update source files and add rhodo test

eessi/testsuite/tests/apps/lammps/lammps.py

@@ -21,6 +21,7 @@ class EESSI_LAMMPS(rfm.RunOnlyRegressionTest):
 
     # Parameterize over all modules that start with LAMMPS
     module_name = parameter(utils.find_modules('LAMMPS'))
+    sourcesdir= 'src/lj'
     executable = 'lmp -in in.lj'
 
     # Set sanity step
@@ -103,3 +104,97 @@ def set_omp_num_threads(self):
         omp_num_threads = self.num_cpus_per_task
         self.env_vars['OMP_NUM_THREADS'] = omp_num_threads
         utils.log(f'env_vars set to {self.env_vars}')
+
+
+@rfm.simple_test
+class EESSI_LAMMPS_rhodo(rfm.RunOnlyRegressionTest):
+    scale = parameter(SCALES.keys())
+    valid_prog_environs = ['default']
+    valid_systems = ['*']
+    time_limit = '30m'
+    device_type = parameter([DEVICE_TYPES[CPU], DEVICE_TYPES[GPU]])
+
+    # Parameterize over all modules that start with LAMMPS
+    module_name = parameter(utils.find_modules('LAMMPS'))
+    sourcesdir= 'src/rhodo'
+    readonly_files = ["data.rhodo"]
+    executable = 'lmp -in in.rhodo'
+
+    # Set sanity step
+    @deferrable
+    def assert_lammps_openmp_treads(self):
+        '''Assert that OpenMP thread(s) per MPI task is set'''
+        n_threads = sn.extractsingle(
+            r'^  using (?P<threads>[0-9]+) OpenMP thread\(s\) per MPI task', self.stdout, 'threads', int)
+        utils.log(f'OpenMP thread(s) is {n_threads}')
+
+        return sn.assert_eq(n_threads, self.num_cpus_per_task)
+
+    @deferrable
+    def assert_lammps_processor_grid(self):
+        '''Assert that the processor grid is set correctly'''
+        grid = list(sn.extractall(
+            '^  (?P<x>[0-9]+) by (?P<y>[0-9]+) by (?P<z>[0-9]+) MPI processor grid', self.stdout, tag=['x', 'y', 'z']))
+        n_cpus = int(grid[0][0]) * int(grid[0][1]) * int(grid[0][2])
+
+        return sn.assert_eq(n_cpus, self.num_tasks)
+
+    @deferrable
+    def assert_total_nr_neigbors(self):
+        '''Assert that the test calulated the right number of neighbours'''
+        neighbours = list(sn.extractall(
+            r'^Total # of neighbors = (?P<neighbours>\S+)', self.stdout, 'neighbours'))
+        n_neighbours = int(neighbours[0])
+
+        return sn.assert_eq(n_neighbours, 12028093)
+
+
+    @sanity_function
+    def assert_sanity(self):
+        '''Check all sanity criteria'''
+        return sn.all([
+            self.assert_lammps_openmp_treads(),
+            self.assert_lammps_processor_grid(),
+            self.assert_total_nr_neigbors(),
+        ])
+
+    @performance_function('img/s')
+    def perf(self):
+        return sn.extractsingle(r'^(?P<perf>[.0-9]+)% CPU use with [0-9]+ MPI tasks x [0-9]+ OpenMP threads', self.stdout, 'perf', float)
+
+    @run_after('init')
+    def run_after_init(self):
+        """hooks to run after init phase"""
+
+        # Filter on which scales are supported by the partitions defined in the ReFrame configuration
+        hooks.filter_supported_scales(self)
+
+        hooks.filter_valid_systems_by_device_type(self, required_device_type=self.device_type)
+
+        hooks.set_modules(self)
+
+        # Set scales as tags
+        hooks.set_tag_scale(self)
+
+    @run_after('setup')
+    def run_after_setup(self):
+        """hooks to run after the setup phase"""
+        # TODO: Have not tested with GPUs yet
+        if self.device_type == 'cpu':
+            hooks.assign_tasks_per_compute_unit(test=self, compute_unit=COMPUTE_UNIT['CPU'])
+        elif self.device_type == 'gpu':
+            hooks.assign_tasks_per_compute_unit(test=self, compute_unit=COMPUTE_UNIT['GPU'])
+        else:
+            raise NotImplementedError(f'Failed to set number of tasks and cpus per task for device {self.device_type}')
+
+    @run_after('setup')
+    def set_omp_num_threads(self):
+        """
+        Set number of OpenMP threads.
+        Set OMP_NUM_THREADS.
+        Set default number of OpenMP threads equal to number of CPUs per task.
+        """
+
+        omp_num_threads = self.num_cpus_per_task
+        self.env_vars['OMP_NUM_THREADS'] = omp_num_threads
+        utils.log(f'env_vars set to {self.env_vars}')