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Getting Started on Emerald

Getting Started on Emerald

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Getting Started on Emerald

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  1. Getting Started on Emerald Research Computing Group

  2. Course Outline • What is Emerald? • Logging into Emerald • File manipulation on Emerald • Submitting jobs on Emerald • Interactive programs on Emerald

  3. Help Documentation • Getting Started on Emerald • http://help.unc.edu/6020 • General overview of Emerald for range of users • Short Course – Getting Started on Emerald • http://help.unc.edu/6479 • Detailed notes for beginning Emerald users

  4. What is Emerald? • 352-processor Linux Cluster • Maintained by Research Computing Group • Appropriate for all users regardless of expertise level • Other Servers: • Cedar/Cypress (128-processor SGI/Altix) • Topsail (4160-processor Dell Linux Cluster) • Mass Storage • Account access

  5. Advantages of Using Emerald • High performance • Large capacity • Parallel processing • Many available software packages • Variety of compiling options

  6. Emerald Linux Cluster

  7. CPU CPU CPU CPU M M M M NETWORK Distributed vs. Shared Memory CPU CPU CPU CPU BUS MEMORY Shared memory - single address space. All processors have access to a pool of shared memory. (examples: Yatta, Cedar/Cypress) Methods of memory access : Bus and Crossbar Distributed memory - each processor has it’s own local memory. Must do message passing to exchange data between processors. (examples: Emerald, Topsail)

  8. Logging Into Emerald • UNIX/Linux/OSX • ssh my_onyen@emerald.unc.edu • Windows: SSH Secure Shell • Setting up a Profile for Emerald • Forwarding X11 packets

  9. Home and Work Directories on Emerald • Home Directory • /afs/isis/home/m/y/my_onyen/ • 250MB quota • ~/private/ • Files backed up daily [ ~/OldFiles] • Space quota/usage in Home Directory: • fslq • Work Directory • /netscr/my_onyen/ • No space limit but periodically cleaned

  10. File Manipulation Commands • SSH Secure File Transfer • Copy files • cp command cp /afs/isis/depts/atn/rcg/example_code/Gaussian/water.com /netscr/my_onyen/. cp /afs/isis/depts/atn/rcg/example_code/sas/test.sas /netscr/my_onyen/. • cp -r • cp -r ~/private/TestDirectory . • Move files • mv commands • mv ~/private/testfile.txt .

  11. File Manipulation Commands • Tar archive • To create a tar file • tar –cvzf TestDirectory.tgz ./ • To see a tar file’s table of content • tar –tvzf TestDirectory.tgz • To untar a tar file • tar –xvzf TestDirectory.tgz

  12. Submitting Jobs: LSF and Packages • LSF (Load Sharing Facility) • Fairly distribute compute nodes among users • 60 processor per user limit • Packages • ipm commands • ipm add (ipm a) • ipm remove (ipm r) • ipm query (ipm q) • Available packages • http://www.renci.org/unc/computing/resources/applications.php

  13. other hosts other hosts Execution host Submission host Master host 3 LIM LIM MLIM Load information 4 2 5 SBD MBD Batch API 11 8 9 Child SBD 1 7 6 queue 12 10 bsub app RES 13 LIM – Load Information Manager MLIM – Master LIM MBD – Master Batch Daemon SBD – Slave Batch Daemon RES – Remote Execution Server User job Details of LSF

  14. Submitting Jobs: bsub Command • bsub command • All files must be in /netscr/my_onyen/ • bsub [- bsub_opts] executable [-exec_opts] • Queues – bqueues command • week • idle • bsub –o • bsub –o out.%J

  15. Submitting Jobs: Following Job Progress • bjobs • bjobs –l JobID • Shows current status of job • bhist • bhist –l JobID • bkill • bkillJobID • Ends job prematurely • bfree

  16. Submitting Jobs: Specialty Scripts • bsas • bsub -q week -R blade sas program.sas • bsas test.sas • bmatlab • bsub -q week -R blade matlab -nodisplay -nojvm -nosplashprogram.m -logfile program.log • bmatlabtest.m

  17. Compiling on Emerald • Compilers • FORTRAN 77/90/95 • C/C++ • Parallel Computing • OpenMP • MPI (MPICH, LAM/MPI, MPICH-GM)

  18. Compiling Details on Emerald

  19. Compiling Details on Emerald • Add a compiler into your working environment • ipm add package_name • Compile a code • command code.f –o executable • Run executable on a compute node using the bsub command • bsub –q week –R blade executable

  20. Submitting Jobs: Job Output • Output sent to email • my_onyen@email.unc.edu • bsub –o • Output saved in working directory • bsub –u email@address • Output sent to specified email address

  21. Interactive Jobs: Setup • X-Windows • Linux/OSX • X11 client • Windows • X-Win32 • Offered on UNC Software Acquisition site • Port forwarding on SSH Secure Shell • Setting up a session on X-Win32

  22. Interactive Jobs: Submission • –Ip • bsub –q int –R blade –Ip sas • bsub –q int –R blade –Ip gv • Specialty Scripts • xsas • xstata

  23. Contacting Research Computing • For assistance with Emerald, please contact the Research Computing Group: • Email: research@unc.edu • Phone: 919-962-HELP • Submit help ticket at http://help.unc.edu