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ddt

Table of Content

Version and Availability
About
Usage
Resources

Versions and Availability

Module Names for ddt on qb3

Machine	Version	Module Name
qb3	19.1.4	ddt/19.1.4

▶ Module FAQ?

The information here is applicable to LSU HPC and LONI systems.

Shells

A user may choose between using /bin/bash and /bin/tcsh. Details about each shell follows.

/bin/bash

System resource file: /etc/profile

When one access the shell, the following user files are read in if they exist (in order):

~/.bash_profile (anything sent to STDOUT or STDERR will cause things like rsync to break)
~/.bashrc (interactive login only)
~/.profile

When a user logs out of an interactive session, the file ~/.bash_logout is executed if it exists.

The default value of the environmental variable, PATH, is set automatically using Modules. See below for more information.

/bin/tcsh

The file ~/.cshrc is used to customize the user's environment if his login shell is /bin/tcsh.

Modules

Modules is a utility which helps users manage the complex business of setting up their shell environment in the face of potentially conflicting application versions and libraries.

Default Setup

When a user logs in, the system looks for a file named .modules in their home directory. This file contains module commands to set up the initial shell environment.

Viewing Available Modules

The command

$ module avail

displays a list of all the modules available. The list will look something like:

--- some stuff deleted ---
velvet/1.2.10/INTEL-14.0.2
vmatch/2.2.2

---------------- /usr/local/packages/Modules/modulefiles/admin -----------------
EasyBuild/1.11.1       GCC/4.9.0              INTEL-140-MPICH/3.1.1
EasyBuild/1.13.0       INTEL/14.0.2           INTEL-140-MVAPICH2/2.0
--- some stuff deleted ---

The module names take the form appname/version/compiler, providing the application name, the version, and information about how it was compiled (if needed).

Managing Modules

Besides avail, there are other basic module commands to use for manipulating the environment. These include:

add/load mod1 mod2 ... modn . . . Add modules
rm/unload mod1 mod2 ... modn  . . Remove modules
switch/swap mod . . . . . . . . . Switch or swap one module for another
display/show  . . . . . . . . . . List modules loaded in the environment
avail . . . . . . . . . . . . . . List available module names
whatis mod1 mod2 ... modn . . . . Describe listed modules

The -h option to module will list all available commands.

▶ Did not find the version you want to use??

If a software package you would like to use for your research is not available on a cluster, you can request it to be installed. The software requests are evaluated by the HPC staff on a case-by-case basis. Before you send in a software request, please go through the information below.

Types of request

Depending on how many users need to use the software, software requests are divided into three types, each of which corresponds to the location where the software is installed:

The user's home directory

Software packages installed here will be accessible only to the user.
It is suitable for software packages that will be used by a single user.
Python, Perl and R modules should be installed here.

/project

Software packages installed in /project can be accessed by a group of users.
It is suitable for software packages that
- Need to be shared by users from the same research group, or
- are bigger than the quota on the home file syste.
This type of request must be sent by the PI of the research group, who may be asked to apply for a storage allocation.

/usr/local/packages

Software packages installed under /usr/local/packages can be accessed by all users.
It is suitable for software packages that will be used by users from multiple research groups.
This type of request must be sent by the PI of a research group.

How to request

Please send an email to sys-help@loni.org with the following information:

Your user name
The name of cluster where you want to use the requested software
The name, version and download link of the software
Specific installation instructions if any (e.g. compiler flags, variants and flavor, etc.)
Why the software is needed
Where the software should be installed (locally, /project, or /usr/local/packages) and justification explaining how many users are expected.

Please note that, once the software is installed, testing and validation are users' responsibility.

About the Software

Arm DDT is a cross-platform debugging tool, compatible with most flavors of Linux on Intel x86_64 (Xeon), IBM Power, NVIDIA CUDA, and Arm hardware.

Usage

DDT requires X-windows to function, so the local machine must have an X11 server installed and running.

▶ X11 FAQ?

From *nix

Since ssh and X11 are already on most client machines running some sort of unix (Linux, FreeBSD, etc), one would simply use the following command:

% ssh -X -Y username@remote.host.tdl

Once successfully logged in, the following command should open a new terminal window on the local host:

% xterm&

An xterm window should appear. If this is not the case, email us.

From Mac OS X

An X11 service is not installed by default, but one is available for installation on the OS distribution disks as an add-on. An alternative would be to install the XQuartz version. Make sure the X11 application is running and connect to the cluster using:

% ssh -X -Y username@remote.host.tdl

From Windows

Microsoft Windows does not provide an X11 server, but there are both open source and commercial versions available. You also need to install an SSH client. Recommended applications are:

MobaXterm - a Windows ssh client with X11 server integrated (recommended)
Xming - a Windows X11 server
PuTTY - a Windows ssh client

When a PuTTY session is created, make sure the "X11 Forwarding Enabled" option is set, and that the X11 server is running before starting the session.

Testing

Once Xming and puTTY have been set up and in stalled, the following will provide a simple test for success:

start Xming
start puTTY
connect to the remote host (make sure puTTY knows about Xming for this host)

Once successfully logged in, the following command should open a new terminal window on the local host:

% xterm&

An xterm window should appear. If this is not the case, refer to "Trouble with Xming?" or email us.

Note About Cygwin

Cygwin is still a useful environment, but is too complicated and contains too many unnecessary parts when all one wants is to interface with remote X11 sessions.

Advanced Usage

The most important connection that is made is from the user's client machine to the first remote host. One may "nest" X11 forwarding by using the ssh -XY command to jump to other remote hosts.

For example:

1. on client PC (*nix or Windows), ssh to remotehost1

2. on remotehost1 (presumably a *nix machine), ssh -XY to remotehost2

3. on remotehost2 (presumably a *nix machine), ssh -XY to remotehost3

...

8. on remotehost8 (presumably a *nix machine), ssh -XY to remotehost9

9. on remotehost9, running an X11 application like xterm should propagate the remote window back to the initial client PC through all of the additional remote connects.

Compile the program with debugging enabled. This typically requires using the -O0 and -g command line switches.
When using a version of MVAPICH2 newer than 1.2, there are two versions of the MPI task manager to choose from. One uses the MPD daemons and the other uses a mechanism based on SSH. The latter is preferred as it gives much better scaling performance at high process counts. To specify its use, set the DDTMPIRUN environment variable to the absolute path of the launch manager you wish to use (if you use mpirun the mpd daemons must be managed manually):

$ export DDTMPIRUN=`which mpirun_rsh`

or

$ export DDTMPIRUN=`which mpirun`

Resources

DDT Users Guide is available on line.

Last modified: September 10 2020 11:58:50.

ddt