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Step by step guide

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Toon Willems edited this page Jul 24, 2012 · 11 revisions
## Introduction

This step-by-step guide will guide you through putting together a self-contained compiler toolkit, and using that toolkit to build a software package. It is assumed you have already configured EasyBuild.

For more information on what a compiler toolkit is and why EasyBuild uses them, see the Compiler toolkits wiki page.

In this guide, we will put together the goalf toolkit, which consists of:

  • the GNU Compiler Collection (GCC), a set of open-source C/C++/Fortran compilers named gcc, g++ and gfortran,
  • the OpenMPI library, which provides support for building MPI (Message Passing Interface) applications,
  • the ATLAS and LAPACK libraries, which provide highly tuned linear algebra routines,
  • the FFTW library, which provides fast discrete Fourier transform routines,
  • the ScaLAPACK library, which provides MPI-enabled LAPACK routines.

Note that the name we give to the toolkit is arbitrary; you might as well name it myToolkit.

The build times specified for each of the toolkit components below are estimates, based on the build times observed on an otherwise unloaded Dell E6420 laptop with a quad-core Intel Core i5 2.4GHz processor and 8GB of physical memory, running 64-bit Fedora 16 Linux with a 3.x kernel.

Note: the various .eb easyconfigs mentioned below are also available in the EasyBuild package, see the easybuild/easyconfigs subdirectory, and are also used by the quick demo.

## Step 1: Compilers

The first step is to build the set of compilers that will be used in our toolkit. They are used further on for building the libraries that make up our toolkit and for building the software packages we wish to deploy on our system.

We aim to make this entire process as self-contained as possible, by reducing the dependencies on existing (external) system libraries. This is important for compilers that already are part of a toolchain, as they most often rely on the presence of certain tools in the system.

GCC supports a so-called bootstrap build, in which the compiler is built in 3 stages: once using the system compiler, once with the compiler obtained from stage 1, and finally using the compiler from stage 2.

This bootstrap build procedure is implemented by the GCC easyblock that comes with EasyBuild, so you do not need to worry about it.

Simply provide EasyBuild with an easyconfig that describes which GCC version you wish to build, and you will obtain a self-contained GCC build.

Step 1.1 Create easyconfig for GCC

Create an easyconfig file GCC-4.6.3.eb with the following contents:

name="GCC"
version='4.6.3'

homepage='http://gcc.gnu.org/'
description="The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
             as well as libraries for these languages (libstdc++, libgcj,...)."

toolkit={'name':'dummy', 'version': 'dummy'}

sources=['%s-%s.tar.gz' % (name.lower(), version),
         'gmp-5.0.4.tar.bz2',
         'mpfr-3.0.1.tar.gz',
         'mpc-0.9.tar.gz',
        ]
sourceURLs=['http://ftpmirror.gnu.org/%(name)s/%(name)s-%(version)s' %
                {'name': name.lower(), 'version': version}, # GCC auto-resolving HTTP mirror
            'http://ftpmirror.gnu.org/gmp', # idem for GMP
            'http://ftpmirror.gnu.org/mpfr', # idem for MPFR
            'http://www.multiprecision.org/mpc/download', # MPC official
           ]
languages=['c','c++','fortran','lto']

moduleclass='compiler'

# building GCC sometimes fails if make parallelism is too high, so we limit it
maxparallel=4

Most of entries in the easyconfig should be clear (if not, see Easyconfig files).

Some remarks:

  • The dummy toolkit specifies that we use the system compiler to kickstart the GCC bootstrap build. However, after completing the build procedure, the resulting GCC will be self-contained because it did not use the system compiler in the final build stage.

  • EasyBuild will try and download the requires source files given the paths in sourceURLs, unless they are available in the source path already.

  • The languages config entry is specific to the GCC easyblock, and specifies for which programming languages support should be enabled.

  • Because of problems with parallel building for some of the libraries on which GCC depends, we limit parallel building to a maximum of 4 simultaneous jobs. EasyBuild auto-detects how many cores you have in your system, and will build in parallel accordingly.

Step 1.2 Build and install GCC

Instruct EasyBuild to build GCC by providing it the easyconfig:

<path>/easybuild/eb GCC-4.6.3.eb

Building GCC v4.6.3 with a bootstrap build as performed by the GCC easyblock takes about 35 minutes (on the aforementioned system).

Step 1.3 Verify installation

Once the installation is complete, you should see a message like COMPLETED: Installation ended successfully appearing, both on the command line output and in the log file created by EasyBuild.

To verify that EasyBuild has produced a working GCC build, load the GCC/4.6.3 module provided and check the version:

module load GCC/4.6.3
gcc --version | grep ^gcc

This should yield something like gcc (GCC) 4.6.3 as output.

You could also automate this step by specifying:

sanityCheckCommand = (None, '--version')

in the easyconfig file.

## Step 2: MPI library

The next step is to build OpenMPI, that will serve as MPI library in the goalf compiler toolkit.

Again, just create an easyconfig and build/install OpenMPI using EasyBuild.

Step 2.1: Create easyconfig for OpenMPI

Create an easyconfig OpenMPI-1.4.5-no-OFED.eb with the following contents:

name='OpenMPI'
version='1.4.5'
versionsuffix="-no-OFED" # no InfiniBand support, so add version suffix

homepage='http://www.open-mpi.org/'
description="The Open MPI Project is an open source MPI-2 implementation."

toolkit={'name': 'GCC','version': '4.6.3'}

sources=['%s-%s.tar.gz'%(name.lower(),version)]
sourceURLs=['http://www.open-mpi.org/software/ompi/v%s/downloads' % '.'.join(version.split('.')[0:2])]

configopts='--with-threads=posix --enable-shared '

moduleclass='lib'

sanityCheckPaths = {
                   'files':["bin/%s" % binfile for binfile in ["ompi_info", "opal_wrapper", "orterun"]] +
                           ["lib/lib%s.so" % libfile for libfile in
                                    ["mca_common_sm", "mpi_cxx", "mpi_f77" ,"mpi_f90",
                                     "mpi", "openmpi_malloc", "open-pal", "open-rte"]],
                    'dirs':["include/openmpi/ompi/mpi/cxx"]
                    }

Some specific remarks with regard to this easyconfig:

  • EasyBuild adds a version suffix -no-OFED for this build, because we do not enable InfiniBand (IB) support (using the OFED stack) in this OpenMPI build procedure. For the sake of this demo, we do not bother with installing required dependencies that allow enabling IB support.

  • We use the GCC built in the previous step as a toolkit for building OpenMPI, as specified by the toolkit entry in the easyconfig.

  • OpenMPI follows the more-or-less standard configure/make/make install build procedure. Hence there is no real need for a dedicated OpenMPI easyblock. This means that EasyBuild will instead fall back to the default Application easyblock that implements this configure/make/make install build procedure.

  • Non-default configure options are specified using the configopts entry. Here, we detail which files and directories are expected to be installed using the sanityCheckPaths config entry.

Step 1.2 Build and install OpenMPI

Instruct EasyBuild to build OpenMPI by providing it with the easyconfig:

<path>/easybuild/eb OpenMPI-1.4.5-no-OFED.eb

Building and installing OpenMPI should only take about 7 minutes.

## Step 3: BLAS and LAPACK libraries

Step 3.1: Building/installing ATLAS

Step 3.1.1: Create easyconfig for ATLAS

name='ATLAS'
version='3.8.4'

homepage='http://math-atlas.sourceforge.net'
description="""ATLAS (Automatically Tuned Linear Algebra Software) is the application of
the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis
on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear
algebra kernel library."""

toolkit={'name':'GCC','version':'4.6.3'}
toolkitopts={'pic':True}

sources=['%s%s.tar.bz2'%(name.lower(),version)]
sourceURLs=[('http://sourceforge.net/projects/math-atlas/files/Stable/%s' % version,'download')]

lapack='LAPACK'
lapackver='3.4.0'

dependencies=[(lapack, lapackver)]
versionsuffix='-%s-%s' % (lapack, lapackver)

patches=['ATLAS-3.8.4_illegal-instruction-fix.patch']

## build full LAPACK library with supplied netlib LAPACK
full_lapack=True

## fix for http://math-atlas.sourceforge.net/errata.html#sharedProbe
configopts="-Ss f77lib '-L$(SOFTROOTGCC)/lib64 -lgfortran'"

## ignore check done by ATLAS for CPU throttling;
## you should set this to False (or remove it)
## and disable CPU throttling (requires root privileges) if you can
ignorethrottling=True

moduleclass='lib'

Step 3.1.2: Build and install ATLAS

Step 3.2: Building/install LAPACK

Step 3.2.1: Create easyconfig for LAPACK

name='LAPACK'
version='3.4.0'

homepage='http://www.netlib.org/lapack/'
description="""LAPACK is written in Fortran90 and provides routines for solving systems of simultaneous linear equations,
least-squares solutions of linear systems of equations, eigenvalue problems, and singular value problems."""

toolkit={'name':'GCC','version':'4.6.3'}
toolkitopts={'pic':True}

sources=['%s-%s.tgz'%(name.lower(),version)]
sourceURLs=[homepage]

moduleclass='lib'

Step 3.2.2: Build and install LAPACK

## Step 4: FFTW library

Step 4.1: Create easyconfig for FFTW

name='FFTW'
version='3.3.1'

homepage='http://www.fftw.org'
description="FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data"

toolkit={'name':'GCC','version':'4.6.3'}
toolkitopts={'optarch':True, 'pic':True}

sources=['%s-%s.tar.gz'%(name.lower(),version)]
sourceURLs=[homepage]

mpilib='OpenMPI'
mpiver='1.4.5'
mpisuff='-no-OFED'

dependencies=[(mpilib, mpiver, mpisuff)]

versionsuffix='-%s-%s%s' % (mpilib, mpiver, mpisuff)

configopts="--enable-sse2 "

## the MPI opts from FFTW2 are valid options but unused until FFTW3.3
configopts+="--with-openmp --with-pic --enable-mpi "

moduleclass='lib'

Step 4.2: Build and install FFTW

(more soon)

## Step 5: ScaLAPACK library

Step 5.1: Create easyconfig for ScaLAPACK

name='ScaLAPACK'
version='1.8.0'

homepage='http://www.netlib.org/scalapack/'
description="The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers."

compname='GCC'
compver='4.6.3'
comp='%s-%s' % (compname, compver)

toolkit={'name':compname,'version':compver}
toolkitopts={'pic':True}

sources=['%s-%s.tgz'%(name.lower(),version)]
sourceURLs=[homepage]

mpilib='OpenMPI'
mpiver='1.4.5'
mpisuff='-no-OFED'
mpi="-%s-%s%s"%(mpilib, mpiver, mpisuff)

blaslib='ATLAS'
blasver='3.8.4'
blas="-%s-%s"%(blaslib, blasver)

lapacklib='LAPACK'
lapackver='3.4.0'
lapack="-%s-%s"%(lapacklib, lapackver)

blacslib='BLACS'
blacsver='1.1'
blacs="-%s-%s"%(blacslib, blacsver)

versionsuffix="%s%s%s%s"%(mpi, blas, lapack, blacs)

dependencies=[(mpilib, mpiver, mpisuff),
              (blaslib, blasver, lapack),
              (lapacklib, lapackver),
              (blacslib, blacsver, mpi)
              ]

## parallel build tends to fail, so disabling it
parallel=1

moduleclass='lib'

Step 5.2: Build and install ScaLAPACK

(more soon)

## Step 6: Compiler toolkit

Step 5.1: Create easyconfig for goalf compiler toolkit

easyblock="toolkit"

name='goalf'
version='1.1.0'
versionsuffix='-no-OFED'

homepage='(none)'
description="""GNU Compiler Collection (GCC) based compiler toolkit, including OpenMPI for MPI support, ATLAS (BLAS support), LAPACK, FFTW and ScaLAPACK."""

toolkit={'name':'dummy','version':'dummy'}

compname='GCC'
compver='4.6.3'
comp='%s-%s' % (compname, compver)

mpilib='OpenMPI'
mpiver='1.4.5'
mpisuff='-no-OFED'
mpi='%s-%s%s' % (mpilib, mpiver, mpisuff)

blaslib='ATLAS'
blasver='3.8.4'
blas='%s-%s'%(blaslib, blasver)

lapacklib='LAPACK'
lapackver='3.4.0'
lapack='%s-%s'%(lapacklib, lapackver)

## compiler toolkit depencies
dependencies=[(compname, compver),
              (mpilib, mpiver, '-%s%s'%(comp,mpisuff)),
              (blaslib, blasver, '-%s-%s'%(comp,lapack)),
              (lapacklib, lapackver, '-%s'%comp),
              ('FFTW', '3.3.1', '-%s-%s'%(comp,mpi)),
              ('ScaLAPACK','1.8.0', '-%s-%s-%s-%s-BLACS-1.1'%(comp,mpi,blas,lapack))
             ]

moduleclass='compiler'

Step 5.2: Install goalf compiler toolkit

(more soon)

## Step 7: Building software with compiler toolkit

(more soon)

## Step 8: Updating the compiler: automatic dependency resolution

Step 8.1: Create easyconfigs

Step 8.1: Install new compiler toolkit using robot for automatic dependency resolution

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