TGQR 2010Q4 Report.pdf - Teragridforum.org

PI Name
Joseph Hargitai,
Albert Einstein
College of Medicine
Catherine Cooper,
Washington State U.
RP(s)
Involved
Name of
software
Nature of improvement
SDSC Hadoop SDSC staff worked to integrate Hadoop with the
global filesystem, local SSDs, and the scheduling
infrastructure. The PI is currently testing the
implementation.
TACC Underworld TACC staff member Yaakoub El Khamra worked
with the research team and the code developer to
develop a version of the code that works on Ranger.
This version of the code is the bleeding-edge
version and modules are still being modified and
tested. The PI is planning to submit an ASTA
request in order to received continued support.
Neutron Science
TeraGrid Gateway
ORNL Amber Consulted with user on desired Amber version.
Initiated arrangements to install Amber11 on NSTG
cluster
Given the strong interest by our user community in utilizing the potential of GPGPU systems, it is
noteworthy to mention, in particular, the assistance given by TACC staff members to three
research groups on Longhorn:
5.3.2
• Lucas Wilcox (PI Omar Ghattas) ran a GPU-accelerated discontinuous Galerkin (DG)
seismic wave propagation code on up to 478 GPUs of longhorn, achieving excellent
strong scaling and near-perfect weak scaling. His largest run on 478 GPUs used a mesh
with 6 billion nodes and 56 billion degrees of freedom.
• Tom Fogal (PI Hank Childs) ran a GPU-accelerated volume rendering code on an 8192-
cubed helium flame combustion dataset on 256 GPUs. This is among the largest data
ever to be directly visualized, and this GPU-based code achieved performance on 256
GPUs that would require 100,000s of CPU cores to match (they performed a similar run
on Jaguar for comparison).
• David LeBard ran a GPU-accelerated fast-analysis molecular dynamics code on 128
GPUs of Longhorn, achieving between 10x to 100x over CPU-based versions.
More Frequent User Support Issues/Questions
Among the system or site specific user issues referred to the RPs for resolution, the most frequent
had to do with login/access and account management issues (e.g. TeraGrid Portal password
versus resource specific passwords, password resets, security credentials, adding and removing
users, locating environment variables, allocations on machines leaving and joining the TeraGrid).
In decreasing order of frequency, issues with job queuing (e.g. which queues to use for various
types of jobs, throughput issues, scripting and execution issues); software availability and use
(finding, setting up, building, optimizing and running); system availability and performance
problems (e.g. memory limit questions, compute node failures, I/O timeouts, requests to kill
jobs); file systems (e.g. permissions and quotas, corrupted files), and wide area data transfer and
archive systems questions were also encountered.
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