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 launch_command( self, cmd, dry=False, mount_points=None, verbose=True, ): full_cmd = self.create_slurm_command(cmd, mount_points=mount_points) # full_cmd = self.create_singularity_cmd(cmd, mount_points=mount_points) utils.add_to_script( full_cmd, path=self.TMP_FILE, verbose=True, overwrite=self._overwrite_script, )