Deploying A PILATUS 6M For Protein Crystallography At

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Deploying a PILATUS 6M forProtein Crystallography atIMCA-CATJoe DigilioJ. Lewis Muir15 July 2010


EXPERIMENT BASICSDetectorSampleShutterX-rays

STEP-ROTATIONStart of RotationOpen ShutterExposureClose ShutterEnd of Rotation

CONTINUOUS-ROTATIONStart of RotationOpen ShutterMultipleExposuresClose ShutterEnd of Rotation


DECTRIS PILATUS 6M 2.3 ms readout time 5 V TTL external trigger/gate 12 Hz frame rate

ALIO GONIOMETER Air bearing Phi (rotation axis) 90 deg/s Phi velocity 2.5 μm runout for all axes Delta Tau Turbo PMAC Clipper Use “gain scheduling” for X and Y

IMPLEMENTATIONUserJDirectorImcaisEPICS Motor RecordExphiAreaDetectorPMAC PLCCamserverPMAC CLIPPERPhi AxisShutterPILATUS 6M

Imcais1. Sets up Exphi2. Sets up areaDetector3. Moves Phi

Exphi Shutter controlled via Turbo PMAC Clipper digital output point Exposure trigger controlled via Turbo PMAC Clipper digital output point


PMAC PLC ProgramCLOSEEND GATHERDELETE GATHERDELETE TRACE Runs as regular PLC Not compiled M-variable for positionPossible optimizations: Run PLC at servo priority Use position-compare functionP1 0P4 0P7 M0P8 M2P10 0P11 0P12 0OPEN PLC 3 CLEAR; Open exposure shutter if requested, and start timerIF (M0! P7)M0 P7IF (M0 1)I5111 P6*8388608/I10ENDIFENDIF; Close exposure shutter if maximum exposure time reachedIF (M0 1 AND P6! 0 AND I5111! 0)P7 0M0 0P1 0P12 0ENDIF; Start exposure trigger pulse if requested, and start timerIF (M2! P8)M2 P8IF (M2 1)I5112 10*8388608/I10ENDIFENDIF.

AreaDetector PILATUS Driver Added CBF image support Added MX settings support Use External Trigger mode Use PILATUS 6M internal timer

AreaDetector PILATUS Driver

CRYSTALLOGRAPHY 3 minute dataset (180 images, 1 deg. image width, 1 s exposure) Test data suggests 1.5 minute dataset is OK too Data quality comparable to step-rotation mode with ADSC Q210r


COMPUTING OVERVIEW Fast and Reliable Storage Fast Network Fast Workstations

STORAGE REQUIREMENTS Aggregate Throughput: 500‐700MB per second Approximately 50TB Highly Available Scalable (size and performance) Avoid vendor lock‐in Compatible with detector server (openSUSE 10.3) POSIX Compliant Modular (reconfigurable to another solution)

DATA FLOWXDS AutoProcessing200 MB / dataset72 MB/s72 MB/sPilatus 6MDetector12 fps200 MB / dataset72 MB/sDetector Computer(openSUSE 10.3)Storage ThroughputNote: 72MB/s 12x6MB/s1 dataset 360-1440 framesWrites: Sustained: 72 MB/s ; Peak: 472MB/sDetector Server: 72MB/sAuto-Processing: 200 MB / datasetSecondary Processing: 200 MB / datasetReads: Sustained: 294 MB/s ; Peak: 694MB/sAuto-Processing: 72MB/sSecondary Processing: 72MB/sViewing: 6MB/sExternal Storage: 72MB/s processed dataExternal Storage: 72MB/s processed dataSecondaryProcessing(manual orclustered)Storage72 MB/s 200 MB72 MB/s 200 MB! 6 MB/sviewing:JDirector, etcExternal Storage(USB, Firewire,eSATA)External Storage(USB, Firewire,eSATA)

LUSTRE FILE SYSTEM High-Availability Scalable Size: up to 64PB Performance: scales nearly linearly to the number of OSTs Server Read Caching: reduces load on storage backend Used in similar environments (eg, LS-CAT) Open Source Thriving community (even after Oracle’s acquisition of Sun)

LUSTRE CONFIGURATIONLustre Two MetaData Servers (MDS) - Active/Passive Failover Two Object Storage Servers (OSS) - Active/Active Failover On-site installation by DataDirect NetworksHigh Availability: Heartbeat and PacemakerMDS/OSS Servers Dual Quad-Core Xeons 12 - 24GB RAM

STORAGE HARDWAREDataDirect Networks S2A6620 Four 8x Fibre Channel Connections 80TB Raw Storage (File Data) 80x 1TB SATA drives 8x 10 drive RAID6 arrays ( 7.5TB each) 60TB usable3TB Raw Storage (MetaData) 10x 300GB 10k RPM SAS drives

TInfiniband SwitchDetectorServer Primary: Backup:InfiniBand DDR (20Gb/s)OSTOSSGigabit iniBandFibre ChannelOST

WORKSTATIONS Data Collection Data Backup Data Processing (x2) Specs Dual Quad-Core Xeons 24GB RAMProcess datasets in 5-15 minutes

OVERALL PERFORMANCEGreater than 500MB/s aggregate

FUTURE Tweak settings on DDN S2A6620 Tweak Lustre parameters Improve data processing times Evaluate automated data processing

ACKNOWLEDGEMENTSBill Allcock (ANL-LCF)Kevin Battaile (IMCA-CAT)Heiner Billich (SLS)Stefan Brandstetter (DECTRIS)Keith Brister (LS-CAT)Peter DenisonEric Eikenberry (DECTRIS)Brian Finley (ANL-CIS)Andrew Foster (Diamond)Cheetah Goletz (ANL-LCF)Oleg Makarov (GM/CA-CAT)Ariel Martinez (DDN)Anne Mulichak (IMCA-CAT)Matthew Pearson (Diamond)Nick Rees (Diamond)Mark Rivers (GSECARS)Sergey Stepanov (GM/CA-CAT)Michael Sternberg (ANL-CNM)Kit Westneat (DDN)

Jul 15, 2010 · Delta Tau Turbo PMAC Clipper . Exphi Shutter controlled via Turbo PMAC Clipper digital output point Exposure trigger controlled via Turbo PMAC Clipper digital output point. Exphi. PMAC PLC Program CLOSE END GATHER DELETE GATHER DELETE TRACE

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