Question about the application
Clicked A Few Times
2:58:27 PM PST - Tue, Nov 6th 2012
Hi all,

This is my first post on this community. I have a "technical" question about the NWChem software. Is it considered as an I/O intensive application or it is more of compute (i.e. CPU) intensive?

Thanks...

Forum Vet
3:17:15 PM PST - Tue, Nov 6th 2012
That's a difficult question to answer. Many of our default algorithms use disk and can become I/O intensive. However, those same algorithms can be directed to do "direct" calculations, avoiding disk and becoming compute intensive. A third variable is when you run in parallel, where the network bandwidth and latency can become an issue for certain algorithms.

Thanks,

Bert


Quote:Dhaminah Nov 6th 9:58 pm
Hi all,

This is my first post on this community. I have a "technical" question about the NWChem software. Is it considered as an I/O intensive application or it is more of compute (i.e. CPU) intensive?

Thanks...

Clicked A Few Times
3:24:31 PM PST - Tue, Nov 6th 2012
Thanks Bert,

Let's neglect the network for the moment and assume we're running the application on a single machine with local storage - disk - across the many cores available. Would the type of storage play a significant role on the application performance. As an example, if we are using the RAM (by creating filesystems from the RAM storage available) vs using regular HDD; is this going to make any difference?

Quote:Bert Nov 6th 2:17 pm
That's a difficult question to answer. Many of our default algorithms use disk and can become I/O intensive. However, those same algorithms can be directed to do "direct" calculations, avoiding disk and becoming compute intensive. A third variable is when you run in parallel, where the network bandwidth and latency can become an issue for certain algorithms.

Thanks,

Bert


Quote:Dhaminah Nov 6th 9:58 pm
Hi all,

This is my first post on this community. I have a "technical" question about the NWChem software. Is it considered as an I/O intensive application or it is more of compute (i.e. CPU) intensive?

Thanks...

Forum Vet
6:14:01 PM PST - Tue, Nov 6th 2012
If disk is used it is because the data does not fit in memory anymore, so your example does not apply. NWChem will use as much of the RAM as is available, then resorts to storing the rest on disk, and if there is not enough disk it will recompute. For many systems, disks are very slow so storing in memory followed by recomputing is often faster.

But, do not assume you will have spare RAM to put a disk file system on.

Are you trying to decide what to buy to run NWChem on?

Bert



Quote:Dhaminah Nov 6th 10:24 pm
Thanks Bert,

Let's neglect the network for the moment and assume we're running the application on a single machine with local storage - disk - across the many cores available. Would the type of storage play a significant role on the application performance. As an example, if we are using the RAM (by creating filesystems from the RAM storage available) vs using regular HDD; is this going to make any difference?

Quote:Bert Nov 6th 2:17 pm
That's a difficult question to answer. Many of our default algorithms use disk and can become I/O intensive. However, those same algorithms can be directed to do "direct" calculations, avoiding disk and becoming compute intensive. A third variable is when you run in parallel, where the network bandwidth and latency can become an issue for certain algorithms.

Thanks,

Bert


Quote:Dhaminah Nov 6th 9:58 pm
Hi all,

This is my first post on this community. I have a "technical" question about the NWChem software. Is it considered as an I/O intensive application or it is more of compute (i.e. CPU) intensive?

Thanks...

Clicked A Few Times
2:48:32 PM PST - Wed, Nov 7th 2012
Thanks again Bert,

I'm trying to improve the application by improving the I/O performance. That said, the very first question that I want to answer is whether the disk performance is actually a bottelneck and that if we improve it the overall application performance will get improved as well. Does that make sense to you?

Can I have your email, please?


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