Taking Compute to Data

June 25-27, 2019

iRODS User Group Meeting 2019

Utrecht , Netherlands

Daniel Moore

Applications Engineer, iRODS Consortium

Taking Compute to Data

The Compute to Data Use Case

Data is assumed to already be routed to an appropriate storage 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

"Compute To Data" Pattern - Salient Features

Implemented as an iRODS rulebase -

    following the Template Method pattern

  1. If necessary, replicate input data to an appropriate resource
  2. Check permissions
  3. Launch compute container (Docker) :
    1. Process input data via Jupyter notebook
    2.  Save results
  4. Register the resultant directory into iRODS
  5. Apply metadata to newly registered results

Components of the System

System Component

Job Initialization

Container Technology

User Provided Compute

 

Implementation

iRODS Rule Base

Docker

Jupyter Notebook

 

Getting Started

git clone https://github.com/irods/irods_training
sudo apt-get -y install \
   irods-externals-cmake3.5.2-0 \
   irods-externals-clang3.8-0 \
   irods-externals-qpid-with-proton0.34-0 \
   irods-dev
export PATH=/opt/irods-externals/cmake3.5.2-0/bin:$PATH

Clone irods_training repository and configure build tools

If necessary:

Getting Started

cd
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_4.2.6~xenial_amd64.deb

cd
mkdir build_register_microservice
cd build_register_microservice
cmake ../irods_training/advanced/hpc_compute_to_data/msvc__msiregister_as_admin/
make package
sudo dpkg -i irods-microservice-register_as_admin-4.2.6-ubuntu16-x86_64.deb

Install packages for the compute-to-data example

cd /home/ubuntu/irods_training/advanced/hpc_compute_to_data/jupyter_notebook

docker build -t testimages/jupyter-digital-filter .

Build Docker image for processing

Getting Started - Python extensions to iRODS

 sudo apt-get -y install python-pip

Also, install python's pip package:

Make sure the Python rule engine plugin is installed.

 sudo apt-get -y install irods-rule-engine-plugin-python
 pip install docker --user

As service account user irods, install the Python Docker API

sudo usermod -aG docker irods

Add irods user to the docker group:

(You might have to restart  the irods server)

      $ sudo service irods restart

or:   $ sudo su irods -c '~/irodsctl restart'

Further Setup and Configuration

Place Python Rule Engine stanza after native RE stanza:

 sudo nano /etc/irods/server_config.json

"rule_engines": [
    {
      "instance_name": "irods_rule_engine_plugin-irods_rule_language-instance",
      "plugin_name": "irods_rule_engine_plugin-irods_rule_language",
                 ...
      "shared_memory_instance": "irods_rule_language_rule_engine"
    },
    {
      "instance_name": "irods_rule_engine_plugin-python-instance",
      "plugin_name": "irods_rule_engine_plugin-python",
      "plugin_specific_configuration": {}
    },

 . . .

Create /etc/irods/core.py with the following  import:

from compute_to_data import *

Continued... Data-to-Compute Set-up / Configuration 

iadmin mkuser alice rodsuser 
iadmin moduser alice password apass

This demonstration will be run as rodsuser 'alice'

Configure the Tagged Resources - if necessary

Make two unix file system resources

iadmin mkresc lts_resc unixfilesystem `hostname`:/tmp/irods/lts_resc
iadmin mkresc dsp_resc unixfilesystem `hostname`:/tmp/irods/dsp_resc

Annotate them with appropriate metadata given their roles

  - defined in the configuration as part of the contract

As the irods service account

imeta add -R lts_resc COMPUTE_RESOURCE_ROLE LONG_TERM_STORAGE
imeta add -R dsp_resc COMPUTE_RESOURCE_ROLE SIGNAL_PROCESSING

Finally ...

ubuntu$ iinit
 ERROR: environment_properties::capture: missing environment file. should be at [/home/ubuntu/.irods/irods_environment.json]
One or more fields in your iRODS environment file (irods_environment.json) are
missing; please enter them.
Enter the host name (DNS) of the server to connect to: localhost
Enter the port number: 1247
Enter your irods user name: alice
Enter your irods zone: tempZone
Those values will be added to your environment file (for use by
other iCommands) if the login succeeds.

Enter your current iRODS password:

ubuntu$ ils
/tempZone/home/alice:
ubuntu$

Remember to log in as 'alice' in the ubuntu training account:

The configuration interface

Define interfaces for any necessary conventions

  • Metadata attributes and values
  • Metadata values for implemented roles

 

Single Point of Truth - Template Method Pattern

  • execute defined preconditions
  • run user's requested container

 

Users may utilize metadata conventions within a rule to provide inputs to the generalized container service.

Reminder ...

Implemented as an iRODS rulebase -

    following the Template Method pattern

  1. If necessary, replicate input data to an appropriate resource
  2. Check permissions
  3. Launch compute container (Docker) :
    1. Process input data via Jupyter notebook
    2.  Save results
  4. Register the resultant directory into iRODS
  5. Apply metadata to newly registered results (but not today...)

The iRODS Rule Language Rule File

main {
  container_dispatch("containers.run","/tempZone/home/alice/task_config.json","dsp_resc","","")
}
INPUT null
OUTPUT ruleExecOut

Note - add a delay() directive for asynchronous behavior.

Contents of /home/ubuntu/spawn_remote_containers.r

The Python Rulebase

 

Located at : /home/ubuntu/irods_training/advanced/hpc_compute_to_data/compute_to_data.py

 

 

 

The Digital Signal Processing container

FROM jupyter/base-notebook

ARG  irods_gid=999
ENV  IRODS_GID ${irods_gid}

USER root

RUN apt-get update && apt-get install -y vim less

RUN groupadd -g $IRODS_GID irods && usermod -aG irods jovyan

RUN sed -i "s/jovyan:x:[0-9]*:[0-9]*\(.*\)/jovyan:x:999:999\1/" /etc/passwd

ADD lpfilter.ipynb /home/jovyan/work/.

COPY mymodule/ /home/jovyan/work/mymodule/

RUN chown jovyan.users /home/jovyan/work/lpfilter.ipynb

COPY mymodule/ /home/jovyan/work/mymodule

RUN chown -R jovyan.users /home/jovyan/work/mymodule

RUN chown -R 999:999 /home/jovyan && chown -R 999:999 /opt/conda

USER jovyan

RUN conda init

RUN conda install -y -c conda-forge matplotlib numpy

RUN jupyter trust /home/jovyan/work/lpfilter.ipynb

CMD [ '/bin/bash' ]

The Jupyter Notebook

 

Located at : /home/ubuntu/irods_training/advanced/hpc_compute_to_data/jupyter_notebook/lpfilter.ipynb

 

 

The notebook:

  - loads an input waveform

  - applies a digital lowpass filter

  - plots 3 graphs of the results

  - saves graphs and filtered data

Compute to Data - Digital Filter Testing

ubuntu $ icd ; imkdir notebook_input notebook_output
ubuntu $ cd ; iput task_config.json
ubuntu $ for x in {1..512}; do echo $((x%24)) ; done >input.dat
ubuntu $ iput input.dat notebook_input
ubuntu $ ils -lr
/tempZone/home/alice:
 alice             0 demoResc          853 2019-06-21.16:05 & task_config.json
 C- /tempZone/home/alice/notebook_input
/tempZone/home/alice/notebook_input:
 alice             0 demoResc         1318 2019-06-21.16:05 & input.dat
 C- /tempZone/home/alice/notebook_output
/tempZone/home/alice/notebook_output:
ubuntu $ irule -F spawn_remote_containers.r
ubuntu $ ils -lr
/tempZone/home/alice:
 alice             0 demoResc          853 2019-06-21.16:05 & task_config.json
 C- /tempZone/home/alice/notebook_input
/tempZone/home/alice/notebook_input:
 alice             0 demoResc         1318 2019-06-21.16:05 & input.dat
 alice             1 dsp_resc         1318 2019-06-21.16:06 & input.dat
 C- /tempZone/home/alice/notebook_output
/tempZone/home/alice/notebook_output:
 alice             0 dsp_resc            0 2019-06-21.16:06 & .8d63a286-943e-11e9-8013-12cc2f55e24c
 C- /tempZone/home/alice/notebook_output/8d63a286-943e-11e9-8013-12cc2f55e24c
/tempZone/home/alice/notebook_output/8d63a286-943e-11e9-8013-12cc2f55e24c:
 alice             0 dsp_resc            0 2019-06-21.16:06 & .8d63a286-943e-11e9-8013-12cc2f55e24c
 alice             0 dsp_resc         3200 2019-06-21.16:06 & lowpass_filtered_input.dat
 alice             0 dsp_resc       359430 2019-06-21.16:06 & lowpass_filter_processing.html

Compute to Data - Digital Filter Results

sudo su - irods

cd /tmp/irods/dsp_resc/home/alice/notebook_output

python -m SimpleHTTPServer 8080

picture here of results

Navigate to HTML file under notebook_output

Thank you

Any Questions?

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