_on('py-setuptools', type='build')
     depends_on('py-enum34', type='build')
     depends_on('py-python-utils@2.4.0', type='build')