Curie's software documentation

If you have any remarks or suggestions, please contact the support team by email : hotline.tgcc@cea.fr

Notice: most of the software or libraries can be accessed by the module command (use module help, list, avail, etc.. on curie): contact the support team if you want to add or modify a module.

Contents

  1. Curie's software documentation

  2. Mathematical libraries

  3. Storage softwares and data handling

  4. Calculation codes

  5. Visualization softwares and data handling

  6. Profiling and Debugging sofwares

  7. Development

  8. Others

Mathematical libraries

Name

Version

Module

Associated variables

Documentation

Comment

boost

1.45.0

boost/1.45.0

$BOOST_INC_DIR,    $BOOST_LIB_DIR

Boost Homepage

C++ library

fftw

2.1.5

fftw/2.1.5

$FFTW2_INC_DIR,    $FFTW2_LIB_DIR

FFTW Homepage

C subroutine library for computing the discrete Fourier transform (DFT)

3.2.2

fftw/3.2.2

$FFTW3_INC_DIR,    $FFTW3_LIB_DIR

gsl

1.14

gsl/1.14

$GSL_INC_DIR,    $GSL_LIB_DIR

GSL Homepage

Numerical library for C and C++ programmers(Gnu Scientific Library)

intel mkl

11.1.072

intel/11.1.072

$MKL_LIBS,    $MKL_SCA_LIBS,     $MKL_LIB_DIR

Intel Homepage

Intel® MKL is a library of math routines for science, engineering, and financial applications

12.0.084

intel/12.0.084

petsc

3.1-p6

petsc/3.1

$PETSC_INC_DIR,    $PETSC_LIB_DIR

PETSc Homepage

Suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations

Storage softwares and data handling

Name

Version

Module

Associated Variables

Documentation

Comment

hdf5

1.8.5

hdf5/1.8.5

$HDF5_INC_DIR,    $HDF5_LIB_DIR

HDF5 Homepage

HDF5 is a data model, library, and file format for storing and managing data

metis

4.0.1

$metis/4.0.1

$METIS_INC_DIR,    $METIS_LIB_DIR

METIS Homepage

Serial Graph Partitioning and Fill-reducing Matrix Ordering

mumps

4.9.2

mumps/4.9.2

$MUMPS_INC_DIR,    $MUMPS_LIB_DIR

MUMPS Homepage

A parallel sparse direct solver

nco

4.0.5

nco/4.0.5

$NCO_INC_DIR , $NCO_LIB_DIR

nco Homepage

The netCDF Operators (NCO) are a suite of standalone, command-line programs like, e.g., ls or mkdir

netcdf

4.1.1

netcdf/4.1.1

$NETCDF_INC_DIR , $NETCDF_LIB_DIR

Netcdf Homepage

Set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data

parmetis

3.1.1

parmetis/3.1.1

$PARMETIS_INC_DIR ,     $PARMETIS_LIB_DIR

Parmetis Homepage

Parallel Graph Partitioning and Fill-reducing Matrix Ordering

phdf5

1.8.5

phdf5/1.8.5

$HDF5_INC_DIR,    $HDF5_LIB_DIR

PHDF5 Homepage

Parallel HDF5

ptscotch

5.1.11

ptscotch/5.1.11

$PTSCOTCH_INC_DIR,    $PTSCOTCH_LIB_DIR

PTSCOTCH Homepage

Parallel scotch

scotch

5.1.11

scotch/5.1.11

$SCOTCH_INC_DIR,    $SCOTCH_LIB_DIR

SCOTCH Homepage

Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning

Calculation codes

Most of the codes require no access path to the binary file. The binary file is automaticly defined by loading the module. However, some of them require additionnal environment variables. You can visualize them by using the command :module show [nom_module].

Name

Version

Module

Documentation

Comment

User restrictions

abinit

6.4.2

abinit/6.4.2

ABINIT Homepage

Parallel molecular dynamics code

code saturne

2.0.0

saturne/2.0.0

Code_Saturne Homepage

EDF's general purpose Computational Fluid Dynamics (CFD) software

cpmd

3.13.2

cpmd/3.13.2

CPMD Homepage

Plane wave/pseudopotential implementation of Density Functional Theory, particularly designed for ab-initio molecular dynamics

Need to belong to the cpmd group (Conditions)

espresso

4.2.1

espresso/4.2.1

Quantum-Espresso Homepage

integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It includes PWSCF code.

gaussian

9-B.01

gaussian/09-B01

Gaussian Homepage

Provides capabilities for electronic structure modeling

gaussian group only

gromacs

4.5.3

gromacs/4.5.3

GROMACS Homepage

Versatile package to perform molecular dynamics

namd

2.7

namd/2.7

Namd Homepage

Parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems

Need to belong to the namd group Upload new attachment "NAMD_Download_Restrictions.pdf"

siesta

2.0.2

siesta/2.0.2

SIESTA Homepage

Spanish Initiative for Electronic Simulations with Thousands of Atoms

Siesta group

vasp

5.2.11

vasp/5.2.11

VASP Homepage

VASP Vienna Ab-initio Simulation Package

Vasp group (A licence is needed)

Visualization softwares and data handling

Name

Version

Module

Associated Variables

Documentation

Comment

cdo

1.4.6

cdo/1.4.6

CDO Homepage

CDO is a collection of command line Operators to manipulate and analyse Climate and forecast model Data. Supported data formats are GRIB, netCDF, SERVICE, EXTRA and IEG

ferret

6.6.1

ferret/6.6.1

$FER_DIR

Ferret Homepage

Logiciel de visualisation et d'analyse adapté aux besoins des océanographes et des météorologistes

qt

4.7.1

qt/4.7.1

Qt Homepage

Graphical library

Profiling and Debugging sofwares

Name

Version

Module

Associated Variables

Documentation

Comment

ddd

3.3.12

ddd/3.3.12

DDD Homepage

GNU DDD is a graphical front-end for command-line debuggers such as GDB, DBX, WDB, Ladebug, JDB, XDB, the Perl debugger, the bash debugger bashdb, the GNU Make debugger remake, or the Python debugger pydb

ddt

2.6.1

ddt/2.6.1

$DDTPATH

Userguide DDT pdf and Curie's Manual

Comprehensive graphical debugger for scalar, multi-threaded and large-scale parallel applications that are written in C, C++ and Fortran

papi

4.1.1

papi/4.1.1

$PAPI_INC_DIR,    $PAPI_LIB_DIR,    $PAPI_LIBS

PAPI Homepage

Profiling tool

paraver

3.99

paraver/3.99

PARAVER HOMEPAGE

Profiling tool

scalasca

1.3.2

scalasca/1.3.2

Scalasca Homepage

Graphical performance analysis of parallel applications

valgrind

3.6.0

valgrind/3.6.0

http://valgrind.org/

Profiling tool and memory analysis

Development

Name

Version

Module

Associated Variables

Documentation

Comment

cmake

2.8.3

cmake/2.8.3

CMake Homepage

Compilation tool (as Make)

gcc

4.5.1

gcc/4.5.1

GCC GNU Homepage

The GNU compiler collection

intel

11.1.072

intel/11.1.072

INTEL COMPILER PAGE

The Intel compiler collection

12.0.084

intel/12.0.084

jdk

1.6.0-23

jdk/1.6.0-23

JAVA HOMEPAGE

Sun Microsystems product aimed at Java developers

bullmpi

0.17.2

bullmpi/0.17.2

BULL HOMEPAGE

MPI Library

0.18.1

bullmpi/0.18.1

bullxmpi

1.0.1

bullxmpi/1.0.1

BULL HOMEPAGE

MPI Library

swig

2.0.1

swig/2.0.1

Swig Homepage

Software development tool that connects programs written in C and C++ with a variety of high-level programming languages. SWIG is used with different types of target languages including common scripting languages such as Perl, PHP, Python, Tcl and Ruby.

Others

Software documentation (last edited 2011-04-28 by hotline.tgcc@cea.fr)