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Finding Help and Documentation

Once you have connected to the AVIDD head node successfully, you may need to look up system documentation at times.

AVIDD is a very standard Linux and so documentation can be found in all the standard places. First there is a man directory in /usr. This is one of the traditional UNIX locations for this directory and it is frequently linked to /usr/share/man on other systems, but not on the AVIDD cluster. You will find manual entries in this directory that refer to GPFS the General  Parallel File System. The most important ones talk about manipulating ACLs, Access  Control Lists, on GPFS.

Most standard Linux commands, including GNU  compilers, have their manual entries in /usr/share/man. However, X11  applications and libraries live in a separate directory tree of their own in /usr/X11R6 and there they have their own manual directory in /usr/X11R6/man.

There is also a directory tree in /usr called local and some system applications are installed there together with their documentation. You will find their manual entries in /usr/local/share/man. There is also a directory /usr/local/man, which contains documentation for the PBS system, installed in /usr/pbs.

Program man reads  file /etc/man.config (you can read it too) in order to find about locations of various manuals. If a directory that contains some manuals, e.g., /usr/local/share/man, is not mentioned on that file, you will have to invoke the command with the -M switch, e.g.,

$ man -M /usr/local/share/man root

Apart from manual entries there are also additional documents and sometimes even tutorials in various doc directories. There is a doc directory in /usr/share and another one in /usr/local/share.

The GNU project distributes  its  documentation in the info format for reading with emacs and with a stand-alone program info. There may be more than one info directories on a system, in which case they should be declared on a file called default.el in the main Emacs Lisp directory. The main Emacs Lisp directory on the AVIDD head nodes is /usr/share/emacs/21.2/lisp, but there is no default.el there  (at the time I'm writing this section). If you need to add more info directories, you can redefine the emacs info directory list in your .emacs file as follows:

(setq Info-default-directory-list
   '( "/usr/share/info/"
      "/usr/share/texmf/info/" ))
or you can append a directory to the existing path like this:
(setq Info-default-directory-list
   (nconc Info-default-directory-list
      (list "/usr/share/maxima/info")))

A source of great wisdom is always the /etc/motd file. This file will flash on every connection to the cluster unless you create a file .hushlogin in your AVIDD home directory.

There  is also a WWW page that describes the AVIDD cluster and you will find it at There is a nice photograph of one of the blade racks on this page too.

I asked the AVIDD administrators to mount this page at a more obvious WWW location, e.g., or just, but I was told by a gentleman  named Craig Stewart that ``doing something with web addresses as you suggest becomes entirely beyond our capabilities.'' So there.

Other very important systems, like MPI, have their own directory trees. For example, the Argonne  MPI  system, MPICH, lives in /usr/local/mpich and extensive MPI documentation can be found in /usr/local/mpich/gcc/doc or in /usr/local/mpich/intel70/doc (depending on whether you want to use GNU or Intel compiler for your MPI applications). Corresponding manual pages live in /usr/local/mpich/gcc/man and /usr/local/mpich/intel70/man respectively.

LAM MPI, a system  developed at the Ohio  Supercomputer Center, which is currently maintained by Indiana University, lives in /usr/local/lam-7.0 and you will find its man pages there too.

HDF-4.1 with its man pages can be found in /usr/local/hdf.

HDF5, ROMIO (a version of MPI IO that  works with MPICH) and parallel DB2 are  not installed on the AVIDD cluster yet. But I'll put a note here as soon we have the software.

next up previous index
Next: Working with Data on Up: Working with the AVIDD Previous: Connecting to the AVIDD
Zdzislaw Meglicki