CHPC

Center for High Performance Computing

Software

OS

The cluster was set up with Rocks Clusters Suite, version 6.1.1. This operating system is based on CentOS 6.5, which in turn is still using a Linux Kernel version <3.0 (2.6.32). Since CentOS 6 is a long-term supported operating system, the available software might not always be the newest or not available altogether. To approach this issue, software can be found in two other directories: Both directories are shared and are (auto-) mounted on every node in the cluster.

C/C++ compiler

Included with CentOS 6.5 is the GCC toolchain v4.4.7. For a newer C/C++ compiler there are the following options:
Command GCC Version Source
scl enable devtoolset-1.1 bash 4.7.2 CentOS Devs
scl enable devtoolset-3 bash 4.9.2 Software Collections
scl enable devtoolset-4 bash 5.3.1 Software Collections
scl enable devtoolset-6 bash 6.2.1 Software Collections
Just issue one of the commands and you can use a different or newer compiler!

/share/apps

This shared folder is the older one. Although in this folder much more software is located than listed here, using any other is discouraged for various reasons.
Directory Program Version Information
accelrys7.0 Materials Studio 7.0 with Castep support
allinea Allinea DDT 4.2.1 64 bit Debugger, with Intel Xeon Phi KNC support
allinea5 Allinea DDT 5.0.1 64 bit Debugger, with Intel Xeon Phi KNC support
MATLAB/R2013a Matlab Release 2013a

/home/apps

This shared folder is the newer one and is actually a subfolder beneath the home share. The following software is directly installed in /home/apps, meaning the path /home/apps/bin lets you use the binaries of them:
Program Version Information
autoconf 2.69
autogen 5.18.4
automake 1.14.1
boost libraries 1.57.0 multithreaded build
CGAL 4.7
cmake 3.4.2
cryptopp 5.6.2
Eigen3 3.2.3
emacs 24.4.1
fftw 3.3.4
gmp 6.0.0a
guile 2.0.11
hdf 4.2.11 shared and static libraries, jpeg and libz support; without fortran support
hdf5 1.8.14 parallel build, fortran and HL API support, shared libs available
libffi 3.2.1
libtool 2.4.4
libunistring 0.9.4
mpfr 3.1.2
OpenBLAS 0.2.15 Compiled on an AMD Opteron Processor 6320
pnetcdf 1.6.1 parallel netcdf without fortran support
proj 4.9.1
scons 2.3.4 works with python 2.7 in /home/apps
scotch 6.0.3 compiled against the system's openmpi
sparsehash 2.0.2
swig 3.0.3 make check tests fail at "checking Examples/perl5/extend
szip 2.1
tar 1.28
valgrind 3.10.1
zlib 1.2.8 64 bit build

Subdirs

The following software is each located in its own subdirectory in /home/apps
Directory Program Version Information
amd/acml ACML AMD Core Math Library, please look further down for version information
amd/apml APML 1.0 AMD Advanced Platform Management Link
amd/libm LibM 3.1 AMD LibM 3.1
beast BEAST 1.8.4 Bayesian Evolutionary Analysis Sampling Trees
cloog CLooG 0.18.1 The CLooG Code Generator in the Polyhedral Model's Home
gmp GMP 6.1.0 The GNU Multiple Precision Arithmetic Library
hwloc111 hwloc 1.11.7 Portable Hardware Locality, static and shared build
isl ISL 0.15 Integer Set Library: library for manipulating sets and relations of integer points
jdk18 JDK 8u25 Sun Oracle Java JDK
jdk1.8.0_71 JDK 8u71/72 Sun Oracle Java JDK
jdk1.8.0_131 JDK 8u131 Sun Oracle Java JDK
libevent218 libevent 2.1.8 an event notification library
MATLAB/R2015a MATLAB R2015a MATLAB
MATLAB/R2017a MATLAB R2017a MATLAB
mpc MPC 1.0.3 Mpc is a C library for the arithmetic of complex numbers
mpfr mpfr 3.1.3 MPFR library
nwchem NWChem 6.5 MPI and Python support, compiled with system's tools (gcc, Python 2.6.6)
open64/sdk/v1.0 AMD SDK 1.0 open64 compiler suite 4.2.4, ACML 4.4.0, AMD LibM 2.1
open64/compiler-suite open64 4.5.2.1 x86 open64 copmiler suite
opencv24 openCV 2.4.10
opencv3 openCV 3.0 beta
openmpi211 Open MPI 2.1.1 Support for SGE and openIB Verbs, built against libevent218, hwloc111, pmix122
parallel-studio Intel Cluster Studio XE 2015 Intel C compiler, debugger, Composer, Inspector
pmix122 PMIx 1.2.2 PMI Exascale (PMIx), built against hwloc111 and libevent218, shared an static
python27 python 2.7.8 Anaconda 2.1 package, many scientific modules included
python34 python 3.4.1 Anaconda3 2.1 package, many scientific modules included
zlib zlib 1.2.8 64 bit static build

ACML

In the following table, information on the AMD acml installations is given. They mainly differentiate by the compiler used for compilation and are further divided in subdirectories.
Directory Version Information
gfortran 5.3.1 compiled with gfortran
gfortran6 6.1 compiled with gfortran, was originally verison 5.3.1 with version 6.1 update
ifort 5.3.1 compiled with Intel fortran compiler
open64 5.3.1 compiled with open64
pgi 5.3.1 compiled with PGI

Python modules

Atop of the scientific modules in the Anaconda(3) package(s), the following modules are also installed for both Python Installations in /home/apps:
Module Version Information
ffc 1.5.0
fiat 1.5.0
instant 1.5.0
hdf5 1.8.14 included hdf5 module version 1.8.13 was overwritten to get parallel support
ufl 1.5.0
And finally, in /home/apps/python27 is the following package included
dolfin 1.5.0
which has support for openmp, mpi, scotch, zlib, python, sphinx, hdf5, vtk.