sciama, the software side · 3. basic building block 4 these are the building blocks of sciama and...
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Sciama, the Software side
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Agenda• Memory Models• Running Jobs, Selecting Packages and
Compiling• OpenMP• MPI• OpenMP / MPI mixed mode• Sciama Information
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Memory Models
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Basic Building Block
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These are the building blocks of Sciama and similar commodity HPC’s.
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Distributed Memory Model
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Largest (sensible) job is 24Gbytes in this distributed
memory model
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Shared Memory Model
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Shared Memory Models Can Support very large processes
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Shared Memory Model Supports OpenMP and MPI (and Hybrid)
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Running Jobs, Selecting Packages and Compiling
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ICG‐HPC Stack
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RedHat Clone
(CERN)
Two main Enterprise Linux players:-
RedHat & SUSE Licensed
Stability is all important.No need for latest andgreatest (Fedora 16)
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Running Jobs
• Run an application already loaded in the environment.
– Use “module avail”
to check what is installed
• Get a new application installed so you can run it.– Contact [email protected]
to get the software installed
• Compile your own application from source code.– You will need to select the compiler(s) and libraries using the “module”
command described. Request dependencies to be installed but not always
possible.
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Running Jobs• You should never run any large processes on a login server. Login servers are
shared by others so any intense processing will slow down the responsiveness
others experience.
• All major applications / compilations should be done on a compute node
• There are two ways to do this both using the “qsub”
command to submit a job to a
queue :‐
– Create an interactive shell on a compute node:‐qsub
–IX
# I=Interactive
X=allow X server windowsThis will give you a command prompt in the current
shell.
– Run a batch job on a compute node(s) :‐qsub
<job‐script>This will start / queue a job according to the directives specified in the job script.
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Installed S/W
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Compiling
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Sciama
Traffic
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Compile Options
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“gdb”
GNU Debugger[burtong@login1 ~]$ gdbGNU gdb
(GDB) Red Hat Enterprise Linux (7.0.1‐23.el5_5.1)Copyright (C) 2009 Free Software Foundation, Inc.License GPLv3+: GNU GPL version 3 or later
<http://gnu.org/licenses/gpl.html>
This is free software: you are free to change and redistribute it.There is NO WARRANTY, to the extent permitted by law. Type "show
copying"
and "show warranty" for details.This GDB was configured as "x86_64‐redhat‐linux‐gnu".For bug reporting instructions, please see:<http://www.gnu.org/software/gdb/bugs/>.(gdb)
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Intel Debugging
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Vtune
Qsub –I -X Very good help
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Inspector
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OpenMP ( Open Multi Processing)
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Largest (sensible) job is 24Gbytes in this distributed memory model
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Multi Threading
• Multiple cores allow for multi treaded applications.• OpenMP
is an enabler
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Shared memory (cooperating threads)• OpenMP• POSIX Threads• Cilk• Threaded Building Blocks• etc, etc
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OpenMP
Identical instances ofparallel region spawnedAs threads
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OpenMP
–
“C”
or Fortran
Compiler looks for directives and creates a multi- threaded executable.
Use –fopenmp as a compiler option
Possibly several parallel sections in one program.
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Running openmp.exe
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MPI ( Message Passing Interface )
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Inter node memory sharing not (usually ) possible
• Gives rise to “distributed memory”
Model• Need the likes of OpenMPI
(Message Passing Interface)
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MPI allows parallel programming in distributed memory model
• MPI enables parallel computation• Message Buffers are used to pass data between processes• Standard tcp-ip network used
Buffers also usedWithin same node.
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MPI Principles (1)
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MPI Principles (2)
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MPI Principles (3)
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First of all you need the a program …
Can be “C” or
Fortran .
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Select Compiler
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The run script
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Run the Job
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“mpitest”
Output
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OpenMP
/ MPI mixed mode and memory models
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Hybrid OpenMP
and MP programming possible
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MPI – OpenMP Mix
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Free Cores
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Sciama
Information
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Live Sciama
Information
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Sciama
Docs and A/c Request