high end computing at cardiff university focus on campus grids james osborne
TRANSCRIPT
![Page 1: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/1.jpg)
High End Computing at Cardiff University
Focus on Campus Grids
James Osborne
![Page 2: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/2.jpg)
Contents
High End Computing SpectrumFacilities at CardiffCondor at CardiffSuccess StoriesHigh End Computing FuturesQuestions
![Page 3: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/3.jpg)
High End Computing Spectrum
![Page 4: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/4.jpg)
The HEC Spectrum
HPCTightly Coupled
Supercomputers
NUMA Machines£ Million+
HTCLoosely Coupled
Small Clusters
Campus Grids£ Thousand
£ H Thousand
Large Clusters
SMP£ H Thousand
£ Million
![Page 5: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/5.jpg)
The HPC End
HPCTightly Coupled
Supercomputers
Bluegene L
131,072 CPUs
![Page 6: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/6.jpg)
The HTC End
HTCLoosely Coupled
Campus Grids
Condor@Cardiff
600+ CPUs
![Page 7: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/7.jpg)
Facilities at Cardiff
![Page 8: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/8.jpg)
Facilities at Cardiff - Helix
Large ClustersHelix
200 CPUs
Owned by PHARM, CHEMY, EARTH, BIOSI
![Page 9: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/9.jpg)
Facilities at Cardiff - SGI
Small ClustersSGI Origin 300
32 CPUs
Owned by WeSC
![Page 10: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/10.jpg)
Facilities at Cardiff - Condor
Campus GridsCondor@Cardiff
600+ CPUs
Owned by insrv
![Page 11: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/11.jpg)
Condor at Cardiff
![Page 12: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/12.jpg)
What is Condor ?
Condor is a software system that creates a High-Throughput Computing (HTC) environment
Condor effectively utilizes the computing power of workstations that communicate over a network
Condor's power comes from the ability to effectively harness resources under distributed ownership
![Page 13: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/13.jpg)
What is a Condor Pool ?
A pool is a collection of workstations that communicate over a network
Central Manager
master
collector
negotiator
schedd
startd
= ClassAd Communication Pathway
= Process Spawned
Submit-Only
master
schedd
Execute-Only
master
startd
Execute-Only
master
startd
![Page 14: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/14.jpg)
What is a Condor Job ?
A command line windows executable All files in a self-contained directory structure Condor runs jobs in a sandbox ..\execute\... Condor runs jobs as user condor-reuse-vm1
One or more input filesOne or more output filesA submit script
One or more logs – useful for debugging
![Page 15: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/15.jpg)
What Goes In A Submit Script ?
Running myprog 100 timesuniverse = vanilla
executable = myprog.exe
input = myin.$(PROCESS)
output = myout.$(PROCESS)
error = myerr.$(PROCESS)
queue 100
![Page 16: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/16.jpg)
What Else Can Go In ?
root_dir = c:\mydirectory
transfer_files = ALWAYS
transfer_input_files = $(ROOT_DIR)\afile.txt
transfer_output_files = $(ROOT_DIR)\afile.txt
log = mylog.$(PROCESS)
notification = NEVER | ERROR
arguments = -arg1 -arg2
![Page 17: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/17.jpg)
What Else Can Go In ?
requirements = OpSys == “WINNT51”
Machine == “hostname.cf.ac.uk”
![Page 18: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/18.jpg)
How Do I Submit A Job ?
In the first instance by sending all your files to [email protected] to allow us to tailor your jobs to our environment
In time by seeking permission to submit your own jobs to [email protected] to allow us to enable your workstation as a submit host Currently requires IP address change
![Page 19: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/19.jpg)
How Do I Submit A Job ?
Submitting your jobcondor_submit myscript.sub
Checking your job’s progresscondor_q
Checking the poolcondor_status
![Page 20: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/20.jpg)
Terms of Use
Any local researcher can use the campus grid on the proviso that they… write a short summary of their research that
we can use to publicise their use of the campus grid
provide references to journal articles and conference proceedings containing appropriate acknowledgements
![Page 21: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/21.jpg)
Success Stories
![Page 22: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/22.jpg)
Prof Tim Wess
OPTOMX-Ray DiffractionDetermine shape of moleculesTime on a single workstation = 2-3 DaysTime on the campus grid = 2-3 HoursSpeed-up factor of ~20
Chair of Non-Crystalline Diffraction Community & Chair of CCP13 for Non-Crystalline Materials
![Page 23: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/23.jpg)
Prof Tim Wess
“This capability provides the final link in the chain that Cardiff has established to solve macromolecular structures”
“Our involvement with synchrotron sources such as DIAMOND … and the residence of CCP 13 … ensures that we are well placed to be in the vanguard of structure determination”
Chair of Non-Crystalline Diffraction Community & Chair of CCP13 for Non-Crystalline Materials
![Page 24: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/24.jpg)
Soyeon Lee
CARBSMontecarlo Simulation20,000 parameters for 90 different modelsTime on a single workstation = 42 DaysTime on the campus grid = 2 DaysSpeed-up factor of ~20
Research Student
![Page 25: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/25.jpg)
Dr Kevin Ashelford
BIOSIDistributed SearchIdentify corrupt records in a DNA databaseTime on a single workstation = 2.4 YearsTime on the campus grid = 2.6 WeeksSpeed-up factor of ~50
Research Fellow
![Page 26: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/26.jpg)
Dr Kevin Ashelford
“This is a significant contribution to microbial research and will hopefully be the required impetus for the world-wide research community to improve current methods”
![Page 27: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/27.jpg)
High End Computing Futures
![Page 28: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/28.jpg)
The HEC Spectrum
HPCTightly Coupled
Supercomputers
NUMA Machines£ Million+
HTCLoosely Coupled
Small Clusters
Campus Grids£ Thousand
£ H Thousand
Large Clusters
SMP£ H Thousand
£ Million
SGI Origin 300
Helix Condor@Cardiff
![Page 29: High End Computing at Cardiff University Focus on Campus Grids James Osborne](https://reader035.vdocuments.mx/reader035/viewer/2022081603/56649d985503460f94a83606/html5/thumbnails/29.jpg)
The HEC Spectrum
HPCTightly Coupled
Supercomputers
NUMA Machines£ Million+
HTCLoosely Coupled
Small Clusters
Campus Grids£ Thousand
£ H Thousand
Large Clusters
SMP£ H Thousand
£ Million
SGI Origin 300
SRIF 3
Helix Condor@Cardiff