Computational Science Environment (CSE)
In efforts to provide a common platform for utilizing and developing data analysis and assessment applications in heterogeneous High Performance Computing (HPC) environments, the Classified Data Analysis and Assessment Center (CDAAC) has developed the Computational Science Environment (CSE). CSE is a new module based software release structure for the software platform once known as the Interdisciplinary Computing Environment (ICE).
CSE provides a stable suite of data analysis and assessment tools, applications and libraries that are common across most HPC environments and developers workstations. In addition, CSE provides an experimental, cutting-edge suite of developer tools that can enhance the data analysis and assessment process. CSE includes the eXtensible Data Model and Format (XDMF), a common data hub where HPC codes and tools can efficiently exchange data values and meaning. CSE consist of many tools like Python, VTK and ParaView that can assist with day-to-day visualization requirement. CSE provides a common platform that enables the development of full featured portable HPC applications.
CSE is now available on MJM, HUMVEE, Sketch and 64-bit RH4 and RH5 workstations. Note that the current CSE contains only a subset of packages and features that we ultimately intend to distribute. Hence, the documentation presented can be temporarily incomplete as developers integrate new packages.
1. Initial CSE module Setup
1.1 Initial module setup at ARL (mjm, harold, sketch, tow)
On the existing HPC systems where modules are automatically integrated into their environment, users only need to know that the CSE modules exist and the procedure to load the CSE main module. The name of the main CSE module is cseinit .
1.2 Initial module setup at AFRL (Hawk)
1.2.1 Initialize modules using .cshrc
To initialize modules on your machine add the following to your .cshrc:
module use /app2/cse/modules/COTS
1.2.2 Initialize modules from the command line
Initialize modules from the command line by executing the following command:
> module use /app2/cse/modules/COTS
2. Machines without modules (64-bit Linux Workstations)
On non-HPC systems such as desktop workstations, the modules software is included with the CSE distribution. The CSE distribution is available using rdist for RHEL4 and RHEL5 linux workstations from an ARL server. For information on how to gain access to the CSE software, please contact the vis@arl.army.mil. Once CSE is installed, the user is required to initialize modules using one of the following methods.
2.1 Initialize modules using .cshrc
To initialize modules on your machine add the following to your .cshrc:
if (-e /usr/cta/CSE/modules/init/tcsh) then source /usr/cta/CSE/modules/init/tcsh module use /usr/cta/CSE/modules/COTS endif
2.3 Initialize modules from the command line
> /usr/cta/CSE/modules/init/tcsh > module use /usr/cta/CSE/modules/COTS
3. Loading and Viewing CSE modules
The CSE module layout is based on simplicity (see packages only if you want to see them) and uses a consistent naming schema that attempts to avoid future naming/package conflicts. The central idea is to simplify the process associated with establishing the proper environment to execute a particular application. The end-user will not be required to establish environment variables or modify library paths to get common applications to work properly. To illustrate how to load different CSE packages several examples are provided.
3.1 Example 1: View and load a CSE application module
To view and load a cse application module:
- Load main cse module:
> module load cseinit
- List the modules:
> module avail cse/doxygen/1.5.9 cse/paraview/3.6.2 cse/xframework/latest cse/doxygen/latest cse/paraview/latest cse-beta cse/graphviz/2.22.2 cse/xframework/2008.10 cse-tools
- Load desired module.
Loading the main CSE module (cseinit) will make the application list (ParaView, Visit, OpenMPI ...) available to load. CSE will commonly provide several versions of the same package, by default the latest version of a particular package is cse/{package}/latest. Loading cse-tools is discussed in the following example.
3.2 Example 2: View and load a CSE tool module
To view and load a cse tool module:
- Load main cse module:
> module load cseinit
- Load cse tools module:
> module load cse-tools
- List the modules:
> module avail -------------------/usr/cta/CSE.010710/modules/rel-tools---------------- cse/cmake/2.8.0.5 cse/netdmf/latest cse/qt/latest cse/cmake/latest cse/numpy/1.3.0 cse/scons/1.0.0 cse/freealut/1.1.0 cse/numpy/latest cse/scons/latest cse/freealut/latest cse/openal/0.0.8 cse/sip/4.7.4 cse/git/1.6.5.2 cse/openal/latest cse/sip/4.9.1 cse/git/latest cse/pypcap/1.1 cse/sip/latest cse/hdf5/1.6.8 cse/pypcap/latest cse/swig/1.3.37 cse/hdf5/latest cse/pyqt/4.6.1 cse/swig/latest cse/libpcap/1.0 cse/pyqt/latest cse/tcltk/8.4.19 cse/libpcap/latest cse/pyro/3.6 cse/tcltk/latest cse/libxml2/2.7.4 cse/pyro/latest cse/vtk/5.4.2 cse/libxml2/latest cse/python/2.5.2 cse/vtk/latest cse/mesa/7.0.4 cse/python/latest cse/xdmf/2009.12.01 cse/mesa/latest cse/qt/4.3.3 cse/xdmf/latest cse/netdmf/2009.12.16 cse/qt/4.5.2 ---------------- /usr/cta/CSE.010710/modules/rel-apps ------------------ cse/doxygen/1.5.9 cse/paraview/3.4.0 cse/xframework/latest cse/doxygen/latest cse/paraview/3.6.2 cse-beta cse/graphviz/2.22.2 cse/paraview/latest cse-tools cse/graphviz/latest cse/xframework/2008.10
- Load desired module.
Note that CSE will commonly provide several versions of the same package, by default the latest version of a particular package is cse/{package}/latest. Loading cse-beta is discussed in the following example.
3.3 Example 3: View and load a CSE beta module
To view and load a CSE beta module:
- Load main cse module:
> module load cseinit
- Load cse beta module:
> module load cse-beta
- List the modules:
> module avail -----------------/usr/cta/CSE.010710/modules/beta-apps ------------------ cse/paraview/3.7.0 cse-tools-beta ---------------- /usr/cta/CSE.010710/modules/rel-apps ------------------ cse/doxygen/1.5.9 cse/paraview/3.4.0 cse/xframework/latest cse/doxygen/latest cse/paraview/3.6.2 cse-beta cse/graphviz/2.22.2 cse/paraview/latest cse-tools cse/graphviz/latest cse/xframework/2008.10
- Load desired module.
Note that CSE will commonly provide several versions of the same package, by default the latest version of a particular package is cse/{package}/latest. Loading cse-beta-tool is discussed in the following example.
3.4 Example 4: View and load a CSE beta tool module
To view and load a CSE beta tool module:
- Load main cse module:
> module load cseinit
- Load cse beta module:
> module load cse-beta
- Load cse tools beta module:
> module load cse-tools-beta
- List the modules:
> module avail -----------------/usr/cta/CSE.010710/modules/beta-tools ------------------ cse/xdmf/2009.01.13 cse/vtk/2009.01.03 -----------------/usr/cta/CSE.010710/modules/beta-apps ------------------ cse/paraview/3.7.0 cse-tools-beta ---------------- /usr/cta/CSE.010710/modules/rel-apps ------------------ cse/doxygen/1.5.9 cse/paraview/3.4.0 cse/xframework/latest cse/doxygen/latest cse/paraview/3.6.2 cse-beta cse/graphviz/2.22.2 cse/paraview/latest cse-tools cse/graphviz/latest cse/xframework/2008.10
- Load desired module.
Note that CSE will commonly provide several versions of the same package, by default the latest version of a particular package is cse/{package}/latest.
4. List of Applications
The current list of CSE applications are:
- Paraview
- Doxygen
- Graphviz
- XframeWork
5. List of Tools
The current list of CSE tools are:
- cmake
- git
- hdf5
- libpcap
- libxml2
- mesa
- netdmf
- numpy
- pypcap
- pyqt
- pyro
- python
- qt
- scipy
- scons
- sip
- swig
- tcltk
- vtk
- xdmf
- openmpi (on some machines)