AceCloud Documentation

How to Setup AceCloud

Sign Up to AWS

AceCloud uses your existing Amazon Web Services account for its compute power. If you don’t yet have an AWS account, register at this site. You will need to supply credit card details for billing purposes.

Install the AceCloud Client Software

For the full AceCloud experience, including automatic execution on EC2 and transparent scaling to large numbers of simulations, the AceCloud client software must be installed on your workstation and configured to use your Amazon account. The AceCloud client is currently automatically installed when installing HTMD. Installation instructions can be found at this page.

Configuring AceCloud

AceCloud requires configuration before it can be used. Once the software is installed, run the command:

acecloud --setup

This will open two browser windows. In the first, complete any login prompt and then subscribe to the AceCloud Amazon Marketplace product. Follow the instructions in the termination window to obtain AWS access credentials from the page opened in the second window.

How to Use AceCloud

The AceCloud client runs ACEMD and Gromacs simulations on Amazon AWS resources. It performs all file copying and VM instantiation operations automatically - once configured with AWS access credentials the user does not need to interact directly with the AWS Console. The syntax for all AceCloud operations is given by:

acecloud --help

Running simulations

AceCloud can run any ACEMD or GROMACS (version 5) simulation, subject to the following restrictions:

  • All necessary files put reside in the submission directory or in a sub-directory thereof.
  • For ACEMD, the input file must be called input
  • For GROMACS, the input file must be called topol.tpr

To submit a simulation to AceCloud, first, prepare the input in a directory, and then run:

acecloud --submit [group/name] [directory-name]

where [group/name] is a two-level identifier for the simulation (example: project2/run10). Regardless, the submitted simulation is named using the absolute path of the submission directory. The simulation results will be retrieved back to the submission directory, so multiple submissions from the same directory are not permitted.

Checking simulations progress

Check the progress of simulations with:

acecloud --status

This summarizes all simulations, grouped by project. Simulations will be in one of the following states:

  • PENDING: Simulation has yet to start running
  • RUNNING: Simulation is in progress
  • COMPLETED: Simulation has finished running and results are ready to retrieve
  • PREEMPTED: Simulation has terminated early due to spot market pre-emption of the AWS instance.

Retrieving simulations results

The output of a simulation becomes available once the job is complete. To retrive it, run:

acecloud --retrieve [group/name]

The output is automatically placed in the directory from which the input files were originally obtained. Original files be recreated if no longer there.

Important Notes on AWS use

  • We recommend running short (less than 3 days) simulations with frequent restarts, rather than one long simulation. AceCloud uses AWS Spot Instances. Spot instance pricing is variable depending on demand. Rarely, in times of peak demand, the spot price may exceed the default AceCloud bid price of 0.70$ and the running simulations may be aborted and results lost. Current spot pricing can be displayed running:
acecloud --print-spots
  • The price that you pay is the current spot price, not the price you have set as the maximum bid.
  • The total output of an AceCloud simulation is limited to 1 GB. No check is made that this has been exceeded, please ensure that you have configured the simulation correctly to not exceed this.
  • AWS accounts have a default limit of 10 concurrent spot instances. If you need to run more instances, higher limits can be requested per-region via the AWS Console here

AceCloud (c) Acellera - no redistribution in whole or part

 Syntax: acecloud [--profile [config-profile]] [args]:

   --submit [group/name] [directory]  [--spot | --ondemand]  :
   --delete [group/name]         :
   --status [group/name]         :
   --retrieve [group/name]       :
   --print-config                : Show AWS configuration
   --print-spots                 : Show Current spot prices
   --profile [name]              : Add to above to select AWS
                                   Config section in config file
   --costcode [code]             : Used for tagging instances
   --setup                       : Perform first-time software setup
   --help

This software requires a subscription to the AceCloud AWS Marketplace product
available from https://aws.amazon.com/marketplace/pp/B01N3SBK3Z