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Si Liu NCAR/CISL/OSD/USS Consulting Service Group

National Center for Atmospheric Research Computation and Information Systems Laboratory Facilities and Support Overview Feb 14, 2010. Si Liu NCAR/CISL/OSD/USS Consulting Service Group.

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Si Liu NCAR/CISL/OSD/USS Consulting Service Group

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  1. National Center for Atmospheric ResearchComputation and Information Systems Laboratory Facilities and Support OverviewFeb 14, 2010 Si Liu NCAR/CISL/OSD/USS Consulting Service Group

  2. CISL’s Mission for User Support“CISL will provide a balanced set of services to enable researchers to securely, easily, and effectively utilize community resources”CISL Strategic Plan CISL also supports special colloquia, workshops andcomputational campaigns; giving these groups of usersspecial privileges and access to facilities and servicesabove and beyond normal service levels.

  3. CISL Facility Navigation and usage of the facility requires a basic familiarity with a number of the functional aspects of the facility. • Computing systems • Bluefire • Frost • Lynx • NWSC machine • Usage • Batch • Interactive • Data Archival • MSS • HPSS • GLADE • Data Analysis & Visualization • Mirage and Storm • Allocations and security • User support

  4. Allocations • Allocations are granted in General Accounting Units (GAUs) • Monitor GAU usage through the CISL portal: http://cislportal.ucar.edu/portal(requires UCAS password) • Charges are assessed overnight and will be available for review for runs that complete by midnight. • GAUs charged = wallclock hours used * number of nodes used * number of processors in that node * computer factor * queue charging factor • The computer charging factor for bluefire is 1.4.

  5. Security • CISL Firewall • Internal networks are separated from the external Internet • protect servers from malicious attacks from external networks • Secure Shell • Use SSH for local and remote access to all CISL systems. • One-time passwords for protected systems • Cryptocard • Yubikey

  6. Computing System - Bluefire • IBM clustered Symmetric MultiProcessing (SMP) system • Operating System: AIX (IBM-proprietary UNIX) • Batch system: Load Sharing Facility (LSF) • File system: General Parallel File System (GPFS) • 127 32-Way 4.7 GHz nodes • 4,064 POWER6 processors • SMT enabled (64 SMT threads per node) • 76.4 TFLOPS • 117 Compute nodes (70.4 TFLOPS peak) • 3,744 POWER6 processors (32 per node) • 69 compute nodes have 64 GB memory • 48 compute nodes have 128 GB memory • 10 other nodes • 2 Interactive sessions/Login nodes (256 GB memory) • 2 Debugging and Share queue nodes (256 GB memory) • 4 GPFS/VSD nodes • 2 Service nodes

  7. Computing System – Bluefire, continued • Memory • L1 cache is 128 KB per processor. • L2 cache is 4 MB per processor on-chip. • The off-chip L3 cache is 32 MB per two-processor chip, and is shared by the two processors on the chip. • 48 nodes contain 128 GB of shared memory, and 69 nodes contain 64 GB per processor of shared memory. • Disk storage • 150 TeraBytes of usable file system space • 5 GB home directory; backed up and not subject to scrubbing. • 400 GB /ptmp directory; not backed up • High-speed interconnect : Infiniband Switch • 4X Infiniband DDR links capable of 2.5 GB/sec with 1.3 microsecond latency • 8 links per node

  8. Computing System - Frost • Four-rack, IBM Blue Gene/L system • Operating system: SuSE Linux Enterprise Server 9. • Batch System: Cobalt from ANL • File system: The scratch space (/ptmp) is GPFS. Home directories are NFS mounted. • 4096 compute nodes (22.936 TFLOPS peak) • 1024 compute nodes per rack • Two 700MHz PowerPC-440 CPUs, 512MB of memory, and two floating-point units (FPUs) per core • One I/O node for every 32 compute nodes • Four front-end cluster nodes. • IBM OpenPower720 server • Four POWER5 1.65GHz CPUs • 8GB of memory

  9. Computing System – Lynx • Single cabinet Massively Parallel Processing supercomputer. • Operating system: Cray Linux Environment • Compute Node Linux (CNL) – based on SuSE Linux SLES 10 • Batch System: • MOAB workload manager • Torque (aka OpenPBS) resource manager • Cray’s ALPS (Application Level Placement Scheduler) • File system: Luster file system • 912 compute processors (8.026 TFLOPS peak) • 76 compute nodes, 12 processors per node • Two hex-core AMD 2.2 GHz Opteron chips  • Each processor has 1.3 gigabytes of memory and totaling 1.216 terabytes of memory in the system. • 10 I/O nodes • A single dual-core AMD 2.6 GHz Opteron chip and 8 gigabytes of memory. • 2 login nodes, 4 nodes reserved for system functions. • 4 nodes are for external Lustrefilesystem and GPFS file system testing.

  10. A Job Script on Bluefire #!/bin/csh # LSF batch script to run an MPI application #BSUB -P 12345678 # project number (required) #BSUB -W 1:00 # wall clock time (in minutes) #BSUB -n 64 # number of MPI tasks #BSUB -R "span[ptile=64]" # run 64 tasks per node #BSUB -J matadd_mpi # job name #BSUB -o matadd_mpi.%J.out # output filename #BSUB -e matadd_mpi.%J.err # error filename #BSUB -q regular # queue # edit exec header to enable using 64K pages ldedit -bdatapsize=64K -bstackpsize=64K -btextpsize=64K matadd_mpi.exe # set this env for launch as default processor binding setenv TARGET_CPU_LIST "-1" mpirun.lsf /usr/local/bin/launch ./matadd_mpi.exe For more examples, see the /usr/local/examples directory.

  11. Submitting, Deleting, and Monitoring Jobs on Bluefire • Job submission • bsub < script • Monitor jobs • bjobs • bjobs -u all • bjobs -q regular -u all • bhist -n 3 -a • Deleting a job • bkill[jobid] • System batch load • batchview

  12. "Big 3“ to get a best performance on bluefire • Simultaneous Multi-Threading(SMT) • a second, on-board "virtual" processor • 64 virtual cpus in each node • Multiple page size support • The default page size: 4 KB. • 64-KB page size when running the 64-bit kernel. • Large pages (16 MB) and "huge" pages (16 GB) • Processor binding

  13. Submitting, Deleting, and Monitoring Jobs on Frost • Submitting a job • cqsub -n 28 -c 55 -m vn \ -t 00:10:00 example • Check job status • cqstat • Deleting a job • cqdel [jobid] • Altering jobs • qalter -t 60 -n 32 --mode vn 118399

  14. A job script on Lynx #!/bin/bash #PBS -q regular #PBS -l mppwidth=60 #PBS -l walltime=01:30:00 #PBS –N example #PBS -e testrun.$PBS_JOBID.err #PBS -o testrun.$PBS_JOBID.out cd $PBS_O_WORKDIR aprun -n 60 ./testrun

  15. Submitting, Deleting, and Monitoring Jobs on Lynx • Submitting a job • qsub [batch_script] • Check job status • qstat –a • Deleting a job • qdel [jobid] • Hold or release a job • qhold [jobid] qrls [jobid] • Change attributes of submitted job • qalter

  16. NCAR Archival System • NCAR Mass Store Subsystem - (MSS) • Currently stores 70 million files, 11 petabytes of data • Library of Congress (printed collection) • 10 Terabytes = 0.01 Petabytes • Mass Store holds 800 * Library of Congress • Growing by 2-6 Terabytes of new data per day • Data holdings increasing exponentially • 1986 - 2 Tb • 1997 - 100 Tb • 2002 - 1000 Tb • 2004 - 2000 Tb • 2008 - 5000 Tb • 2010 – 8000 Tb

  17. Migrating from the NCAR MSS to HPSS • MSS and its interfaces will be replaced by High Performance Storage System (HPSS) in March 2011. • When the conversion is complete, the existing storage hardware currently in use will still be in place, but it will be under HPSS control. • Users will not have to copy any of their files from the MSS to HPSS. There will be a period of downtime. • The MSS Group will be working closely with users during this transition.

  18. The differences between MSS and HPSS • What will be going away: • msrcp and all DCS libraries. • The MSS ftp server. • All DCS metadata commands for listing files, and manipulating files. • Retention periods, the weekly "Purge" and email purge notices, the "trash can" for purged/deleted files, and the "msrecover" command. • Read and write passwords on MSS files. • What we will have instead: • Hierarchical Storage Interface (HSI), which will be the primary interface that NCAR will be supporting for data transfers to/from HPSS along with metadata access and data management. • GridFTP (under development) • HPSS files have NO expiration date. They remain in the archive until they are explicitly deleted. Once deleted, they cannot be recovered. • Posix-style permission bits for controlling access to HPSS files and directories. • Persistent directories. • Longer filenames (HPSS full pathnames can be up to 1023 characters). • Higher maximum file size (HPSS files can be up to 1 Terabyte).

  19. Charges for MSS and HPSS The current MSS charging formula is: GAUs charged = .0837*R + .0012*A +N(.1195*W + .205*S) • R = Gigabytes read • W = Gigabytes created or written • A = Number of disk drive or tape cartridge accesses • S = Data stored, in gigabyte-years • N = Number of copies of file: = 1 if economy reliability selected = 2 if standard reliability selected

  20. HPSS Usage • To request an account • TeraGrid users should send email to: help@teragrid.org • NCAR users should contact CISL Customer Support: cislhelp@ucar.edu • The HPSS uses HSI as its POSIX compliant interface. • HSI uses Kerberos as an authentication mechanism.

  21. Kerberoshttp://www2.cisl.ucar.edu/docs/hpss/kerberos • Authentication service • Authentication – validate who you are • Service – with a server, set of functions, etc. • Kerberos operates in a domain • Default is UCAR.EDU • Domain served by a KDC • Key Distribution Center • Server (dog.ucar.edu) • Different pieces (not necessary to get into this) • Users of the service • Individual people • Kerberized Services (like HPSS)

  22. Kerberos Commands • kinit • Authenticate with KDC, get your TGT • klist • List your ticket cache • kdestroy • Clear your ticket cache • kpasswd • Change your password

  23. Hierarchical Storage Interface (HSI) • POSIX like interface • Different Ways to Invoke HSI • Command line invocation • hsicmd • hsi get myhpssfile (in your default dir on HPSS) • hsi put myunixfile (in your default dir on HPSS) • Open an HSI session • hsi to get in and establish session; end, exit, quit to get out • restricted shell like environment • hsi “in cmdfile” • File of commands scripted in “cmdfile” • Navigating HPSS while in HSI session • pwd , cd, ls, cdls

  24. Data Transfer • Writing data – put command • [HSI]/home/user1> put file.01 • [HSI]/home/user1> put file.01 : new.hpss.file • Reading data – get command • [HSI]/home/user1-> get file.01 • [HSI]/home/user1-> get file.01 : new.hpss.file Detailed documentation for HSI can be found at http://www.ucar.edu/docs/hpss

  25. GLADE centralized file service • High performance shared file system technology • Shared work spaces across CISL's HPC resources • Multiple different spaces based requirements. • /glade/home/username • /glade/scratch/username • /glade/proj*

  26. Data Analysis & Visualization • Data Analysis and Visualization • High-end servers available 7 x 24 for interactive data analysis, data-postprocessing and visualization. • Data Sharing • Shared data access within the Lab. Access to the NCAR Archival Systems and NCAR Data Sets. • Remote Visualization • Access DASG's visual computing platforms from the convenience of your office using DASG's tcp/ip based remote image delivery service. • Visualization Consulting • Consult with DASG staff on your visualization problems.   • Production Visualization • DASG staff can in some instances generate images and/or animations of your data on your behalf.

  27. Software Configuration (Mirage-Storm). • Development Environments • Intel C, C++, F77, F90 • GNU C, C++, F77, Tools • TotalView debugger • Software Tools • VAPOR • NCL, NCO, NCARG • IDL • Matlab • Paraview • ImageMagick • VTK

  28. User Support • CISL homepage: • http://www2.cisl.ucar.edu/ • CISL documentation • http://www2.cisl.ucar.edu/docs/user-documentation • CISL HELP • Call (303)497-1200 • Email to cislhelp@ucar.edu • Submit an extraview ticket • CISL Consulting Service • NCAR Mesa Lab Area 51/55, Floor 1B

  29. Information We Need From You • Machine name • Job ID, date • Nodes job ran on, if known • Description of the problem • Commands you typed • Error code you are getting • These are best provided in ExtraView ticket or via email to cislhelp@ucar.edu.

  30. Working on mirage • Log on to ‘mirage’ • ssh –X –l username mirage3.ucar.edu • One-time password using CryptoCard or Yubikey • Use 'free' or 'top' to see if there is currently enough resources • Enabling your Yubikey token • Your yubikey has been activated and is ready for use. • The yubikey is activated by the warmth of your finger not the pressure in pushing the button. • Using your Yubikey token • When you are logging in to mirage, your screen displays a response: Token_Response: • Enter you PIN number on the screen (do not hit enter) then touch the yubikey button. This will insert a new one-time password(OTP) and a return.

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