Compilers

by

Compiling GNU 5.2.0 on CentOS 6

1. Prerequisites:

You will need

  1. gmp 4.3.1-7.el6_2.2
  2. mpfr  2.4.1-6.el6
  3. mpc 0.19-1.el6.rf and
  4. isl-0.14

For 1 to 3, do take a look at Compiling GNU 4.8.1 on CentOS 6. For 4, do take look at Compiling isl-0.15 library

2a. Update linked library at /etc/ld.so.conf

# touch /etc/ld.so.conf.d/library.conf
/usr/local/isl-0.15/lib
/usr/local/mpfr-2.4.2/lib
/usr/local/mpc-0.8.1/lib
/usr/local/gmp-4.3.2/lib

2b. Update your .bashrc

export LD_LIBRARY_PATH=/usr/local/mpfr-2.4.2/lib:/usr/local/mpc-0.8.1/lib:/usr/local/gmp-4.3.2/lib:/usr/local/isl-0.15/lib

3. Compile. This will take a while.

# tar -zxvf  gcc-4.8.1.tar.gz
# cd gcc-4.8.1
# mkdir build-gcc
# cd build-gcc
# ../configure --prefix=/usr/local/gcc-5.2.0 
--with-mpfr=/usr/local/mpfr-2.4.2 
--with-mpc=/usr/local/mpc-0.8.1 
--with-gmp=/usr/local/gmp-4.3.2
--with-isl=/usr/local/isl-0.14
--disable-multilib
--disable-libmpx
--enable-shared
--enable-languages=c,c++,fortran,go,objc,obj-c++  
--host x86_64-redhat-linux-gnu 
--build x86_64-redhat-linux-gnu
# make -j 16
# make install

References:

  1. Encountering error -static-libstdc++ not implemented when compiling GNU 4.8.1 on CentOS 6
  2. Configure Error when compiling GCC 5.2.0 on CentOS 6.6
by

Install GCC 4.8.1 and other Scientitic Packages via Yum on CentOS

Do take a look at Linux @ CERN for the documentation on how to use yum to install devtoolset which contain the following packages. The latest version for CentOS 6 is devtoolset-2.1. Here is a summary of the Linux @ CERN

CentOS 6 / SL 6

Developer Toolset 2.1 provides following tools:

  • gcc/g++/gfortran – GNU Compiler Collection – version 4.8.2
  • gdb – GNU Debugger – version 7.6.34
  • binutils – A GNU collection of binary utilities – version 2.23.52
  • elfutils – A collection of utilities and DSOs to handle compiled objects – version 0.155
  • dwz – DWARF optimization and duplicate removal tool – version 0.11
  • systemtap – Programmable system-wide instrumentation system – version 2.1
  • valgrind – Tool for finding memory management bugs in programs – version 3.8.1
  • oprofile – System wide profiler – version 0.9.8
  • eclipse – An Integrated Development Environment – version 4.3.1 (Kepler)

CentOS 5 / SL 5

Developer Toolset 1.1 provides following tools:

  • gcc/g++/gfortran – GNU Compiler Collection – version 4.7.2
  • gdb – GNU Debugger – version 7.5
  • binutils – A GNU collection of binary utilities – version 2.23.51
  • elfutils – A collection of utilities and DSOs to handle compiled objects – version 0.154
  • dwz – DWARF optimization and duplicate removal tool – version 0.7
  • systemtap – Programmable system-wide instrumentation system – version 1.8
  • valgrind – Tool for finding memory management bugs in programs – version 3.8.1
  • oprofile – System wide profiler – version 0.9.7

Installation and Enablement

CentOS 6 / SL 6

Save repository information as /etc/yum.repos.d/slc6-devtoolset.repo on your system:

# cd /etc/yum.repos.d/ 
# wget -O /etc/yum.repos.d/slc6-devtoolset.repo http://linuxsoft.cern.ch/cern/devtoolset/slc6-devtoolset.repo
# yum install devtoolset-2 --nogpgcheck
# scl enable devtoolset-2 bash

CentOS 5 / SL 5

Save repository information as /etc/yum.repos.d/slc5-devtoolset.repo on your system:

# cd /etc/yum.repos.d/
# wget -O /etc/yum.repos.d/slc5-devtoolset.repo http://linuxsoft.cern.ch/cern/devtoolset/slc5-devtoolset.repo
# yum install devtoolset-1.1
# scl enable devtoolset-1.1 bash
by

Compiling GNU Scientific Library (GSL) gsl-1.16 on CentOS 6

The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. It is free software under the GNU General Public License.

The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. There are over 1000 functions in total with an extensive test suite.

Step 1: The current version of GSL is gsl-1.16.tar.gz

Step 2: You may want to use the latest GCC 4.8.1 to compile. For more information on how to compile GCC 4.8.1, see Compiling GNU 4.8.1 on CentOS 6. This compilation will help to fix all the components required for gsl-1.16

Step 3: After packing gsl, To compile

# cd /root/gsl-1.15/
# mkdir build-gsl
# cd build-gsl
# ../configure --prefix=/usr/local/gsl-1.16/
# make 
# make install
by

Compiling GCC 4.7.2 on CentOS 5

Step 1: Download the following prerequistics applications libraries from ftp://gcc.gnu.org/pub/gcc/infrastructure/

  1. gmp-4.3.2.tar.bz2
  2. mpfr-2.4.2.tar.bz2
  3. mpc-0.8.1.tar.gz

1. Install gmp-4.3.2

# bunzip2 gmp-4.3.2.tar.bz2
# tar -zxvf gmp-4.3.2.tar
# cd gmp-4.3.2
# ./configure --prefix=/usr/local/gmp-4.3.2
# make
# make install

2. Install mpfr-2.4.2 (requires gmp-4.3.2 as prerequisites)

# bunzip2 mpfr-2.4.2.tar.bz2
# tar -zxvf mpfr-2.4.2.tar
# cd mpfr-2.4.2
# ./configure --prefix=/usr/local/mpfr-2.4.2 --with-gmp=/usr/local/gmp-4.3.2/
# make
# make install

3. Install mpc-0.8.1 (requires gmp-4.3.2 and mpfr-2.4.2 as prerequisites ) 

# tar -zxvf mpc-0.8.1.tar.gz
# cd mpc-0.8.1
#./configure --prefix=/usr/local/mpc-0.8.1/ --with-gmp=/usr/local/gmp-4.3.2/ --with-mpfr=/usr/local/mpfr-2.4.2
# make
# make install

4. Update your LD_LIBRARY_PATH at your ~/.bashrc

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpc-0.8.1:/usr/local/mpfr-2.4.2/lib:/usr/local/gmp-4.3.2/lib

5. Install the glibc-devel.i686. For more information, do look at Error when compiling GCC 4.8.1 (linuxtoolkit.blogspot.com)

6. Finally install GNU CC 4.7.2

# tar -zxvf  gcc-4.7.2.tar.gz
# cd gcc-4.7.2
# mkdir build-gcc
# cd build-gcc
# ../configure --prefix=/usr/local/gcc-4.7.2 \ 
--with-mpfr=/usr/local/mpfr-2.4.2 \ 
--with-mpc=/usr/local/mpc-0.8.1 \
--with-gmp=/usr/local/gmp-4.3.2 \
--with-mpfr-include=/usr/local/mpfr-2.4.2/include \
--with-mpc-include=/usr/local/mpc-0.8.1/include
# make all-gcc
# make install-gcc
by

Compiling GNU 4.8.1 on CentOS 6

I encountered error when compiling GCC 4.8.1 on CentOS 6 I have the prequistics (via yum installed)

  1. gmp 4.3.1-7.el6_2.2
  2. mpfr  2.4.1-6.el6
  3. mpc 0.19-1.el6.rf

But still I enountered the error

configure: error: Building GCC requires GMP 4.2+, MPFR 2.4.0+ and MPC 0.8.0+. 
Try the --with-gmp, --with-mpfr and/or --with-mpc options to specify their locations.  
Source code for these libraries can be found at their respective hosting sites as well as 
at ftp://gcc.gnu.org/pub/gcc/infrastructure/

To resolve the issue, download from the ftp://gcc.gnu.org/pub/gcc/infrastructure/ the following application and compile them.

  1. gmp-4.3.2.tar.bz2
  2. mpfr-2.4.2.tar.bz2
  3. mpc-0.8.1.tar.gz

1. Install gmp-4.3.2

# bunzip2 gmp-4.3.2.tar.bz2
# tar -zxvf gmp-4.3.2.tar
# cd gmp-4.3.2
# ./configure --prefix=/usr/local/gmp-4.3.2
# make
# make install

2. Install mpfr-2.4.2 (requires gmp-4.3.2 as prerequisites)

# bunzip2 mpfr-2.4.2.tar.bz2
# tar -zxvf mpfr-2.4.2.tar
# cd mpfr-2.4.2
# ./configure --prefix=/usr/local/mpfr-2.4.2 --with-gmp=/usr/local/gmp-4.3.2/
# make
# make install

3. Install mpc-0.8.1 (requires gmp-4.3.2 and mpfr-2.4.2 as prerequisites ) 

# tar -zxvf mpc-0.8.1.tar.gz
# cd mpc-0.8.1
#./configure --prefix=/usr/local/mpc-0.8.1/ --with-gmp=/usr/local/gmp-4.3.2/ --with-mpfr=/usr/local/mpfr-2.4.2
# make
# make install

4. Update your LD_LIBRARY_PATH reflect /usr/local/mpc-0.8.1/lib In your .bash_profile include the following

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/mpc-0.8.1

5. Install the glibc-devel.i686. For more information, do look at Error when compiling GCC 4.8.1 (linuxtoolkit.blogspot.com)
6. Finally install GNU CC 4.8.1

# tar -zxvf  gcc-4.8.1.tar.gz
# cd gcc-4.8.1
# mkdir build-gcc
# cd build-gcc
# ../configure --prefix=/usr/local/gcc-4.8.1 --with-mpfr=/usr/local/mpfr-2.4.2 --with-mpc=/usr/local/mpc-0.8.1 --with-gmp=/usr/local/gmp-4.3.2
# make
# make install
by

Compiling BLACS on CentOS 5

1. You have to compile OpenMPI 1.4.x with g77 and gfortran. I’m compiling with OpenIB and Torque as well

./configure --prefix=/usr/local/mpi/gnu-g77/ \
F77=g77 FC=gfortran \
--with-openib \
--with-openib-libdir=/usr/lib64 \
--with-tm=/opt/torque

2. Download BLACS from www.netlib.org/blacs. Remember to download both mpiblacs.tgz and the mpiblacs-patch03.tgz

# cd /root
# tar -xzvf mpiblacs.tgz
# tar -xzvf mpiblacs-patch03.tgz
# cd BLACS
# cp ./BMAKES/BMake.MPI-LINUX Bmake.inc

3. Edit Bmake.inc according to the recommendation from OpenMPI FAQ

# Section 1:
# Ensure to use MPI for the communication layer

   COMMLIB = MPI

# The MPIINCdir macro is used to link in mpif.h and
# must contain the location of Open MPI's mpif.h. 
# The MPILIBdir and MPILIB macros are irrelevant
# and should be left empty.

   MPIdir = /path/to/openmpi-1.4.3
   MPILIBdir =
   MPIINCdir = $(MPIdir)/include
   MPILIB =

# Section 2:
# Set these values:

   SYSINC =
   INTFACE = -Df77IsF2C
   SENDIS =
   BUFF =
   TRANSCOMM = -DUseMpi2
   WHATMPI =
   SYSERRORS =

# Section 3:
# You may need to specify the full path to
# mpif77 / mpicc if they aren't already in
# your path. IF not type the whole path out.

   F77            = /usr/local/mpi/gnu-g77/bin/mpif77
   F77LOADFLAGS   =

   CC             = /usr/local/mpi/gnu-g77/bin/mpicc
   CCLOADFLAGS    =

4. Following the recommendation from BlACS Errata (Necessary flags for compiling the BLACS tester with g77)

blacstest.o : blacstest.f
	$(F77) $(F77NO_OPTFLAGS) -c $*.f
to:
blacstest.o : blacstest.f
	$(F77) $(F77NO_OPTFLAGS) -fno-globals -fno-f90 -fugly-complex -w -c $*.f

5. Compile the Blacs tests. You should see

# cd /root/BLACS/TESTING
# make clean
# make

You should see xCbtest_MPI-LINUX-1 and xFbtest_MPI-LINUX-1

6. Tun the Tests

# mpirun -np 5 xCbtest_MPI-LINUX-0
# mpirun -np 5 xFbtest_MPI-LINUX-0

7. If the test is successful, you may wish to copy the BLACS library to /usr/local/lib. But I like to  separate my compiled libraries separately to /usr/local/blacs/lib

# cp /root/BLACS/LIB*.a /usr/local/blacs/lib
# chmod 555 /usr/local/blacs/lib/*.a
by

Compiling LAPACK on CentOS 5

Download the lapack latest stable version (lapack-3.3.0.tgz) from http://www.netlib.org/lapack

# cd /root
# tar -xzvf lapack-3.3.0.tgz
# cd /root/lapack-3.3.0
# cp make.inc.example make.inc

Assuming Edit make.inc. Assuming the Compiling ATLAS on CentOS 5

#BLASLIB = ../../blas$(PLAT).a
BLASLIB = /usr/local/atlas/lib/libf77blas.a /usr/local/atlas/lib/libatlas.a

Compile lapack package

# make

Copy the libraries to

# mkdir /usr/local/lapack/lib
# cp /root/lapack-3.3.0/*.a /usr/local/lapack/lib
# cd /usr/local/lapack/lib/
# chmod 555 *.a

Other related Information

  1. Compiling ATLAS on CentOS 5
by

Compiling ATLAS on CentOS 5

This tutorial is to help you compile ATLAS (Automatically Tuned Linear Algebra Software) with gFortran. For those who are using Intel Compiler, you have the reliable Intel MKL (Math Kernel Library)

First thing first, some comparison between ATLAS and MKL.

ATLAS

ATLAS The Automatically Tuned Linear Algebra Software (ATLAS) provides a complete implementation of the BLAS API 3 and a subset of LAPACK 3. A big number of instructions-set specific optimizations are used throughout the library to achieve peak-performance on a wide variety of HW-platforms.

ATLAS provides both C and Fortran interfaces.

ATLAS is available for all HW-platforms capable of running UNIX or UNIX-like operating systems as well as Windows ™.

MKL

Intel’s Math Kernel Library (MKL) implements a set of linear algebra, fast Fourier transforms and vector math functions. It includes LAPACK 3, BLAS 3 and extended BLAS and provides both C and Fortran interfaces.

MKL is available for Windows ™ and Linux (x86/i686 and above) only.

Download the latest stable package from ATLAS (http://sourceforge.net/projects/math-atlas/files/Stable/). The current stable version is atlas3.8.0.tar.gz. Do note that ATLAS don’t like configuration on its original location, hence the need to create ATLAS_BUILD directory.

# cd /root
# tar -xzvf atlas3.8.3.tar.gz
# mkdir /root/ATLAS_BUILD
# cd /root/ATLAS_BUILD
# /root/ATLAS/configure

You will need to turn off CPU Throttling. For CentOS and Fedora, you will use

# /usr/bin/cpufreq-selector -g performance

For more information, you can see my blog entry Switching off CPU Throttling on CentOS or Fedora

Compile ATLAS

make
make check
make ptcheck
make time
make install

By default, ATLAS installed to /usr/local/atlas

Finally remember to add /usr/local/atlas/lib to your LD_LIBRARY_PATH

Notes:

    1. Linux Cluster Application Site
    2. ScaLAPACK, LAPACK, BLACS and ATLAS on OpenMPI & Linux installation tutorial
    by

    Building OpenMPI with Intel Compilers

    Modified from Performance Tools for Software Developers – Building Open MPI* with the Intel® compilers

    Step 1: Download the OpenMPI Software from http://www.open-mpi.org/ . The current stable version at point of writing is OpenMPI 1.3.2

    Step 2: Download and Install the Intel Compilers from Intel Website. More information can be taken from Free Non-Commercial Intel Compiler Download

    Step 3: Add the Intel Directory Binary Path to the Bash Startup

    At my ~/.bash_profile directory, I’ve added

    export PATH=$PATH:/opt/intel/Compiler/11.0/081/bin/intel64

    At command prompt

    # source .bashrc

    Step 4: Configuration Information

    # source /opt/intel/Compiler/11.0/081/bin/compilervars.sh
    # gunzip -c openmpi-1.2.tar.gz tar xf -
# cd openmpi-1.2
#./configure --prefix=/usr/local CC=icc CXX=icpc F77=ifort FC=ifort
# make all install

    Step 5: Setting PATH environment for OpenMPI
    At my ~/.bash_profile directory, I’ve added.

    export PATH=/usr/local/bin:${PATH} 
export LD_LIBRARY_PATH=/opt/intel/Compiler/11.0/081/lib/intel64:${LD_LIBRARY_PATH}
(The LD_LIBRARY_PATH must point to /opt/intel/Compiler/11.0/081/lib/intel64/libimf.so)

    Step 6: test

    $ mpicc --v
cc version 12.1.5 (gcc version 4.4.6 compatibility)