Applications

From Molecular Modeling Wiki

Contents 1 General Information 1.1 Scope of this page 1.2 Parallel calculations 1.3 List 2 Turbomole 5.10 / 6.0 3 Amber 10

General Information

Scope of this page

The description of applications on this page is valid for newer clusters starting from lithium, through uranium, barium, thallium, and newer. It is also partially valid for francium and helium, but there may be some differences.

Parallel calculations

Multiprocessor clusters are built to be able to run calculations in a parallel way. However, using parallel calculations on a cluster requires a special approach when integrating parallelized applications with a queueing system, and almost each application needs to be configured and tuned individually. It is necessary to follow strict rules to use the cluster in an efficient way - please read the application notes below to find specific demands of the installed applications.

List

Turbomole 5.10 / 6.0 [1]
Amber 10 [2]

Turbomole 5.10 / 6.0

The TurboMole program is supplied in a form of binary files (no source code) which are compiled and linked with an HP implementation of MPI libraries, what imposes strict requiements to the environment setup of parallel calculations. TurboMole needs to have some variables defined and files created to be able to run in parallel, especially when parallel run across machines is reqired.

To submit a parallel TurboMole job:

1. Copy a sample script /usr/local/programs/common/turbomole/turbomole-5.10/sub/dscf_sample_mp or /usr/local/programs/common/turbomole/turbomole-6.0/sub/dscf_sample_mp to your data directory and rename it.
2. Edit the script and modify the part starting with a comment MODIFY HERE; do not modify other parts, unless you know what you do.
3. If your TuboMole control file contains $scfintunit section, specify the file location as file=/scratch/<username>/<filename> where <username> is your login name and <filename> is an arbitrary file name. Please note that saving the file into your home directory will most likely lead to a very slow calculation and may even cause entire cluster slowdown.
4. Submit the calculation with

   qsub -q <queue_name> -pe hpmpi <n> <scriptname>

   where <queue_name>is a queue name, <n> is a number of processors, and <scriptname> is a name of the script you used in step 1.

Note:

Please note that parallel environment (the parameter you enter after -pe option in qsub) for TurboMole is hpmpi (not mpi) - these two environments may not be interchanged!

To submit a single-processor TurboMole job:

1. Copy a sample script /usr/local/programs/common/turbomole/turbomole-5.10/sub/dscf_sample_sp or /usr/local/programs/common/turbomole/turbomole-6.0/sub/dscf_sample_sp to your data directory and rename it.
2. Edit the script and modify the part starting with a comment MODIFY HERE; do not modify other parts, unless you know what you do.
3. If your TuboMole control file contains $scfintunit section, specify the file location as file=/scratch/<username>/<filename> where <username> is your login name and <filename> is an arbitrary file name. Please note that saving the file into your home directory will most likely lead to a very slow calculation and may even cause entire cluster slowdown.
4. Submit the calculation with

   qsub -q <queue_name> <scriptname>

   where <queue_name> is a queue name, <n> is a number of processors, and <scriptname> is a name of the script you used in step 1.

Note:

The older TurboMole versions (before 5.10) use different system of parallel libraries and thus cannot be run (in multiprocessor mode) the same way as decribed above. Please contact us if you need to run older version in parallel.

Amber 10

The Amber suite consists of a set of programs and utilities. It is generaly impossible to create a universal submission script, so it is user's responsibility to prepare a script and submit it properly.

To submit a parallel Amber job:

1. Copy a sample script /usr/local/programs/common/amber/amber10/sub/amber_sample_mp to your data directory and rename it.
2. Edit the script and modify the part starting with a comment MODIFY HERE; do not modify other parts, unless you know what you do.
3. Submit the calculation with

   qsub -q <queue_name> -pe mpi_alt <n> <scriptname>

   where <queue_name> is a queue name, <n> is a number of processors, and <scriptname> is a name of the script you used in step 1.
4. Please note that parallel environment for Amber is mpi_alt (not mpi) and that it is not the same as for TurboMole (mpi_alt versus hpmpi) - these two environments may not be interchanged!

To submit a single-processor Amber job:

1. Copy a sample script /usr/local/programs/common/amber/amber10/sub/amber_sample_sp to your data directory and rename it.
2. Edit the script and modify the part starting with a comment MODIFY HERE; do not modify other parts, unless you know what you do.
3. Submit the calculation with

   qsub -q <queue_name> <scriptname>

   where <queue_name> is a queue name and <scriptname> is a name of the script you used in step 1.