EAS PC Cluster User Guide

This page is a bare-bones user manual for the PCP cluster. Please send comments about missing, incorrect or confusing information to support eas slu edu /P>

General Overview

The EAS cluster1 is a 9-node PC cluster for parallel (MPI) and serial (task-farm) computation. The front end, bora.eas.slu.edu, is used for interactive work (e.g., editing, compiling, and submitting jobs). The compute nodes (b01, b02, ..., b08) are managed through the Portable Batch System (PBS) and you should not log into them.

Login access to bora should be through ssh. Insecure access through telnet or rsh is not allowed. Security is an important concern on the x86 cluster (as it is on all EAS systems) so please be careful. Please read the EAS policy on passwords. Login access to the compute nodes should be through PBS only.

The default login shell is bash.

The standard environment setup is in /home/defaults/bashrc. Your .bashrc file should already include this file. This should allow you to do everything described here without modifying your environment. All man pages should also be accessible by default. When software changes on the cluster, we will automatically update the global bashrc to reflect the changes. If you don't source the global file, your programs may stop working. If you find that we missed something that should be in the global file, please let us know rather than changing just your own environment.

The cluster is running the PGI CDK Cluster Development Kit It includes pghpf, pgf90, pgf77, pgc++, pgcc, pgdbg, and pgprof.

Online documentation is available via netscape

under the URL file:/usr/pgi/doc/index.htm

Compiling Code with MPICH

We do not provide the mpi(compiler) scripts. There are too many ways that these can cause confusion. There is an installed version on mpich

that was provided with the PGI CDK. To use that you add the library name to the compile line or the makefile library line.

An example from the mpihello program:

pgf77 -o mpihello mpihello.f -lfmpich -lmpich

The fmpich library provides the fortran hooks to the mpich library.

Description of node attributes

Node attributes on the EAS cluster are all the same:

512 MB RAM

1200 MB swap

1 GB/sec Ethernet

Software available on the cluster:

This rest of this page provides a brief introduction to the software available on the cluster. Some of this software is part of the Cluster Development Kit (CDK) and some is specific to the EAS cluster. EAS-specific software is labelled (EAS).

Unless otherwise noted, the software can be accessed by adding /usr/local/pkg/[package-name]/bin to your $PATH variable. Source code, if any, can be found in /usr/local/src/[package-name].

For packages available in multiple versions, /usr/local/{src,pkg}/[package-name] is usually a symbolic link to the most recent version. Other versions can usually be accessed directly using the package name with the appropriate version number appended (e.g. /usr/local/pkg/package-3.1).

(label) [package-name] description of package

• (EAS) [acroread] Adobe Acrobat reader

• (CDK) [asci] Libraries of Basic Linear Algebra Subroutines (BLAS) and extended precision arithmetic (real*10, real*20) tuned for Intel Pentium (from the ASCI project at Sandia National Lab). These are the standard subroutines for vector and matrix operations used across the high performance computing industry. You can access these routines by adding -lblas -lextprecision to your compile or link command. This is licensed software and must not be redistributed. Source code for the tuned routines is not available.

• (EAS) [gcc] RedHat version of the GNU compiler system. This is a symlink to a recent (hopefully stable) version of the GCC suite of compilers, which includes C++, C, Fortran77, compilers.

• (CDK) [lapack] LAPACK library for dense linear algebra. You can access these routines by adding -llapack -lblas to your compile or link command. Documentation is at Netlib, on the LAPACK page.

• (CDK) [mpich] Message Passing Interface (MPI) implementation from Argonne National Lab. This is the standard package for parallel programming on a CDK cluster. You must use the special mpif77, mpif90, mpicc, mpiCC compiler commands to compile and link MPI programs. By default, the PGI Fortran compilers and GNU C compilers are used. You should use the PBS qsub command to run a program built with MPI. Man pages are in /usr/local/pkg/mpich/man. The MPI standard and other info can be found at the MPICH home page.

• (CDK) [pbs] Portable Batch System. This package controls access to the compute nodes of the x86 cluster. Contains the important qsub and qstat commands. Some details about PBS on the EAS cluster can be found here. Commands and man pages are available by default. Try man pbs to start. Additional general info about PBS can be found at the PBS home page.

• (CDK) [pgi] Portland Group compilers for C++, C, Fortran and HPF (pgCC, pgcc, pgf77, pgf90, pghpf). Also a profiler and debuggers (pgprof, pgdbx, Xpgdbx). All commands are available by default. These compilers tend to produce code that is faster than the code produced by the GNU compilers. This is licensed software. You can install the package on another system. Ask Eric Haug for installation info. Man pages are available for all commands (try man -k portland). Additional documentation is at file:/net/bora/usr/pgi/doc/index.htm If your web browser cannot access this page, run netscape from bora.eas.slu.edu instead of your local system.

Terms of use on the cluster

Users are guaranteed no level of service on this cluster. This cluster is a development system. We cannot make any guarantees to cluster availability. We use this cluster to test device drivers and operating system software, so you should expect it to be a bit unstable. We do, occasionally, lose user data and user jobs. We will sometimes shut the cluster down without notification. If you need results for a conference tomorrow, or need your data backed up nightly, you should use another system. Last modified: 30 Sep 2002
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