Apache ANT Java development software
Apache Ant is a Java library and command-line tool who's mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. ANT is accessed via Modules.
> module load ant
> module load ...your_needed_java_ver...
Eclipse IDE
Eclipse is a multi-language software development environment comprising an integrated development environment (IDE) and an extensible plug-in system.
Load the following:
> salloc -N1 -c1 -p interactive
> module load java/1.6.0_64bit
> module load eclipse/1.4.1-x86_64
> srun ...srun options... eclipse
When finished, type exit to release the allocation.
Python Compiler
Installed python modules: matplotlib, numpy, Networkx, Biopython
To check docs online while logged into cluster:
> pydoc matplotlib
Complete Python docs
A guide to Python Modules
For info about what system-wide python based packages are installed:
$ module load python/2.7.6 To see what python apps are available: $ pip list |
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Perl Compiler
Perl is a stable, cross platform programming language. Perl is extensible. There are over 500 third party modules available from the Comprehensive Perl Archive Network (CPAN).
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Portland documentation is on the vendor website or on the cluster in the install tree found at: /opt/shared/pgi/
MPI related
OpenMPI , Mvapich and Mvapich2 are is available on the cluster as a loadable module. Once the corresponding module is loaded, your environment will provide access to the various MPI compilers.
> module load openmpi
For example, OpenMPI provides the following:
mpic++ mpicxx mpicc mpiCC mpif77 mpif90
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The cluster 64-bit login node requires Gnu GCC 64-bit compiler and as a result becomes the default native compiler. No Module setup is required.
Documentation is available at GCC online documentation or from the following man pages:
> man gcc
> man g77
> man gfortran
Note, the system default install of gcc is ver. 4.1. This can be an issue for some types of dependencies. For example, the gfortran option for openmp usage requires gcc ver. 4.7 or newer. You may access this version by the following:
> module load gcc
G95
G95 is a stable, production Fortran 95 compiler available for multiple cpu architectures and operating systems. There are two versions on the cluster, The module command makes a distinction. Using "module load g95" gets the 32-bit version and "module load g95-64" gets the 64-bit version.
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To access icc:
> module load icc
> > srun ...srun options... icc ....your options....
Local Fortran documentation in HTML format can be found at:
>firefox file:////opt/intel/fce/10.1.017/doc/main_for/index.htm
or via manpages depending on what Module is loaded:
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Fortran quick reference is available by typing:
> man ifort
> ifort -help
Shell script programming
Check the site shellcheck for a debug tool.
Thread programming
In shared memory multiprocessor architectures, such as SMPs, threads can be used to implement thread based parallelism. The cluster compute nodes are smp nodes with 8 cores. C and C++ compilers will have one or more compile options for threads. The cluster has pthreads installed and for more information see the man pages:
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The cluster's gcc compiler supports openmp threads. Check the gcc docs for related information. Note the possible need to access a compute node in an Exclusive Host LSF manner. This would allow one's threads to use all cores on one host. A simple example such as:
-bash-3.2$ bsub -queue express -R bigmem -x ./yourcodeexecutablesrun ...srun options... ./yourcode_executable
would obtain a node for exclusive host access with large memory.
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