Taking Data to Compute
TODAY, 2017
Renaissance Computing Institute
UNC-Chapel Hill
Jason Coposky
@jason_coposky
Executive Director, iRODS Consortium
Taking Data to Compute
Integrating iRODS into a compute environment
iRODS as a compute orchistrator
iRODS commands for staging data for compute
iRODS commands for capturing data products
iRODS API built into Application
Compute Application
Compute Job
Job Scheduler
The Data to Compute Use Case
Focus on the right side of the picture
Goals - Develop a thumbnailing service for iRODS
- Select an appropriate resource to house the data for compute
- Replicate the data to the compute resource
- Send a job to the compute scheduler to generate thumbnails
- Register the thumbnails into the catalog
- Replicate the thumbnails back to long term storage
- Trim replicas on compute resource
Goals - Develop generic interface concept for compute
- Develop a metadata driven interface for labeling resources which provide computational capabilities - ultimately relies upon convention
- Separate configuration from implementation - isolate deployment specific concepts
- Consider a rule base as an extension of iRODS - rules are not just data management policy
Components of the System
System Component
Job Scheduler
Job Launching Script
Tools to Execute
Job Endpoint
Implementation
User's Choice
bash
Image Magick convert
iRODS Rule Base
(user extension of the iRODS API)
Getting Started
Installing Condor Repositories
wget -qO - http://research.cs.wisc.edu/htcondor/ubuntu/HTCondor-Release.gpg.key | sudo apt-key add -
echo "deb [arch=amd64] http://research.cs.wisc.edu/htcondor/ubuntu/stable/ $(lsb_release -sc) contrib" | sudo tee /etc/apt/sources.list.d/condor.list
echo "deb [arch=amd64] http://research.cs.wisc.edu/htcondor/ubuntu/development/ $(lsb_release -sc) contrib" | sudo tee /etc/apt/sources.list.d/condor.list
Installing Condor and Image Magick
sudo apt-get update
sudo apt-get -y install condor imagemagick
sudo service condor restart
Getting Started
Clone the training repository
git clone https://github.com/irods/irods_training
Build and install the training package
sudo apt-get -y install irods-externals-* irods-dev
export PATH=/opt/irods-externals/cmake3.5.2-0/bin/:/opt/irods-externals/clang3.8-0/bin/:$PATH
mkdir build_hpc
cd build_hpc
cmake ../irods_training/advanced/hpc_data_to_compute/
make package
sudo dpkg -i ./irods-hpc-data-to-compute-example_4.2.0~trusty_amd64.deb
Package Contents
$ dpkg -c ./irods-hpc-data-to-compute-example_4.2.0~trusty_amd64.deb drwxr-xr-x root/root 0 2017-05-07 18:03 ./etc/ drwxr-xr-x root/root 0 2017-05-07 18:03 ./etc/irods/ -r--r--r-- root/root 9586 2017-05-07 16:58 ./etc/irods/thumbnail.re -r--r--r-- root/root 1656 2017-05-07 16:58 ./etc/irods/thumbnail_configuration.re drwxr-xr-x root/root 0 2017-05-07 18:03 ./var/ drwxr-xr-x root/root 0 2017-05-07 18:03 ./var/lib/ drwxr-xr-x root/root 0 2017-05-07 18:03 ./var/lib/irods/ -r--r--r-- root/root 298 2017-05-07 16:58 ./var/lib/irods/create_thumbnails.r -r--r--r-- root/root 360 2017-05-07 16:58 ./var/lib/irods/find_thumbnails.r drwxr-xr-x root/root 0 2017-05-07 18:03 ./var/lib/irods/msiExecCmd_bin/ -r-xr--r-- root/root 335 2017-05-07 16:58 ./var/lib/irods/msiExecCmd_bin/submit_thumbnail_job.sh -r--r--r-- root/root 70 2017-05-07 16:58 ./var/lib/irods/msiExecCmd_bin/thumbnail.submit
Configure the rule engine
Add the two additional rule bases to server_config.json
"rule_engines": [
...
"re_rulebase_set": [
"thumbnail_configuration",
"thumbnail",
"core"
],
...
]
Remember that order matters
Configure the LTS and Image Processing Resources
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
cp ~/irods_training/stickers.jpg /tmp
sudo mkdir -p /tmp/irods/thumbnails
sudo chown -R irods:irods /tmp/irods
Stage data and destination directory for thumbnail creation
Design by Contract - the configuration interface
Define interfaces for any necessary conventions
- Metadata attributes and values
- Naming conventions for logical and physical paths
- Metadata values for implemented roles
- Interface to job scheduler for launching compute
Single Point of Truth - allows for the use of the same
'end-points' for various metadata standards and naming conventions
Design by Contract - the configuration interface
For the thumbnail service we will need to:
- Get the metadata attribute string that holds the role
- Get the tag for an Image Compute resource
- Get the tag for a Long Term Storage resource
- Get the logical collection name for thumbnails
- Get the physical path for a thumbnail
- Get the name of a thumbnail
- Get a list of desired thumbnail sizes
Design by Contract - the configuration interface
Provide an interface for our chosen metadata convention
get_compute_resource_role_attribute(*t) { *t = "COMPUTE_RESOURCE_ROLE" } get_image_compute_type(*t) { *t = "IMAGE_PROCESSING" } get_long_term_storage_type(*t) { *t = "LONG_TERM_STORAGE" }
Design by Contract - the configuration interface
Provide an interface for job submission
submit_thumbnail_job(*server_host, *size_str, *src_phy_path, *dst_phy_path ) {
remote(*server_host, "") {
*cmd_opt = '/usr/bin/convert -thumbnail *size_str *src_phy_path *dst_phy_path'
*err = errormsg(msiExecCmd(
"submit_thumbnail_job.sh",
*cmd_opt, "null", "null", "null", *std_out_err), *msg);
msiGetStdoutInExecCmdOut(*std_out_err,*std_out);
writeLine("serverLog", "XXXX - STDOUT [*std_out]")
msiGetStderrInExecCmdOut(*std_out_err,*std_err);
writeLine("serverLog", "XXXX - STDERR [*std_err]")
if(*err != 0) {
writeLine( "serverLog", "FAILED: [*cmd_opt] [*err] [*msg]" );
failmsg(*err,*cmd_opt)
}
} # remote
}
Design by Contract - the configuration interface
Provide an interface for naming conventions
get_thumbnail_collection_name(*col_name, *obj_name, *thumb_coll_name) {
*fn = trimr(*obj_name, ".")
*thumb_coll_name = *col_name ++ "/" ++ *fn ++ "_thumbnails"
}
get_thumbnail_physical_path(*dst_dir, *thumb_name, *phy_path) {
*phy_path = *dst_dir ++ "/" ++ *thumb_name
}
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" )
#*size_list = list( "128x128" )
}
Design by Contract - the configuration interface
Abstraction of job submission via shell script
#!/bin/bash
# $1 - executable
# $2 - thumbnail option
# $3 - sizing string
# $4 - source physical path
# $5 - destination physical path
/usr/bin/condor_submit /var/lib/irods/msiExecCmd_bin/thumbnail.submit -append "executable ${1}" -append "arguments ${2} ${3} ${4} ${5}"
Thumbnail Service - helper functions
Local functions to simplify queries and complex operations
split_path(*p, *tok, *col, *obj) get_resource_name_by_role(*resc_name, *attr, *value) get_resource_name_by_id(*resc_id, *resc_name) get_resource_id_by_name(*resc_name, *resc_id) 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)
Thumbnail Service - helper function implementation
split_path(*p, *tok, *col, *obj) { *col = trimr(*p, *tok) *obj = substr(*p, strlen(*col)+1, strlen(*p)) } get_resource_name_by_role(*resc_name, *attr, *value) { *resc_name = "NULL" foreach(*row in SELECT DATA_RESC_NAME WHERE META_RESC_ATTR_NAME = '*attr' AND META_RESC_ATTR_VALUE = '*value') { *resc_name = *row.DATA_RESC_NAME } # foreach } get_resource_name_by_id(*resc_id, *resc_name) { *resc_name = "NULL" foreach(*row in SELECT RESC_NAME WHERE RESC_ID = '*resc_id') { *resc_name = *row.RESC_NAME } # foreach } get_resource_id_by_name(*resc_name, *resc_id) { *resc_id = "NULL" foreach(*row in SELECT RESC_ID WHERE RESC_NAME = '*resc_name') { *resc_id = *row.RESC_ID } # foreach } get_resource_host_by_id(*resc_id, *resc_host) { *resc_host = "NULL" foreach(*row in SELECT RESC_LOC WHERE RESC_ID = '*resc_id') { *resc_host = *row.RESC_LOC } # foreach }
Thumbnail Service - helper function implementation
get_resc_id_for_data_object_resident_on_image_node( *obj_name, *col_name,
*compute_resc_role_attr, *image_compute_type, *src_resc_id) {
*src_resc_id = "NULL"
*image_resc_id = "NOT_FOUND"
foreach(*row in SELECT DATA_RESC_ID WHERE DATA_NAME = '*obj_name' AND COLL_NAME = '*col_name') {
*id = *row.DATA_RESC_ID
foreach(*v in SELECT META_RESC_ATTR_VALUE WHERE RESC_ID = '*id' and
META_RESC_ATTR_NAME = '*compute_resc_role_attr' ) {
if(*image_compute_type == *v.META_RESC_ATTR_VALUE) {
*image_resc_id = *id
break
}
} # values
} # out_ids
}
get_phy_path_for_object_on_resc_id(*obj_name, *resc_id, *phy_path) {
*phy_path = "NULL"
foreach(*row in SELECT DATA_PATH WHERE DATA_NAME = '*obj_name' AND RESC_ID = '*resc_id') {
*phy_path = *row.DATA_PATH;
}
}
Thumbnail Service - helper functions
Find the resource tagged for image processing and replicate the data object
replicate_object_to_image_node( *src_obj_path, *compute_resc_role_attr, *image_compute_type, *img_resc_name, *src_resc_id ) { get_resource_name_by_role( *img_resc_name, *compute_resc_role_attr, *image_compute_type); if("NULL" == *img_resc_name) { failmsg(-1,"get_resource_name_by_role failed [*lts_resc_name][*compute_resc_role_attr][*image_compute_type]") } # "Take the Data to the Compute" - replicate to an image compute node *err = errormsg(msiDataObjRepl( *src_obj_path, "destRescName=*img_resc_name", *out_param), *msg) if(0 != *err) { failmsg(*err, "msiDataObjRepl failed for [*src_obj_path] [*img_resc_name] - [*out_param]") } *src_resc_id = "NULL" # set the src resc id to the new image compute node id get_resource_id_by_name(*img_resc_name, *src_resc_id) }
Thumbnail Service - helper functions
register_and_replicate_thumbnail(*server_host, *obj_path, *src_resc_name, *phy_path, *dst_resc_name) {
delay( "<EF>5s REPEAT UNTIL SUCCESS</EF>") {
remote(*server_host, "") {
*long_term_resource = "demoResc"
writeLine("serverLog", "register_and_replicate_thumbnail :: [*obj_path] [*src_resc_name] [*phy_path] [*dst_resc_name]");
*err = errormsg(msiPhyPathReg(*obj_path, *src_resc_name, *phy_path, "null", *status), *msg);
if(0 != *err) {
failmsg(*err, "msiPhyPathReg failed for [*obj_path] [*src_resc_name] [*phy_path] [*status]")
}
*err = errormsg(msiDataObjRepl(
*obj_path,
"destRescName=*dst_resc_name",
*out_param), *msg)
if(0 != *err) {
failmsg(*err, "msiDataObjRepl failed for [*obj_path] [*dst_resc_name] - [*out_param]")
}
*err = errormsg(msiDataObjUnlink(
"objPath=*obj_path++++replNum=0++++unreg=",
*out_param), *msg)
if(0 != *err) {
failmsg(*err, "msiDataObjUnlink failed for [*obj_path] [*out_param]")
}
} # remote
}
}
Register a thumbnail and replicate it to another resource then trim the source replica
Thumbnail Service - the function interface
Functions which rely on the configuration abstraction to do the work of generating the thumbnails
create_thumbnail_collection(*src_obj_path, *dst_phy_dir) create_thumbnail(*src_obj_path, *dst_obj_path, *dst_phy_path, *size_str) create_thumbnail_impl(*src_obj_path, *dst_obj_path, *dst_phy_path, *size_str) get_list_of_thumbnails(*src_obj_path, *thumbnail_list)
These functions represent an extension of the iRODS API
- first through the rule engine, potentially through the API plugin interface
Thumbnail Service - the function interface
create_thumbnail_collection(*src_obj_path, *dst_phy_dir) { split_path(*src_obj_path, "/", *col_name, *obj_name *thumb_coll_name = "NULL" get_thumbnail_collection_name(*col_name, *obj_name, *thumb_coll_name); writeLine( "serverLog", "XXXX - thumb_coll_name [*thumb_coll_name]" ) *err = errormsg(msiCollCreate(*thumb_coll_name, 1, *out), *msg) if( *err < 0 ) { writeLine("serverLog", "msiCollCreate failed: [*err] [*msg] [*out]") failmsg(*err, *msg) } get_thumbnail_sizes(*thumb_sizes) foreach( *sz in *thumb_sizes ) { get_thumbnail_name(*obj_name, *sz, *thumbnail_name); *dst_obj_path = *thumb_coll_name ++ "/" ++ *thumbnail_name writeLine( "serverLog", "XXXX - [*src_obj_path] [*sz] [*thumbnail_name] [*dst_obj_path]" ) *dst_phy_path = "NULL" get_thumbnail_physical_path(*dst_phy_dir, *thumbnail_name, *dst_phy_path) create_thumbnail( *src_obj_path, *dst_obj_path, *dst_phy_path, *sz) } }
Thumbnail Service - interface functions
Text
create_thumbnail(*src_obj_path, *dst_obj_path, *dst_phy_path, *size_str) {
*err = errormsg(msiObjStat(*dst_obj_path,*obj_stat), *msg);
if(0 != *err) {
writeLine("serverLog", "msiObjStat failed for [*dst_obj_path] [*err]")
create_thumbnail_impl(
*src_obj_path,
*dst_obj_path,
*dst_phy_path,
*size_str );
}
}
Thumbnail Service - interface functions
get_list_of_thumbnails(*src_obj_path, *thumbnail_list) { *thumbnail_list = list() split_path(*src_obj_path, "/", *col_name, *obj_name) # derive a collection name from the logical path *thumb_coll_name = "NULL" get_thumbnail_collection_name( *col_name, *obj_name, *thumb_coll_name) # get the list of possible sizes get_thumbnail_sizes(*thumb_sizes) foreach( *sz in *thumb_sizes ) { get_thumbnail_name(*obj_name, *sz, *thumbnail_name); *dst_obj_path = *thumb_coll_name ++ "/" ++ *thumbnail_name # does the thumbnail exist *err = errormsg(msiObjStat(*dst_obj_path,*obj_stat), *msg) if( 0 == *err ) { # it does exist, add it to the list *thumbnail_list = cons(*dst_obj_path, *thumbnail_list) } } }
Thumbnail Service - interface functions
create_thumbnail_impl(*src_obj_path, *dst_obj_path, *dst_phy_path, *size_str) { split_path(*src_obj_path, "/", *col_name, *obj_name) # 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") } writeLine("serverLog", "image_compute_type [*image_compute_type]") *lts_compute_type = "NULL" get_long_term_resc_type(*lts_compute_type) if("NULL" == *lts_compute_type) { failmsg(-1,"get_long_term_resc_type failed") } writeLine("serverLog", "lts_compute_type [*lts_compute_type]") *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") } writeLine("serverLog", "compute_resc_role_attr [*compute_resc_role_attr]")
1 - 4 :: capture metadata
Thumbnail Service - interface functions
2 - 4 :: Determine resources and replicate to compute
*lts_resc_name = "NULL" get_resource_name_by_role( *lts_resc_name, *compute_resc_role_attr, *lts_compute_type); if("NULL" == *lts_resc_name) { failmsg(-1,"get_resource_name_by_role failed [*lts_resc_name][*compute_resc_role_attr][*lts_compute_type]") } writeLine("serverLog", "lts_resc_name [*lts_resc_name]") *src_resc_id = "NULL" get_resc_id_for_data_object_resident_on_image_node( *obj_name, *col_name, *compute_resc_role_attr, *image_compute_type, *src_resc_id) writeLine("serverLog", "src_resc_id [*src_resc_id]") *img_resc_name = "NULL" # does data object not reside on the required resource? if("NULL" == *src_resc_id) { replicate_object_to_image_node( *src_obj_path, *compute_resc_role_attr, *image_compute_type, *img_resc_name, *src_resc_id ) if("NULL" == *src_resc_id) { failmsg(-1, "get_resource_id_by_name failed for [*img_resc_name]") } } writeLine("serverLog", "src_resc_id [*src_resc_id]")
Thumbnail Service - interface functions
3-4 :: determine resource parameters for the job
*src_resc_name = "NULL" get_resource_name_by_id(*src_resc_id, *src_resc_name) if("NULL" == *src_resc_name) { failmsg(-1,"get_resource_name_by_id failed for [*src_resc_id]") } writeLine("serverLog", "src_resc_name [*src_resc_name]") *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,"failed for [*obj_name] [*src_resc_id]") } writeLine("serverLog", "src_phy_path [*src_phy_path]") *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]") } writeLine("serverLog", "server_host [*server_host]")
Thumbnail Service - interface functions
4-4 :: launch job and capture products
# launch image computation job submit_thumbnail_job( *server_host, *size_str, *src_phy_path, *dst_phy_path) # launch registration and replication register_and_replicate_thumbnail( *server_host, *dst_obj_path, *src_resc_name, *dst_phy_path, *lts_resc_name); }
Thumbnail Service - user space invocation
create_thumbnails { *err = errormsg(create_thumbnail_collection(*src_obj_path, *dst_phy_dir), *msg) if(0 != *err) { writeLine( "stdout", "FAIL: [*err] [*msg]") } } INPUT *src_obj_path="/tempZone/home/rods/stickers.jpg",*dst_phy_dir="/tmp/irods/thumbnails" OUTPUT ruleExecOut
create_thumbnails.r
Thumbnail Service - user space invocation
find_thumbnails { *thb_list = list() *err = errormsg(get_list_of_thumbnails(*src_obj_path, *thb_list), *msg) if(0 != *err) { writeLine( "stdout", "FAIL: [*err] [*msg]") } foreach( *t in *thb_list ) { writeLine("stdout", "thumbnail [*t]") } } INPUT *src_obj_path="/tempZone/home/rods/stickers.jpg" OUTPUT ruleExecOut
find_thumbnails.r
Thumbnail Service - testing
irods@icat:~$ iput /tmp/stickers.jpg irods@icat:~$ ils -l /tempZone/home/rods: rods 0 demoResc 2157087 2017-05-09.18:42 & stickers.jpg
irods@icat:~$ irule -F create_thumbnails.r irods@icat:~$ ils -l /tempZone/home/rods: rods 0 demoResc 2157087 2017-05-09.18:42 & stickers.jpg rods 1 img_resc 2157087 2017-05-09.18:43 & stickers.jpg C- /tempZone/home/rods/stickers_thumbnails irods@icat:~$ ils -l /tempZone/home/rods/stickers_thumbnails /tempZone/home/rods/stickers_thumbnails: rods 1 lts_resc 229954 2017-05-09.18:43 & stickers_thumbnail_1024x1024.jpg rods 1 lts_resc 6456 2017-05-09.18:43 & stickers_thumbnail_128x128.jpg rods 1 lts_resc 19355 2017-05-09.18:43 & stickers_thumbnail_256x256.jpg rods 1 lts_resc 63036 2017-05-09.18:43 & 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]
Slide title here
- All rules should be created and tested in user space before being installed as a rule base
- Rules may be refactored into a microservice plugin
- Rules may be refactored into a C++ rule engine plugin
- Rules may be refactored into an API plugin
Taking Data to Compute
By jason coposky
Taking Data to Compute
Training to accompany the one page data management design pattern: https://irods.org/images/data_to_compute.jpg
- 1,989