Flexible IO and Integration for Scientific Codes Through The Adaptable IO System (ADIOS)

1ADIOS – http://www. adiosapi.org Jay Lofstead

Flexible IO and Integration for Scientific Codes

Through The Adaptable IO System (ADIOS)

Jay Lofstead (GT), Scott Klasky (ORNL), Karsten Schwan(GT), Norbert Podhorszki (ORNL), Chen Jin (ORNL)

June 23, 2008


Outline

• Motivation

• Design Goals

• Architecture

• Related Work

• Supported Features

• Examples

• Codes & Performance

• Future Work

• Collaborators


Motivation

• Multiple HPC architectures• Cray, IB-based clusters, BlueGene

• Many different APIs• MPI-IO, POSIX, HDF5, netCDF• GTC (fusion) has changed IO routines 8 times so

far based on moving platforms

• Different IO patterns• Restarts, analysis, diagnostics• Different combinations provide different levels of

I/O performance


Design Goals

• ADIOS Fortran and C based API almost as simple as standard POSIX IO

• External configuration to describe metadata and control IO settings

• Take advantage of existing IO techniques (no new native IO methods)

Fast, simple-to-write, efficient IO for multiple platforms without changing the source code


Design Goals

ADIOS Contributions:

1. Data Grouping: Multiple, independently controlled IO settings• diagnostics, restarts, analysis, viz

2. Optional data items: Different data from different processes• Single group write has header from a single proc and data from all

3. Data sizes change dynamically: Datasets vary in size• Run size changes data sizes; also AMR codes

4. Constructed output is special: Reused buffers must be handled properly

• stack temporaries...

5. IO memory is second to science: Buffer space for IO is strictly limited

• respect the memory needs of the scientific codes


Design Goals

Provide support for these future features:

• Provide integration opportunities for other systems• Workflow• In situ visualization• Other simulations

• Provenance collection

• Other data management tools• Science aware data compression


Architecture

• Thin API• XML file

• data groupings with annotation

• IO method selection• buffer sizes

• Common tools• Buffering• Scheduling

• Pluggable IO routines

ExternalMetadata(XML file)

Scientific Codes

ADIOS API

DART

LIVE/DataTap

MPI-IO

POSIX IO

HD

F-5

pnetCDF

Viz Engines

Others (plug-in)

buffering schedule feedback


Architecture

• Data groupings• logical groups of related items written at the same

time.• Not necessarily one group per writing event

• IO Methods• Choose what works best for each grouping• Vetted and/or written by experts for each

• POSIX (Wei-keng Lao Northwestern)• MPI-IO (Steve Hodson, ORNL)• MPI-IO Collective (Wei-keng Lao Northwestern)• NULL (Jay Lofstead GT)• Ga Tech DataTap Asynchronous (Hasan Abbasi GT)• others..


Related Work• Specialty APIs

• HDF-5 – complex API• Parallel netCDF – no structure

• File system aware middleware• MPI ADIO layer – File system connection,

complex API

• Parallel File systems• Lustre – Metadata server issues• PVFS2 – client complexity• LWFS – client complexity• GPFS, pNFS, Panasas


Supported Features

• Platforms tested• Cray CNL (ORNL Jaguar)• Cray Catamount (ORNL old-Jaguar and

SNL Redstorm)• Linux Infiniband (ORNL Ewok)

• IO Methods• MPI-IO independent, MPI-IO collective,

POSIX, NULL, Ga Tech DataTap asynchronous, Rutgers DART asynchronous


Examples

• Setup/Cleanup codecall adios_init (‘config.xml’)

...

call adios_finalize (my_rank)

• adios_init – reads the XML file (once for every process)

• adios_finalize – provide opportunity for cleanup


Examples

• IO codecall adios_open (handle, ‘filename’,

‘groupname’)

call adios_write (handle, ‘varname’, var)

ADIOS_WRITE(handle,var_name)

...

call adios_close (handle)


Examples

• IO codecall adios_open (handle, ‘filename’,

‘groupname’)

ADIOS_GWRITE (handle)

call adios_close (handle)

- ADIOS_GREAD coming soon


Examples

• IO hints (for asynchronous IO)• call adios_end_iteration ()

• pacing hints for asynchronous transport methods

• use in conjunction with ‘iterations’ attribute of method element in XML

• call adios_begin_calculation ()• hint for asynchronous IO that a low-IO phase is

starting

• call adios_end_calculation ()• hint for asynchronous IO that a low-IO phase is

ending


Examples• XML file contents (data elements)<adios-config host-language=“Fortran”><adios-group name=“restart” coordination-

communicator=“comm” coordination-var=“cvar”>

<var name=“elements” type=“integer” write=“no”/>

<var name=“data” type=“double” path=“/” dimensions=“elements”copy-on-write=“yes”/>

</adios-group></adios-config>


Examples• XML file contents (other)

<attribute name=“description” path=“/data” value=“simulation particle data”/>

<global-bounds dimensions=“..” offsets=“..”>

<var .../>

</global-bounds>

<mesh ..../>

<method method=“DataTap” iterations=“50” group=“restart”>params</method>

<method method=“visit” group=“restart”/>

<buffer size-MB=“100” allocate-time=“now”/>


Codes & Performance

• Codes• GTC (fusion), Chimera (supernova), GTS

(fusion), XGC0 (fusion), XGC1 (fusion), Flash (astrophysics), S3D (combustion)

• Performance Measurements• GTC: nearly 25 GB/sec• GTS: 12 GB/sec• Chimera: 6.5% reduction in wall clock time


Codes & Performance


Codes & Performance

Old GTC IO

New GT ADIOS/DataTap IO

12 GB/restart

GT

C O

n R

izzo

at

OR

NL


Codes & Performance

• June 7, 2008: 24 hour GTC run on Jaguar at ORNL• 93% of machine (28,672 cores)• MPI-OpenMP mixed model on quad-core

nodes (7168 MPI procs)• three interruptions total (simple node

failure) with 2 10+ hour runs• Wrote 56 TB of data at 20 GB/sec (21 TB

for post analysis)• IO overhead 3% of wall clock time• Mixed IO methods of synchronous MPI-IO

and POSIX IO configured in the XML file


Support Tools

• bpdump – similar to h5dump

• bp2h5 – convert output file to HDF5

• bp2nc – convert output to netCDF


Future Work

• Work on read functionality

• Index files

• Additional native transports• direct parallel HDF5 and parallel netCDF• asynchronous MPI• Visit• others as demanded


Future Work

• Offload to staging area for other processing


Collaborators

• Chen Jin, Scott Klasky, Stephen Hodson, James B. White III, Weikuan Yu (Oak Ridge National Laboratory)

• Hasan Abbasi, Greg Eisenhauer, Karsten Schwan, Matthew Wolf, Fang Zheng (Georgia Tech)

• Wei-keng Liao, Alok Choudhary, Northwestern University

• Manish Parashar, Ciprian Docan, Rutgers University.

• Ron Oldfield, Sandia Labs


References• Jay Lofstead, Scott Klasky, Karsten Schwan, Norbert

Podhorszki, Chen Jin. “Flexible IO and Integration for Scientific Codes Through The Adaptable IO System (ADIOS).” In CLADE 2008 at HPDC, Boston, MA, June 2008. ACM.

• Hasan Abbasi, Matthew Wolf, Karsten Schwan. “Live data workspace: A flexible, dynamic and extensible platform for petascale applications.” In Cluster Computing, Austin, TX, September 2007. IEEE International.

• Chen Jin, Scott Klasky, Stephen Hodson, Weikuan Yu (Oak Ridge National Laboratory) Jay Lofstead, Hasan Abbasi, Karsten Schwan, Matthew Wolf (Georgia Tech) Wei-keng Liao, Alok Choudhary(Northwestern University) Manish Parashar, Ciprian Docan, Rutgers University. Ron Oldfield (Sandia National Laboratories). “Adaptive IO System (ADIOS).” In CUG 2008. Helsinki, Findland, May 2008.

• Sarp Oral. NCCS Jaguar GTC 128 Nodes Test Results. http://users.nccs.gov/~oral/jagregtests/gtc128.html.

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Flexible IO and Integration for Scientific Codes Through The Adaptable IO System (ADIOS)