Condo - Available Software

System Software
 Condo nodes run Red Hat Enterprise Linux 6.6 and use TORQUE (PBS) for 
 resource and job management.

 The application of operating system patches occurs as security needs dictate.  
 All nodes allow for unlimited stack usage, as well as unlimited core dump size 
 (though disk space and server quotas may still be a limiting factor). 

 For information on job schedulers refer to the 
 Managing jobs using the PBS job scheduler Section.

Intel Compilers:
 Fortran compiler (ifort) 
 C and C++ Compilers (icc and icpc) 

 MPI (Using Infiniband):
  Intel MPI with Intel Fortran  ( mpiifort)
  Intel MPI with Intel C and C++ ( mpiicc , mpicpc)
  For information on Intel MPI Library Compiler Drivers refer to Section 2.1 of 
  the Intel MPI Library for Linux OS Reference Manual.

Performance and Debugging tools
 Allinea DDT Debugger (/shared/allinea/tools/bin/ddt)
 For information on DDT refer to the Using the DDT Debugger Section.

 GNU Debugger (/usr/bin/gdb)
 This debugger can be used to debug serial programs written in C and C++.

 Intel Debugger (idb, idbc, idbc_mic)
 Intel debugger can be used to debug jobs that run on regular Intel CPUs and/or 
 Intel Xeon Phi Accelerator cards.
 Issue 'man idb' on 'share' or 'stream' to find information on this debugger.

Scientific Libraries
 MPI Message Passing Library (mpirun MPI Tutorial) 
 MKL Optimized Scientific Library that includes BLAS, LAPACK and FFTs. Refer to the
 Intel Math Kernel Library Link Line Advisor to choose the correct linking options.

Application Software
 Groups are responsible for installing their own group specific software, 
 since they usually are more expert at the software that is specific to their 
 discipline.  This also allows the groups to install whatever version they 
 want in their group's directories without affecting any other group on the 
 system, and to update on their own schedule without having to wait for a 
 system administrator to do it.

 Some groups are using the modules facility to manage installed software with
 several versions, like R or OpenFoam.  To see what modulefile directories are
 available by default, issue 
 module avail

 For any of the NAMES listed, you can issue:
 module load  NAME
 and now 
 module list
 will show that NAME
 and whatever software is enabled by that module can now be used.
 module unload  NAME
 will unload the software module NAME and you should be back where
 you were before loading the module.

  For example, 
    module load LAS/compilers/gcc/4.9.3  
  will load a newer version of the Gnu compilers,
    module load engr/openfoam-2.2.2
  will load that version of the OpenFoam CFD software, and
    module load LAS/gromacs/5.0.5  
  will load the version 5.0.5 of the Molecular Mechanics package Gromacs.

 If you make your own module DIRECTORY, then issuing
 module use  DIRECTORY
 allows those module files to be added to the list of modules which are
 avalable to you.

 The order in which modules are loaded is imoportant when there 
 are commands or libraries of the ssame name, such as different 
 versions of MPI or of compilers.  In general, the last module
 loaded will have precedence.

 If help is needed to install a specific software please contact