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piny-md

About

PINY_MD is a molecular dynamics simulation tool.

Version and Availability

Softenv Keys for piny-md on painter
Machine Version Softenv Key
painter Aug 30 2005 +piny-md-intel-11.1-mvapich-1.1
▶ Display Softenv Keys for piny-md all clusters
Machine Version Softenv Key
eric Aug 30 2005 +piny-md-intel-11.1-mvapich-1.1
qb Aug 30 2005 +piny-md-intel-11.1-mvapich-1.1
oliver Aug 30 2005 +piny-md-intel-11.1-mvapich-1.1
louie Aug 30 2005 +piny-md-intel-11.1-mvapich-1.1
poseidon Aug 30 2005 +piny-md-intel-11.1-mvapich-1.1
painter Aug 30 2005 +piny-md-intel-11.1-mvapich-1.1
▶ Softenv FAQ?

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

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

Using the softenv command, a user may view the list of available packages. Currently, it can not be ensured that the packages shown are actually available or working on the particular machine. Every attempt is made to present an identical environment on all of the LONI clusters, but sometimes this is not the case.

Example,

$ 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
....
Listing of Available Packages

See Packages Available via SoftEnv on LSU HPC and LONI.

For a more accurate, up to date list, use the softenv command.

Caveats

Currently there are some caveats to using this tool.

  1. packages might be out of sync between what is listed and what is actually available
  2. resoft and soft utilities are not; to update the environment for now, log out and login after modifying the ~/.soft file.
Availability

softenv is available on all LSU HPC and LONI clusters to all users in both interactive login sessions (i.e., just logging into the machine) and the batch environment created by the PBS job scheduler on Linux clusters and by loadleveler on AIX clusters..

Packages Availability

This information can be viewed using the softenv command:

% softenv
Managing Environment with 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

Usage

Usage requires invoking the PINY_MD command and providing it with the name of an input file as an argument. Generically, it looks like:

    $ piny_md_machine sim_input
  

To find the name assigned to the executable, use the soft-dbq to examine the softenv key used for PINY. It will give the path to executable. For instance:

$ soft-dbq +piny-md-intel-11.1-mvapich-1.1
     
This is all the information associated with
the key or macro +piny-md-intel-11.1-mvapich-1.1.

-------------------------------------------

Name: +piny-md-intel-11.1-mvapich-1.1
Description: @types: Applications @name: piny-md @version: Aug 30,
2005 @build: mvapich-1.1-intel-10.1 @about: PINY_MD(c) is a
multipurpose, object-oriented molecular simulation package developed
as a collaborative effort between Indiana University, New York
University and the University of Pennsylvania.
Flags: none
Groups: none
Exists on: Linux

-------------------------------------------

On the Linux architecture,
the following will be done to the environment:

  The following environment changes will be made:
    PATH = ${PATH}:/usr/local/packages/piny-md/intel-11.1-mvapich-1.1/bin
$ ls /usr/local/packages/piny-md/intel-11.1-mvapich-1.1/bin
piny_md_par

This shows the path to PINY_MD and the existance of a single executable name piny_md_par. The _par indicates it is a parallel build, and the key name shows it was built with mvapich 1.1.

Setting up a simulation is the hard part of using the program. For guidance there, please refer to the Resources below.

Resources

Last modified: March 31 2014 12:21:36.