(ATS3-GS03) Accelrys Enterprise Platform Architecture Deeper Dive

Jason BenedictSr. Architect, Platform R&Djason.benedict@accelrys.com

The information on the roadmap and future software development efforts are intended to outline general product direction and should not be relied on in making a purchasing decision.

• Core services and security• Job launching• Process management• Latency and scalability data• Clustering methods

Agenda

LIMS

IsentrisNotebookVaultDocsORACLE

…

ExperimentWorkflow

InstrumentInterfaces

ReportsWorkRequest

SchedulingExperiment Design

RegistrationBiologyModeling & Simulation

Virtual Chemistry

Data Mining & Analytics

Imaging

3rd Party Applications

Accelrys Enterprise PlatformWeb Applications Thick Client Applications

SharePoint & Office Applications

Web Application Framework Client Integration APIs MS Office Integration

OtherLEA

SOA Integration

Scientific and Generic Services Data Management Services

Accelrys Enterprise Platform

Accelrys Enterprise Platform Integration

DBs

Pipeline Pilot Enterprise Server

Protocol Runtime Environment (scisvr)VB Script

(On Client)

Run Program Java Perl Python

VB Script (On

Server)

Admin Portal Help PortalWeb Apps Web Services API

.NET SOAP & HTTP

Telnet / FTP SSH / SCP ODBC /

JDBC

VB Script Cmd Line Java Classes

Perl Scripts

.NET Classes

RESTService

SOAP Service Cmd Line

Server IntegrationExtend pipelines with new components that integrate your code, data and services.

Professional ClientRun Protocol

Command Line Client

Web Browser

Web Port

JavaScript Client SDK

JavaScript Client

.NET Client SDK

.NET Client

Java Client SDK

Java Client

Web Services API

SOAP Client

Client IntegrationBuild clients that connect to Pipeline Pilot and run protocol services.

REST API

Grid System Integration (optional)

File System

Pipeline Server Architecture

Apache HTTP Server

Authentication and Authorization Security Module

XMLDB Service

Locator Service

RunnerService

LoggingService

File AccessService

Protocol Web

Services

Admin Portal

Help Portal

Data Flow Services

XMLDB User Data Job Data

Corporate Directory

CMS

SOA

DB’s

runjob CGI

WSDL CGI

Mod_balancer

Mod_proxy

Apache Tomcat

Query Service

Scheduler

1 .. N1 .. 1

Launching Asynchronous (polling) Jobs

Apache HTTP ServerAuthentication and Authorization Security Module

Runner Service

Need to fork scisvr?

scisvr(.exe) JVMCLR

Job Folder

2.1.

Create job directory with compressed protocol.xml and uploaded input files

3. 4.

Poll job status via sts file

Monitor Job existence via lck file and process status

5.

Read result file from disk and return to client through Apache

Write sts file and results files to job directory

Write lck file to lck directory

Apache HTTP Server

XMLDB

Launching Synchronous (blocking) Jobs

Authentication and Authorization Security Module

Runner Service

Need to fork scisvr?

scisvr(.exe) JVMCLR

2.1.

Get protocol XML from Protocol DB

3.

Connect to scisvr pipe. Send protocol XML and request parameters

4.

Send notification to apache via pipe when done

5.

Stream results back to Apache on pipe

XMLDB XMLDB

Write lck file to lck directory

Job Settings

• Set Max Running Jobs to 2x available cores

• Set Blocking Job timeout between 10-30 seconds, not more due to client starvation

• Maximum Number of Parallel Processing is a guideline, not a strict maximum. Set to 2x cores

• Set Maximum Job Daemons Per Pool to 2x available cores

• Job Readiness Refresh Rate assists with multipurpose servers which can become “cold”

• Read application specific recommendations for more details

– Identified by __poolid=<name> parameter on request.– Needs to be sent from the

client, not from the saved protocol

– Latency of 20-200 ms– Creates a pool of scisvr.exe

processes dedicated to that pool

– Enables caching of expensive resources:• JVM• CLR• Database connections• Protocol DB Shortcuts

and References

Process Management - Pools

– Impersonation create a small pool for each user for each pool

– Lower the pool sizes to accommodate this behaviors

Process Management – Pools w/ Impersonation

Scisvr Pool Settings – Config filesSetting Default Description

Start Servers 0 Number of initial processes in this pool, created when apache starts

Min Spare Servers 1 Min number of idle processes to keep alive

Max Spare Servers 1 Max number of “available”processes to keep alive

Max Spare Servers Trim Time 0 Time to wait (seconds) before pruning “Available” servers exceeding Max Spare Servers value

Max Servers 16 The total number of servers to allow for this pool

Max Queue Depth 32 maximum number of jobs to queue before rejected. Can be 0 or -1 for infinite

Max Requests Per Server -1 Maximum number of requests to handle in a single server before exiting, -1 is infinite

Time to Live 300 Idle timeout (seconds) for pooled server to live

Warm-up Protocol Path to initial protocol to run

Memory Threshold 80 Max % phys mem use by all proc’s before pruning

Individual Usage Threshold 15 Max % phys mem use by one proc before pruning

Web Job Launch Scalability Improvements

Framework overhead on blocking, pooled jobs on 8 core Windows 2008 R2 (64 bit)

Web Job Launch Scalability Improvements LinuxFor simple chemistry fetch of 10 records to JSON on 8 core RedHat Linux ES5 (64 bit)

Identical tests on Windows 2008 RS on identical hardware

Performance Tuning Document

• Guide available on Accelrys Forums– http://doc.accelrys.com/library/PipelinePilot/doc/performance

_tuning.pdf

Public Cluster

16

Clients

Primary Pipeline Pilot Server

SecondaryPipelinePilot Servers

Login

Execute

NFS

Users

Users

Private Cluster

17Clients

Primary Pipeline Pilot Server

SecondaryPipelinePilot Servers

Login

NFS

Execute

Users

Users

Users

Grid (SGE, PBS, LSF, other)

18Clients

Primary Pipeline Pilot serverandgrid submission server

Grid Nodes: do not require Apache HTTPD

Login

NFS

Execute

Users

Users

Users

Grid software and SOAP

IP-based Load Balancing 1

19

Clients

Reverse Proxyor

IP-based Load Balancer

Login

Execute

Users

Users

Symmetrical Pipeline Pilot Server Nodes Shared Storage

XMLDB

Job FoldersUser Folders

File share

• What we learned– Apache service and launching system– Job launching and settings– Process management for pooling– How pooling has improved latency (snappiness)– Clustering and grids

Summary

The information on the roadmap and future software development efforts are intended to outline general product direction and should not be relied on in making a purchasing decision.

For more information on the Accelrys Tech Summits and other IT & Developer information, please visit:https://community.accelrys.com/groups/it-dev