Merge branch 'unstable' of github.com:ParaToolsInc/taucmdr into oneapi

Fixed typo and whitespace error during conflict resolution

.github/workflows/CI.yml

@@ -26,7 +26,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-18.04, ubuntu-16.04]
+        os: [ubuntu-18.04] #, ubuntu-20.04
         backend: ['tinydb', 'sqlite']
         python_version: ['3.7']
     env:
@@ -145,16 +145,17 @@ jobs:
 
       - name: Pylint PR Comment
         if: matrix.os == 'ubuntu-18.04'
-        uses: marocchino/sticky-pull-request-comment@v1
+        uses: marocchino/sticky-pull-request-comment@v2
         with:
-          GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
           header: pylint-comment
           path: ./pylint.md
+          recreate: true
 
       - name: Upload Coverage info
         if: always()
-        uses: codecov/codecov-action@v1
+        uses: codecov/codecov-action@v2
         with:
+          token: ${{ secrets.CODECOV_TOKEN }}
           flags: unittests,CI
           name: codecov-${{ matrix.os }}
           fail_ci_if_error: true # optional (default = false)

.github/workflows/nightly.yml

@@ -1,7 +1,7 @@
-# The last two jobs, unit testing and runnng TAU=full installation wait until the first finishes and re-uses the TAU=minimal install
 # Unfortunately, there is a lot of duplicated code that could be simplified/eliminated with YAML anchors and aliases,
 # but GitHub Actions does not yet support YAML anchors and aliases.
-# Clever use of global environment variables could help eliminate some of it, but the best options would be to just use aliases and anchors
+# Clever use of global environment variables could help eliminate some of it, but the best options would be to just use
+# aliases and anchors
 
 name: TAU nightly testing
 
@@ -20,69 +20,77 @@ env:
 
 jobs:
   Install-taucmdr-minimal:
+    name: Install and Test TAU Commander
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
       matrix:
-        os: [ubuntu-18.04, ubuntu-16.04]
-        python_version: ['2.7']
-
+        os: [ubuntu-18.04] #, ubuntu-20.04
+        python_version: ['3.7']
+    env:
+      OS: ${{ matrix.os }}
+      PY_VER: ${{ matrix.python_version }}
     steps:
       - uses: actions/checkout@v2
         with:
           fetch-depth: 9999
 
       - name: Install system packages
         run: |
+          # Ensure that we have default system compilers and MPI for testing
           sudo apt-get update -qq || true
           sudo apt-get install -y --no-install-recommends gcc g++ gfortran mpi-default-bin mpi-default-dev
 
-      # - name: Setup Python
-      #   uses: actions/setup-python@v1
-      #   with:
-      #     python-version: '3.6'
-      #     architecture: 'x64'
-
       - name: System info
         id: info
         run: |
+          # Get info for debugging and set some environment variables to use later
           uname -a
           mount
+          df -h
           gcc --version
           echo "github.event_name: ${{ github.event_name }}"
           echo "github.ref:        ${{ github.ref }}"
           echo "matrix.os:         ${{ matrix.os }}"
+          echo "Pythons found:"
+          type -a python
+          while read -r line ; do "${line##* is }" --version; done <<< $(type -a python)
           export INSTALLDIR="${HOME}/${INSTALLDIR}"
           echo "::set-output name=install_dir::${INSTALLDIR}"
-          echo "::set-env name=INSTALLDIR::${INSTALLDIR}"
+          echo "INSTALLDIR=${INSTALLDIR}" >> "${GITHUB_ENV}"
           echo "::set-output name=home_dir::${HOME}"
           echo "::set-output name=taucmdr_system::${INSTALLDIR}/${__TAUCMDR_SYSTEM_PREFIX__}"
-          echo "::set-env name=__TAUCMDR_SYSTEM_PREFIX__::${INSTALLDIR}/${__TAUCMDR_SYSTEM_PREFIX__}"
+          echo "__TAUCMDR_SYSTEM_PREFIX__=${INSTALLDIR}/${__TAUCMDR_SYSTEM_PREFIX__}" >> "${GITHUB_ENV}"
+          echo "::set-output name=branch::${GITHUB_REF#refs/*/}"
+          echo "BRANCH=${GITHUB_REF#refs/*/}" >> "${GITHUB_ENV}"
+          echo "BRANCH: ${GITHUB_REF#refs/*/}"
 
-# No caching available for cron jobs
+      # No caching available for cron jobs
 
       - name: Install TAU Commander
         run: |
           make INSTALLDIR="${INSTALLDIR}" install
-          echo "::add-path::${INSTALLDIR}/conda/bin"
+          echo "${INSTALLDIR}/conda/bin" >> $GITHUB_PATH
           export PATH="${INSTALLDIR}/conda/bin:${PATH}"
           which python
           which pip
           python -m pip install -U pip
           python -m pip install -U --prefix "${INSTALLDIR}/conda" -r requirements-dev.txt
           cd "${HOME}"
           zip -vr taucmdr-nightly.zip ${INSTALLDIR##*/} -x "taucmdr/system/src/*" -x "taucmdr/conda/*"
+          type -a python
+          while read -r line ; do "${line##* is }" --version; done <<< $(type -a python)
 
       - name: Upload TAU Commander install log
         if: always()
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v2
         with:
           name: taucmdr-tau-minimal-debug-log-${{ matrix.os }}
           path: ${{ steps.info.outputs.home_dir }}/.local/taucmdr/debug_log
 
       - name: Upload TAU Commander minimal install
         if: always()
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v2
         with:
           name: taucmdr-installation-${{ matrix.os }}
           path: ${{ steps.info.outputs.home_dir }}/taucmdr-nightly.zip
@@ -103,20 +111,22 @@ jobs:
         run: |
           rm ~/.local/taucmdr/debug_log || true
           export __TAUCMDR_DB_BACKEND__=tinydb
+          rm -f ./coverage.xml || true
           coverage run setup.py test
+          coverage xml
 
       - name: Test TAU Commander with SQLite backend
         run: |
           export __TAUCMDR_DB_BACKEND__=sqlite
           coverage run setup.py test
+          coverage xml
 
       - name: Build sphinx docs
-        run: |
-          python setup.py build_sphinx
+        run: python setup.py build_sphinx
 
       - name: Upload TAU Commander unit test log
         if: always()
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v2
         with:
           name: taucmdr-unit-test-debug-log-${{ matrix.os }}
           path: ${{ steps.info.outputs.home_dir }}/.local/taucmdr/debug_log
@@ -133,7 +143,7 @@ jobs:
 
       - name: Upload nightly TAU validate
         if: always()
-        uses: actions/upload-artifact@v1
+        uses: actions/upload-artifact@v2
         with:
           name: taucmdr-full-tau-validate-${{ matrix.os }}-${{ github.sha }}
           path: ${{ steps.info.outputs.home_dir }}/tau-tests-validate

Dockerfile

@@ -6,7 +6,7 @@ RUN DEBIAN_FRONTEND=noninteractive set -v && \
         rm -rf /var/lib/apt/lists/* && \
         localedef -i en_US -c -f UTF-8 -A /usr/share/locale/locale.alias en_US.UTF-8 && \
         useradd -ms /bin/bash tau
-ENV LANG=en_US.UTF-8 INSTALLDIR=/home/tau/taucmdr
+ENV LANG=en_US.UTF-8 INSTALLDIR=/home/tau/taucmdr __TAUCMDR_DEVELOPER__=1
 COPY .gitignore .gitattributes .version.sh LICENSE README.md Makefile setup.py MANIFEST.in requirements-dev.txt /tmp/taucmdr/
 COPY scripts /tmp/taucmdr/scripts
 COPY packages /tmp/taucmdr/packages
@@ -15,7 +15,7 @@ COPY examples /tmp/taucmdr/examples
 COPY .testfiles /tmp/taucmdr/.testfiles
 COPY .git /tmp/taucmdr/.testfiles
 WORKDIR /tmp/taucmdr
-RUN ls -la ; make clean ; make install ; chown -R tau:tau ${INSTALLDIR}
+RUN ls -la ; make clean ; mkdir ${INSTALLDIR}; make install; chown -R tau:tau ${INSTALLDIR}
 USER tau
 WORKDIR /home/tau/src
 ENV PATH="/home/tau/taucmdr/conda/bin:$PATH:/home/tau/taucmdr/bin"

Makefile

@@ -56,8 +56,8 @@ endif
 
 # Get build system locations from configuration file or command line
 ifneq ("$(wildcard setup.cfg)","")
-	BUILDDIR = $(shell grep '^build-base =' setup.cfg | sed 's/build-base = //')
-	INSTALLDIR = $(shell grep '^prefix =' setup.cfg | sed 's/prefix = //')
+	BUILDDIR ?= $(shell grep '^build-base =' setup.cfg | sed 's/build-base = //')
+	INSTALLDIR ?= $(shell grep '^prefix =' setup.cfg | sed 's/prefix = //')
 endif
 ifeq ($(BUILDDIR),)
 	BUILDDIR=build
@@ -128,9 +128,9 @@ else
 	endif
 endif
 
-CONDA_VERSION = latest
+CONDA_VERSION = v2.2.0
 
-CONDA_REPO = https://github.com/ParaToolsInc/CommanderConda/releases/$(CONDA_VERSION)/download
+CONDA_REPO = https://github.com/ParaToolsInc/CommanderConda/releases/download/$(CONDA_VERSION)
 CONDA_PKG = CommanderConda3-$(CONDA_OS)-$(CONDA_ARCH).sh
 CONDA_URL = $(CONDA_REPO)/$(CONDA_PKG)
 CONDA_SRC = system/src/$(CONDA_PKG)

README.md

@@ -71,8 +71,10 @@ TAU Commander developers should visit the [developer documentation](http://parat
 Acknowledgements
 ================
 
-This work is supported by the United States Department of Energy under
-DoE SBIR grant DE-SC0009593.
+Initial development of TAU Commander was supported by the United States
+Department of Energy under DOE SBIR award DE-SC0009593. Development of support
+for machine learning and artificial intelligence applications is supported by
+the United States Department of Energy under DOE SBIR award DE-SC0019700.
 
 The work on extending TAU Commander for OpenSHMEM was supported by the
 United States Department of Defense (DoD) and used resources of the

packages/taucmdr/cf/compiler/__init__.py

@@ -427,7 +427,7 @@ class InstalledCompilerCreator(type):
     and `icc` would be probed twice. With this metaclass, ``b is a == True`` and `icc` is only invoked once.
     """
     def __call__(cls, absolute_path, info, **kwargs):
-        assert isinstance(absolute_path, str) and os.path.isabs(absolute_path)
+        assert absolute_path == '' or (isinstance(absolute_path, str) and os.path.isabs(absolute_path))
         assert isinstance(info, _CompilerInfo)
         # Don't allow unchecked values into the instance cache
         if kwargs:
@@ -636,7 +636,10 @@ def probe(cls, command, family=None, role=None):
         assert isinstance(role, _CompilerRole) or role is None
         absolute_path = util.which(command)
         if not absolute_path:
-            raise ConfigurationError("Compiler '%s' not found on PATH" % command)
+            if family is None:
+                absolute_path = ''
+            else:
+                raise ConfigurationError("Compiler '%s' not found on PATH" % command)
         command = os.path.basename(absolute_path)
         LOGGER.debug("Probe: command='%s', abspath='%s', family='%s', role='%s'",
                      command, absolute_path, family, role)
@@ -764,6 +767,11 @@ def __init__(self, family):
                         LOGGER.warning(err)
                         continue
                     self.members.setdefault(role, []).append(installed)
+        for role, info_list in family.members.items():
+            for info in info_list:
+              if family.name == 'None':
+                  installed = InstalledCompiler(info.command, info)
+                  self.members.setdefault(role, []).append(installed)
         if not self.members:
             cmds = [info.command for info_list in family.members.values() for info in info_list]
             raise ConfigurationError(f"{self.family.name} {self.family.kbase.description} not found.",

packages/taucmdr/cf/compiler/cuda.py

@@ -38,5 +38,7 @@
 IBM = CUDA_COMPILERS.add('IBM', family_regex=r'^IBM XL', version_flags=['-qversion'],
                          FC='xlcuf')
 
+NONE = CUDA_COMPILERS.add('None', CXX='', FC='')
+
 CUDA_CXX = CUDA_COMPILERS.roles['CXX']
 CUDA_FC = CUDA_COMPILERS.roles['FC']

packages/taucmdr/cf/compiler/mpi.py

@@ -66,6 +66,10 @@
                          show_wrapper_flags=['-craype-verbose', '--version', '-E'],
                          CC='cc', CXX='CC', FC='ftn')
 
+NONE = MPI_COMPILERS.add('None', #family_regex='',
+                         CC='', CXX='', FC='')
+
+
 MPI_CC = MPI_COMPILERS.roles['CC']
 MPI_CXX = MPI_COMPILERS.roles['CXX']
 MPI_FC = MPI_COMPILERS.roles['FC']

packages/taucmdr/cf/software/tau_installation.py

@@ -236,6 +236,7 @@ def __init__(self, sources, target_arch, target_os, compilers,
                  forced_makefile=None,
                  dyninst=False,
                  mpit=False,
+                 unwinder='libunwind',
                  unwind_depth=0):
         """Initialize the TAU installation wrapper class.
 
@@ -274,7 +275,7 @@ def __init__(self, sources, target_arch, target_os, compilers,
             measure_mpi (bool): If True then measure time spent in MPI calls.
             measure_openmp (str): String specifying OpenMP measurement method, one of "ignore", "ompt", or "opari".
             measure_cuda (bool): If True then measure time spent in CUDA calls.
-            meaure_level_zero (bool): If True then use Intel oneAPI level 0 tool iterface
+            meaure_level_zero (bool): If True then use Intel oneAPI level 0 tool interface
             measure_shmem (bool): If True then measure time spent in SHMEM calls.
             measure_heap_usage (bool): If True then measure memory usage.
             measure_system_load (bool): If True then measure the system load.
@@ -298,6 +299,7 @@ def __init__(self, sources, target_arch, target_os, compilers,
             sampling_period (int): Sampling period in microseconds; set to 0 to use architecture specific defaults.
             track_memory_footprint (bool): If True then track memory footprint.
             mpit (bool): If True then enable MPI-T profiling interface.
+            unwinder (str): Tool used to unwind code
             forced_makefile (str): Path to external makefile if forcing TAU_MAKEFILE or None.
         """
         assert minimal in (True, False)
@@ -350,6 +352,7 @@ def __init__(self, sources, target_arch, target_os, compilers,
         assert isinstance(sampling_period, int)
         assert track_memory_footprint in (True, False)
         assert isinstance(forced_makefile, str) or forced_makefile is None
+        assert isinstance(unwinder, str)
         super().__init__('tau', 'TAU Performance System',
                                               sources, target_arch, target_os, compilers,
                                               REPOS, COMMANDS, None, None)
@@ -421,13 +424,14 @@ def __init__(self, sources, target_arch, target_os, compilers,
         self.track_memory_footprint = track_memory_footprint
         self.tags = tags
         self.forced_makefile = forced_makefile
+        self.unwinder = unwinder
         self.dyninst = dyninst
         self.unwind_depth = unwind_depth
         self.uses_pdt = not minimal and (self.source_inst == 'automatic' or self.shmem_support)
         self.uses_binutils = not minimal and (self.target_os is not DARWIN) and 'binutils' in sources
-        self.uses_libunwind = not minimal and (self.target_os is not DARWIN) and 'libunwind' in sources
-        self.uses_libdwarf = not minimal and (self.target_os is not DARWIN) and 'libdwarf' in sources
+        self.uses_libunwind = not minimal and (self.target_os is not DARWIN) and 'libunwind' in sources and self.unwinder == 'libunwind'
         self.uses_libelf = not minimal and (self.target_os is not DARWIN) and 'libelf' in sources
+        self.uses_libdwarf = not minimal and (self.target_os is not DARWIN) and 'libdwarf' in sources and self.uses_libelf
         self.uses_papi = not minimal and bool(len([met for met in self.metrics if 'PAPI' in met]))
         self.uses_scorep = not minimal and (self.profile == 'cubex')
         self.uses_ompt = not minimal and (self.measure_openmp == 'ompt')
@@ -452,7 +456,7 @@ def __init__(self, sources, target_arch, target_os, compilers,
         for met in self.metrics:
             mets.extend(met.split(','))
         self.metrics = mets
-        uses = lambda pkg: sources[pkg] if forced_makefile else getattr(self, 'uses_'+pkg)
+        uses = lambda pkg: sources.get(pkg, False) if forced_makefile else getattr(self, 'uses_'+pkg)
         for pkg in 'binutils', 'libunwind', 'libelf', 'libdwarf', 'papi', 'pdt', 'ompt', 'libotf2', 'sqlite3', 'level_zero':
             if uses(pkg):
                 self.add_dependency(pkg, sources)
@@ -778,7 +782,8 @@ def configure(self):
                     '-tag=%s' % self.uid,
                     '-arch=%s' % self.tau_magic.name,
                     '-bfd=%s' % binutils.install_prefix if binutils else None,
-                    '-unwind=%s' % libunwind.install_prefix if libunwind else None,
+                    '-unwinder=%s' % self.unwinder,
+                    '-unwind=%s' % libunwind.install_prefix if self.unwinder == 'libunwind' and libunwind else None,
                    ] if flag]
             if util.create_subprocess(cmd, cwd=self._src_prefix, stdout=False, show_progress=True):
                 raise SoftwarePackageError('TAU configure failed')
@@ -862,7 +867,8 @@ def configure(self):
                   '-fortran=%s' % fortran_magic if fortran_magic else None,
                   '-bfd=%s' % binutils.install_prefix if binutils else None,
                   '-papi=%s' % papi.install_prefix if papi else None,
-                  '-unwind=%s' % libunwind.install_prefix if libunwind else None,
+                  '-unwinder=%s' % self.unwinder,
+                  '-unwind=%s' % libunwind.install_prefix if self.unwinder == 'libunwind' and libunwind else None,
                   '-dwarf=%s' % libdwarf.install_prefix if libdwarf else None,
                   '-elf=%s' % libelf.install_prefix if libdwarf else None,
                   '-scorep=%s' % scorep.install_prefix if scorep else None,

packages/taucmdr/cli/commands/project/list.py

@@ -81,6 +81,7 @@ def main(self, argv):
         if single:
             storage = levels[0]
             ctrl = Project.controller(storage)
+            # pylint: disable=unexpected-keyword-arg
             proj = ctrl.one({'name': keys[0]}, context=False)
             for cmd, prop in ((target_list_cmd, 'targets'),
                               (application_list_cmd, 'applications'),

packages/taucmdr/cli/commands/target/copy.py

@@ -35,6 +35,7 @@
 from taucmdr.cf.compiler.host import HOST_COMPILERS
 from taucmdr.cf.compiler.mpi import MPI_COMPILERS
 from taucmdr.cf.compiler.shmem import SHMEM_COMPILERS
+from taucmdr.cf.compiler.cuda import CUDA_COMPILERS
 from taucmdr.cf.software.tau_installation import TauInstallation
 
 
@@ -96,6 +97,10 @@ def _construct_parser(self):
 
         group = parser.add_argument_group('Symmetric Hierarchical Memory (SHMEM) arguments')
         self._configure_argument_group(group, SHMEM_COMPILERS, '--shmem-compilers', 'shmem_family')
+
+        group = parser.add_argument_group('CUDA arguments')
+        self._configure_argument_group(group, CUDA_COMPILERS, '--cuda-compilers', 'cuda_family')
+
         return parser
 
     def main(self, argv):

packages/taucmdr/cli/commands/target/edit.py

@@ -37,6 +37,7 @@
 from taucmdr.cf.compiler.host import HOST_COMPILERS
 from taucmdr.cf.compiler.mpi import MPI_COMPILERS
 from taucmdr.cf.compiler.shmem import SHMEM_COMPILERS
+from taucmdr.cf.compiler.cuda import CUDA_COMPILERS
 from taucmdr.cf.software.tau_installation import TauInstallation
 
 
@@ -99,6 +100,9 @@ def _construct_parser(self):
 
         group = parser.add_argument_group('Symmetric Hierarchical Memory (SHMEM) arguments')
         self._configure_argument_group(group, SHMEM_COMPILERS, '--shmem-compilers', 'shmem_family')
+
+        group = parser.add_argument_group('CUDA arguments')
+        self._configure_argument_group(group, CUDA_COMPILERS, '--cuda-compilers', 'cuda_family')
         return parser
 
     def _update_record(self, store, data, key):