Software on Palma

We use the environment module approach to manage the user environment for different software, library or compiler versions on Palma. The distinct advantage of the modules approach is that the user is no longer required to explicitly specify paths for different executable versions, and try to keep the MANPATH and related environment variables coordinated. With the modules approach, users simply "load" and "unload" modules to control their environment. Type

module avail

to list all the modules which are available to be loaded. Notice that most of them indicate associated version numbers. Modules make it easy to switch between versions of a package. Specifying a module name without a version number will select the default production version.

Modules can be added with the call

module add name

where name indicates the complete name of the module. This can be done in the .bashrc so you do not have to load the modules needen by default every time you log in.

module li

shows the already loaded modules.

In the following part, there is an overview of the installed software on Palma with the appropriate module names.

Compiler

Serial Compiler

Sets the environment variables CC, CXX, FC and FLAGS_FAST

compiler/intel/12	Version 12 of the Intel compiler suite, inkl. C/C++ and Fortran
intel/cc/11.1.059	Intel C and C++ compiler
intel/fc/11.1.059	Intel Fortran compiler
studio/12.2	Oracle Studio compiler, only for testing purposes
pgi/11.3	PGI compiler

MPI

Sets the environment variables MPICC, MPICXX, MPIF77 and MPIF90

mpi/intel/4.0.0.028

Intel MPI in version 4, should be used as standard MPI environment

Further variants:

mpi/intel/3.2.2.006	Older version, only for compatibility purposes
intel/mpi/3.2.2.006	The same module
mpi/mpich2/intel/1.2.1p1	MPICH2, if explicitely required by the code
mpi/mpich2/intel/1.3.1b
mpi/mpich2/intel/1.3.2
mpi/mvapich2/intel/1.6-rc2	MVAPICH2, might run, if Intel MPI does not run on arbitrary many processors
mpi/mvapich2/intel/stable
mpi/openmpi/gcc/1.4	OpenMPI, if explicitely required by the code, compiled with the GNU compiler
mpi/openmpi/intel/1.5.1	the same with Intel compiler

Libraries

fftw/intel/2.1.5	Fastest Fourier Transform in the West, compiled with Intel compiler
fftw/intel/3.2.2
fftw/intel/3.3-b1	FFTW, current beta version
fftw/studio/3.2.2	FFTW, compiled with Oracle Studio
hdf5/parallel/1.8.4	parallel version of HDF5
hdf5/serial/1.8.4	serielle version of HDF5
netcdf/serial/4.1.1
netcdf/serial/intel/4.1.2
petsc/intel/3.0.0-p12
petsc/intel/3.1-p8	Portable, Extensible Toolkit for Scientific Computation Link zur Homepage
slepc/intel/3.0.0-p7
slepc/intel/3.1-p6	Scalable Library for Eigenvalue Problem Computations, Extension of PETSC Link zur Homepage
nag/fnl6i04dcl
dislin/10.0
dislin/10.1
intel/mkl/10.2.4.032	Intel Math Kernel Library Dokumentation

Debugger/Profiler

Allinea DDT

Paralleldebugger for MPI and OpenMP. (Link to vendor homepage) We have a license for up to 16 processes that is shared by all users. Please use only as many processes as necessary. To use the program, load the module

ddt/2.6.1

, after that, it can be startet by the command ddt.

OMPP

ompp/0.7.0

OpenMP profiler for C/C++ and Fortran Link to manual

Marmot

marmot/intel/2.4.0

MPI Checker Link to homepage

Marmot can be used to check MPI code for bugs like deadlocks. Usage:

• Substitute compiler call by marmotcc, marmotcxx, marmotf77 or marmotf90
• Run program with MARMOT_LOGFILE_TYPE=1 mpirun -np(n+1) ./program
• A HTML file es created that gives hints for bugs

Oracle Studio

studio/12.2

Compiler suite, with profiling tools for serial und parallel codes

Intel Trace Analyzer and Collector

intel/itac/7.2.2

MPI Profiler

Intel Inspector

tools/intel-inspector/xe_2011

memory error and thread checker tool for C, C++, C# .NET, and Fortran

Usage:

• (optional) to be able to find the location of found bugs in the source code, compiler with the option "-g"
• execute the GUI via "inspxe-gui"
• Create a new project
• Choose "New Analysis"
• Let the inspector search for problems like memory problems, memory leaks, data races and deadlocks

Intel VTune

tools/vtune/xe_2011

Find performance bottlenecks

Attention! Due to a bug in the processors of palma1, VTune must not be used to collect data on palma1 under no circumstances. Please use palma50 for this purpose.

• The GUI is called via "amplxe-gui"

Miscellaneous

Matlab Mathematica and Maple

The modules for the current Version of Matlab, Mathematica and Maple are called

mathematica/8.0

matlab/R2011a

maple/Maple14

To start these programs with a GUI on a node with the batch system, see this guide

R

Usage:

module rm intel/mpi
module add mpi/openmpi/gcc/1.4

Reserve a node

qsub -I -A ...
mpirun -np 8 -machinefile $PBS_NODEFILE --mca

Execute program Quit Rmpi

mpi.close.Rslaves()
mpi.quit()