From HPC

Please contact support if you need/what different software or libraries install. Appropriate licenses will need to be provide.

Contents 1 Compilers 1.1 Intel 10.1 Proffesional (2 concurrent licenses) 1.2 GNU Compilers 1.2.1 C/C++ compiler options/tuning 1.3 R 1.4 Java 1.5 OpenMP 1.6 openMPI 2 Software 2.1 Stata10

Compilers

Listed below are the compilers currently installed and supported. If there is a language or compiler you would like, please speak to IT Services.

Intel 10.1 Proffesional (2 concurrent licenses)

The Intel compilers are highly optermized for the cpu's in the gecko cluster. They also include the Maths Kernel Library (BLAS, LAPACK, etc), please see Intel documentation for more information.

• C/C++ (icc/icpc)
• Fortran (ifort)

• Intel Fortran Information
• Intel Fortran Documentation
• Intel C/C++ Information
• Intel C/C++ Documentation

GNU Compilers

• C/C++ (gcc/g++)
• Fortran (gfortran)

C/C++ compiler options/tuning

Note: You can also try optimization level 3, change -02 to -03

• i686 (32 bit)

CHOST="i686-pc-linux-gnu"
CFLAGS="-march=nocona -O2 -pipe -fomit-frame-pointer"
CXXFLAGS="${CFLAGS}"

• x86-64 (64 bit)

CHOST="x86_64-pc-linux-gnu"
CFLAGS="-march=nocona -O2 -pipe" 
CXXFLAGS="${CFLAGS}"

Improve make speed

MAKEOPTS="-j2"

R

Version 2.7.2

R is a language and environment for statistical computing and graphics.

http://www.r-project.org/

Java

Versions 1.4, 1.5, 1.6 in 32bit and 64bit flavours, enabled/loaded via modules

OpenMP

OpenMP website http://openmp.org/wp/

Both the GNU and Intel compilers support OpenMP.

GNU

gcc -fopenmp
g++ -fopenmp
gfortran -fopenmp

Intel

icc -openmp
icpc -openmp
ifort -openmp

openMPI

Software

Stata10

stata-se (Stata SE 32bit command line, for use on cluster)

xstata-se (Stata SE 32bit GUI, for use only on head node to check/change do files etc)