Include QMCPACK

.github/workflows/h5bench-hdf5-1.12.0.yml

@@ -28,7 +28,12 @@ jobs:
           cd build
 
           cmake .. \
-            -DH5BENCH_ALL=ON
+            -DH5BENCH_METADATA=ON \
+            -DH5BENCH_EXERCISER=ON \
+            -DH5BENCH_AMREX=ON \
+            -DH5BENCH_OPENPMD=ON \
+            -DH5BENCH_E3SM=ON \
+            -DH5BENCH_QMCPACK=OFF
           make -j 2
           make install
 

.github/workflows/h5bench-hdf5-1.13.0.yml

@@ -22,9 +22,16 @@ jobs:
 
       - name: Dependencies
         run: |
+          sudo apt-get update
+          sudo apt-get install libblas-dev liblapack-dev -y
+
           # VOL-ASYNC
           git clone --recursive https://github.com/hpc-io/vol-async.git /opt/vol-async
 
+          # FFTW
+          wget https://www.fftw.org/fftw-3.3.10.tar.gz
+          tar zxf fftw-3.3.10.tar.gz
+
       - name: Build Argobots
         run: |
           export ABT_DIR=/opt/argobots
@@ -37,6 +44,14 @@ jobs:
           make -j 2
           make install
 
+      - name: Build FFTW
+        run: |
+          cd fftw-3.3.10
+
+          ./configure
+
+          sudo make install
+
       - name: Build VOL-ASYNC
         run: |
           export HDF5_DIR=/opt/hdf5
@@ -266,6 +281,13 @@ jobs:
           cd build-sync
           ./h5bench --debug --abort-on-failure ../samples/sync-e3sm.json
 
+      - name: Test h5bench SYNC qmcpack
+        run: |
+          export LD_LIBRARY_PATH=/opt/hdf5/lib:$LD_LIBRARY_PATH
+
+          cd build
+          ./h5bench --debug --abort-on-failure ../samples/sync-qmcpack.json
+
       - name: Test h5bench ASYNC write/read
         run: |
           export HDF5_DIR=/opt/hdf5

.github/workflows/h5bench-hdf5-develop.yml

@@ -22,14 +22,18 @@ jobs:
       - name: Dependencies
         run: |
           sudo apt-get update
-          sudo apt-get install cmake gcc gdb libtool zlib1g-dev python3 libopenmpi-dev -y
+          sudo apt-get install cmake gcc gdb libtool zlib1g-dev python3 libopenmpi-dev libblas-dev liblapack-dev -y
 
           # HDF5
           git clone https://github.com/HDFGroup/hdf5.git
 
           # VOL-ASYNC
           git clone --recursive https://github.com/hpc-io/vol-async.git /opt/vol-async
 
+          # FFTW
+          wget https://www.fftw.org/fftw-3.3.10.tar.gz
+          tar zxf fftw-3.3.10.tar.gz
+
       - name: Build HDF5 develop
         run: |
           export HDF5_DIR=/opt/hdf5
@@ -59,6 +63,14 @@ jobs:
           make -j 2
           make install
 
+      - name: Build FFTW
+        run: |
+          cd fftw-3.3.10
+
+          ./configure
+
+          sudo make install
+
       - name: Build VOL-ASYNC
         run: |
           export HDF5_DIR=/opt/hdf5
@@ -405,6 +417,17 @@ jobs:
           cd build-sync
           ./h5bench --debug --abort-on-failure ../samples/sync-e3sm.json
 
+      - name: Test h5bench SYNC qmcpack
+        run: |
+          export HDF5_HOME=/opt/hdf5
+          export ABT_HOME=/opt/argobots
+          export ASYNC_HOME=/opt/vol-async
+
+          export LD_LIBRARY_PATH=$ASYNC_HOME/lib:$HDF5_HOME/lib:$ABT_HOME/lib:$LD_LIBRARY_PATH
+
+          cd build-sync
+          ./h5bench --debug --abort-on-failure ../samples/sync-qmcpack.json
+
       - name: Test h5bench ASYNC write/read
         run: |
           export HDF5_DIR=/opt/hdf5

.gitmodules

@@ -9,3 +9,6 @@
 [submodule "e3sm"]
 	path = e3sm
 	url = https://github.com/Parallel-NetCDF/E3SM-IO
+[submodule "qmcpack"]
+	path = qmcpack
+	url = https://github.com/QMCPACK/qmcpack

CMakeLists.txt

@@ -28,6 +28,7 @@ option(H5BENCH_EXERCISER        "Enable Exerciser benchmark"        OFF)
 option(H5BENCH_AMREX            "Enable AMReX benchmark"            OFF)
 option(H5BENCH_OPENPMD          "Enable OpenPMD benchmark"          OFF)
 option(H5BENCH_E3SM             "Enable E3SM benchmark"             OFF)
+option(H5BENCH_QMCPACK          "Enable QMCPACK benchmark"          OFF)
 
 message(STATUS "h5bench baseline: ON")
 
@@ -39,13 +40,15 @@ if(H5BENCH_ALL)
     set(H5BENCH_AMREX ON)
     set(H5BENCH_OPENPMD ON)
     set(H5BENCH_E3SM ON)
+    set(H5BENCH_QMCPACK ON)
 endif()
 
 message(STATUS "h5bench METADATA: ${H5BENCH_METADATA}")
 message(STATUS "h5bench EXERCISER: ${H5BENCH_EXERCISER}")
 message(STATUS "h5bench AMREX: ${H5BENCH_AMREX}")
 message(STATUS "h5bench OPENPMD: ${H5BENCH_OPENPMD}")
 message(STATUS "h5bench E3SM: ${H5BENCH_E3SM}")
+message(STATUS "h5bench QMCPACK: ${H5BENCH_QMCPACK}")
 
 # HDF5 Dependency #############################################################
 #
@@ -258,6 +261,29 @@ configure_file(${CMAKE_SOURCE_DIR}/src/h5bench.py ${CMAKE_BINARY_DIR}/h5bench CO
 configure_file(${CMAKE_SOURCE_DIR}/src/h5bench_version.py ${CMAKE_BINARY_DIR}/h5bench_version.py COPYONLY)
 configure_file(${CMAKE_SOURCE_DIR}/src/h5bench_configuration.py.in ${CMAKE_BINARY_DIR}/h5bench_configuration.py)
 
+# QMCPACK #####################################################################
+#
+# https://github.com/QMCPACK/qmcpack
+
+if(H5BENCH_QMCPACK)
+    if(CMAKE_COMPILER_IS_GNUCC AND CMAKE_CXX_COMPILER_VERSION VERSION_GREATER_EQUAL 9.2.0)
+        if(${HDF5_VERSION} VERSION_GREATER_EQUAL "1.12.1")
+            set(ENV{HDF5_ROOT} ${HDF5_HOME})
+            set(QMC_BUILD_SANDBOX_ONLY ON)
+
+            add_subdirectory(qmcpack)
+
+            execute_process(
+                COMMAND ${CMAKE_COMMAND} -E copy ${CMAKE_BINARY_DIR}/qmcpack/bin/restart ${CMAKE_BINARY_DIR}/h5bench_qmcpack
+            )
+        else()
+            message(FATAL_ERROR "QMCPACK requires at least HDF5 1.12.1")
+        endif()
+    else()
+        message(FATAL_ERROR "QMCPACK requires at least gcc-9.2")
+    endif()
+endif()
+
 # Install binaries ############################################################
 
 install(
@@ -332,6 +358,15 @@ if(H5BENCH_AMREX)
     endif()
 endif()
 
+if(H5BENCH_QMCPACK)
+    install(
+        FILES
+        h5bench_qmcpack
+        PERMISSIONS OWNER_EXECUTE OWNER_WRITE OWNER_READ
+        DESTINATION bin
+    )
+endif()
+
 # Testing #####################################################################
 
 add_subdirectory(${CMAKE_CURRENT_SOURCE_DIR}/tests)

docs/source/index.rst

@@ -35,6 +35,7 @@ Exerciser            ``h5bench_exerciser``       |:white_check_mark:| |:white_la
 OpenPMD (write)      ``h5bench_openpmd_write``   |:white_check_mark:| |:white_large_square:|   |:white_large_square:|   |:white_large_square:| 
 OpenPMD (read)       ``h5bench_openpmd_read``    |:white_check_mark:| |:white_large_square:|   |:white_large_square:|   |:white_large_square:| 
 E3SM-IO              ``h5bench_e3sm``            |:white_check_mark:| |:white_large_square:|   |:white_large_square:|   |:white_check_mark:| 
+QMCPACK              ``h5bench_qmcpack``         |:white_check_mark:| |:white_large_square:|   |:white_large_square:|   |:white_check_mark:|  
 ==================== =========================== ==================== ======================== ======================== ========================
 
 .. toctree::
@@ -54,6 +55,7 @@ E3SM-IO              ``h5bench_e3sm``            |:white_check_mark:| |:white_la
    openpmd
    exerciser
    e3sm
+   qmcpack
 
 .. toctree::
    :maxdepth: 2

docs/source/qmcpack.rst

@@ -0,0 +1,38 @@
+QMCPACK
+========
+
+QMCPACK is an open-source production-level many-body ab initio Quantum Monte Carlo code for computing the electronic structure of atoms, molecules, 2D nanomaterials and solids. The solid-state capabilities include metallic systems as well as insulators.
+
+QMCPACK has a checkpoint/restart miniapp which has been integrated into `h5bench`. It dumps walker configurations and random number seeds to the HDF5 files and then reads them in and check the correctness. To have good performance at large scale, HDF5 version >= 1.10 is needed.
+
+You can find more information in QMCPACK `GitHub repository <https://github.com/QMCPACK/qmcpack>`_.
+
+Configuration
+-------------
+
+You can configure QMCPACK benchmark with the following options. Notice that if you use the ``configuration.json`` approach to define the runs for ``h5bench``, we will automatically generate the final configuration file based on the options you provide in the JSON file. For standalone usage of this benchmark, you can refer to E3SM-IO repository.
+
+====================== ==============================================================================
+**Parameter**          **Description**                                                             
+====================== ==============================================================================
+``i``                  Number of Monte Carlo steps
+``g``                  Tiling (``tiling_1 tiling_2 tiling_3``)
+``s``                  Random seed
+``w``                  Number of walkers
+``r``                  Maximum pair distance (i.e., ``rmax``)
+====================== ==============================================================================
+
+JSON Configuration (recomended)
+^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
+
+To run an instance of AMReX HDF5 benchmark you need to include the following in the ``benchmarks`` property of your ``configuration.json`` file:
+
+.. code-block::
+
+    {
+        "benchmark": "qmcpack",
+        "configuration": {
+            "i": "100",
+            "g": "4 4 1"
+        }
+    }

samples/sync-qmcpack.json

@@ -0,0 +1,22 @@
+{
+    "mpi": {
+        "command": "mpirun",
+        "configuration": "--allow-run-as-root --oversubscribe -np 2 "
+    },
+    "vol": {
+
+    },
+    "file-system": {
+
+    },
+    "directory": "storage",
+    "benchmarks": [
+        {
+            "benchmark": "qmcpack",
+            "configuration": {
+                "i": "100",
+                "g": "4 4 1"
+            }
+        }
+    ]
+}

src/h5bench.py

@@ -32,6 +32,7 @@ class H5bench:
     H5BENCH_OPENPMD_WRITE = 'h5bench_openpmd_write'
     H5BENCH_OPENPMD_READ = 'h5bench_openpmd_read'
     H5BENCH_E3SM = 'h5bench_e3sm'
+    H5BENCH_QMCPACK = 'h5bench_qmcpack'
 
     def __init__(self, setup, prefix=None, debug=None, abort=None, validate=None, filter=None):
         """Initialize the suite."""
@@ -236,6 +237,8 @@ def run(self):
                 self.run_openpmd(id, benchmark)
             elif name == 'e3sm':
                 self.run_e3sm(id, benchmark)
+            elif name == 'qmcpack':
+                self.run_qmcpack(id, benchmark)
             else:
                 self.logger.critical('{} - Unsupported benchmark/kernel')
 
@@ -855,6 +858,70 @@ def run_e3sm(self, id, setup):
         except Exception as e:
             self.logger.error('Unable to run the benchmark: %s', e)
 
+    def run_qmcpack(self, id, setup):
+        """Run the QMCPACK benchmark."""
+        if not self.is_available(self.H5BENCH_QMCPACK):
+            self.logger.critical('{} is not available'.format(self.H5BENCH_QMCPACK))
+
+            sys.exit(os.EX_UNAVAILABLE)
+
+        try:
+            start = time.time()
+
+            configuration = setup['configuration']
+
+            parameters = []
+
+            # Create the configuration parameter list
+            for key in configuration:
+                if key not in ['d'] and configuration[key]:
+                    parameters.append('-{} {} '.format(key, configuration[key]))
+
+            # Waiting for https://github.com/QMCPACK/qmcpack/pull/4343 to be merged
+            # parameters.append('-d {}/{} '.format(self.directory, id))
+
+            if self.prefix:
+                benchmark_path = self.prefix + '/' + self.H5BENCH_QMCPACK
+            else:
+                if os.path.isfile(h5bench_configuration.__install__ + '/' + self.H5BENCH_QMCPACK):
+                    benchmark_path = h5bench_configuration.__install__ + '/' + self.H5BENCH_QMCPACK
+                else:
+                    benchmark_path = self.H5BENCH_QMCPACK
+
+            command = '{} {} {}'.format(
+                self.mpi,
+                benchmark_path,
+                ' '.join(parameters)
+            )
+
+            self.logger.info(command)
+
+            # Make sure the command line is in the correct format
+            arguments = shlex.split(command)
+
+            stdout_file_name = '{}/{}/stdout'.format(self.directory, id)
+            stderr_file_name = '{}/{}/stderr'.format(self.directory, id)
+
+            with open(stdout_file_name, mode='w') as stdout_file, open(stderr_file_name, mode='w') as stderr_file:
+                s = subprocess.Popen(arguments, stdout=stdout_file, stderr=stderr_file, env=self.vol_environment)
+                sOutput, sError = s.communicate()
+
+                if s.returncode == 0 and not self.check_for_hdf5_error(stderr_file_name):
+                    self.logger.info('SUCCESS (all output files are located at %s/%s)', self.directory, id)
+                else:
+                    self.logger.error('Return: %s (check %s for detailed log)', s.returncode, stderr_file_name)
+
+                    if self.abort:
+                        self.logger.critical('h5bench execution aborted upon first error')
+
+                        sys.exit(os.EX_SOFTWARE)
+
+            end = time.time()
+
+            self.logger.info('Runtime: {:.7f} seconds (elapsed time, includes allocation wait time)'.format(end - start))
+        except Exception as e:
+            self.logger.error('Unable to run the benchmark: %s', e)
+
 
 def main():
     PARSER = argparse.ArgumentParser(