Difference between revisions of "Desmond"

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== Description ==
== Description ==


''From the Desmond web site'': '''Desmond'''Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.  
''From the Desmond web site'': '''Desmond''' is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.  


{{AppStandardHeader|2016.2|desmond}}
{{AppStandardHeader|2016.2|desmond}}




== Running Desmond on CIRCE/SC ==
<br />
=== Using Desmond in Batch Mode ===


{{AppRunningOnCIRCE}}
The user manuals related to Desmond are essential to understanding the application and making the most of it.  The guides and this page should be all you need to get started with your simulations.


If, for example, you have a Dalton input file named dalton.in, and a molecule file named dalton.mol, you would set up a submit script like this:
{{SLURMAppParams}}


The script below (for testing, name it “dalton-test.sh”) can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.
*Desmond Documentation directory: /apps/desmond/2016.2/docs
*Desmond Users Guide: /apps/desmond/2016.2/docs/maestro/desmond_users_guide.pdf
*Quick Start Guides: /apps/desmond/2016.2/docs/maestro/desmond_quick_start/
 
If, for example, you have a Desmond input file named example.cfg, you would set up a submit script like this:
 
*The script below (for testing, name it "desmond-test.sh") can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue.  For help on submitting jobs to the queue, see our [[Guide_to_SLURM|SLURM User's Guide]]. Scripts are provided as examples only.  Your executables, tools, and options for SLURM will vary.


<pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#E0E0E0; color:black;">
<pre style="white-space:pre-wrap; width:55%; border:1px solid lightgrey; background:#E0E0E0; color:black;">
#!/bin/bash
#!/bin/bash
#
#
#SBATCH --comment=dalton-test
#SBATCH --comment=desmond-example
#SBATCH --ntasks=8
#SBATCH --ntasks=8
#SBATCH --job-name=dalton-test
#SBATCH --job-name=dalton-test
Line 22: Line 31:
#SBATCH --time=01:00:00
#SBATCH --time=01:00:00


#### SLURM 8 processor Dalton test to run for 1 hour.
#### Slurm 8 processor Desmond test to run for 1 hour.


module purge
module purge
module load apps/dalton/2.0
module load apps/desmond/2016.2
 
mpirun desmond --destrier mpi -tpp 1 --include example.cfg


mpirun dalton dalton.in dalton.mol
</pre>
</pre>
&nbsp;<br>
&nbsp;<br>
Next, you can change to your job’s directory, and run the sbatch command to submit the job:
 
*Then, you can change to your job's directory, and run the sbatch command to submit the job:


<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
[user@login0 ~]$ cd my/jobdir
[user@login0 ~]$ cd my/job/directory
[user@login0 jobdir]$ sbatch ./dalton-test.sh</pre>
[user@login0 jobdir]$ sbatch .desmond-test.sh/</pre>


*You can view the status of your job with the “squeue -u <username>” command
*You can view the status of your job with the “squeue -u <username>” command


{{Documentation}}
=== Using Desmond Graphical Interfaces on CIRCE/SC ===
*Dalton Home Page
'''Please Note: Interactive Desmond processing/simulation jobs lasting more than 30 minutes should be run in an SRUN session, NOT on the login nodes.'''
**http://dirac.chem.sdu.dk/daltonprogram.org
 
*Dalton User's Guide
{{X11Connection}}
**http://daltonprogram.org/www/resources/dalton2013manual.pdf
 
** /opt/apps/dalton/2.0/dalton20manual.pdf
1. Next, start an interactive SRUN session by running the command below with example resources:
 
<pre style="white-space:pre-wrap; width:70%; border:1px solid lightgrey; background:#000000; color:white;">
[user@login0 ~]$ srun --time=02:00:00 --nodes=1 --cpus-per-task=8 --pty /bin/bash
</pre>
 
This will request an interactive session on a compute node, with 8 processor cores, for a duration of 2 hours. For help on submitting jobs to the queue, see our [[Guide_to_SLURM|SLURM User's Guide]].
 
2. If all goes well, you should get dropped into an interactive shell on the execution host (this may take some time depending on system usage). You will now need to load the Desmond module as described above and then start the Maestro interface:
 
<pre style="white-space:pre-wrap; width:45%; border:1px solid lightgrey; background:#000000; color:white;">
[user@login0 ~]$ module add apps/desmond/2016a
[user@login0 ~]$ maestro
</pre>
 
3. Once you are finished, you can simply type "exit" at the Linux command prompt to exit the SRUN session.


{{BKETOR}}
{{BKETOR}}
*Dalton Known Tests
*Available Desmond Tutorials
**/opt/apps/dalton/2.0/tests
**/apps/desmond/2016.2/tutorials


{{AppStandardFooter}}
{{AppStandardFooter}}

Latest revision as of 14:23, 31 May 2022

Description

From the Desmond web site: Desmond is a software package developed at D. E. Shaw Research to perform high-speed molecular dynamics simulations of biological systems on conventional commodity clusters, general-purpose supercomputers, and GPUs. The code uses novel parallel algorithms and numerical techniques to achieve high performance and accuracy on platforms containing a large number of processors, but may also be executed on a single computer.

Version

  • 2016.2

Authorized Users

  • CIRCE account holders
  • RRA account holders
  • SC account holders

Platforms

  • CIRCE cluster
  • RRA cluster
  • SC cluster

Modules

Desmond requires the following module file to run:

  • apps/desmond/2016.2


Running Desmond on CIRCE/SC


Using Desmond in Batch Mode

The user manuals related to Desmond are essential to understanding the application and making the most of it. The guides and this page should be all you need to get started with your simulations.

  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.
  • Desmond Documentation directory: /apps/desmond/2016.2/docs
  • Desmond Users Guide: /apps/desmond/2016.2/docs/maestro/desmond_users_guide.pdf
  • Quick Start Guides: /apps/desmond/2016.2/docs/maestro/desmond_quick_start/

If, for example, you have a Desmond input file named example.cfg, you would set up a submit script like this:

  • The script below (for testing, name it "desmond-test.sh") can be copied into your job directory (the folder with your input files) and modified so that you can submit batch processes to the queue. For help on submitting jobs to the queue, see our SLURM User's Guide. Scripts are provided as examples only. Your executables, tools, and options for SLURM will vary.
#!/bin/bash
#
#SBATCH --comment=desmond-example
#SBATCH --ntasks=8
#SBATCH --job-name=dalton-test
#SBATCH --output=output.%j.dalton-test
#SBATCH --time=01:00:00

#### Slurm 8 processor Desmond test to run for 1 hour.

module purge
module load apps/desmond/2016.2

mpirun desmond --destrier mpi -tpp 1 --include example.cfg

 

  • Then, you can change to your job's directory, and run the sbatch command to submit the job:
[user@login0 ~]$ cd my/job/directory
[user@login0 jobdir]$ sbatch .desmond-test.sh/
  • You can view the status of your job with the “squeue -u <username>” command

Using Desmond Graphical Interfaces on CIRCE/SC

Please Note: Interactive Desmond processing/simulation jobs lasting more than 30 minutes should be run in an SRUN session, NOT on the login nodes.

Establishing a GUI connection to CIRCE/SC

To use Desmond, you will need to connect to CIRCE/SC with GUI redirection, either using:

  • CIRCE/SC Desktop Environment
  • SSH with X11 redirection
    • If connecting from OSX or Linux via SSH, please ensure that you use one of the following commands to properly redirect X11: 
      • [user@localhost ~]$ ssh -X circe.rc.usf.edu
        or
      • [user@localhost ~]$ ssh -X sc.rc.usf.edu

1. Next, start an interactive SRUN session by running the command below with example resources: 

[user@login0 ~]$ srun --time=02:00:00 --nodes=1 --cpus-per-task=8 --pty /bin/bash

This will request an interactive session on a compute node, with 8 processor cores, for a duration of 2 hours. For help on submitting jobs to the queue, see our SLURM User's Guide.

2. If all goes well, you should get dropped into an interactive shell on the execution host (this may take some time depending on system usage). You will now need to load the Desmond module as described above and then start the Maestro interface: 

[user@login0 ~]$ module add apps/desmond/2016a
[user@login0 ~]$ maestro

3. Once you are finished, you can simply type "exit" at the Linux command prompt to exit the SRUN session.

Benchmarks, Known Tests, Examples, Tutorials, and Other Resources

  • Available Desmond Tutorials
    • /apps/desmond/2016.2/tutorials

More Job Information

See the following for more detailed job submission information:

Reporting Bugs

Report bugs with Desmond to the IT Help Desk: rc-help@usf.edu

Retrieved from "https://wiki.rc.usf.edu/index.php?title=Desmond&oldid=2711"