KAUST Supercomputing Laboratory Newsletter 13th January 2016

XSEDE HPC Workshop: OpenMP

The registration page for the XSEDE HPC Monthly Workshop Series - January 20th - OpenMP session is up.
The portal registration page can be found here:
https://portal.xsede.org/course-calendar/-/training-user/class/454/sessi...
If there is enough interest, KSL will investigate the possibility of streaming this course live in the Library computer room on the 20th of January.

KSL Workshop Series:  Optimizing I/O on Shaheen II

Thursday, February 4, 2016

KAUST Supercomputing Laboratory (KSL) invites you to the second Shaheen II Seminar Series on maximizing efficient use of the parallel file system.  It will provide an overview of Parallel I/O, explore using various profiling tools for validating I/O performance, and cover best practices for efficient I/O operations.  The focus will be on scientific codes for climate, seismic, and biology applications. 
 
This seminar is for all Shaheen II users dealing with large files, or a large number of files.
Seats are limited. Please register your interest at: https://www.surveymonkey.com/r/H6FNM7C
 
Venue/Time: Computer Lab Room, 3rd floor at the Library, from 9:30am-11:00am
 
Agenda:
        09:30am - Optimizing I/O on Shaheen II
        10:00am - Interactive Exercises on Shaheen II
        10:30am - Q&A with KSL team (bring all your HPC questions)
 

Neser Last Day of Service

Please note this system has now been decommissioned.

Shaheen I/ Neser Data

We will continue to have the Shaheen I/Neser ‘home' and ‘project' filesystems available until at least 31st July 2016. However, please note that the ‘scratch' filesystem will be taken off-line and deleted on the 1st February 2016.
For data that is needed for projects on Shaheen II, rather than copying it yourself, please contact us and we can assist in moving the data as we have dedicated systems for this that have direct access to both storage subsystems.

Tip of the Week:Dynamically Linking Applications

By default, on Shaheen II Cray XC40, compiling and linking libraries to build an application will make use of static linking, which is recommended for most applications. However, using dynamic libraries is necessary for some applications. In this case, users can link applications dynamically by either setting the environment variable CRAYPE_LINK_TYPE to dynamic or by adding the -dynamic flag during linking.

  • Example of building program with dynamic linking, export the environment variable and compile your code normally.
export CRAYPE_LINK_TYPE=dynamic
ftn -o my_exe_dynamic  my_program.f90
  • Same example by using linker flag:
ftn -dynamic -o my_exe_dynamic my_program.f90

At runtime you also need to export CRAY_ROOTFS=DSL in your job script.

Please note that using dynamically linked applications does have a performance impact especially with a large number of processes.  This is due to the runtime linking process and symbol lookup in the shared objects during the startup of the program or when the loading of the dynamically loaded library is called.

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