[gmx-users] Re: Gromacs on "HPC workstations" ?

Nicola Fantini nicola.fantini at cloudbroker.com
Wed Apr 18 15:54:18 CEST 2012

Dear Jonathan,

as there is a growing number of cloud providers offering HPC resources,
cloud solutions are becoming certainly an attractive alternative compared to
the purchase of your own equipment.

The prime criteria for choosing either option should be your expected
distribution of workload over time. If you expect to have a constant, high
workload, having your own equipment might be more cost effective. Local cost
(system engineering, adequate space, electricity cost, ...) and availability
will have a major influence on this. However, if your workload is periodic,
has spikes or you cannot predict it at all for the next few years, cloud is
definitively an option, either for all of the processing or just for burst

The typical cost of running a 64-cores machine is approximately 2-3$ per
hour, which adds up to 250$ - 400$ for 5 days, including the complete
hardware infrastructure and hardware operation. Cloud infrastructure
providers often do not give detailed information on their actual hardware
but refer rather to reference infrastructure / equivalents, as they usually
offer access to virtual machines on shared hardware. However, for HPC
purposes there are also cloud and on demand offerings that provide access to
physical machines, with the corresponding detailed hardware information

Regarding making Gromacs work in the cloud, you can either setup and operate
your own cloud infrastructure using an Infrastructure as a Service (IaaS)
provider or use an existing Software as a Service (SaaS) offering directly
making Gromacs or other applications available as a service via the
internet. Both service types are charged pay-per-use, with the pricing
schemes depending on the provider, functionality, service levels, support,
etc. SaaS offerings may be slightly more expensive, but have the advantage
that you do not need to worry at all about the cloud infrastructure setup
and operations, but can focus on using Gromacs.

Based on our experience in developing our own cloud platform and making
applications like Gromacs available in the cloud, you should consider for a
cloud solution:
- variety / specification of accessible hardware, for example for jobs of
different size
- deployment of Gromacs (and perhaps other MD applications) on the cloud
- mechanism to provision and de-provision the resources, avoiding idle
resources and thus unnecessary costs
- scalability mechanism if more than one resource is being used
- setup of a queuing system to optimally utilize the resources
- command line and/or web browser access to the application to run jobs
- scripting possibilities / programmatic access (API), if desired
- fault tolerance mechanisms for larger/many jobs
- file transfer and storage mechanisms
- security / encryption if confidential data are involved
- authentication and accounting if managing multiple users
- pricing and charging mechanisms of the cloud provider (credit card,
prepaid, monthly bill, etc.)
- access only to external resources or also to internal ones (e.g., private

Another alternative to above will be web portal / gateway solutions such as
the ones developed in the EU FP7 project SCI-BUS (http://www.scibus.org),
which offers access to both academic cluster and grid infrastructures as
well as to public and private cloud infrastructures and will have ready to
use applications and workflows.

Hope this helps! Please do not hesitate to contact me in case you have any

Best regards,


P.S.: By the way, we are currently seeking Gromacs use cases / demo cases
for our cloud platform. If you are interested to look into this in more
detail, please contact me directly.

Nicola Fantini
CloudBroker GmbH
Technoparkstrasse 1 CH-8005 Zurich Switzerland
nicola.fantini at cloudbroker.com 
Mobile:  +41 79 355 02 17 Phone: +41 44 633 79 35


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