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Overview

Cardiac is built around a Sun Microsystems, Inc. 8000p Blade Center, with 80 Sun Microsystem X8440 blade servers interconnected by Voltaire, Inc.'s low-latency Infiniband switching technology. The cluster was purchased using a grant awarded to Dr. Larry Chinitz, head of Cardiac Electrophysiology and Dr. Glenn I. Fishman, Director of the Division of Cardiology at the NYU Langone Medical Center, along with a contribution from ITS. The cluster's principal user is Professor Charles S. Peskin (Dept. of Mathematics, CIMS), along with NYU researchers Boyce Griffith and David McQueen. The group's primary focus is to construct a functional computer model of the beating human heart.

Up to 75% of the cluster resources are dedicated to Professor Charles Peskin's group. The NYU community is allocated a minimum of 25% of the cluster's resources, more when available. Allocations are dynamic and flexible to allow for best utilization of the instrument. See this article for a description of Professor Peskin's group and work.

For additional details, or for information about how to access Cardiac, please email hpc@nyu.edu.

Hardware Specifications

System Name

Cardiac

Vendor/Model

1 Sun 8000p Blade Center; 80 Sun Microsystem X8440 blade servers

Network

DDR IB  

Operating System

Linux

Number of Login Nodes

1

Number of Compute Nodes

62

Number of CPU Cores

1264

Total Memory

2.47 Terabytes

Theoretical Peak Performance

9.12 Teraflops

CPU Manufacturer / Model

ADM Barcelona 8356.

CPU Speed

2.3GHz clock speed

Memory per Node

32GB (2GB per core)

Login and Compute Nodes

The table below shows the Login Nodes available on the Cardiac Cluster.

Login Node

Processors

Memory

cardiac1.es.its.nyu.edu

2 AMD Barcelona 8356 @ 2.33GHz

32GB

The table below shows the Compute Nodes available on the Cardiac Cluster. |

Compute Nodes

Count

Processors

Memory

CPUs per Node

compute-0-0 to compute-0-9

10

4 AMD Barcelona 8356 @ 2.33GHz

32GB

16

compute-1-0 to compute-1-9

10

4 AMD Barcelona 8356 @ 2.33GHz

32GB

16

compute-2-0 to compute-2-9

10

4 AMD Barcelona 8356 @ 2.33GHz

32GB

16

compute-3-0 to compute-3-9

10

4 AMD Barcelona 8356 @ 2.33GHz

32GB

16

compute-4-0 to compute-4-9

10

4 AMD Barcelona 8356 @ 2.33GHz

32GB

16

compute-5-0 to compute-5-9

10

4 AMD Barcelona 8356 @ 2.33GHz

32GB

16

compute-6-0 to compute-6-9

10

4 AMD Barcelona 8356 @ 2.33GHz

32GB

16

compute-7-0 to compute-7-8

9

4 AMD Barcelona 8356 @ 2.33GHz

32GB

16

Networks

The table below shows the File Systems available on the Cardiac Cluster.

Network

Vendor

Purpose

Speed

Ethernet

Dell

Management, Serving /home over NFS to nodes

1 GB/sec

Infiniband

Voltaire

High-Speed, low-latency, MPI, Lustre

20 GB/sec

File Systems

The table below shows the File Systems available on the Cardiac Cluster.

Mountpoint

Size

FS Type

Backed up?

Availability

Variable

Value

/home

113GB

NFS

Yes

All nodes (login, compute) through NFS over 1GB/sec ethernet.

$HOME

/home/NetID

/stage

11TB

NFS

Yes

Only the login node have a 1GB/sec connection to /archive through NFS.

$STAGE

/stage/NetID

/scratch.lustre

94TB

Lustre

NO

All nodes (login, compute) through DDR Infiniband.

N/A

/scratch.lustre/NetID

/scratch

301TB

NFS

NO

All nodes (login, compute) through NFS over 1GB/sec ethernet.

$SCRATCH

/scratch/NetID

/archive

102TB

ZFS

Yes

Only the login node have a 1GB/sec connection to /archive through NFS.

$ARCHIVE

/archive/NetID

Cardiac Queues

Cardiac is a shared resource between a private owner and HPC/ITS ("Public"). MOAB FS, or "fair share" policy, is used to allocate resources between the private and public researchers to ensure priorities and to maximize utilization. The fair share policy aims to balance the 75/25% ownership ratio to flexibly increase the usage targets when private nodes are idle.

Type

Name of Queue

Maximum
Walltime

Max CPU 
  Core/User

Max Queued
  Per User

Maximum
 Nodes

Node Allocation
      Type

Active

Ownership

User Share

Parallel

p12

12 hours

   192,384

 

 

Exclusive

Yes

Public

25% +

Parallel

p48

48 hours

   96,192

 

 

Exclusive

Yes

Public

25% +

Serial

ser2

48 hours

   72,144

 

 

Shared

Yes

Public

25% +

Serial

serlong

96 hours

   32/64

 

 

Shared

Yes

Public

25% +

Interactive

interactive

4 hours

   2

 

2

Shared

Yes

Public

N/A

Parallel

card

no limit

no limit

no limit

 

Exclusive

Yes

Private

75%

Serial

s-card

no limit

no limit

no limit

 

Shared

Yes

Private

75%

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