1 / 15

HPCC Mid-Morning Break

HPCC Mid-Morning Break. Interactive High Performance Computing Dirk Colbry, Ph.D. Research Specialist Institute for Cyber Enabled Discovery. Running Jobs on the HPC. Submission scripts are used to run jobs on the cluster. The developer nodes are used to compile, test and debug programs.

antionette-frankie
Download Presentation

HPCC Mid-Morning Break

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. HPCC Mid-Morning Break Interactive High Performance Computing Dirk Colbry, Ph.D. Research Specialist Institute for Cyber Enabled Discovery

  2. Running Jobs on the HPC • Submission scripts are used to run jobs on the cluster. • The developer nodes are used to compile, test and debug programs. • However, the developer nodes are powerful systems too. We don’t want to waste their compute power.

  3. Advantages of running Interactively • You do not need to write a submission script. • You do not need to wait in the queue. • You can provide input and feedback to your programs as they are running.

  4. Disadvantages of running Interactively • All the resources on developer nodes are shared between all users. • Any single process is limited to 2 hours of cpu time. If a process runs longer than 2 hours it will be killed. • Programs that over utilize the resources on a developer node (preventing other to use the system) can be killed without warning.

  5. Developer Nodes

  6. Developer Nodes

  7. Compiling • Most users use the developer nodes for developing their software. • If you are using a makefile you can compile using more processors with the –j option. • Make –j32 • Will make with 32 core threads

  8. Testing MPI jobs • Use mpirun instead of mpiexec • Need a hostfile > echo $HOST >> ./hostfile > echo $HOST >> ./hostfile > echo $HOST >> ./hostfile > echo $HOST >> ./hostfile • MPIRUN example: > mpirun –np 4 –hostfile ./hostfilemycommand

  9. Running in the background • You can run a program in the background by typing an “&” after the command. • You can make a program keep running even after you log out of your ssh session by using “nohup command”. • You can run an entire session in the background even if you log in and out of your ssh session by using the “screen” command. • All three of these options are common to linux and tutorials can be found online.

  10. What is X11? • Method for running Graphical User Interface (GUI) across a network connection. SSH X11 Personal Computer Running x11 server Cluster

  11. What is needed for X11 • X11 server running on your personal computer • SSH connection with X11 enabled. • Fast Network connection • Preferably on campus.

  12. Programs that can use X11 • matlab – Matrix Laboratory Software • R - statistical computing and graphics • firefox – Web browser • totalview – C/C++/fortran debugger • gedit, gvim, emacs – Text editors • And others…

  13. Installing an X-server • We have a tutorial for installing a windows X-server. • Search for “X-Server” on the HPCC wiki • https://wiki.hpcc.msu.edu/display/hpccdocs/Installing+an+X-server+on+Windows • There are lots of x11 servers • Xming • cygwin

  14. Example Programs • Totalview

  15. Star-P – Shared Memory Matlab • See wiki page to get started: • https://wiki.hpcc.msu.edu/display/hpccdocs/Star-P+and+MATLAB • Running Starp > module load starp > starp &

More Related