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paraview

About

Paraview is an open-source, multi-platform data analysis and visualization application.

Versions and Availability

Softenv Keys for paraview on supermike2
Machine Version Softenv Key
supermike2 4.4.0 +Paraview-4.4.0-Intel-13.0.0-openmpi-1.6.2
▶ Softenv 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):

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

Softenv

SoftEnv is a utility that is supposed to help users manage complex user environments with potentially conflicting application versions and libraries.

System Default Path

When a user logs in, the system /etc/profile or /etc/csh.cshrc (depending on login shell, and mirrored from csm:/cfmroot/etc/profile) calls /usr/local/packages/softenv-1.6.2/bin/use.softenv.sh to set up the default path via the SoftEnv database.

SoftEnv looks for a user's ~/.soft file and updates the variables and paths accordingly.

Viewing Available Packages

The command softenv will provide a list of available packages. The listing will look something like:

$ softenv
These are the macros available:
*   @default
These are the keywords explicitly available:
+amber-8                       Applications: 'Amber', version: 8 Amber is a
+apache-ant-1.6.5              Ant, Java based XML make system version: 1.6.
+charm-5.9                     Applications: 'Charm++', version: 5.9 Charm++
+default                       this is the default environment...nukes /etc/
+essl-4.2                      Libraries: 'ESSL', version: 4.2 ESSL is a sta
+gaussian-03                   Applications: 'Gaussian', version: 03 Gaussia
... some stuff deleted ...
Managing SoftEnv

The file ~/.soft in the user's home directory is where the different packages are managed. Add the +keyword into your .soft file. For instance, ff one wants to add the Amber Molecular Dynamics package into their environment, the end of the .soft file should look like this:

+amber-8

@default

To update the environment after modifying this file, one simply uses the resoft command:

% resoft

The command soft can be used to manipulate the environment from the command line. It takes the form:

$ soft add/delete +keyword

Using this method of adding or removing keywords requires the user to pay attention to possible order dependencies. That is, best results require the user to remove keywords in the reverse order in which they were added. It is handy to test out individual keys, but can lead to trouble if changing multiple keys. Changing the .soft file and issuing the resoft is the recommended way of dealing with multiple changes.

Usage

Sample usage for remote visualization:

  1. Start ParaView server pvserver on the cluster using compute node, do *not* start pvserver from the head node, e.g.:
    qsub -I -l nodes=1:ppn=20,walltime=1:00:00 -q workq -A your_allocation_name
    
    After you get the interactive session, start your pvserver from the *compute node*, e.g. smicXXX:
    module load paraview/4.3.1/INTEL-140-MVAPICH2-2.0
    mpirun -np 8 pvserver --server-port=11111
    
    *For unknown reason you might need to limit the number of pvserver process to 8
  2. Establish an SSH tunnel:
    Use the following command from your *local* terminal, note that the compute node number smicXXX should be the name of your compute node:
    ssh -L11111:smicXXX:11111 -N your_user_name@smic.hpc.lsu.edu
    
    Type your password and leave the terminal open.
  3. Connect to the remote server using ParaView on your desktop:
    Start the same version of paraview as installed on cluster, e.g. Pavaview 4.3.1 from your *local* terminal and use File > Connect to the forwarded localhost port.

Please refer to Resources section for more detailed usage information.

Resources

Last modified: June 25 2015 20:36:54.