Category: General HPC

Content related to high performance computing in general.

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Citations & Acknowledgements

Proper acknowledgement of computational resources and HPC staff support in research at Auburn University is critical in soliciting HPC funding. Although metrics, such as the number of jobs ran, cluster utilization and proc-hrs used, indicate that HPC resources are in demand, acknowledgement in research publications is the primary means of proving that Auburn University’s HPC resources are actually in line...

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Prologues and Epilogues

Job prologues and epilogues allow you to execute shell scripts before your job starts, or after it completes. In torque, you can specify a prologue or epilogue with the resource (-l) switch, i.e… qsub -l nodes=1:ppn=20,epilogue=/path/to/epilogue.sh Then, what the script does is entirely up to you.  You may want to perform pre or post file processing, copy operations, or even...

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Job Dependency and Intragroup Contention

The allocation and scheduling of resources by the Torque\Moab workload manager is a complex process. When there are multiple jobs being submitted to the same reservation, this becomes even further complicated, and can lead to unexpected results. To facilitate preemption, the scheduler performs a node selection algorithm and attempts to free these nodes by breaking down any running jobs. In...

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Running MATLAB Jobs

Hopper provides X11 forwarding so that you can interact with software that provides a GUI, which in many cases can be a convenient way to prepare or run jobs. However, if used incorrectly, use of this feature can lead to high load on the login node and result in your processes being terminated. In the case of MATLAB, College of...

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Reservations

Hopper implements a shared-maximum model of scheduling which guarantees that each principle investor and their lab group has access to the resources that they have purchased, while also providing extra computational power through leveraging underutilized processors. This model relies heavily on Moab “reservations” which are similar to traditional queues, but are defined in terms of ownership. Like queues, reservations serve...

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Ownership and Preemption

As a “condo-model” cluster, Hopper is funded by a group of financial stakeholders known as Principle Investigators.  Each PI maintains ownership of a subset of nodes within the cluster, and is guaranteed purchased processing power on demand.  In mild contrast to this, a secondary goal of the machine is to promote efficiency through allowing all cluster researchers to leverage any...

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Building the Hopper Cluster Part II: Networking

On Tuesday, January 19th, 2016 work started on the networking phase of the Auburn University “Hopper” High Performance Compute Cluster. This phase involved the routing of hundreds of InfiniBand, Ethernet and Fiber Optic cables, enabling high speed communication between the previously installed servers. The InfiniBand network architecture provides the cluster with high speed, low latency shared disk access and the...

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Building the Hopper Cluster Part I: Nodes

On Monday, January 5, the build began on the new HPC cluster in the AU Data Center. Resembling an old fashioned ‘barn raising’, OIT and Lenovo personnel unboxed and racked equipment in step one of constructing Auburn’s newest and most powerful research computer. Work continues with the goal to be operational by mid-February.  

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Excluding a Host

As with all cluster problems you encounter, if you know of a problematic host in the cluster, please send an email to hpcadmin@auburn.edu.  It may take some time for the cluster admins to respond, so in the meantime, you can avoid that host with the following syntax… bsub -R “select[hname!=node000]” … qsub -l h=!node001 Additionally, you can specify one or...

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OpenMPI in Xcode 6.1

To debug OpenMPI programs in Xcode 6.1… First build a recent version of OpenMPI.  From the Terminal… > curl -O http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.3.tar.gz > tar -xvzf openmpi-1.8.3.tar.gz > cd openmpi-1.8.3 > ./configure –prefix=/usr/local/lib/openmpi-1.8.3/ CFLAGS=-m64 CXXFLAGS=-m64 FFLAGS=-m64 FCFLAGS=-m64 > make > make install Start a new project.  Select OS X -> Application -> Command Line Application Select Project -> Build Settings -> Add /usr/local/lib/openmpi-1.8.3/include to...