m.s mabakane

M.S MABAKANE

HPC USERS AND ADMINISTRATORS WORKSHOP

INDUCTION COURSE

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APPLY FOR SYSTEM ACCOUNTBelow is the summary of account application process:

Apply online using: http://www.chpc.ac.za/index.php/contact-us/apply-for-resources-form

Application recorded in the helpdesk system

Committee approve/reject the application

User sign CHPC Use Policy

User account created in the system

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LOGIN INTO THE SYSTEMSTo login to the systems, ssh into the following hostnames:

Sun cluster: sun.chpc.ac.za

GPU cluster: gpu.chpc.ac.za

The users connects to the systems using 10 GB/s network bandwidth from anywhere in South Africa and 100 MB/s outside of the country.

The amount of network speed determines the level of accessing or copying data into systems. For more info about login and use of HPC systems, please visit: wiki.chpc.ac.za.

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COPYING DATADifferent modes can be used to copy data into or out of the HPC systems:

Linux machine: scp -r username@hostname:/directory-to-copy.

The windows users can use an application, namely, Winscp to copy data from the computer to the HPC clusters.

Moreover, WinSCP can also be used to copy data from the clusters to the users computer.

Basic information on how to install Ubuntu Linux operating system can be found on: https://help.ubuntu.com/community/Installation. For more info on how to install and use WinSCP, please visit these website: http://winscp.net/eng/docs/guide_install.

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HPC SYSTEMS

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sun cluster

Blue Gene/P

GPU cluster SA Grid system

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Sun Cluster

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OVERVIEW OF SUN CLUSTER

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DIFFERENT COMPONENTS OF SUN SYSTEM

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Nehalem Harpertown

Sparc

WestmereDell Visualization node

Sparc

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CLUSTER NEHALEM HARPERTOWN WESTMERE DELL SPARC VIZ

Operating system

Centos 5.8 Centos 5.8 Centos 5.8 Centos 5.8 Solaris 10 Redhat 5.1

File system /opt/gridware/export/home/luster/SCRATCH 1, 2, 3, 4, 5

/opt/gridware/export/home/luster/SCRATCH1, 2, 3, 4, 5

/opt/gridware/export/home/luster/SCRATCH 1, 2, 3, 4, 5

/opt/gridware/export/home/luster/SCRATCH 1, 2, 3, 4, 5

/scratch/home/scratch/work

/scratch/home/scratch/work

CPU* Intel Xeon 2.93 Ghz

Intel Xeon 3.0 Ghz

Intel Xeon 2.93 Ghz

Intel Xeon 2.93 Ghz

Sparcv9 AMD Opteron 2.93 GHZ

Memory 12 GB 16 GB 24 36 2TB 64 GB

For more information visit: http://wiki.chpc.ac.za/quick:start#what_you_have

DIFFERENT COMPONENTS OF SUN SYSTEM (cont…)

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FILESYSTEM STORAGEThe sun system is equipped with five important different directories used to store data in Lustre filesystem. Below is the major directories within the storage:

/opt/gridware/compilers

/opt/gridware/libraries /opt/gridware/applications

/export/home/username

/export/home/username/scratch

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STORAGE & BACK-UP POLICIESCHPC has implemented quota policies to govern the storage capacity of the supercomputing system.

User are allowed to store up a maximum of 10 GB data in their home directories.

The system provide a grace period of seven days for users who exceeded 10 GB in the home directories.

User’s home directory is backed-up. No back-up for scratch.

Data older than 90 days is deleted in the user’s scratch directory.

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COMPILERSDifferent compilers are available to compile various parallel programs in the sun system. The modules are used to load the following available compilers in the user environment:

GNU & Intel compilers:

G.C.C 4.1.2 (gfortran, gcc and g++) -> /usr/bin

G.C.C 4.7.2 (gfortran, gcc and g++) -> module add gcc/4.7.2

Intel 12.1.0 with MKL and IntelMPI (ifort, icc, icpc) -> module add intel2012

Intel 13.0.1 with MKL and IntelMPI -> module add intel-XE/13.0

Sun Studio (suncc, sunf95, c++filt) -> module add sunstudio

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MESSAGE PASSING IINTERFACE (MPI)Various message passing interface (mpi) are used to parallelize applications on the sun system and this include:

OpenMPI 1.6.1 compiled with gnu (mpicc, mpiCC, mpif90 and mpif77) -> module add openmpi/openmpi-1.6.1-gnu

OpenMPI 1.6.1 compiled with intel (mpicc, mpiCC, mpif90 and mpif77) -> module add openmpi/openmpi-1.6.1-intel

OpenMPI 1.6.5 compiled with gnu (mpicc, mpiCC, mpif90 and mpif77) -> module add openmpi/openmpi-1.6.5-gnu & module add openmpi/openmpi-1.6.5_gcc-4.7.2

OpenMPI 1.6.5 compiled with Intel (mpicc, mpiCC, mpif90 and mpif77) -> module add openmpi/openmpi-1.6.5-intel & module add openmpi/openmpi-1.6.5-intel-XE-13.0

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APPLICATIONSDifferent scientific and commercial groups utilise various parallel applications to perform computational calculations using sun cluster. The most popular applications in the cluster are as follows:

Weather Research Forecast (WRF) WRF-Chem DL_POLY ROMS (Regional Oceanic Modelling system) Gaussian VASP Gadget Material and Discovery studio CAM Quantum Espresso

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MOAB AND TORQUEMoab cluster suite is a scheduling tool used to control jobs on both sun cluster.

Moreover, torque is utilised to monitor the computational resources available in the clusters.

Basic moab commands:

msub - submit job showq - check status of the job canceljob - cancel job in the cluster

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EXAMPLE OF MOAB SCRIPT#!bin/bash #MSUB -l nodes=3:ppn=12 #MSUB -l walltime=2:00:00 #MSUB -l feature=dell|westmere #MSUB -m be #MSUB -V #MSUB -o /lustre/SCRATCH2/users/username/file.out #MSUB -e /lustre/SCRATCH2/users/username/file.err #MSUB -d /lustre/SCRATCH2/users/username/ #MSUB -mb ##### Running commands nproc=`cat $PBS_NODEFILE | wc -l` mpirun -np $nproc <executable> <output>

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GPU Cluster

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GPU CLUSTER

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COMPUTE NODES

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24 GB of memory

16 Intel Xeon processors (2.4 Ghz)

4 X Nvidia Tesla GPU cards

96 GB local hard drive capacity

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FILE SYSTEM The GPU cluster is attached to 14 terabytes managed using GPFS across the entire supercomputer. The cluster has the following file system structure:

/GPU/home

/GPU/opt

All the libraries and compilers are located in /GPU/opt. On the other hand, /GPU/home is used to store user’s applications and output data.

No back-up and storage policies on the GPU system

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COMPILERS and MPIDifferent kinds of libraries are used to compile and execute parallel applications simulating in the GPU system:

Intel compiler 12.1.0 with MKL and MPI (ifort, icc, icpc) -> module load intel/12.0

Intel compiler 13.0.1 with MKL and IntelMPI -> module load intel/13.0

G.C.C 4.6.3 (gfortran, gcc and g++) -> module load gcc/4.6.3

Mpich 2.1.5 compiled with gnu (mpirun, mpicc, mpif90) -> module load mpich2/1.5

Mvapich compiled with Intel (mpirun, mpicc, mpif90) -> module load mvapich2/intel/1.9

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APPLICATIONS Below is the list of available applications running in the GPU cluster:

Emboss

NAMD

AMBER

Gromacs

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QUESTIONS

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OPERATIONAL SERVICES

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SLA BETWEEN CHPC & USERSThe CHPC has developed the service level agreement with the users to ensure smooth operations and utilisation of the supercomputing system.

To this end; CHPC is responsible for ensuring that users’ queries are responded and resolved on-time. Below is the breakdown of queries associated with the resolution time:

Create user accounts, login and ssh - 1 day Network - 1 dayStorage - 2 daysInstalling softwares and libraries - 3 days Compiling & Porting applications - 3 days

All the queries and incidents are recorded in the helpdesk system.

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HELPDESK STATISTICS

L1 - all calls resolved within 24 hrs e.g. ssh, login and user creationL2 - all calls such storage, third party software and hardware resolved within 48 hrs L3 - all calls resolved within 72 hrs. e.g. compilers, software and applications

Service Level Resolved Total received Percentage Target

Level 1 – (L1) 229 230 99% 97%

Level 2 – (L2) 19 19 100% 95%

Level 3 – (L3) 165 179 92% 80%

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CUSTOMER SATISFACTIONIn the 2nd quarter of 2013/14; customer satisfaction survey was conducted in order to understand the users satisfaction with regard to the services provided by the centre.

Furthermore, the aim of the survey was to collect critical suggestions, complaints and compliments that may lead to improve the overall operational services within the CHPC. The survey was categorised into the following pillars:

Helpdesk System performanceSchedulerTraining and workshop CHPC Website and wiki

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CUSTOMER SURVEY

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CUSTOMER SURVEY (cont…)

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QUESTIONS & DISCUSSION!!

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ADMINISTRATING SUPERCOMPUTING SYSTEMS

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DIFFERENT TYPES OF SUPERCOMPUTERS Supercomputers are regarded as the fastest computers that can perform millions/trillions of calculations within a short period of time. These supercomputing systems can be classified into various categories such as:

Distributed-memory systems

Shared-memory machines

Vector systems

Most of the scientists utilise these fastest computers to compute parallel applications and generate scientific output as quick as possible.

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PERFORMANCE OF PROGRAMS ON SUPERCOMPUTERSThe performance of parallel applications is mainly affected by interplays of factors such as (Adve and Vernon, 2004; Ebnenasir and Beik, 2009):

Limited network bandwidthUnevenly distribution of message-passingSlow read/write requests within the storageLogic of the parallel codeHigh memory latency in the processing nodesHigh processor utilisation in the execution nodesAdve, V.S., and Vernon, M.K. (2004). Parallel program performance prediction using deterministic task graph analysis. ACM Transactions on Computer Systems. 22(1): 94-136. Ebnenasir, A., and Beik, R. (2009). Developing parallel programs: a design-oriented perspective. Proceedings of the 2009 IEEE 31st international conference on software engineering. Vancouver: IEEE Computer Society, pp. 1-8.

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THE PERFORMANCE OF THE SUPERCOMPUTERS Different components (e.g. processor, memory, network) play an important role in determining the performance of the supercomputers such as clusters, massive-parallel processing and shared-memory machines.

In the CHPC - sun cluster, execution nodes are equipped with different processors and memory to simulate applications.

The performance of the execution nodes is therefore important to compute parallel programs and generate output as quick as possible.

In this case, we look at the statistics of computational resources used to process applications in the sun cluster.

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Machine Usage On Sun Cluster

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TOP USERS V/S JOBS

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TOP USERS V/S CPU

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APPLICATIONS V/S CPU

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WAITING TIME IN THE QUEUE

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JOBS V/S WALLTIME

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Sun Storage

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OVERVIEW OF THE STORAGE

LUSTRE FILESYSTEMLustre is a distributed parallel file system used to manage, share and monitor data in the storage. In the sun cluster, it is configured to administer the following storage capacity:

1 Petabytes (SCRATCH 5)

480 terabytes (SCRATCH 1, 2, 3 and 4)

Both sub-storage systems (480 terabytes and 1 petabytes) are shared across the entire cluster. On this front, ClusterStor manager is used to monitor and reports the status of 1 petabytes sub-storage.

Different scripts are used to monitor and control the shared 480 terabytes.

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ClusterStor Manager

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ClusterStor Manager (cont…)

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SCRIPTS TO MONITOR LUSTRE

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Sun - Compute Nodes

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GANGLIA MONITORING TOOLGanglia is a graphical-user interface tool used to monitor components such as memory, processor and network of the system. In the sun cluster, it is used to monitor the following computational architectures:

Nehalem

Harpertown

Dell

Westmere

It can further be able to provide the status of the individual execution nodes within the supercomputing system.

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GANGLIA MONITORING TOOL (cont..)

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xCAT (Extreme Cloud Administration Toolkit )xCAT is the software tool used to enable easy administration and deployment of Linux machines in a distributed parallel environment. The CHPC administrators use xCAT to perform administration tasks such as:

Provisioning of the node (s)

Power on/off the node (s)

Query status of the node (s)

Add post-scripts for the nodes

Distribution of user accounts details in the nodes

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Sun - Security

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CLUSTER SECURITYThe security is one of the most important critical and challenging factors of administrating the supercomputing system. The CHPC - Sun system protect itself from virus and intruders by applying the following security measures:

Normal user only allowed to attempt login for 10 times

Root user only allowed to attempt login for 2 times

Users not allowed to ssh into the compute nodes

Full-time availability, reliability and accessibility of the system depend on the security measures taken to ensure no virus, intruders and hackers has unlawful access to the systems.

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SCRIPTS TO MONITOR SECURITY

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SUN - NETWORK

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STRUCTURE OF THE NETWORK

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QUESTIONS

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ACKNOWLEDGEMENTSI would like to acknowledge the following for their contributions on this presentation:

CHPC - Technical team & Langton Nkiwane (Eclipse Holdings) for their advises about the supercomputing infrastructures.

Brenda Skosana (CSIR) & Zoleka Nkukuma (CSIR) for their assistance in logistics of all the attendees.

Wilson Maruping (CHPC) for tireless effort to provide helpdesk statistics.

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m.s mabakane

Documents

hpc systems

system accountbelow

system cont

supercomputing system

users computer

gb data

users home directory

zathe users