What is MCSR

1
(No Transcript)
2
What is MCSR?

• Who is MCSR?
• What Does MCSR Do?
• Who Does MCSR Serve?
• What Kinds of Accounts?
• Why Does Mississippi Need Supercomputers?
• What Kinds of Research?
• What Kinds of Instruction?
• What Kinds of Workshops?
• How Much Does it Cost?
• What Kinds of Software?
• What Supercomputers and Clusters?

3
What is MCSR?

• Mississippi Center for Supercomputer Research
• Established in 1987 by the Mississippi
  Legislature
• Mission Enhance Computational Research
  Climate at Mississippis 8 Public Universities
• also Support High Performance Computing
  (HPC) Education in Mississippi

4
What Does MCSR Do?

• We make Mississippi scientists
• - more competitive for federal grants
• - more productive in research
• We provide extraordinary learning opportunities
  for Mississippi college students
• - instructional accounts
• - computing workshops
• - helpdesk support

5
Who Does MCSR Serve?

• MCSR serves faculty, researchers, and students at
  all of Mississippis 8 public universities
• Alcorn State University
• Jackson State University
• Mississippi Sate University
• Mississippi Valley State University
• The University of Southern Mississippi
• Delta State University
• The University of Mississippi
• Mississippi University for Women

6
Who Uses More MCSR Computing Time?
7
What Types of Computing Access is Available?

• Research Accounts
• - provided for faculty and student researchers
• - good for the duration of employment or
  enrollment
• Instructional Accounts
• - provided at an instructors request
• - for all students enrolled in a semester course
• - valid for the duration of the semester
• - can be converted to research account

8
Research vs. Class Accounts?
9
Who Uses Research Accounts?
10
Who Uses Instructional Accounts?
11
What Types of Courses Use MCSR?

• Over 82 University Courses Supported since 2000
• C/C, Fortran, MPI, OpenMP, MySQL,
  HTML,Javascript, Matlab, PHP, Perl, .

http//www.mcsr.olemiss.edu/education.php
12
Why Do Mississippi Researchers Need
Supercomputers?

• Economics researchers in a poor state like
  Mississippi can still make a big splash.
• Computational simulations are faster, cheaper,
  and safer than laboratory experiments alone.

13
What Kinds of Research _at_ MCSR?

• 90 of MCSR calculations are computational
  chemistry
• Cleanup of high explosive materials.
• Design of high energy density rocket fuels
• The chemical underpinnings of high powered lasers
• Mutation studies of enzyme activity
• Designing weather-proofing coatings for machinery
• Other Areas
• Hurricane forecasting
• Blast resistant Coatings
• Better 3-D imaging for diagnosing brain tumors

14
What Types of Workshops by MCSR?

• MCSR consultants taught over 140 free seminars in
  FY08.
• Over 60 training topics available, and growing.
• Fixed schedule or on-demand.
• Unix/programming, Math Software, Stats Software,
  Computational Chemistry Software

15
(No Transcript)
16
Do Researchers and Students Pay to Use MCSR?

• No. MCSR services are provided at no cost to the
  individual, department, or institution.
• Funded researchers may ask for priority access.
• Mississippi researchers may claim the value of
  MCSR computing services received as an in-kind
  contribution from their institution when seeking
  federal grants.

17
How Much Does MCSR Cost Mississippi?
18
What Is the Value of MCSR to Mississippi?

• RETURN ON INVESTMENT
• GRANTS SUPPORTED / MCSR BUDGET
• For FY 2008
• 32,832,097 / 845,535
• 38.30 per dollar spent

19
What Software Environments _at_ MCSR

• Programming
• C/C, FORTRAN, Java, Perl, PHP, MPI
• Science/Engineering
• PV-Wave, IMSL, GSL, Math Libraries, Abaqus
• Math/Statistics
• SAS, SPSS, Matlab, Mathematica
• Chemistry
• Gaussian, Amber, NWChem, GAMESS, CPMD, MPQC,
  MolPro, GROMACS

20
What Supercomputers _at_ MCSR?
21
Supercomputers at MCSR sweetgum

• - SGI Origin 2800 128-CPU Supercomputer
• - 64 GB of shared memory

22
Supercomputers at MCSR redwood

• - 224 CPU SGI Altix 3700 Supercomputer- 224 GB
  of shared memory

23
Supercomputers at MCSR mimosa

• 253 CPU Intel Linux Cluster Pentium 4
• Distributed memory 500MB 1GB per node
• Gigabit Ethernet

24
Supercomputers at MCSR mimosa
25
Supercomputers at MCSR sequoia

• 22 nodes
• 176 cores
• 352 GB Memory
• 20 TB Storage
• InfiniBand Interconnect

26
Supercomputers at MCSR sequoia
27
Introduction to Parallel Programming at MCSR

• Message Passing Computing
• Processes communicate via calls to message
  passing library routines
• Programmers parallelize algorithm and add
  message calls
• At MCSR, this is via MPI programming with C or
  Fortran
• Sweetgum Origin 2800 Supercomputer (128 CPUs)
• Mimosa Beowulf Cluster with 253 Nodes
• Redwood Altix 3700 Supercomputer (224 CPUs)
• Sequoia Altix XE 310 InfiniBand Cluster (176
  cores)
• Shared Memory Computing
• Threads coordinate/communicate results via shared
  memory variables
• Care must be taken not to modify the wrong memory
  areas
• At MCSR, this is via OpenMP programming with C or
  Fortran on sweetgum, redwood, or sequoia

28
Speed-Up
http//www.mcsr.olemiss.edu/Engr692_TimingWorshkee
t.xls
29
What MCSR Systems for USM Class Accounts

• Sweetgum
• MPI or OpenMP
• 1 to 16 CPUs
• Up to 900mb per CPU
• PBS scripts preferred
• PBS l ncpus4
• Interactive computations will be killed after 30
  minutes
• Queues SM-4P, SM-8P, MM-8P, MM-16P
• Processors Mix of 195 MHz and 300 MHz
• O/S Irix (like Unix)
• Compilers SGIs Fortran, C/C, GNU C/C, w/
  SGI MPT

30
(No Transcript)
31
(No Transcript)
32
What MCSR Systems for USM Class Accounts

• Mimosa
• MPI
• 1 to 18 nodes
• 400 GB Memory per node
• PBS Scripts Only (no interactive jobs allowed)
• PBS l nodes4
• Queues MCSR-CA
• Processors single 1.4 GHz P4/node
• O/S SUSE Linux 10.3
• Compilers Portland Group (PGI) Fortran, C/C
  w/mpich
• qstat f (to find out what nodes your job is
  running on)

33
(No Transcript)
34
(No Transcript)
35
What MCSR Systems for USM Class Accounts

• Sequoia
• OpenMP (multiple processors on the same node)
• MPI (multiple processors on the same or
  different nodes)
• Hybrid (OpenMP within node, MPI across nodes)
• 1 to 4 nodes, 1 to 8 CPUs per node
• PBS Queues SM-4P (for up to 4 CPUs on 1 node)
• MCSR-Test (up to 8 CPUs on each of 4 nodes)
• PBS Scripts Only (no interactive jobs allowed)
• PBS l nodes4ppn8 (to run on all 8 CPUs of
  all 4 nodes)
• PBS l ncpus8select
• 16 GB Memory per node (2 GB per CPU)
• qstat f (to find out what nodes your job is
  running on)

36
(No Transcript)
37
(No Transcript)
38
Sequoia for USM Class Accounts

• To run on 4 nodes, and 8 processors per node (32
  processes)
• PBS l nodes4ppn8
• To run on 2 nodes, and 4 processors per node (8
  processes)
• PBS l nodes2ppn4
• To run on 1 node, and up to 8 processors (OpenMP)
• PBS l nodes1ppn8
• To run on 8 processors, regardless of number of
  nodes
• PBS l ncpus8
• To run 8 processors, with preferences about node
  placement
• PBS l ncpus8
• PBS l placescatter (distribute across as
  many nodes as can)
• PBS l placepack (pack processes onto as few
  nodes as can)
• PBS l placefree (place processes on first
  available processors)

39
Parallel Efficiency