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(ATS4-PLAT01) Core Architecture
Changes in AEP 9.0 and Their Impact
         on Administrators
                                   Steven Bush
                   R&D, AEP Core Infrastructure
                    steven.bush@accelrys.com
Platforms

• Except where noted, the information within this
  presentation applies to both Windows and Linux
  installations.
• Starting in 9.0, AEP server installations are now 64-bit
  only
Services
• 8.5 and earlier
   – 32 and 64 bit
   – Apache
• 9.0
   – 64 bit only
   – Apache
        • Manages running jobs
        • Other services including access to protocol database and files
   – Tomcat
        • Back end service provider
             –   Security filter
             –   Internal configuration and system database
             –   Periodic cleanup tasks
             –   Other scheduled tasks
   – AEPManager (Windows)
        • Responsible for managing the other services
Tomcat Cleanup tasks
• Remove stale job directories
   – Expired and invalid jobs
• Queue processing
   – When max running jobs is reached
• Remove stale lck files
   – <InstallDir>/temp/lck
       • Each running job creates a file with basic information
       • Running jobs reports, when to queue based on lck file count
       • If the job process crashes, the lck file remains
• Clean up /var/tmp files (Linux)
   – Used for OS synchronization files (mutexes, conditions, pipes)
Managing the services (Windows)

• AEPManager service
   – Starts and shuts down Tomcat and Apache
   – Monitors status of each service to restart when necessary
   – Right click “My Computer”, choose “Manage”, Navigate to Services.
     Start/Stop AEPManager.
• Modified ApacheMonitor.exe
   –   Based on Apache Foundation apachemonitor.exe
   –   Shows all installed Apache services
   –   Combines all services within same AEP install directory
   –   8.5 and earlier: use apachemonitor.exe that ships in apache folder
Managing the services (Windows)

• Services Administration Panel
• Processes and Memory
   – Task Manager
   – Process Explorer
      • Improved Task Manager
      • http://technet.microsoft.com/en-US/sysinternals
Managing the services (Linux)

• startserver, stopserver scripts still used
   – Starts and stops both Apache and Tomcat
   – /etc/rc.d used for autostart services
       • Installed by root installation script (scirootinstall)
• ps and top
• “free –m” to check memory (-m = Megabytes)
   – read “-/+ buffers/cache” line for real results
Launch Performance




   Example which reads 500 molecules and returns a bit of JSON text.
   Elapsed Time/Throughput vs Number of Simultaneous Clients
Exporting/Importing Configurations

• Export configuration from administration portal
   – Clone server configurations
   – Set up new nodes for load balancing configuration
Maintenance Mode

• Disable launching jobs without shutting down the server
   – Professional UI can still be used to build protocols
   – Admin portal is still accessible
New Deployment Options
                               8.5        9.0
            Single Server      Yes        Yes
                Windows      32/64 bit   64 bit
                    Linux    32/64 bit   64 bit
           Private Cluster    Linux      Linux
            Public Cluster    Linux      Linux
              Grid Engine     Linux      Linux
      SSL Only/HTTP Only        No        Yes
          Port Forwarded        No        Yes
  Load Balanced Web Farm        No        Yes
New Globals/URL creation

• Should no longer build URLs from server name and port
   – Will not work with reverse proxies and single port setups
   – Had problems on clusters and grids
• Use @ServerRoot and @ServerSSLRoot instead
   – Reflects configuration of server
      •   SSL/HTTP only
      •   Reverse proxy/port forwarded
      •   Load balanced
      •   Clusters and grids
• Old globals will continue to work for basic configurations
New Globals/URL Creation


                                                     8.5                                         9.0


                HTTP URLs     http://$(ServerName):$(ServerPort)/myFile       $(ServerRoot)/myfile


               HTTPS URLs     https://$(ServerName):$(ServerSSLPort)/myFile   $(ServerSSLRoot)/myfile


         Internal HTTP URLs   Same as client                                  @/pilot_settings/ROOT


        Internal HTTPS URLs   Same as client                                  @/pilot_settings/SSLROOT


       Internal Server Name   Same as client                                  @/pilot_settings/InternalServerName


      Shared Data Directory   @ScitegicRoot                                   @SharedPublicDir
Protocol Links

• http://<server>:<port>/auth/launchjob
   – Faster launch times
   – Improved features
       • streaming results
       • Integrated authentication
   – runjob.pl links map to launchjob with _compat=1 flag
SSL and HTTP Only Modes

• Setting found in Admin Portal
   – Server ConfigurationServer Port Usage
• Changes all outgoing URLs to point to correct endpoint
   – In SSL only mode, @ServerRoot becomes https://....
   – In HTTP only mode, @ServerSSLRoot becomes http://....
• Does not turn off second port by default
   – To disable listening on the unused port, contact support
Reverse Proxy
Reverse Proxy

• Deploy behind a port forwarding server
   – Deployment into DMZs
   – Multiple subnet deployments
      • Some clients outside firewall, others inside
• “SSL termination” option
   – Connection to reverse proxy is via SSL
   – From proxy to AEP server is HTTP only
Reverse Proxy: Configuration

• Configure in Admin portal
   – SetupReverse Proxy and Load Balancing
   – Set the default server name for your reverse proxy (e.g.
     firewall.mydomain.net)
       • Add aliases that might be used as well (e.g.
         10.1.2.3,firewall,othername.mydomain.net)
   – Set the port numbers that are available for your reverse proxy
       • Leave HTTP or SSL blank if not used
Reverse Proxy: Configuration
Load Balanced
Load Balanced vs. Cluster vs. Grid
•   Load Balanced (Windows or Linux)
     –   Large numbers of simultaneous users
     –   Individual web requests are distributed
     –   Parallel subprotocols are not distributed
     –   Ideal for short running web based applications that require simultaneous user scalability or failover
     –   Cannot be used for ad-hoc use
•   Cluster (Linux)
     –   Large numbers of long running jobs
     –   Running jobs are distributed
     –   Parallel subprotocols are distributed
     –   Ideal for long running jobs with large parallelization needs
     –   Useful for ad-hoc use
•   Grid (Linux)
     –   Similar to cluster
     –   Load is controlled by third party grid software (eg. OGE, LSF, PBS)
     –   Slowest launch times
     –   Ideal for large numbers of very long running jobs and taking advantage of existing grid systems
     –   Possibly slow for ad-hoc use
Load Balancer Requirements

• Install behind any off the shelf load balancer
   – The AEP server itself does not require affinity, but some
     applications may choose to impose this limitation
   – One requirement for the load balancer: Must preserve the
     HTTP “Host” header.
Load Balanced: Benefits

• Throughput
   – Huge improvement under high usage
• Performance
   – No difference under low usage versus single servers
   – Moderate improvement under high usage
• High Availability
   – If a node goes down, other nodes continue functioning
Load Balanced: Performance




 Example which reads 500 molecules and returns a bit of JSON text tested against 1-3
 nodes. Elapsed Time/Throughput vs Number of Simultaneous Clients
Load Balanced: Restrictions
• Protocol Database is read only
   – Deploy protocols and components using packages
   – Can not build models
   – Intended for applications that rarely change
• Parallel subprotocols do not distribute across nodes
   – Set “Server” to the name of the load balancer instead of “localhost”
• Admin Portal connected through the load balancer can only
  show running jobs
   – Connect to individual nodes for full portal access
   – Use “Export/Import” to update each node
Load Balanced: Shared Data

•   “Folder Locations” in Admin portal
•   Jobs directory
•   Users directory
•   Shared Public directory
    – Use @SharedPublicDir instead of @ScitegicRoot
       • On a single server system, both are equal
Load Balanced: Configuration

• SetupReverse Proxy and Load Balancing
   – Follow same setup as for reverse proxy
   – Check box for “Load Balanced”
• SetupFolder Locations
   – Jobs directory
   – Users directory
   – Shared Public directory
      • Use @SharedPublicDir instead of @ScitegicRoot
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.

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(ATS4-PLAT01) Core Architecture Changes in AEP 9.0 and their Impact on Administrators

  • 1. (ATS4-PLAT01) Core Architecture Changes in AEP 9.0 and Their Impact on Administrators Steven Bush R&D, AEP Core Infrastructure [email protected]
  • 2. Platforms • Except where noted, the information within this presentation applies to both Windows and Linux installations. • Starting in 9.0, AEP server installations are now 64-bit only
  • 3. Services • 8.5 and earlier – 32 and 64 bit – Apache • 9.0 – 64 bit only – Apache • Manages running jobs • Other services including access to protocol database and files – Tomcat • Back end service provider – Security filter – Internal configuration and system database – Periodic cleanup tasks – Other scheduled tasks – AEPManager (Windows) • Responsible for managing the other services
  • 4. Tomcat Cleanup tasks • Remove stale job directories – Expired and invalid jobs • Queue processing – When max running jobs is reached • Remove stale lck files – <InstallDir>/temp/lck • Each running job creates a file with basic information • Running jobs reports, when to queue based on lck file count • If the job process crashes, the lck file remains • Clean up /var/tmp files (Linux) – Used for OS synchronization files (mutexes, conditions, pipes)
  • 5. Managing the services (Windows) • AEPManager service – Starts and shuts down Tomcat and Apache – Monitors status of each service to restart when necessary – Right click “My Computer”, choose “Manage”, Navigate to Services. Start/Stop AEPManager. • Modified ApacheMonitor.exe – Based on Apache Foundation apachemonitor.exe – Shows all installed Apache services – Combines all services within same AEP install directory – 8.5 and earlier: use apachemonitor.exe that ships in apache folder
  • 6. Managing the services (Windows) • Services Administration Panel • Processes and Memory – Task Manager – Process Explorer • Improved Task Manager • http://technet.microsoft.com/en-US/sysinternals
  • 7. Managing the services (Linux) • startserver, stopserver scripts still used – Starts and stops both Apache and Tomcat – /etc/rc.d used for autostart services • Installed by root installation script (scirootinstall) • ps and top • “free –m” to check memory (-m = Megabytes) – read “-/+ buffers/cache” line for real results
  • 8. Launch Performance Example which reads 500 molecules and returns a bit of JSON text. Elapsed Time/Throughput vs Number of Simultaneous Clients
  • 9. Exporting/Importing Configurations • Export configuration from administration portal – Clone server configurations – Set up new nodes for load balancing configuration
  • 10. Maintenance Mode • Disable launching jobs without shutting down the server – Professional UI can still be used to build protocols – Admin portal is still accessible
  • 11. New Deployment Options 8.5 9.0 Single Server Yes Yes Windows 32/64 bit 64 bit Linux 32/64 bit 64 bit Private Cluster Linux Linux Public Cluster Linux Linux Grid Engine Linux Linux SSL Only/HTTP Only No Yes Port Forwarded No Yes Load Balanced Web Farm No Yes
  • 12. New Globals/URL creation • Should no longer build URLs from server name and port – Will not work with reverse proxies and single port setups – Had problems on clusters and grids • Use @ServerRoot and @ServerSSLRoot instead – Reflects configuration of server • SSL/HTTP only • Reverse proxy/port forwarded • Load balanced • Clusters and grids • Old globals will continue to work for basic configurations
  • 13. New Globals/URL Creation 8.5 9.0 HTTP URLs http://$(ServerName):$(ServerPort)/myFile $(ServerRoot)/myfile HTTPS URLs https://$(ServerName):$(ServerSSLPort)/myFile $(ServerSSLRoot)/myfile Internal HTTP URLs Same as client @/pilot_settings/ROOT Internal HTTPS URLs Same as client @/pilot_settings/SSLROOT Internal Server Name Same as client @/pilot_settings/InternalServerName Shared Data Directory @ScitegicRoot @SharedPublicDir
  • 14. Protocol Links • http://<server>:<port>/auth/launchjob – Faster launch times – Improved features • streaming results • Integrated authentication – runjob.pl links map to launchjob with _compat=1 flag
  • 15. SSL and HTTP Only Modes • Setting found in Admin Portal – Server ConfigurationServer Port Usage • Changes all outgoing URLs to point to correct endpoint – In SSL only mode, @ServerRoot becomes https://.... – In HTTP only mode, @ServerSSLRoot becomes http://.... • Does not turn off second port by default – To disable listening on the unused port, contact support
  • 17. Reverse Proxy • Deploy behind a port forwarding server – Deployment into DMZs – Multiple subnet deployments • Some clients outside firewall, others inside • “SSL termination” option – Connection to reverse proxy is via SSL – From proxy to AEP server is HTTP only
  • 18. Reverse Proxy: Configuration • Configure in Admin portal – SetupReverse Proxy and Load Balancing – Set the default server name for your reverse proxy (e.g. firewall.mydomain.net) • Add aliases that might be used as well (e.g. 10.1.2.3,firewall,othername.mydomain.net) – Set the port numbers that are available for your reverse proxy • Leave HTTP or SSL blank if not used
  • 21. Load Balanced vs. Cluster vs. Grid • Load Balanced (Windows or Linux) – Large numbers of simultaneous users – Individual web requests are distributed – Parallel subprotocols are not distributed – Ideal for short running web based applications that require simultaneous user scalability or failover – Cannot be used for ad-hoc use • Cluster (Linux) – Large numbers of long running jobs – Running jobs are distributed – Parallel subprotocols are distributed – Ideal for long running jobs with large parallelization needs – Useful for ad-hoc use • Grid (Linux) – Similar to cluster – Load is controlled by third party grid software (eg. OGE, LSF, PBS) – Slowest launch times – Ideal for large numbers of very long running jobs and taking advantage of existing grid systems – Possibly slow for ad-hoc use
  • 22. Load Balancer Requirements • Install behind any off the shelf load balancer – The AEP server itself does not require affinity, but some applications may choose to impose this limitation – One requirement for the load balancer: Must preserve the HTTP “Host” header.
  • 23. Load Balanced: Benefits • Throughput – Huge improvement under high usage • Performance – No difference under low usage versus single servers – Moderate improvement under high usage • High Availability – If a node goes down, other nodes continue functioning
  • 24. Load Balanced: Performance Example which reads 500 molecules and returns a bit of JSON text tested against 1-3 nodes. Elapsed Time/Throughput vs Number of Simultaneous Clients
  • 25. Load Balanced: Restrictions • Protocol Database is read only – Deploy protocols and components using packages – Can not build models – Intended for applications that rarely change • Parallel subprotocols do not distribute across nodes – Set “Server” to the name of the load balancer instead of “localhost” • Admin Portal connected through the load balancer can only show running jobs – Connect to individual nodes for full portal access – Use “Export/Import” to update each node
  • 26. Load Balanced: Shared Data • “Folder Locations” in Admin portal • Jobs directory • Users directory • Shared Public directory – Use @SharedPublicDir instead of @ScitegicRoot • On a single server system, both are equal
  • 27. Load Balanced: Configuration • SetupReverse Proxy and Load Balancing – Follow same setup as for reverse proxy – Check box for “Load Balanced” • SetupFolder Locations – Jobs directory – Users directory – Shared Public directory • Use @SharedPublicDir instead of @ScitegicRoot
  • 28. 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.