TARDIS cluster runs CentOS Linux version 5.5.

Apart from a large number of packages that are part of a standard CentOS distribution, a number of custom-built software packages are installed on the cluster. All custom packages are located in the /shared directory which is shared over NFS across all nodes, that is, all custom software is immediately accessible from all computer nodes.

List of all custom software

Name Versions Default version Compiled withNotes
GNU Compiler Collection (GCC) 4.3.5, 4.4.4 4.4.4 N/A includes C/C++ and Fortran 77/90/95 compilers
Open MPI 1.4.2 1.4.2
(gcc 4.4.4)
gcc 4.4.4, 4.1.2, open64 with support for Infiniband and SGE
MPICH 1.2.7p1 1.2.7p1 gcc 4.1.3 with support for Infiniband
MPICH2 1.0 1.0 gcc 4.1.3 with support for Infiniband
ACML 4.4.0 4.4.0 N/A with support for gcc and open64
Boost 1.43 1.43 gcc 4.4.4 with boost.mpi
CMake 2.8.2 2.8.2 gcc 4.4.4
CUDA 2.2, 3.1 3.1 N/A
CULA 2.0 1.43 gcc 4.4.4 Basic version
FFTW 2.1.5, 3.2.2 2.1.3 gcc 4.4.4
GSL 1.14 1.14 gcc 4.4.4
HOOMD revision 3830 revision 3830 gcc 4.4.4, boost 1.43, CUDA 3.1, Python 2.7 no support for Yakub electrostatics
HOOMD-YAKUB 1.0 HOOMD gcc 4.1.3, boost 1.33, CUDA 3.1, Python 2.3 older version with support for Yakub electrostatics
KINSOL 2.6.0 2.6.0 gcc 4.1.3, OpenMPI 1.4.2 support for serial and parallel libraries
LAMMPS 11_Aug_2010, 11_Jan_2011 11_Aug_2010 gcc 4.4.4, OpenMPI 1.4.2 general purpose molecular dynamics package
Membrane rev. 184 rev. 184 gcc 4.4.4, gsl 1.14 Monte Carlo code for elastic membranes
Python 2.7 2.7 gcc 4.4.4 with numpy and SciPy
PETSc 3.1-p4 3.1-p4 gcc 4.4.4, OpenMPI 1.4.2 debugging disabled
SLEPc 3.1-p1 3.1-p1 gcc 4.4.4, OpenMPI 1.4.2, PETSc 3.1-p4 debugging disabled
TAO 1.10.1 1.10.1 gcc 4.4.4, OpenMPI 1.4.2, PETSc 3.1-p4 debugging disabled
Subversion 1.6.12 1.6.12 gcc 4.4.4
Sun Grid Engine 6.2u5 6.2u5 N/A


Software list can be accessed from a terminal by typing:

module avail





Output of the previous command will look something like this:


--------------------------------------- /shared/Modules/versions -----------------------------------------
3.2.7

--------------------------------------- /shared/Modules/3.2.7/modulefiles ----------------------------
acml/gfortran64(default)     cuda/3.1(default)     gmp/5.0.1(default)     modules    
mpi/openmpi-open64     acml/gfortran64_mp     cula/2.0     gsl/1.14     mpc/0.8.1(default)
cuda/2.2     gcc/4.4.4(default)     module-info     mpi/openmpi-gcc-4.4(default)





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