Manual for Using Super Computing Resources

1

Manual for using Super Computing Resources

Super Computing Research and Education Centre

at

Research Centre for Modeling and Simulation

National University of Science and Technology

H-12 Campus, Islamabad

2

Table of Contents

1. Computational Resources 03

1.1 Specifications of Super Computer 03

1.1.1 Snapshot of Data Center 04

1.1.2 Rack Diagram of Super Computer 05

1.1.3 Locations of Compilers 06

1.1.4 Locations of Runtimes 06

1.2 Storage Area Network (SAN) Setup 07

1.3 Network Diagram 08

2. Submitting Processes to Super Computer 09

2.1 Steps to Login through SSH 09

2.1.1 Linux Client 09

2.1.2 Windows Client 10

2.2 Steps for Password-less Authentications 11

2.3 Steps for Submitting Jobs on the Cluster 12

2.3.1 Running Parallel MPI Jobs 12

2.3.2 Running Parallel MPI Scripts 13

3. Contact Information 14

3.1 Contact Persons 14

3.2 Contact Address 14

3

1. Computational Resources

RCMS Super Computer is installed in state of art data center with 80 KVA of UPS backup and 12 ton precision cooling system. The data center is protected by FM-200 based Automatic Fire Detection and Suppression System and manual fire extinguishers. CCTV Cameras and Access Control systems are being procured for effective surveillance of data center. Specifications of Super Computer are given below:-

1.1 Specifications of Super Computer

The Super Computer is comprised of 32 Intel Xeon based machines and each one of them is connected to Nvidia Tesla S1070 (each of which contains 4 GPU’s). All nodes are connected by40Gbps QDR InfiniBand Interconnect for internal communication. Ahigh-performance and reliable SAN storage is linked to Servers, accessible by all computational nodes. Table 1shows the detailed specification of RCMS Super Computer.

Cluster Name afrit.rcms.nust.edu.pkBrand HP ProLiant DL380 G6 Servers/ HP

ProLiant DL160se G6 ServerTotal Processors 272 Intel XeonTotal Nodes 34Total Memory 1.312 TBOperating System Redhat Enterprise Linux 5.6Interconnects InfiniBand SwitchStorage HP P2000 SAN Storage 22TB

capacity, SAN Switches, Host Bus Adapters (HBA’s), Fiber Channel Switch with RAID Controllers

Graphic Processing Unit

32 x NVidia Tesla S1070 (each system contains 4 GPU’s)

Table 1: Specification of RCMS Super Computer

4

1.1.1 Snapshot of Data Center

Figure 1: SnapshotofRCMSSuper Computer

Cluster Nodes

afrit.rcms.nust.edu.pk Compute-0-13 Compute-0-24

Compute-0-3 Compute-0-14 Compute-0-25










5

1.1.2 Rack Diagram of Super Computer

Figure 2: Logical Rack DiagramofRCMSCluster

6

1.1.3 Locations of Compilers

Name Command Location

Make utility make /usr/bin/make

GNU C compiler gcc /usr/bin/gcc

GNU C++ compiler g++ /usr/bin/g++

GNU F77 Compiler g77 /usr/bin/g77

MPI C compiler mpicc /usr/mpi/intel/openmpi-1.4.3/bin/mpicc

MPI C++ compiler mpic++ /usr/mpi/intel/openmpi-1.4.3/bin/mpic++

MPI Fortran 77 Compiler mpif77 /usr/mpi/intel/openmpi-1.4.3/bin/mpif77

Java Compiler javac /usr/java/latest/bin/javac

Ant Utility ant /opt/rocks/bin/ant

C compiler cc /usr/bin/cc

F77 Compiler f77 /usr/bin/f77

GFortran Compiler gfortran /usr/bin/gfortran

Fortran95 Compiler f95 /usr/bin/f95

UPC Compiler upcc /share/apps/UPC/upc-installation/upcc

1.1.4 Locations of Runtimes:

Name Command Location

MPI Runtime mpirun /usr/mpi/intel/openmpi-1.4.3/bin/mpirun

Java Virtual Machine java /usr/java/latest/bin/java

UPC Runtime upcrun /share/apps/UPC/upc-installation/upcrun

7

1.2 SAN Setup

Total 22 TB of SAN Storage is available for storing users’ data. Two SAN Switches are installed in UBB Rack. 8 x 8 Gb transceiver installed in each of the SAN Switch. Total 48 slots are available which are occupied with 450GB each.

The system is configured on RAID -1 one unit and RAID-5 on 4 units, each containing 16 drives. One online spare drive is marked in each of the disk enclosure for high availability. In case of drive failure the online spare drive will take over and data will be re-created depending on the RAID level.

Each unit is presented to Storage Node, whose hostname is ‘u2’. NFS Server daemon is installed on ‘u2’. NFS share has been created in order to assign storage to other nodes on network.

The Storage is managed using an application called Storage Management Utility.

Figure 3: SAN Storage

8

1.3 Network Diagram for Super Computer

Figure 4: Network diagram of Super Computing Resources.

9

$ ssh -p 2299 [email protected]

2. Submitting Processes to Super Computer

2.1 Steps to Login using SSH

2.1.1 Linux Client

a) On the shell prompt type:

Where username is the login name assigned by System Administrator

b) The following text will be displayed:

You will have to type ‘yes’ as shown and press enter

c) After pressing enter system will prompt for password. You may enter your password in order to login. Please note that your password will not be displayed for security reasons.

10

2.1.2 Windows Client:

a) An SSH Client will be required in order to login using SSH. You may download PuTTY from http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

b) In Host Name field of putty write IP Address: 111.68.97.5

c) Select SSH as connection type and enter port: 2299.

c) Then click open.

e) On clicking Open you will be asked to enter your username and password. Write your username and password followed by an Enter to login to Super Computer. Pleasenote that your password will not be displayed for security reasons.

http://www.chiark.greenend.org.uk/~sgtatham/putty/download.html

11

$ ssh-keygen –t rsa

$ cd ~$ cat ./.ssh/id_rsa.pub >> ./.ssh/ authorized_keys

2.2 Password-less Authentication

2.2.1 The private / public key pair will be required in order to authenticate you on the target machine. To generate this key pair, type the following in console:

2.2.2 Shell will ask the following questions:

2.2.3 After generating the public key, copy the public key to a file named authorized_keys, as shown below:

Enter file in which to save the key(/export/home2/RCMS/usman/.ssh/id_rsa):(Press enter here)Enter passphrase:(Press enter here or give passphrase)Enter same passphrase again:(Press enter here or give passphrase)

12

#!/bin/bash#myscript.sh## ****************************# Following is the title of the Sequential script. #$ -N SEQ_PRO# The output and errors of the programmes will be written in# SEQ_PRO.OPRO_ID and SEQ_PRO.EPRO_ID respectively.#Path to the executable file./usr/bin/myscript# End of Script

$ chmod 755 myscript.sh

$ qsub -V myscript.sh

$ qstat

$ qdel 19

2.3 Running Scripts on Cluster

2.3.1 Running Sequential Scripts:

a) Create a shell Script

b) Set execute permissions to the script

c) Now submit your script as follows:-

d) In order to see the status of script type the following command followed by enter:

e) In order to del your running script type the following command:

19 is the ID of your script

13

# !/bin/bash# mpi_script.sh# **********************# Following is the name of MPI Script# $ -N MPI_PRO# Following will be the output and error files# MPI_PRO.OPRO_ID and MPI_PRO.EPRO_ID respectively.# $ -pe mpi 16#This will assign 16 cores to the script# $NSLOTS# No of cores allocated by the sun grid engine# machines# a machine file containing names of all available nodesecho "Allocated $NSLOTS slots."mpirun -np $NSLOTS -mca ras gridengine --hostfile machines mpi_script.sh# End of Script

$ chmod 755 mpi_script.sh

$ qsub -V mpi_script.sh

$ qstat

$ qdel 19

2.3.2 Running Parallel MPI Scripts

a) Create a shell script for parallel processing

b) Set execute permissions to the script

c) Now submit your script as follows:-

d) In order to see the status of script type the following command followed by enter:

e) In order to del your running script type the following command:

19 is the ID of your script

14

3. Contact Information:

3.1 Contact Persons:

In case of any inquiry or assistance feel free to contact the following persons:

S. No Designation Name Contact No Email Address

1 Director ScREC Engr. Taufique-ur-Rehman 051-90855730 [email protected]

2 Faculty Member Mr. Tariq Saeed 051-90855731 [email protected]

3 System Administrator

Engr. Muhammad Usman 051-90855717 [email protected]

4 Assistant System Administrator

Mr. Shahzad Shoukat 051-90855714 [email protected]

3.2 Contact Address:

Supper Computing Lab, 1st Floor, Acad1 Block,Research Center of Modeling and Simulation (RCMS)National University of Sciences and Technology, Sector H 12, IslamabadPakistan.

Special Thanks to:

Mr. Hammad Siddiqi, System AdministratorHigh Performance Computing Lab,School of Electrical Engineering and Computer Science,National University of Sciences and Technology, H-12, Islamabadhttp://hpc.seecs.nust.edu.pk/

http://hpc.seecs.nust.edu.pk/

Documents

Manual for Using Super Computing Resources