Application Development Tools

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Development Tools For HPC Applications
Deniz Savas, Michael Griffiths Corporate
Information and Computing Services The University
of Sheffield Email m.griffiths_at_sheffield.ac.uk,
d.savas_at_sheffield.ac.uk
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Outline

• Building Applications
• Gnu compilers, g, g, g77
• Portland compilers, pg, pgf77
• Calling fortran from C and C from fortran
• Using, Building and installing libraries
• Using the make utility
• The Eclipse Development Environment
• Links

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Compilers
Language GNU Portland
C gcc pgcc
C g pgCC
Fortran 77 g77 pgf77
Fortran90/95 pgf90
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Invoking the Compiler

• Compiling FORTRAN Programs
• pgf77 o mycode options mycode.f
• Compiling c/c Programs
• pgcc o mycode options mycode.c

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Options Used with Both gnu and Portland Compilers
Option Action
-c Compile, do not link.
-o exefile Specifies a name for the resulting executable.
-g Produce debugging information (no optimization).
-Ilibrary_name (lower case L) Link the given library into the program. e.g. include math library by using option -lm
-ldirectory-name (upper case I) Add directory to search path for include files
-O N Set optimisation level to N
-Dmacrodefn Define a macro
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Options Used with Portland Compilers
Option Action
-tp k8-64 Specify target processor type to be opteron processor running 64 bit system (Portland only).
-Mvectsse2 Vectorizer option, turn on streaming SIMD extensions (SSE) and SSE2 instructions. SSE2 instructions operate on 64bit floating point data
-Mvectprefetch Generate prefetch instructions
-Mconcur Auto parallelization option
-fastsse Optimal set of options for processors supporting SSE/SSE2, Streaming SIMD Extensions
-fast Full optimisation with function unrolling and code reordering (Portland only).
-g77 libs Link time option allowing object files generated by g77 to be linked into programs (may cause problems with parallel libraries)
-Mbounds Check arrays for out of bounds access
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Options Used with gnu Compilers
Option Action TO CHECK
--version Return version information
-mtunecpu-type -marchcpu-type I386-I64 processor specification options.
-mmmx -msse -msse2 Options to enable sse/sse2 or mmx(windows)
-Wall Show all warnings
-Wno-deprecated Switch off warnings about use of deprecated function (c only)
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Linking a FORTRAN application with NAG libraries

• NAG best and most comprehensive library of
  numerical computing routines available
• Mark20 on iceberg use lnag and lacml with the
  pgf77 or pgf90 compiler
• Example
• pgf90 myprogf90 lnag lacml
• See comprehensive documentation at
• https//iceberg.shef.ac.uk/docs/nag/index.html

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The AMD core math libraries (acml)

• ACML consists of the following main components
• A full implementation of Level 1, 2 and 3 Basic
  Linear Algebra Subroutines (BLAS), with key
  routines optimized for high performance on AMD
  Opteron processors.
• A full suite of Linear Algebra (LAPACK) routines.
  As well as taking advantage of the highly-tuned
  BLAS kernels, a key set of LAPACK routines has
  been further optimized to achieve considerably
  higher performance than standard LAPACK
  implementations.
• A comprehensive suite of Fast Fourier Transforms
  (FFTs) in both single-, double-, single-complex
  and double-complex data types.

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Using the acml libraries

• Building an application using the portland
  compilers
• pgcc myapp.c -I/opt/acml-pg2.6.0/pgi64/include
  -L/opt/acml-pg2.6.0/pgi64/lib -lm lacml
• Building an application using the gnu compilers
• gcc myapp.c -I/opt/acml-gnu2.6.0/gnu64/include
  -L/opt/acml-gnu2.6.0/gnu64/lib -lm lacml
• Examples
• Documentation at https//iceberg.shef.ac.uk/docs/a
  cmldoc/html/index.html
• See http//www.shef.ac.uk/wrgrid/documents/hpc/num
  libs.htmlacmlexamples

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Building Large Applications

• Typically compile program using
• g o myprog myprog.c lm g
• Large programs
• Modularized
• Combine into a single executable
• Building large applications is a multi step
  process
• Compile each source file
• Link resulting objects into an executable

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Example Multi Source Program1

• To build the Monte-carlo model, mc, we do the
  following.
• g c g mc.cpp
• g c g mc_system.cpp
• g c g mc_particle.cpp
• g c -g mc_statistics.cpp
• g o mc mc.o mc_system.o mc_particle.o
  mc_statistics.o lm
• Note only one of the sources has a main function

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Example Multi Source Program2

• If mc_system.cpp is edited we dont need to
  recompile
• mc_statistics, mc_particle or mc
• Rebuild the application as follows
• g c g mc_system.cpp
• g o mc mc.o mc_system.o mc_particle.o
  mc_statistics.o lm
• Automate these steps using make

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Libraries

• Libraries are packaged collections of object
  files
• Standard library contains printf etc..
• Maths library contains sin, cos etc..
• Specify additional libraries with lltnamegt
• Only standard library is provided automatically
• To compile a program with a maths library
• g c myprog myprog.c -lm

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Building your own library

• Benefits of building libraries
• Share standardised functions with community
• Separate functionality from detailed code
• Good way of packing up your most useful routines
  and reusing them
• How to build
• Build libraries using
• Named as libltnamegt.a or libltnamegt.so
• http//www-cs.canisius.edu/PL_TUTORIALS/C/C-UNIX/l
  ibraries

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Example

• Example my util library
• g -c vec.cc
• Generates vec.o
• g -c mat.cc
• Generates mat.o
• Add object files to library
• ar r myutillib.a vec.o
• ar r mylibutil.a mat.o
• Dont use l for your own libraries link as
  follows
• g myprog.cc mylib.a o myprog

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Installing a Library

• General steps
• Download and uncompress source
• Read documentation and build e.g. using configure
• make and make install to build and install
• Update your environment
• Set LD_LIBRARY_PATH
• Compile with -lMyNewLib

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Using the Make Utility

• Used to compile and link programs
• Makefile tells make how to perform link and
  compilation
• Consists of rules with the following shape
• target dependencies
• command

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make

• target name of file generated by a program
• dependency used as input to create target
• Target files are created whenever a dependency
  has changed
• Commands can include
• cc, CC, g, f77, f95, mpf77
• make
• make clean

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make target

• Perform actions to obtain a target from a set of
  dependecies
• Make checks when dependencies last updated
• target dependencies
• rule

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Simple Makefile .. almost trivial!
game game.o gcc -o game game.o game.o
game.c gcc -c game.c clean rm game game.o
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Simple Makefile

• Generates executable called game from a single
  source file called game.c
• Has a sequence of rules
• game
• Rule for building target executable file
• game.o
• Rule for building object files
• clean
• Rule for cleaning executable and object files

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Make multiple source file project
project main.o data.o io.o CC -o project
main.o data.o io.o main.o main.c io.h
data.h CC -c main.c data.o data.c io.h
data.h CC -c data.c io.o io.c io.h CC -c
io.c clean rm project main.o data.o io.o
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Hints for Building Makefiles

• Use at the start of a line for comments
• Use \ at the end of a line for line continuation
• The line defining the rule that follows the
  definition of target and dependencies should
  normally be indented using a tab character and
  NOT whitespace characters

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Makefile with implict rules for compiling a
static library
objects vec.o vecpair.o mat.o flags -fast
-tp k8-64 libmyutil.a (objects) ar -r -o
myutil.a (objects) (flags) vec.o vec.c pgCC
-c vec.c (flags) vecpair.o vecpair.c pgCC -c
vecpair.c (flags) mat.o mat.c pgCC -c mat.c
(flags) clean rm myutil.a (objects)
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Macros Used with Makefiles
_at_ Full name of the current target . lt The
source file of the current (single) dependency .
The part of a filename which matched a suffix
rule. ? The names of all the dependencies
newer than the target separated by
spaces. The names of all the dependencies
separated by spaces, but with duplicate names
removed.
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Suffixes

• Make uses a special target, named .SUFFIXES to
  allow you to define your own suffixes.
• For example, the dependency line.SUFFIXES .foo
  .bar
• tells make that you will be using these special
  suffixes to make your own rules.

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Custom Suffix Rule

• Similar to how make already knows how to make a
  .o file from a .c file, you can define rules in
  the following manner
• .foo.bar tr 'A-Za-z' 'N-ZA-Mn-za-m'
  lt lt gt _at_ .c.o (CC) (CFLAGS) -c lt
• The first rule allows you to create a .bar file
  from a .foo file. (Don't worry about what it
  does, it basically scrambles the file.)
• The second rule is the default rule used by make
  to create a .o file from a .c file.

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Makefile with suffix rule
objects blastest.o flags -fast -tp k8-64
mk4 (objects) pgCC -o mk4 (objects)
(flags) .c.o pgCC -c (flags) lt clean rm
mk4 (objects)
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Using Eclipse

• Advantages
• Starting

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Using Eclipse Advantages

• Open source
• Available for many platforms
• Windows requires cygwin and gnu development tools
  g, g77, gdb, gmake, stl etc..
• Use to develop wide variety of applications in a
  single development environment
• e.g. c, c, f77, f90, java

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Eclipse features

• Perspectives for java, C/C, debug and soon
  fortran development
• Multiple projects
• Browsers
• Help, members, types, namespaces
• Interactive debugging
• Build projects using make or ant

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Starting eclipse

• Type eclipse
• Requests directory for workspace
• N.B. Sometimes necessary to start eclipse using
• eclipse -vm JAVA_HOME/jre/bin/java

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Eclipse C/C Perspective Layout
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Creating a new project

• Managed make project
• Helloworld
• Standard make project
• Hellotest
• Provide a make file

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Creating a standard make project
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Editing Project Settings
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Finishing Steps
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Debug Window
Switch between perspectives
Debug windows
Debug stepping controls
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Running the Debugger
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Setting and Modifying Breakpoint Properties
Right click here to edit breakpoint properties
Right click here to toggle breakpoint
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Links

• http//www.eclipse.org/
• http//www-106.ibm.com/developerworks/library/os-e
  cc/
• A useful tutorial on the eclipse cdt
• http//www.cplusplus.com
• Very useful reference section