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Jazz Application Documentation

Software on the LCRC computers includes the vendor-supplied operating systems and programming environments as well as third-party products installed by the LCRC Systems Team. Most of packages will have man and info pages are available online. Other documentation such as vendor user guides and Jazz usage instructions may be found by clicking on the application's name in the application list.

The LCRC Systems Team installs, maintains, and supports a number of third-party software applications. Most can be used free-of-charge by all LCRC users. Some applications are restricted to only Argonne National Laboratory (ANL) users. Restricted applications are marked as such and an explanation of the restriction may be found by selecting the application's name.

Examples of third-party software are compilation systems such the Intel and Portland Group compilers, applications such as Gaussian 98, and tools and utilities such as PBS and QBank.

Eventually, requests for additional software applications may be made using an online request form, for now, please send mail with the name of the software and any known details to systems@lcrc.anl.gov.

System Utilities and Tools

Application Version Softenv Key Marks Notes

SoftEnv 1.4.2 @default I SoftEnv is used to specify which applications are set up in a user's environment.

Globus 2.2.4 +globus I Globus provides the tools to build computational grids.

Portable Batch Scheduler (PBS) 5.4 @default I PBS provides the interface between user jobs and the Jazz compute nodes.

QBank 2.10.4 @default I QBank is the allocations manager for Jazz.

Condor 6.6.10 @default W Condor provides the interface between user jobs and the Jazz compute nodes that are not currently in use by regular PBS jobs.

Subversion 1.0.9 +subversion I Subversion is a freely available replacement for CVS and can be used for source code versioning.

Compilers & Debuggers

Application Version Softenv Key Marks Notes

PGI 5.2 +pgi-5.2 I L Portland Group, Inc. (PGI) compiler suite for F90 (pf90), F77, C, C++. Up to 5 instances of the pgi compiler suite may be in use at any time. Use of this compiler suite is available to any person with an active Jazz account. Activation of new versions automatically retires prior versions on the system. Priority will be given to Gaussian users should the need arise.

GCC 3 3.2.3 +gcc-compilers I Default version of the standard GNU compiler suite used on Jazz. Includes C, C++, F77 and Java compilers. GCC is open source, public domain software and has no license restrictions.

GCC 4 4.0.2 +gcc-4.0.2 I Version 4 of the standard GNU compiler. Includes C, C++, F95 and Java compilers. GCC is open source, public domain software and has no license restrictions.

G95 0.50 +g95 I G95 Fortran 95 compiler. G95 is open source, public domain software and has no license restrictions.

Intel 8 8.1 +intel-compilers I L Default version of the Intel compiler suite, including the IDB debugger. The compilers are under a 2 concurrent user license. To request use of the profiling tool, send email to systems@lcrc.anl.gov. The Intel suite is available for use by any person with an active Jazz account.

Intel 7 7.1,7.0 +intel-7.1,
+intel-7.0 I L Version 7 of the Intel compiler suite, including the IDB debugger and MKL libraries. The libraries have unlimited usage and the compilers are under a 2 concurrent user license. To request use of the profiling tool, send email to systems@lcrc.anl.gov. The Intel suite is available for use by any person with an active Jazz account.

Intel 6 6.0.1.304 +intel-6.0.1.304 I L Version 6 of the Intel compiler suite. The compilers are under a 2 concurrent user license. To request use of the profiling tool, send email to systems@lcrc.anl.gov. The Intel suite is available for use by any person with an active Jazz account.

Absoft 9.0 +absoft-9.0 I L Absoft Fortran compilers. Up to 4 instances of the Absoft compiler suite may be in use at any time. Use of this compiler suite is available to any person with an active Jazz account. Activation of new versions automatically retires prior versions on the system. Priority will be given to STAR-CD users should the need arise.

NAG 5.0 +nag-f95-5.0 I L NAG F95 compiler. Up to 2 instances of the nag compiler suite may be in use at any time. Use of this compiler suite is available to any person with an active Jazz account. Activation of new versions automatically retires prior versions on the system.

Totalview 6.7.0 +totalview I L Totalview is a commerical parallel debugger. This package is limited in number of seats and number of processors. Up to two instances may be run at any given time, using up to 16 processors. Activation of new versions automatically retires prior versions on the system. Totalview is available to any person with an active Jazz account.

Valgrind 2.2.0 +valgrind I Valgrind is a memory management tool that checks for memory leaks. Valgrind is open source, public domain software and has no license restrictions.

Jumpshot 4 +jumpshot I Jumpshot and the associated slog2 file utilities allow you to visualize the MPI (and other) library calls in your code.

Programming Libraries

Application Version Softenv Key Marks Notes

MPICH 1.2.6 @default I No info available yet

MPICH-GM 1.2.6..13b @default I MPICH-GM is Myricom's version of MPICH.

PVM 3.4.4 +pvm I PVM (Parallel Virtual Machine) is a software package for hooking a heterogeneous collection of Unix and/or Windows computers by a network to be used as a single large parallel computer.
PVM is not well supported at this time. http://www.netlib.org/pvm3/book/node1.html

Geospatial Data Abstraction Library (GDAL) 1.6 +python-openev I GDAL is a translator library for raster geospatial data formats. Freely available.

eGenix.com mx BASE Python Library 2.0.4 +python-egenix-mx-base I Python library for fast text processing, date/time processing and web site programming. Freely available.

Global Array (GA) 3.3.1 +global-arrays I "The Global Arrays (GA) toolkit provides and efficient and portable 'shared-memory' programming interface for distributed-memory computers."

Scientific Applications

Application Version Softenv Key Marks Notes

Matlab 13.1 +matlab I L MATLAB is an integrated technical computing environment that combines numeric computation, advanced graphics and visualization, and a high-level programming language. Activation of new versions immediately retires prior versions on the system. Up to 2 instances may be used at any time. MATLAB is available for use by any person with an active Jazz account.

IDL 5.6 +idl I L Interactive Data Language (IDL) is an interactive, high-level language used to analyize data visually. Up to 1 instance may be used at any time. This is a restricted use package. Users are given access to the software on per-user basis. To request use of the IDL package, send email to systems@lcrc.anl.gov.

Gaussian 98 @all-g98 I L Gaussian 98 is a connected series of programs for performing semi-empirical, density functional theory and ab initio molecular orbital calculations. Gaussian 98 requires the use of the PGI compiler. This is a restricted use package. Users are given access to the software on a per-user basis. To request use of the Gaussian package, send email to systems@lcrc.anl.gov. Use of this package is restricted to non-commercial research.
G98 is now installed and working for both parallel and serial. Please read the documentation accessible through the application name link.

STAR-CD 3.27.052 +starcd or @all-star I L STAR-CD is a Computational Fluid Dynamics code that uses proprietary numerical schemes for steady and transient simulations. It can accept almost any mesh structure and/or cell shape making it ideal for adaptive meshing. Other specialist options include rotating systems, buoyancy-driven flows and combustion modelling. User-supplied subroutines are also available.
STAR-CD requires the use of the Absoft compiler. This is a restricted use package. Access to the software is provided on per-user basis. To request use of STAR-CD, send email to systems@lcrc.anl.gov.

Materials Studio (MSI) 2.2 +msi I L Materials Studio is a scientific software environment for running computational materials science simulations. It was purchased by CMT and is only available for use by members of that division.

Network Common Data Format (NetCDF) 3.6.0-p1 +netcdf or @climate I Platform independent data storage for storing array data, along with associated metadata. Freely available under the terms of the UCAR/Unidata license.

NetCDF Operators (NCO) 2.9.9 +nco or @climate I Operators for manipulating NetCDF data. Freely available under the terms of the GPL. Useful for anyone using NetCDF data.

Ncview 1.92d +ncview or @climate I Ncview is a graphical viewer for NetCDF files. Freely available under the terms of the GPL.

MM5 to NetCDF Convertor NA +mm5-netcdf or @climate I Converts PSU/NCAR MM5 binary output data to the NetCDF format. Freely available to anyone, without license.

VASP 4.6.25 +vasp-4.6.25 R VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.

Parallel Total Energy (PEtot) 2 (not in softenv) I From the PEtot web page, "PEtot stands for parallel total Energy (Etot). It is a parallel plane wave pseudopotential program for atomistic total energy calculation based on density functional theory. It is designed for large system simulations to be run on large parallel computers like IBM SP machines at NERSC, and linux cluster machines. It is developed under U.S. Department of Energy fundings and it is a freely distributed public source code. It has a LBNL BSD license, which means that you can use it and change it for noncommercial purposes. However, we will not be responsible for any potential problems it might cause directly or indirectly due to the running of this code."

Climate Data Analysis Tools (CDAT) 3.3 +cdat I A Python library for manipulating climate data in NetCDF format. Also includes a GUI called "vcdat" which allows you to quickly visualize NetCDF files. Freely available.

Visualization ToolKit (VTK) 4.2 +vtk I VTK is "an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world." It's written in C++ but also has wrappers for Tcl/Tk and Python.

I - Installed and supported W - On list to be installed

P - Installation difficulties R - Requested, waiting approval

C - Use with caution; see notes L - Licenced, restricted use; see notes

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System Utilities and Tools
Application	Version	Softenv Key	Marks		Notes
SoftEnv	1.4.2	@default	I		SoftEnv is used to specify which applications are set up in a user's environment.
Globus	2.2.4	+globus	I		Globus provides the tools to build computational grids.
Portable Batch Scheduler (PBS)	5.4	@default	I		PBS provides the interface between user jobs and the Jazz compute nodes.
QBank	2.10.4	@default	I		QBank is the allocations manager for Jazz.
Condor	6.6.10	@default	W		Condor provides the interface between user jobs and the Jazz compute nodes that are not currently in use by regular PBS jobs.
Subversion	1.0.9	+subversion	I		Subversion is a freely available replacement for CVS and can be used for source code versioning.
Compilers & Debuggers
Application	Version	Softenv Key	Marks		Notes
PGI	5.2	+pgi-5.2	I	L	Portland Group, Inc. (PGI) compiler suite for F90 (pf90), F77, C, C++. Up to 5 instances of the pgi compiler suite may be in use at any time. Use of this compiler suite is available to any person with an active Jazz account. Activation of new versions automatically retires prior versions on the system. Priority will be given to Gaussian users should the need arise.
GCC 3	3.2.3	+gcc-compilers	I		Default version of the standard GNU compiler suite used on Jazz. Includes C, C++, F77 and Java compilers. GCC is open source, public domain software and has no license restrictions.
GCC 4	4.0.2	+gcc-4.0.2	I		Version 4 of the standard GNU compiler. Includes C, C++, F95 and Java compilers. GCC is open source, public domain software and has no license restrictions.
G95	0.50	+g95	I		G95 Fortran 95 compiler. G95 is open source, public domain software and has no license restrictions.
Intel 8	8.1	+intel-compilers	I	L	Default version of the Intel compiler suite, including the IDB debugger. The compilers are under a 2 concurrent user license. To request use of the profiling tool, send email to systems@lcrc.anl.gov. The Intel suite is available for use by any person with an active Jazz account.
Intel 7	7.1,7.0	+intel-7.1, +intel-7.0	I	L	Version 7 of the Intel compiler suite, including the IDB debugger and MKL libraries. The libraries have unlimited usage and the compilers are under a 2 concurrent user license. To request use of the profiling tool, send email to systems@lcrc.anl.gov. The Intel suite is available for use by any person with an active Jazz account.
Intel 6	6.0.1.304	+intel-6.0.1.304	I	L	Version 6 of the Intel compiler suite. The compilers are under a 2 concurrent user license. To request use of the profiling tool, send email to systems@lcrc.anl.gov. The Intel suite is available for use by any person with an active Jazz account.
Absoft	9.0	+absoft-9.0	I	L	Absoft Fortran compilers. Up to 4 instances of the Absoft compiler suite may be in use at any time. Use of this compiler suite is available to any person with an active Jazz account. Activation of new versions automatically retires prior versions on the system. Priority will be given to STAR-CD users should the need arise.
NAG	5.0	+nag-f95-5.0	I	L	NAG F95 compiler. Up to 2 instances of the nag compiler suite may be in use at any time. Use of this compiler suite is available to any person with an active Jazz account. Activation of new versions automatically retires prior versions on the system.
Totalview	6.7.0	+totalview	I	L	Totalview is a commerical parallel debugger. This package is limited in number of seats and number of processors. Up to two instances may be run at any given time, using up to 16 processors. Activation of new versions automatically retires prior versions on the system. Totalview is available to any person with an active Jazz account.
Valgrind	2.2.0	+valgrind	I		Valgrind is a memory management tool that checks for memory leaks. Valgrind is open source, public domain software and has no license restrictions.
Jumpshot	4	+jumpshot	I		Jumpshot and the associated slog2 file utilities allow you to visualize the MPI (and other) library calls in your code.
Programming Libraries
Application	Version	Softenv Key	Marks		Notes
MPICH	1.2.6	@default	I		No info available yet
MPICH-GM	1.2.6..13b	@default	I		MPICH-GM is Myricom's version of MPICH.
PVM	3.4.4	+pvm	I		PVM (Parallel Virtual Machine) is a software package for hooking a heterogeneous collection of Unix and/or Windows computers by a network to be used as a single large parallel computer. PVM is not well supported at this time. http://www.netlib.org/pvm3/book/node1.html
Geospatial Data Abstraction Library (GDAL)	1.6	+python-openev	I		GDAL is a translator library for raster geospatial data formats. Freely available.
eGenix.com mx BASE Python Library	2.0.4	+python-egenix-mx-base	I		Python library for fast text processing, date/time processing and web site programming. Freely available.
Global Array (GA)	3.3.1	+global-arrays	I		"The Global Arrays (GA) toolkit provides and efficient and portable 'shared-memory' programming interface for distributed-memory computers."
Scientific Applications
Application	Version	Softenv Key	Marks		Notes
Matlab	13.1	+matlab	I	L	MATLAB is an integrated technical computing environment that combines numeric computation, advanced graphics and visualization, and a high-level programming language. Activation of new versions immediately retires prior versions on the system. Up to 2 instances may be used at any time. MATLAB is available for use by any person with an active Jazz account.
IDL	5.6	+idl	I	L	Interactive Data Language (IDL) is an interactive, high-level language used to analyize data visually. Up to 1 instance may be used at any time. This is a restricted use package. Users are given access to the software on per-user basis. To request use of the IDL package, send email to systems@lcrc.anl.gov.
Gaussian 98		@all-g98	I	L	Gaussian 98 is a connected series of programs for performing semi-empirical, density functional theory and ab initio molecular orbital calculations. Gaussian 98 requires the use of the PGI compiler. This is a restricted use package. Users are given access to the software on a per-user basis. To request use of the Gaussian package, send email to systems@lcrc.anl.gov. Use of this package is restricted to non-commercial research. G98 is now installed and working for both parallel and serial. Please read the documentation accessible through the application name link.
STAR-CD	3.27.052	+starcd or @all-star	I	L	STAR-CD is a Computational Fluid Dynamics code that uses proprietary numerical schemes for steady and transient simulations. It can accept almost any mesh structure and/or cell shape making it ideal for adaptive meshing. Other specialist options include rotating systems, buoyancy-driven flows and combustion modelling. User-supplied subroutines are also available. STAR-CD requires the use of the Absoft compiler. This is a restricted use package. Access to the software is provided on per-user basis. To request use of STAR-CD, send email to systems@lcrc.anl.gov.
Materials Studio (MSI)	2.2	+msi	I	L	Materials Studio is a scientific software environment for running computational materials science simulations. It was purchased by CMT and is only available for use by members of that division.
Network Common Data Format (NetCDF)	3.6.0-p1	+netcdf or @climate	I		Platform independent data storage for storing array data, along with associated metadata. Freely available under the terms of the UCAR/Unidata license.
NetCDF Operators (NCO)	2.9.9	+nco or @climate	I		Operators for manipulating NetCDF data. Freely available under the terms of the GPL. Useful for anyone using NetCDF data.
Ncview	1.92d	+ncview or @climate	I		Ncview is a graphical viewer for NetCDF files. Freely available under the terms of the GPL.
MM5 to NetCDF Convertor	NA	+mm5-netcdf or @climate	I		Converts PSU/NCAR MM5 binary output data to the NetCDF format. Freely available to anyone, without license.
VASP	4.6.25	+vasp-4.6.25	R		VAMP/VASP is a package for performing ab-initio quantum-mechanical molecular dynamics (MD) using pseudopotentials and a plane wave basis set. The approach implemented in VAMP/VASP is based on a finite-temperature local-density approximation (with the free energy as variational quantity) and an exact evaluation of the instantaneous electronic ground state at each MD-step using efficient matrix diagonalization schemes and an efficient Pulay mixing.
Parallel Total Energy (PEtot)	2	(not in softenv)	I		From the PEtot web page, "PEtot stands for parallel total Energy (Etot). It is a parallel plane wave pseudopotential program for atomistic total energy calculation based on density functional theory. It is designed for large system simulations to be run on large parallel computers like IBM SP machines at NERSC, and linux cluster machines. It is developed under U.S. Department of Energy fundings and it is a freely distributed public source code. It has a LBNL BSD license, which means that you can use it and change it for noncommercial purposes. However, we will not be responsible for any potential problems it might cause directly or indirectly due to the running of this code."
Climate Data Analysis Tools (CDAT)	3.3	+cdat	I		A Python library for manipulating climate data in NetCDF format. Also includes a GUI called "vcdat" which allows you to quickly visualize NetCDF files. Freely available.
Visualization ToolKit (VTK)	4.2	+vtk	I		VTK is "an open source, freely available software system for 3D computer graphics, image processing, and visualization used by thousands of researchers and developers around the world." It's written in C++ but also has wrappers for Tcl/Tk and Python.

I - Installed and supported	W - On list to be installed
P - Installation difficulties	R - Requested, waiting approval
C - Use with caution; see notes	L - Licenced, restricted use; see notes