Taking Compute to Data
June 5-7, 2018
iRODS User Group Meeting 2018
Durham, NC
Daniel Moore
dmoore@renci.org
Applications Engineer, iRODS Consortium
Taking Compute to Data
TODAY, 2018
Renaissance Computing Institute
UNC-Chapel Hill
Daniel Moore
dmoore@renci.org
Application Engineer, iRODS Consortium
The Compute to Data Use Case
Data is considered to be routed to appropriate storage
resource
Goals - Develop generic interface concept for compute
Goals - Develop a thumbnailing service for iRODS
Implemented as an iRODS rulebase -
following the Template Method pattern
Components of the System
System Component
Container Technology
User Provided Compute
Post Compute Container
Job Endpoint
Implementation
Singularity
docker://repo_name/thumbnail_image shub://repo_name/metadata_addtags
iRODS Rule Base
(user extension of the iRODS API)
Getting Started
~/irods_training/advanced/hpc_compute_to_data/ubuntu_14_16/install_singularity.sh
Install Singularity:
As the ubuntu training account
Getting Started
mkdir build_compute_to_data cd build_compute_to_data cmake ../irods_training/advanced/hpc_compute_to_data make package sudo dpkg -i ./irods-hpc-compute-to-data-example_4.2.3~xenial_amd64.deb
Build and Install the Compute to Data package
git clone https://github.com/irods/irods_training sudo apt-get -y install irods-externals-* irods-dev export PATH=/opt/irods-externals/cmake3.5.2-0/bin/:$PATH
Getting Started - if necessary
mkdir build_data_to_compute cd build_data_to_compute cmake ../irods_training/advanced/hpc_data_to_compute/ make package sudo dpkg -i ./irods-hpc-data-to-compute-example_4.2.3~xenial_amd64.deb
Build and Install the Data to Compute package
git clone https://github.com/irods/irods_training sudo apt-get -y install irods-externals-* irods-dev export PATH=/opt/irods-externals/cmake3.5.2-0/bin/:$PATH
Getting Started
cd mkdir build_uuid cd build_uuid cmake ../irods_training/advanced/irods_microservice_plugin_uuid/ make package sudo dpkg -i ./irods-get-uuid-4.2.1-ubuntu14-x86_64.deb
Build and Install the UUID microservice plugin
Text
Configure the rule engine plugin
"rule_engines": [ ... "re_rulebase_set": [ "compute_to_data", "data_to_compute", "core" ], ... ]
sudo su - irods vim /etc/irods/server_config.json
Disable SSL in the iRODS Server for Jargon
acPreConnect(*OUT) { *OUT="CS_NEG_DONT_CARE"; }
Edit /etc/irods/core.re
acPreConnect(*OUT) { *OUT="CS_NEG_REFUSE"; }
becomes
Configure the Tagged Resources - if necessary
Make two unix file system resources
iadmin mkresc lts_resc unixfilesystem `hostname`:/tmp/irods/lts_resc iadmin mkresc img_resc unixfilesystem `hostname`:/tmp/irods/img_resc
Annotate them with appropriate metadata given their roles
- defined in the configuration as part of the contract
imeta add -R lts_resc COMPUTE_RESOURCE_ROLE LONG_TERM_STORAGE
imeta add -R img_resc COMPUTE_RESOURCE_ROLE IMAGE_PROCESSING
Stage data for thumbnail creation
cp ~/irods_training/stickers.jpg /tmp
As the irods service account
As the ubuntu training account
The configuration interface
Define interfaces for any necessary conventions
Single Point of Truth - Template Method Pattern
Users may utilize metadata conventions within a rule to provide inputs to the generalized container service
The Image Compute container
FROM python:3 # Define environment variable ENV SOURCE_IMAGE default_source_image ENV DESTINATION_IMAGE default_destination_image ENV SIZE default_size ENV DESTINATION_COLLECTION default_size WORKDIR / ADD make_thumbnail.py / RUN apt-get install -y libjpeg-dev && pip install pillow # Run app.py when the container launches CMD ["sh", "-c", "python ./make_thumbnail.py ${SIZE}x${SIZE} /src/${SOURCE_IMAGE} /dst/${DESTINATION_IMAGE} ${DESTINATION_COLLECTION}"]
The Python thumbnail utility
import os, sys import json import datetime from PIL import Image # capture incoming parameters size_str = sys.argv[1] src_name = sys.argv[2] dst_name = sys.argv[3] dst_coll = sys.argv[4] # build size array size_vals = size_str.split('x') size = int(size_vals[0]), int(size_vals[1]) # generate thumbnail try: im = Image.open(src_name) im.thumbnail(size) im.save(dst_name, im.format) except IOError: print("cannot create thumbnail for: " + src_name) sys.exit()
1-2 : Build the Thumbnail
The Python thumbnail utility
# create metadata and build json representation for moarlock avu_list = [] avu = {} avu['attribute'] = 'source_image' avu['value'] = os.path.basename(src_name) avu['unit'] = '' avu['irodsPath'] = os.path.basename(dst_name) avu['action'] = 'ADD' avu_list.append(avu) avu = {} avu['attribute'] = 'time_stamp' avu['value'] = '{:%Y-%m-%d %H:%M:%S}'.format(datetime.datetime.now()) avu['unit'] = '' avu['irodsPath'] = os.path.basename(dst_name) avu['action'] = 'ADD' avu_list.append(avu) md_manifest = {} md_manifest['operation'] = avu_list md_manifest['failureMode'] = 'FAIL_FAST' md_manifest['parentIrodsTargetPath'] = dst_coll # write out manifest for moarlock with open('/dst/mdmanifest.json', 'w') as outfile: json.dump(md_manifest, outfile, sort_keys=True, indent=4, separators=(',', ': '))
2-2 : Create the mdmanifest.json file for Moarlock
Example mdmanifest.json
{ "operation":[ { "attribute":"atr1", "value":"val1", "unit":"", "irodsPath":"stickers.jpg", "action":"ADD" } ], "failureMode":"FAIL_FAST", "parentIrodsTargetPath":"/tempZone/home/rods/" } |
The configuration interface
For the thumbnail service we will need to
The configuration interface
Utilize the interface for our chosen metadata convention
get_compute_resource_role_attribute(*t) { *t = "COMPUTE_RESOURCE_ROLE" } get_image_compute_type(*t) { *t = "IMAGE_PROCESSING" }
The configuration interface
get_thumbnail_collection_name(*col_name, *obj_name, *thumb_coll_name) {
*fn = trimr(*obj_name, ".")
*thumb_coll_name = *col_name ++ "/" ++ *fn ++ "_thumbnails"
}
get_thumbnail_name(*file_name, *size, *thumb_name) {
# trim the extension
*fn = trimr(*file_name, ".")
*ext = substr(*file_name, strlen(*fn)+1, strlen(*file_name))
*thumb_name = *fn ++ "_thumbnail_" ++ *size ++ "." ++ *ext
}
get_thumbnail_sizes(*size_list) {
*size_list = list( "128x128", "256x256", "512x512", "1024x1024" )
}
Utilize the interface for naming conventions
Thumbnail Service - helper functions
split_path(*p, *tok, *col, *obj)
get_resource_host_by_id(*resc_id, *resc_host)
get_resc_id_for_data_object_resident_on_image_node(*obj_name, *col_name,
*compute_resc_role_attr, *image_compute_type, *src_resc_id)
get_phy_path_for_object_on_resc_id(*obj_name, *resc_id, *phy_path)
Leverage helper functions from Data to Compute
object_is_image_type(*_f, *_flag) determine_destination_resource(*_obj_path)
Additional helper functions for Compute to Data
Routing the Data - helper function implementation
object_is_image_type(*_f, *_flag) { *_flag = false; if (*_f like "*.jpg" || *_f like "*.jpeg" || *_f like "*.bmp" || *_f like "*.tif" || *_f like "*.tiff" || *_f like "*.rif" || *_f like "*.gif" || *_f like "*.png" || *_f like "*.svg" || *_f like "*.xpm") { *_flag = true; } }
Use file extension to determine image type
Other options: use a Tika service for mime-type, the Cyverse infotyper service, custom microserivce plugin
Routing the Data - match object type to resource
determine_destination_resource(*_obj_path) { *comp_attr = "NULL" get_compute_resource_role_attribute(*comp_attr); *image_flag = false; object_is_image_type(*_obj_path, *image_flag) *resc_name = "lts_resc" # discover LTS resc if(true == *image_flag) { *image_type = "NULL" get_image_compute_type(*image_type) get_resource_name_by_role(*resc_name, *comp_attr, *image_type) } msiSetDefaultResc(*resc_name,"forced"); }
Find the image processing resource and route the ingested data accordingly
Compute to Data Interface
Ingested data must route to appropriate resource given some criteria
acSetRescSchemeForCreate()
launch_compute_container(
*host_name, *port_str, *guid_str, *src_phy_path, *dst_log_path, *container_name, *user_docker_options) launch_thumbnail_compute(*src_obj_path)
Provide a template for containerized compute and an endpoint for creating thumbnails
Routing the Data
acSetRescSchemeForCreate {
determine_destination_resource($objPath)
}
Override the static policy enforcement point for data object creation
Call our helper function, passing the session variable which holds the logical path of the data object
Compute to Data Template Method
launch_compute_container(
*host_name,
*port_str,
*guid_str,
*src_phy_path,
*dst_log_path,
*container_name,
*user_docker_options) {
remote(*host_name, "null") {
# possible future pre-processing here
# build the full docker option string
*cmd_opt = *user_docker_options ++ " " ++ *container_name ++ "\""
# call the users provided container
msiExecCmd("docker_run.sh", *cmd_opt, "null", "null", "null", *std_out_err)
1-2 : Launch the user defined container
Note - add a delay() directive for asynchronous behavior
Compute to Data Template Method
# build option string for Moarlock split_path(*dst_log_path, "/", *dst_col_name, *dst_obj_name) *moar_opts = "\" -v " ++ *src_phy_path ++ ":/var/input -e host=" ++ *host_name ++ " -e zone=tempZone -e port=" ++ *port_str ++ " -e user=rods -e passwd=rods -e irodsout=" ++ *dst_col_name ++ " -e guid=" ++ *guid_str ++ " diceunc/moarlock:1.0\"" # post-processing with Moarlock msiExecCmd("docker_run.sh", *moar_opts, "null", "null", "null", *std_out_err) } # remote } # launch_compute_container
2-2 : Build and launch the Moarlock container
Note: iRODS parameters are currently hardcoded - utilize tickets in future iterations
Compute to Data Thumbnail Rule
launch_thumbnail_compute( *src_obj_path ) { # TODO - ensure image is on image compute resource split_path(*src_obj_path, "/", *col_name, *obj_name) *thumb_coll_name = "NULL" get_thumbnail_collection_name(*col_name, *obj_name, *thumb_coll_name); if("NULL" == *image_compute_type) { failmsg(-1,"get_thumbnail_collection_name failed") } *guid_str = "NULL" msiget_uuid(*guid_str) *dst_dir_name = "/tmp/" ++ *obj_name ++ "-" ++ *guid_str
1-4 : capture target collection and UUID
Compute to Data Thumbnail Rule
# capture configuration parameters *image_compute_type = "NULL" get_image_compute_type(*image_compute_type) if("NULL" == *image_compute_type) { failmsg(-1,"get_image_compute_type failed") } *compute_resc_role_attr = "NULL" get_compute_resource_role_attribute(*compute_resc_role_attr) if("NULL" == *compute_resc_role_attr) { failmsg(-1,"get_compute_resource_role_attribute failed") } *src_resc_id = "NULL" get_resc_id_for_data_object_reside_on_image_node( *obj_name, *col_name, *compute_resc_role_attr, *image_compute_type, *src_resc_id)
2-4 : capture metadata parameters and resource id
Compute to Data Thumbnail Rule
*src_phy_path = "NULL" get_phy_path_for_object_on_resc_id(*obj_name, *src_resc_id, *src_phy_path) if("NULL" == *src_phy_path) { failmsg(-1,"get_phy_path_for_object_on_resc_id failed for <snip>") } split_path(*src_phy_path, "/", *src_dir_name, *src_file_name) *server_host = "NULL" get_resource_host_by_id(*src_resc_id, *server_host); if("NULL" == *server_host) { failmsg(-1,"get_resource_host_by_id failed for [*src_resc_id]") } get_thumbnail_sizes(*thumb_sizes)
3-4 : get source physical path, host name and sizes
Compute to Data Thumbnail Rule
4-4 : build docker option string and call container template
foreach( *sz in *thumb_sizes ) { get_thumbnail_name(*obj_name, *sz, *thumbnail_name); *dst_obj_path = *thumb_coll_name ++ "/" ++ *thumbnail_name *sz_str = str(*sz) *docker_options = "\" -v " ++ *src_dir_name ++ ":/src -v " ++ *dst_dir_name *docker_options = *docker_options ++ ":/dst -e SIZE=" ++ *sz_str *docker_options = *docker_options ++ " -e SOURCE_IMAGE=" ++ *src_file_name *docker_options = *docker_options ++ " -e DESTINATION_IMAGE=" ++ *thumbnail_name *docker_options = *docker_options ++ " -e DESTINATION_COLLECTION=" ++ *thumb_coll_name ++ " " launch_compute_container( *server_host, "1247", *guid_str, *dst_dir_name, *dst_obj_path, "thumbnail", *docker_options) } # for } # launch_thumbnail_compute
Compute to Data - Thumbnail Invocation Rule
launch_compute {
*logical_path="/tempZone/home/rods/stickers.jpg"
launch_thumbnail_compute(*logical_path) } INPUT null OUTPUT ruleExecOut
launch_compute.r
Compute to Data - Thumbnail Testing
irods@icat:~$ iput -fR img_resc /tmp/stickers.jpg irods@icat:~$ irule -F launch_compute.r irods@icat:~$ ils -l /tempZone/home/rods: rods 0 img_resc 2157087 2017-05-29.22:46 & stickers.jpg C- /tempZone/home/rods/stickers_thumbnails irods@icat:~$ ils -l stickers_thumbnails /tempZone/home/rods/stickers_thumbnails: rods 0 img_resc 229954 2017-05-29.22:46 & stickers_thumbnail_1024x1024.jpg rods 0 img_resc 6456 2017-05-29.22:46 & stickers_thumbnail_128x128.jpg rods 0 img_resc 19355 2017-05-29.22:46 & stickers_thumbnail_256x256.jpg rods 0 img_resc 63036 2017-05-29.22:46 & stickers_thumbnail_512x512.jpg irods@icat:~$ irule -F find_thumbnails.r thumbnail [/tempZone/home/rods/stickers_thumbnails/stickers_thumbnail_1024x1024.jpg] thumbnail [/tempZone/home/rods/stickers_thumbnails/stickers_thumbnail_512x512.jpg] thumbnail [/tempZone/home/rods/stickers_thumbnails/stickers_thumbnail_256x256.jpg] thumbnail [/tempZone/home/rods/stickers_thumbnails/stickers_thumbnail_128x128.jpg]
Note: we need to use the -R img_resc as rodsadmin users are not affected by acSetRescSchemeForCreate
Future Work