Cluster Workshop

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Cluster Workshop
For COMP RPG students 17 May, 2010 High
Performance Cluster Computing Centre
(HPCCC) Faculty of Science Hong Kong Baptist
University
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Outline

• Overview of Cluster Hardware and Software
• Basic Login and Running Program in a job queuing
  system
• Introduction to Parallelism
• Why Parallelism
• Cluster Parallelism
• Open MP
• Message Passing Interface
• Parallel Program Examples
• Policy for using sciblade.sci.hkbu.edu.hk
• http//www.sci.hkbu.edu.hk/hpccc/sciblade

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Overview of Cluster Hardware and Software
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Cluster Hardware

• This 256-node PC cluster (sciblade) consist of
• Master node x 2
• IO nodes x 3 (storage)
• Compute nodes x 256
• Blade Chassis x 16
• Management network
• Interconnect fabric
• 1U console KVM switch
• Emerson Liebert Nxa 120k VA UPS

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Sciblade Cluster
256-node clusters supported by fund from RGC
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Hardware Configuration

• Master Node
• Dell PE1950, 2x Xeon E5450 3.0GHz (Quad Core)
• 16GB RAM, 73GB x 2 SAS drive
• IO nodes (Storage)
• Dell PE2950, 2x Xeon E5450 3.0GHz (Quad Core)
• 16GB RAM, 73GB x 2 SAS drive
• 3TB storage Dell PE MD3000
• Compute nodes x 256 each with
• Dell PE M600 blade server w/ Infiniband network
• 2x Xeon E5430 2.66GHz (Quad Core)
• 16GB RAM, 73GB SAS drive

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Hardware Configuration

• Blade Chassis x 16
• Dell PE M1000e
• Each hosts 16 blade servers
• Management Network
• Dell PowerConnect 6248 (Gigabit Ethernet) x 6
• Inerconnect fabric
• Qlogic SilverStorm 9120 switch
• Console and KVM switch
• Dell AS-180 KVM
• Dell 17FP Rack console
• Emerson Liebert Nxa 120kVA UPS

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Software List

• Operating System
• ROCKS 5.1 Cluster OS
• CentOS 5.3 kernel 2.6.18
• Job Management System
• Portable Batch System
• MAUI scheduler
• Compilers, Languages
• Intel Fortran/C/C Compiler for Linux V11
• GNU 4.1.2/4.4.0 Fortran/C/C Compiler

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Software List

• Message Passing Interface (MPI) Libraries
• MVAPICH 1.1
• MVAPICH2 1.2
• OPEN MPI 1.3.2
• Mathematic libraries
• ATLAS 3.8.3
• FFTW 2.1.5/3.2.1
• SPRNG 2.0a(C/Fortran) /4.0(C/Fortran)

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Software List

• Molecular Dynamics Quantum Chemistry
• Gromacs 4.0.7
• Gamess 2009R1,
• Gaussian 03
• Namd 2.7b1
• Third-party Applications
• FDTD simulation
• MATLAB 2008b
• TAU 2.18.2, VisIt 1.11.2
• Xmgrace 5.1.22
• etc

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Software List

• Queuing system
• Torque/PBS
• Maui scheduler
• Editors
• vi
• emacs

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Hostnames

• Master node
• External sciblade.sci.hkbu.edu.hk
• Internal frontend-0
• IO nodes (storage)
• pvfs2-io-0-0, pvfs2-io-0-1, pvfs-io-0-2
• Compute nodes
• compute-0-0.local, , compute-0-255.local

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Basic Login and Running Program in a Job Queuing
System
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Basic login

• Remote login to the master node
• Terminal login
• using secure shell
• ssh -l username sciblade.sci.hkbu.edu.hk
• Graphical login
• PuTTY vncviewer e.g.
• username_at_sciblade vncserver
• New sciblade.sci.hkbu.edu.hk3 (username)'
  desktop is sciblade.sci.hkbu.edu.hk3
• It means that your session will run on display 3.

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Graphical login

• Using PuTTY to setup a secured connection Host
  Namesciblade.sci.hkbu.edu.hk

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Graphical login (cont)

• ssh protocol version

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Graphical login (cont)

• Port 5900 display number (i.e. 3 in this case)

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Graphical login (cont)

• Next, click Open, and login to sciblade
• Finally, run VNC Viewer on your PC, and enter
  "localhost3" 3 is the display number
• You should terminate your VNC session after you
  have finished your work. To terminate your VNC
  session running on sciblade, run the command
• username_at_tdgrocks vncserver kill 3

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Linux commands

• Both master and compute nodes are installed with
  Linux
• Frequently used Linux command in PC cluster
  http//www.sci.hkbu.edu.hk/hpccc/sciblade/faq_scib
  lade.php

cp cp f1 f2 dir1 copy file f1 and f2 into directory dir1
mv mv f1 dir1 move/rename file f1 into dir1
tar tar xzvf abc.tar.gz Uncompress and untar a tar.gz format file
tar tar czvf abc.tar.gz abc create archive file with gzip compression
cat cat f1 f2 type the content of file f1 and f2
diff diff f1 f2 compare text between two files
grep grep student search all files with the word student
history history 50 find the last 50 commands stored in the shell
kill kill -9 2036 terminate the process with pid 2036
man man tar displaying the manual page on-line
nohup nohup runmatlab a run matlab (a.m) without hang up after logout
ps ps -ef find out all process run in the systems
sort sort -r -n studno sort studno in reverse numerical order
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ROCKS specific commands

• ROCKS provides the following commands for users
  to run programs in all compute node. e.g.
• cluster-fork
• Run program in all compute nodes
• cluster-fork ps
• Check user process in each compute node
• cluster-kill
• Kill user process at one time
• tentakel
• Similar to cluster-fork but run faster

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Ganglia

• Web based management and monitoring
• http//sciblade.sci.hkbu.edu.hk/ganglia

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Why Parallelism
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Why Parallelism Passively

• Suppose you are using the most efficient
  algorithm with an optimal implementation, but the
  program still takes too long or does not even fit
  onto your machine
• Parallelization is the last chance.

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Why Parallelism Initiative

• Faster
• Finish the work earlier
• Same work in shorter time
• Do more work
• More work in the same time
• Most importantly, you want to predict the result
  before the event occurs

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Examples

• Many of the scientific and engineering problems
  require enormous computational power.
• Following are the few fields to mention
• Quantum chemistry, statistical mechanics, and
  relativistic physics
• Cosmology and astrophysics
• Computational fluid dynamics and turbulence
• Material design and superconductivity
• Biology, pharmacology, genome sequencing, genetic
  engineering, protein folding, enzyme activity,
  and cell modeling
• Medicine, and modeling of human organs and bones
• Global weather and environmental modeling
• Machine Vision

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Parallelism

• The upper bound for the computing power that can
  be obtained from a single processor is limited by
  the fastest processor available at any certain
  time.
• The upper bound for the computing power available
  can be dramatically increased by integrating a
  set of processors together.
• Synchronization and exchange of partial results
  among processors are therefore unavoidable.

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Multiprocessing Clustering
Parallel Computer Architecture
Distributed Memory Cluster
Shared Memory Symmetric multiprocessors (SMP)
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Clustering Pros and Cons

• Advantages
• Memory scalable to number of processors.
• ?Increase number of processors, size of
  memory and bandwidth as well.
• Each processor can rapidly access its own memory
  without interference
• Disadvantages
• Difficult to map existing data structures to this
  memory organization
• User is responsible for sending and receiving
  data among processors

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TOP500 Supercomputer Sites (www.top500.org)
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Cluster Parallelism
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Parallel Programming Paradigm

• Multithreading
• OpenMP
• Message Passing
• MPI (Message Passing Interface)
• PVM (Parallel Virtual Machine)

Shared memory only
Shared memory, Distributed memory
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Distributed Memory

• Programmers view
• Several CPUs
• Several block of memory
• Several threads of action
• Parallelization
• Done by hand
• Example
• MPI

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Message Passing Model
Message Passing The method by which data from one
processor's memory is copied to the memory of
another processor.
Process A process is a set of executable
instructions (program) which runs on a processor.
Message passing systems generally associate only
one process per processor, and the terms
"processes" and "processors" are used
interchangeably
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OpenMP
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OpenMP Mission

• The OpenMP Application Program Interface (API)
  supports multi-platform shared-memory parallel
  programming in C/C and Fortran on all
  architectures, including Unix platforms and
  Windows NT platforms.
• Jointly defined by a group of major computer
  hardware and software vendors.
• OpenMP is a portable, scalable model that gives
  shared-memory parallel programmers a simple and
  flexible interface for developing parallel
  applications for platforms ranging from the
  desktop to the supercomputer.

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OpenMP compiler choice

• gcc 4.40 or above
• compile with -fopenmp
• Intel 10.1 or above
• compile with Qopenmp on Windows
• compile with openmp on linux
• PGI compiler
• compile with mp
• Absoft Pro Fortran
• compile with -openmp

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Sample openmp example

• include ltomp.hgt
• include ltstdio.hgt
• int main()
• pragma omp parallelprintf("Hello from thread
  d, nthreads d\n", omp_get_thread_num(),
  omp_get_num_threads())

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serial-pi.c

• include ltstdio.hgt
• static long num_steps 10000000
• double step
• int main ()
• int i double x, pi, sum 0.0
• step 1.0/(double) num_steps
• for (i0ilt num_steps i)
• x (i0.5)step
• sum sum 4.0/(1.0xx)
• pi step sum
• printf("Est Pi f\n",pi)

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Openmp version of spmd-pi.c

• include ltomp.hgt
• include ltstdio.hgt
• static long num_steps 10000000
• double step
• define NUM_THREADS 8
• int main ()
• int i, nthreads double pi, sumNUM_THREADS
• step 1.0/(double) num_steps
• omp_set_num_threads(NUM_THREADS)
• pragma omp parallel
• int i, id,nthrds
• double x
• id omp_get_thread_num()
• nthrds omp_get_num_threads()
• if (id 0) nthreads nthrds
• for (iid, sumid0.0ilt num_steps
  iinthrds)
• x (i0.5)step
• sumid 4.0/(1.0xx)

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Message Passing Interface (MPI)
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MPI

• Is a library but not a language, for parallel
  programming
• An MPI implementation consists of
• a subroutine library with all MPI functions
• include files for the calling application program
• some startup script (usually called mpirun, but
  not standardized)
• Include the lib file mpi.h (or however called)
  into the source code
• Libraries available for all major imperative
  languages (C, C, Fortran )

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General MPI Program Structure
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Sample Program Hello World!

• In this modified version of the "Hello World"
  program, each processor prints its rank as well
  as the total number of processors in the
  communicator MPI_COMM_WORLD.
• Notes
• Makes use of the pre-defined communicator
  MPI_COMM_WORLD.
• Not testing for error status of routines!

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Sample Program Hello World!
include ltstdio.hgt include mpi.h
// MPI compiler header file void
main(int argc, char argv) int nproc,myrank,i
err ierrMPI_Init(argc,argv)
// MPI initialization // Get number of MPI
processes MPI_Comm_size(MPI_COMM_WORLD,nproc)
// Get process id for this
processor MPI_Comm_rank(MPI_COMM_WORLD,myrank)
printf (Hello World!! Im process d of
d\n,myrank,nproc) ierrMPI_Finalize()
// Terminate all MPI
processes
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Performance

• When we write a parallel program, it is important
  to identify the fraction of the program that can
  be parallelized and to maximize it.
• The goals are
• load balance
• memory usage balance
• minimize communication overhead
• reduce sequential bottlenecks
• scalability

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Compiling Running MPI Programs

• Using mvapich 1.1
• Setting path, at the command prompt, type
• export PATH/u1/local/mvapich1/binPATH
• (uncomment this line in .bashrc)
• Compile using mpicc, mpiCC, mpif77 or mpif90,
  e.g.
• mpicc o cpi cpi.c
• Prepare hostfile (e.g. machines) number of
  compute nodes
• Compute-0-0
• Compute-0-1
• Compute-0-2
• Compute-0-3
• Run the program with a number of processor node
• mpirun np 4 machinefile machines ./cpi

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Compiling Running MPI Programs

• Using mvapich 1.2
• Prepare .mpd.conf and .mpd.passwd and saved in
  your home directory
• MPD_SECRETWORDgde1234-3
• (you may set your own secret word)
• Setting environment for mvapich 1.2
• export MPD_BIN/u1/local/mvapich2
• export PATHMPD_BINPATH
• (uncomment this line in .bashrc)
• Compile using mpicc, mpiCC, mpif77 or mpif90,
  e.g.
• mpicc o cpi cpi.c
• Prepare hostfile (e.g. machines) one hostname
  per line like previous section

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Compiling Running MPI Programs

• Pmdboot with the hostfile
• mpdboot n 4 f machines
• Run the program with a number of processor node
• mpiexec np 4 ./cpi
• Remember to clean after running jobs by
  mpdallexit
• mpdallexit

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Compiling Running MPI Programs

• Using openmpi1.2
• Setting environment for openmpi
• export LD-LIBRARY_PATH/u1/local/openmpi/
• libLD-LIBRARY_PATH
• export PATH/u1/local/openmpi/binPATH
• (uncomment this line in .bashrc)
• Compile using mpicc, mpiCC, mpif77 or mpif90,
  e.g.
• mpicc o cpi cpi.c
• Prepare hostfile (e.g. machines) one hostname
  per line like previous section
• Run the program with a number of processor node
• mpirun np 4 machinefile machines ./cpi

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Submit parallel jobs into torque batch queue

• Prepare a job script, say omp.pbs like the
  following
• !/bin/sh
• Job name
• PBS -N OMP-spmd
• Declare job non-rerunable
• PBS -r n
• Mail to user
• PBS -m ae
• Queue name (small, medium, long, verylong)
• Number of nodes
• PBS -l nodes1ppn8
• PBS -l walltime000800
• cd PBS_O_WORKDIR
• export OMP_NUM_THREADS8
• ./omp-test
• ./serial-pi
• ./omp-spmd-pi
• Submit it using qsub
• qsub omp.pbs

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Another example of pbs scripts

• Prepare a job script, say scripts.sh like the
  following
• !/bin/sh
• Job name
• PBS -N Sorting
• Declare job non-rerunable
• PBS -r n
• Number of nodes
• PBS -l nodes4
• PBS -l walltime080000
• This job's working directory
• echo Working directory is PBS_O_WORKDIR
• cd PBS_O_WORKDIR
• echo Running on host hostname
• echo Time is date
• echo Directory is pwd
• echo This jobs runs on the following processors
• echo cat PBS_NODEFILE
• Define number of processors
• NPROCSwc -l lt PBS_NODEFILE

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Parallel Program Examples
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Example 1 Estimation of Pi (OpenMP)

• include ltomp.hgt
• include ltstdio.hgt
• static long num_steps 10000000
• double step
• define NUM_THREADS 8
• int main ()
• int i, nthreads double pi, sumNUM_THREADS
• step 1.0/(double) num_steps
• omp_set_num_threads(NUM_THREADS)
• pragma omp parallel
• int i, id,nthrds
• double x
• id omp_get_thread_num()
• nthrds omp_get_num_threads()
• if (id 0) nthreads nthrds
• for (iid, sumid0.0ilt num_steps
  iinthrds)
• x (i0.5)step
• sumid 4.0/(1.0xx)

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Example 2a Sorting quick sort

• The quick sort is an in-place, divide-and-conquer,
  massively recursive sort.
• The efficiency of the algorithm is majorly
  impacted by which element is chosen as the pivot
  point.
• The worst-case efficiency of the quick sort,
  O(n2), occurs when the list is sorted and the
  left-most element is chosen.
• If the data to be sorted isn't random, randomly
  choosing a pivot point is recommended. As long as
  the pivot point is chosen randomly, the quick
  sort has an algorithmic complexity of O(n log n).
  
• Pros Extremely fast.
• Cons Very complex algorithm, massively recursive

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Quick Sort Performance
Processes Time
1 0.410000
2 0.300000
4 0.180000
8 0.180000
16 0.180000
32 0.220000
64 0.680000
128 1.300000
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Example 2b Sorting -Bubble Sort

• The bubble sort is the oldest and simplest sort
  in use. Unfortunately, it's also the slowest.
• The bubble sort works by comparing each item in
  the list with the item next to it, and swapping
  them if required.
• The algorithm repeats this process until it makes
  a pass all the way through the list without
  swapping any items (in other words, all items are
  in the correct order).
• This causes larger values to "bubble" to the end
  of the list while smaller values "sink" towards
  the beginning of the list.

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Bubble Sort Performance
Processes Time
1 3242.327
2 806.346
4 276.4646
8 78.45156
16 21.031
32 4.8478
64 2.03676
128 1.240197
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Monte Carlo Integration

• "Hit and miss" integration
• The integration scheme is to take a large number
  of random points and count the number that are
  within f(x) to get the area

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Monte Carlo Integration

• Monte Carlo Integration to Estimate Pi

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Example 2 Prime prime/prime.c prime/prime.f90 pr
ime/primeParallel.c prime/Makefile prime/machines
Compile by the command make Run the serial
program by ./primeC or ./primeF Run the
parallel program by mpirun np 4 machinefile
machines ./primeMPI
Example 1 omp omp/test-omp.c omp/serial-pi.c omp
/spmd-pi.c Compile program by the command
make Run the program in parallel
by ./omp-spmd-pi Submit job to PBS by qsub
omp.pbs
Example 4 pmatlab pmatlab/startup.m pmatlab/RUN.
m pmatlab/sample-pi.m Submit job to PBS by qsub
Qpmatlab.pbs
Example 3 Sorting sorting/qsort.c sorting/bubble
sort.c sorting/script.sh sorting/qsort
sorting/bubblesort Submit job to PBS queuing
system by qsub script.sh
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Policy for using sciblade.sci.hkbu.edu.hk
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Policy

1. Every user shall apply for his/her own computer
   user account to login to the master node of the
   PC cluster, sciblade.sci.hkbu.edu.hk.
2. The account must not be shared his/her account
   and password with the other users.
3. Every user must deliver jobs to the PC cluster
   from the master node via the PBS job queuing
   system. Automatically dispatching of job using
   scripts or robots are not allowed.
4. Users are not allowed to login to the compute
   nodes.
5. Foreground jobs on the PC cluster are restricted
   to program testing and the time duration should
   not exceed 1 minutes CPU time per job.

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Policy (continue)

• Any background jobs run on the master node or
  compute nodes are strictly prohibited and will be
  killed without prior notice.
• The current restrictions of the job queuing
  system are as follows,
• The maximum number of running jobs in the job
  queue is 8.
• The maximum total number of CPU cores used in one
  time cannot exceed 512.
• The restrictions in item 7 will be reviewed
  timely for the growing number of users and the
  computation need.