Software

The search.di.uminho.pt cluster is based on the Rocks 5.2.1 cluster management distribution. The following rolls are installed: area51, base, bio, ganglia, hpc, java, kernel, os, viz, web-server, service-pack 5.2.2, torque, myrinet_mx, cuda, modules-5.2, intel-11, login-5.2 and mpich2-intel-11.

The software base included In these rolls or installed separatelly includes the following applications and libraries:

Package: Versions:
Linux kernel (CentOS 5.3) 2.6.18-128.1.14
Cluster management Rocks 5.2.1
torque 2.3.6-1
Maui 3.2.6p21
Environment modules (”module avail”) 3.2.6
Bacula 3.0.3
Compilers GCC compiler suite 4.1.2 20080704 (Red Hat 4.1.2-44)
Intel compilers suite 11.1
nvcc compiler 2.0, V0.2.1221; 4.0
MPI stacks OpenMPI 1.3.3, 1.3.4, 1.4
Mpich  
Mpich2  
Profiling Intel VTune 9.1
mpiP 3.1.2
Libraries Intel Math Kernel Library  
GotoBLAS  
BLACS  
Boost 1.47
FFTW2 2.1.5
FFTW3 3.2.2; 3.3
NAMD 2.7b2
VMD 1.8.7
XMD 2.5.34-1
PBRT 1.04
Gromacs 4.0.5; 4.0.7; 4.5.5
Lammps 14Nov2011
HMMER  
NCBI BLAST  
MpiBLAST  
Biopython  
ClustalW  
MrBayes  
T_Coffee  
Emboss  
Phylip  
Fasta  
Glimmer  
TIGR Assembler  
OpenEXR 1.6.1
IlmBase 1.0.1
Glew 1.5.2