Home » portaltest page » Using CIPRES Resources

Using CIPRES Resources

CIPRES provides access to compute resources are made available by the US National Science Foundation as part of its mission to provide cyberinfrastructure for the advancement of Science. Gateways are unique in offering any scientist the opportunity to easily access some of the best computational resources in the world. At present, users receive 1,000 hours of ACCESS resources through CIPRES as part of a six month free trial. More time is available on a subscription basis.

Our use policies are provided here.

If you see a message you don't understand, let us know. We provide some tools to monitor job progress. If your job fails, the most efficient way to describe the problem to us is shown here:

Configuring Your Job for optimal running:
ACCESS resources improve performance by dividing up jobs into multiple individual processes, and mapping them across as many processors as possible while still maintaining a sensible benefit. We have benchmarked the codes offered by CIPRES to determine how jobs of various sizes can be run most efficiently.  We have distilled this information into a few user-parameters that describe your data set. When you upload your data, we abstract as much of this information as possible, and use it to run job as efficiently as possible.

Setting the time of your job:
The time you enter in this box sets the number of clock hours the job will be allowed to run. The time you enter is the limit in clock time from the time your job begins to execute. The clock does not start immediately when you submit, but when your job reaches the end of the queue and begins to run.

How long can I run?:
Jobs that use CPUs may be configured to run for as much as 168 hours. Jobs that use GPUs are limited to 120 hours. Many jobs can be restarted. If you need a longer run than the interface allows, please let us know. There is generally no harm in overestimating your run time. We will reserve the time in your allocation while the job runs, but once the job is completed, your account will only be charged for the amount of time you actually use.

How long will my job run?  For many programs, you can try to figure out how long your run will take by performing some test runs with the data set you are analyzing. You can, for example, make two test MrBayes runs that require only a few generations (I usually use 1000 and 10000), take the run times, and make a line through them. The slope gives you the time per generation for this data set on this resource. Similarly, you can run bootstrapping tools for a few generations to get an idea of how long the run will take.

How does CIPRES charge for running jobs? When you submit a job, the application will evaluate the maximum total resource your run could take if it runs for the full configured time. This is the number of cores used times the maximum number of hours the job is set to run. For example, if your run uses 8 cores, and the max time is set for 168 hours, your run could take up to 1344 cpu hours. When you submit, the application will "reserve" 1344 hours in your account. If the job completes in 1 hour, the application will charge your account 8 hours (8 cores x 1 hour) and will "release" the remaining 1336 hours. While the job is running, if you have less than 1344 hours remaining in your account, you will not be able to submit a new job. Once the job completes, and the time is released, you will be able to submit again.

Status of ACCESS Resources: The success of your run will depend in part on whether or not the machine is "up" and running. You can use the links below to check the status of the machines. CIPRES jobs run on the ACCESS resource called Expanse. You can check its status, and for any planned maintenance here.

If there is a tool or a feature you need, please let us know.