Nanco a large hpc cluster for rbni russell berrie nanotechnology institute
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Nanco: a large HPC cluster for RBNI (Russell Berrie Nanotechnology Institute). Anne Weill – Zrahia Technion,Computer Center October 2008. Resources needed for applications arising from Nanotechnology. Large memory – Tbytes High floating point computing speed – Tflops

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Nanco: a large HPC cluster for RBNI (Russell Berrie Nanotechnology Institute)

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Nanco a large hpc cluster for rbni russell berrie nanotechnology institute

Nanco: a large HPC cluster for RBNI(Russell Berrie Nanotechnology Institute)

Anne Weill – Zrahia

Technion,Computer Center

October 2008


Resources needed for applications arising from nanotechnology

Resources needed for applications arising from Nanotechnology

  • Large memory –Tbytes

  • High floating point computing speed –Tflops

  • High data throughput – state of the art …


Smp architecture

SMP architecture

P

P

P

P

Memory


Cluster architecture

Cluster architecture

Processor

Memory

Processor

Memory

Interconnection network


Why not a cluster

Why not a cluster

  • Single SMP system easier to purchase/maintain

  • Ease of programming in SMP systems


Why a cluster

Why a cluster

  • Scalability

  • Total available physical RAM

  • Reduced cost

  • But …


Nanco a large hpc cluster for rbni russell berrie nanotechnology institute

Having an application which exploits the parallel capabilities

requires

Studying the application or

applications which

will run on the cluster


Things to include in design

Things to include in design


Our choices

Our choices


Other requirements

Other requirements

  • Space, power ,cooling constraints , strength of floors

  • Software configuration:

  • Operating system

  • Compilers & application deve. tools

  • Load balancing and job scheduling

  • System management tools


Configuration

Configuration

M

M

M

P

P

P

P

P

P

node2

node64

node1

Infiniband Switch


Before finalizing our choice

Before finalizing our choice …

One should check , on a similar system :

  • Single processor peak performance

  • Infiniband interconnect performance

  • SMP behaviour

  • Non commercial parallel applications behaviour


Parallel applications issues

Parallel applications issues

  • Execution time

  • Parallel speedup Sp= T1/Tp

  • Scalability


Benchmark design

Benchmark design

  • Must give a good estimate of performance of your application

  • Acceptance test -should match all its components


Comparison of performance

Comparison of performance


Execution time of monte carlo parallel code mpi

Execution time of Monte-Carlo parallel code (MPI)


What did work

What did work

  • Running MPI code interactively

  • Running a serial job through the queue

  • Compiling C code with MPI


What did not work

What did not work

  • Compiling F90 or C++ code with MPI

  • Running MPI code through the queue

  • Queues do not do accounting per CPU


P ara llel performance results

Parallel performance results

Theoretical peak

2.1 Tflops

Nanco performance on HPL:

0.58 Tflops


Comparison with sun benchmark

Comparison with Sun Benchmark


E xecution ti me comparison of compilers

Execution time –comparison of compilers


Perfor mance with different optimizations

Performance with different optimizations


Conclusions from acceptance tests

Conclusions from acceptance tests

  • New gcc (gcc4) is faster than Pathscale for some applications

  • MPI collective communication functions are differently implemented in various MPI versions

  • Disk access times are crucial - use attached storage when possible


Scheduling decisions

Scheduling decisions

  • Assessing priorities between user groups

  • Assessing parallel efficiency of different job types (MPI,serial ,OPenMP) /commercial software and designing special queues for them

  • Avoiding starvation by giving weight to the urgency parameter


Observations during production mode

Observations during production mode

  • Assessing user’s understanding of machine – support in writing scripts and efficient parallelization

  • Lack of visualization tools – writing of script to show current usage of cluster


Utilization of cluster

Utilization of cluster


Utilization of nanco sep08

Utilization of nanco sep08


Nanco jobs by type

Nanco jobs by type


Conclusion

Conclusion

  • Benchmark correct design is crucial to test capabilities of proposed architecture

  • Acceptance tests allow to negotiate with vendors and give insights on future choices

  • Only after several weeks and running of the cluster at full capacity can we make informed decisions on management of the cluster


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