CCL: Remote access to high performance computing

[Renier Dreyer <renier.dreyer(-)crunchyard.com>]

Hi All

As mentioned there are numerous online providers.

There are however some differences that I would like to point out:

1) Some cloud based providers such as Amazon and Google virtualize their environment through a hypervisor. This means that you are sharing the actual hardware with other users as well as the extra overhead of the hypervisor.

2) Network speeds are 10GbE for these providers across their entire netowrk.

3) I would agree that for small simulations (4 cores) it is better to invest in a good desktop or server.

For large simulation that require many cores, this means that simulation will run between 7 and 10 times slower than running on a dedicated HPC system. HPC systems also provide immediate access to 100's or thousands of cores.

The cost per simulation would then also be much more expensive.

For example:

Running a 64 water molecule CP2K simulation on a 32 core compute instance on AWS take 45 minutes. Running the same simulation on CrunchYard takes 7 minutes using 4 cores.

AWS cost: US$1.12

CrunchYard cost commercial: US$ 0.2

CrunchYard cost academic: US$ 0.02

Additionally there is no setup and management needed for CrunchYard as all submissions are through the website portal with packages pre-installed (for advanced users there is a scripting option :)

Kind Regards

Renier

On Sun, May 10, 2015 at 2:21 AM, Brian Skinn bskinn#,#alum.mit.edu <owner-chemistry]^[ccl.net> wrote:

All,

I utilized the free trial offer for Google Cloud Compute to evaluate its cost structure for computational chemistry applications (ORCA quantum calculations, to be exact).   It ended up being far more economical to just buy a refurbished server to run at home, rather than rent the CPU time from somewhere else.  Of course, this is in large part because I have sufficient familiarity with Linux to configure, administer and maintain such a server.  If that expertise is not available to you, renting the CPU time may well be the better deal.  If CrunchYard does not support the computational software you require, you should be able to install just about anything onto a G Cloud Instance.

Google Compute tracks the free trial by giving a $300 account credit and then just billing normally.  For my own records, I tracked the decrease in funds over my testing period.  I've laid that data into a Google Spreadsheet; it can be viewed here.  I've enabled comments for all viewers, so if anyone has questions feel free to either email me at bskinn-AT-alum-DOT-mit-DOT-edu, or to tag comments into the sheet.

Amazon Web Services is another big player for cloud computing.  I surveyed their pricing briefly; I think Google's services would end up being less expensive, but in large part I went with Google's trial offer because it was much easier to get it started & I think the terms were less restrictive.

Good luck,

Brian

On Sat, May 9, 2015 at 5:40 PM, Computational Chemist computationalchemist++ymail.com <owner-chemistry(-)ccl.net> wrote:

Thank you Sergio, Victor, Chris and Wojciech for replying.

I am doing this research at Alexandriah University, Egypt. I want to do comparable molecular dynamics simulations on three HCV protease genotypes. For each simulation, I need 4 processors with  2GB RAM for each processor. I expect the calculations to take 6-8 months. I can use AMBER or Gomacs or NAMD.

 Thank you,

Dina

On Saturday, May 9, 2015 10:35 PM, Wojciech Kolodziejczyk dziecial**icnanotox.org <owner-chemistry**ccl.net> wrote:

The answer is YES they are.

2015-05-09 13:45 GMT-05:00 Jim Kress jimkress35=gmail.com <owner-chemistry###ccl.net>:

I recommend (and use) CrunchYard:

https://www.crunchyard.com/default.aspx

 

Jim

 

> From: owner-chemistry+jimkress35==gmail.com(!)ccl.net [mailto:owner-chemistry+jimkress35==gmail.com(!)ccl.net] On Behalf Of Computational Chemist computationalchemist * http://ymail.com/" target="_blank">ymail.com
Sent: Saturday, May 09, 2015 11:03 AM
To: Kress, Jim
Subject: CCL: Remote access to high performance computing

 

Dear All,

 

I need more computer resources so that I can do large scale molecular dynamics simulations. Are there any high performance computing centers that provide international access for users through application, proposals, fees...etc

 

Thank you so much.

 

Dina