def launch_command(
self,
cmd,
dry=False,
mount_points=None,
verbose=False,
):
full_cmd = self.create_singularity_cmd(cmd, mount_points=mount_points)
utils.add_to_script(
full_cmd,
path=self.TASK_FILE,
verbose=True,
overwrite=self._overwrite_task_script,
)
cmd_list = utils.CommandBuilder()
cmd_list.append('module load gcc openmpi')
cmd_list.append('ht_helper.sh -m "python/3.5" -t {}'.format(
self._taskfile_path_on_brc))
sbatch_cmd = slurm_util.wrap_command_with_sbatch(
cmd_list.to_string(),
self._slurm_config,
self._n_tasks_total,
)
utils.add_to_script(
sbatch_cmd,
path=self.SBATCH_FILE,
verbose=True,
overwrite=True,
)
def create_slurm_command(self, cmd, mount_points=None):
singularity_cmd = self.create_singularity_cmd(
cmd,
mount_points=mount_points,
)
full_cmd = slurm_util.wrap_command_with_sbatch(
singularity_cmd,
self._slurm_config,
n_tasks=1,
)
return full_cmd
