hpcflow.sdk.submission.shells.bash.Bash

class hpcflow.sdk.submission.shells.bash.Bash(*args, **kwargs)

Bases: Shell

Class to represent using bash on a POSIX OS to generate and submit a jobscript.

Methods

format_save_parameter
format_stream_assignment
get_version_info	Get bash version information.
prepare_JS_path
prepare_element_run_dirs
process_JS_header_args
wrap_in_subshell	Format commands to run within a subshell.

Attributes

DEFAULT_EXE
JS_DIRECT_HEADER
JS_ELEMENT_ARRAY
JS_ELEMENT_LOOP
JS_ENV_SETUP_INDENT
JS_EXT
JS_HEADER
JS_INDENT
JS_MAIN
JS_SCHEDULER_HEADER
JS_SHEBANG
executable
linux_release_file
shebang_executable

DEFAULT_EXE = '/bin/bash'

JS_DIRECT_HEADER = '{shebang}\n\n{header}\n'

JS_ELEMENT_ARRAY = 'JS_elem_idx=$(({scheduler_array_item_var} - 1))\n{main}\ncd $WK_PATH\n'

JS_ELEMENT_LOOP = 'for ((JS_elem_idx=0;JS_elem_idx<{num_elements};JS_elem_idx++))\ndo\n{main}\ndone\ncd $WK_PATH\n'

JS_ENV_SETUP_INDENT = '    '

JS_EXT = '.sh'

JS_HEADER = '{workflow_app_alias} () {{\n(\n{env_setup}{app_invoc}\\\n    --config-dir "{config_dir}"\\\n    --config-invocation-key "{config_invoc_key}"\\\n    "$@"\n)\n}}\n\nWK_PATH=`pwd`\nWK_PATH_ARG=$WK_PATH\nSUB_IDX={sub_idx}\nJS_IDX={js_idx}\nEAR_ID_FILE="$WK_PATH/artifacts/submissions/${{SUB_IDX}}/{EAR_file_name}"\nELEM_RUN_DIR_FILE="$WK_PATH/artifacts/submissions/${{SUB_IDX}}/{element_run_dirs_file_path}"\n'

JS_INDENT = '  '

JS_MAIN = 'elem_need_EARs=`sed "$((${{JS_elem_idx}} + 1))q;d" $EAR_ID_FILE`\nelem_run_dirs=`sed "$((${{JS_elem_idx}} + 1))q;d" $ELEM_RUN_DIR_FILE`\n\nfor ((JS_act_idx=0;JS_act_idx<{num_actions};JS_act_idx++))\ndo\n\n  need_EAR="$(cut -d\'{EAR_files_delimiter}\' -f $(($JS_act_idx + 1)) <<< $elem_need_EARs)"\n  if [ "$need_act" = "0" ]; then\n      continue\n  fi\n\n  run_dir="$(cut -d\'{EAR_files_delimiter}\' -f $(($JS_act_idx + 1)) <<< $elem_run_dirs)"\n  cd $WK_PATH/$run_dir\n\n  {workflow_app_alias} internal workflow $WK_PATH_ARG write-commands $SUB_IDX $JS_IDX $JS_elem_idx $JS_act_idx\n  {workflow_app_alias} internal workflow $WK_PATH_ARG set-ear-start $SUB_IDX $JS_IDX $JS_elem_idx $JS_act_idx\n  . {commands_file_name}\n  {workflow_app_alias} internal workflow $WK_PATH_ARG set-ear-end $SUB_IDX $JS_IDX $JS_elem_idx $JS_act_idx\n\ndone\n'

JS_SCHEDULER_HEADER = '{shebang}\n\n{scheduler_options}\n{header}\n'

JS_SHEBANG = '#!{shebang_executable} {shebang_args}'

property executable: List[str]

format_save_parameter(workflow_app_alias, param_name, shell_var_name)

format_stream_assignment(shell_var_name, command)

get_version_info(exclude_os=False)

Get bash version information.

Parameters:

exclude_os (bool | None) – If True, exclude operating system information.

Return type:

Dict

property linux_release_file

prepare_JS_path(js_path)

Parameters:

js_path (Path) –

Return type:

str

prepare_element_run_dirs(run_dirs)

Parameters:

run_dirs (List[List[Path]]) –

Return type:

List[List[str]]

process_JS_header_args(header_args)

Parameters:

header_args (Dict) –

Return type:

Dict

property shebang_executable: List[str]

wrap_in_subshell(commands)

Format commands to run within a subshell.

This assumes commands ends in a newline.

Parameters:

commands (str) –

Return type:

str