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Supercomputing Environments

File Systems
Dot Files
Compiling Systems
Parallel Environments

Access [Back to top]

Before anyone can access a high performance computing system at OSC, they must have a valid account for the given system. To apply for an account, see Accounts.

Once you have an account, use the ssh command to access the systems. See the table below for appropriate hostnames.

Table 1. Hostnames and Operating Systems

System	Hostname	Operating System
Itanium 2 Cluster	ipf-login1.osc.edu	LINUX
Glenn	glenn.osc.edu	LINUX

Environment [Back to top]

All high performance computing systems at OSC run a flavor of UNIX. For more information, see Table 1.

File Systems

Each user is assigned a permanent file area known as their home filesystem.

On all of the machines users share the same home filesystem that is mounted from our Mass Storage System. Your home area is the same whenever you login to any one of those systems.

In addition to your home areas, each system has a temporary area known as /tmp. On the cluster systems, /tmp is not shared between nodes. This is typically a very large area where users may execute codes that produce large intermediate files. A few items to note about /tmp are

the system removes files last accessed more than 24 hours previously
there are no disk charges associated with /tmp
files on /tmp are not backed-up by the system
files on /tmp cannot be migrated to tape

When using /tmp, either create a directory under /tmp with the same name as your userid or use the TMPDIR environment variable which is automatically assigned a unique directory name for the duration of an interactive or batch session.

Dot Files

The Center provides a few basic skeleton files to help you get started. These files are often referred to as dot files because they begin with a ".". Typically, they do not appear in a directory listing. To display a listing of these files, use ls -a command. The files are

.forward: File containing your local e-mail address.; Note: the system and the center often rely on communications via e-mail. If your local e-mail address changes, please change the contents of the .forward file.
.profile: Start-up shell script for Korn, POSIX, and Bourne shell users. Users may modify this file to add/override any environment variables or conventions that were established by the system. For a list of current environment variables on a given system, enter the env command.
.login: Start-up shell script for C shell users. Users may modify this file to add/override any environment variables or conventions that were established by the system. For a list of current environment variables on a given system, enter the env command.
.cshrc: Start-up shell script for C shell users that is executed each time a new C shell is invoked. Users may modify this file to establish variables and aliases.; Note: A similar file for Korn shell users is identified with the ENV environment variable set in the .profile script.

Do not redefine your PATH environment variable without including ${PATH}. If you hard-code your PATH, it will break the modules software which all of the OSC systems use to make software packages available, and as a result you may not be able to compile or submit batch jobs. The following is a better way to modify your PATH variable:

Korn shell (.profile): PATH="${PATH}:${HOME}/bin"
export PATH
C shell (.cshrc): setenv PATH ${PATH}:${HOME}/bin

For most systems, the default shell (command processor) is the Korn shell. To change the default shell, contact oschelp@osc.edu.

Compiling Systems

Table 2. Compiling Systems and Commands

System	Compiling
System	System	Command
Itanium 2 Cluster	Fortran	ifort
Itanium 2 Cluster	C and C++	icc
Glenn	Fortran	g77 ifort (Intel) pgf90 (PGI) mpif77 mpif90
Glenn	C and C++	gcc / g++ icc (Intel) pgcc (PGI) pgCC (PGI) mpicc

Parallel Environments

Table 3 provides a summary of the parallel environments and types of memory available on the high-performance computers at OSC.

Table 3. Parallel Environments

System	Programming Models	Memory
Itanium 2 Cluster	automatic (-parallel) assisted HPF MPI OpenMP	distributed between nodes shared between two processors in a node
Glenn	Portland group:automatic (-Mconcur) Intel:automatic (-parallel) assisted HPF MPI OpenMP	distributed between nodes shared between two processors in a node

Batch Processing [Back to top]

The following links go to sample batch requests for the given system.

Table 4. Batch Processing

System	Batch System	Submit	Monitor	Delete
Itanium 2 Cluster	PBS	qsub	qstat	qdel
Glenn	PBS	qsub	qstat	qdel

Performance Analysis and Optimization [Back to top]

Performance analysis and tuning is an important part of code development, particularly for large, resource-limited applications. Optimization allows you to get results quicker and/or minimize resource consumption. For general information on measuring code performance, including typical and ideal performance characteristics of the OSC machines, and basic optimization strategies, see:

The links in Table 5 provide basic information on the most useful performance analysis tools available on the OSC systems, including ways of determining standard performance metrics, e.g., the MFLOP rating.

Table 5. Performance Analysis Tools