Larger Memory Models

Message boards : Number crunching : Larger Memory Models

To post messages, you must log in.

1 · 2 · Next

AuthorMessage
Paul

Send message
Joined: 29 Oct 05
Posts: 193
Credit: 64,858,035
RAC: 24
Message 86813 - Posted: 14 Jul 2017, 17:43:36 UTC

Is there a way to request work units that require large memory models? I now have a few systems with more than 1GB RAM per core and would like to see that RAM put to good use. Currently the largest work unit I have is using about 650MB and most are using less than 400MB.
Thx!

Paul

ID: 86813 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator

Send message
Joined: 22 Aug 06
Posts: 4018
Credit: 0
RAC: 0
Message 86815 - Posted: 15 Jul 2017, 14:54:11 UTC

Not at this time. But, with the new servers in place, that sort of change should now be more approachable than it was previously.
Rosetta Moderator: Mod.Sense
ID: 86815 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Paul

Send message
Joined: 29 Oct 05
Posts: 193
Credit: 64,858,035
RAC: 24
Message 86823 - Posted: 18 Jul 2017, 10:44:57 UTC - in response to Message 86815.  

I looked at one of my machines this morning & it had at least 10 processes using more than 1GB of RAM each! I thought the project team just started throwing me larger processes. This is the fist time I have seen my machine using more than 32GB of RAM. I love to see better resource utilization.
Thx!

Paul

ID: 86823 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator

Send message
Joined: 22 Aug 06
Posts: 4018
Credit: 0
RAC: 0
Message 86826 - Posted: 18 Jul 2017, 13:49:26 UTC

That was more of a coincidence. However, on occasion, there are tasks that require more memory, and rather than allocating them to a specific subgroup, the Project Team was able to precent them from going out to systems with low memory. With the new servers, they may be able to make the scheduler more proactive in assigning such tasks.
Rosetta Moderator: Mod.Sense
ID: 86826 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Sam

Send message
Joined: 27 Dec 10
Posts: 7
Credit: 8,710,442
RAC: 17
Message 86832 - Posted: 21 Jul 2017, 3:31:20 UTC - in response to Message 86826.  

I would love to volunteer my machines to have the resource intensive work units =D

Will this be possible on the new servers?
ID: 86832 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile David E K
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 1 Jul 05
Posts: 1018
Credit: 4,334,829
RAC: 0
Message 86836 - Posted: 21 Jul 2017, 17:13:41 UTC

This is my fault. I was asked by someone in the lab to increase the length limit on Robetta, our publicly available structure prediction server, so I did but since realized the memory issue. I've reverted the length limit until we can figure out a good approach to handle them. Sorry. There may still be some jobs left over. These are medically relevant targets.
ID: 86836 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Mod.Sense
Volunteer moderator

Send message
Joined: 22 Aug 06
Posts: 4018
Credit: 0
RAC: 0
Message 86850 - Posted: 25 Jul 2017, 14:36:54 UTC
Last modified: 25 Jul 2017, 14:41:47 UTC

I caught these tasks using over 1GB of memory on Windows 7.
pq170720_Sh29_1_DHR09_000603_0050_C_0001...
D2D2F222xtal_AB_5_3gaf_3s55_0007_0001.pdb_unaD2D2F222_17_07_19_36_34_globalDocking_5_SAVE_ALL_OUT...
Rosetta Moderator: Mod.Sense
ID: 86850 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1686
Credit: 6,629,809
RAC: 98
Message 86859 - Posted: 26 Jul 2017, 13:32:44 UTC

It's a problem to introduce, in user profile's, a button with something like "Permit wus with high usage memory"??
Every user can decide or not to accept these wus.
ID: 86859 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile David E K
Volunteer moderator
Project administrator
Project developer
Project scientist

Send message
Joined: 1 Jul 05
Posts: 1018
Credit: 4,334,829
RAC: 0
Message 86862 - Posted: 26 Jul 2017, 17:59:09 UTC

On the list of things to do. great idea. I'll remind/alert the lab about the memory issues. thanks.
ID: 86862 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Juha

Send message
Joined: 28 Mar 16
Posts: 13
Credit: 705,034
RAC: 0
Message 86948 - Posted: 2 Aug 2017, 19:18:19 UTC - in response to Message 86862.  

There is no need to introduce a button for tasks with high memory usage. BOINC server already handles this out of the box. The server sends only such tasks to a host that have rsc_memory_bound less than the memory limit set in host's/user's computing preferences. If user doesn't want memory filled with tasks all he or she needs to do is lower the memory limit in computing preferences.

That does mean that the project needs to fill rsc_memory_bound accurately. The few tasks that I sampled had rsc_memory_bound=1e8 bytes but actual memory usage was 300-400 MB. Naughty.
ID: 86948 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Chilean
Avatar

Send message
Joined: 16 Oct 05
Posts: 711
Credit: 26,669,447
RAC: 0
Message 86950 - Posted: 2 Aug 2017, 20:42:51 UTC

On a related topic: I've found that current WUs use considerably less RAM than they did before. If I'm not wrong... R@H WUs used to take about half a GB per WU (thus the popular "1GB-per-core rule of thumb").
ID: 86950 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Trotador

Send message
Joined: 30 May 09
Posts: 108
Credit: 214,424,832
RAC: 0
Message 86959 - Posted: 3 Aug 2017, 16:29:28 UTC

The amount of memory used by each WU type varies widely as it depends on the simulation programmed by the scientific that created it.

Now, I'm seeing up to 1.3 Gb in many "yh170802_" units, close to 1GB in "JWdesRMf_closed_" units and around 200Mb in "A211_" ones
ID: 86959 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jim1348

Send message
Joined: 19 Jan 06
Posts: 881
Credit: 52,257,545
RAC: 2
Message 86962 - Posted: 3 Aug 2017, 19:19:23 UTC - in response to Message 86959.  

Now, I'm seeing up to 1.3 Gb in many "yh170802_" units,

Interesting. I never bothered to look before. But BoincTasks shows a "yh17802" using 1329 MB of real memory, and 1508 MB of virtual memory.
I suppose the "real memory" is the one to pay attention to for DRAM purposes. Fortunately, with 32 GB of main memory, it has not been an issue.
ID: 86962 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Trotador

Send message
Joined: 30 May 09
Posts: 108
Credit: 214,424,832
RAC: 0
Message 86966 - Posted: 4 Aug 2017, 9:58:18 UTC

New king :)

"JWC6-62dock-new..." up to 1,5Gb RAM occupation
ID: 86966 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Chilean
Avatar

Send message
Joined: 16 Oct 05
Posts: 711
Credit: 26,669,447
RAC: 0
Message 86969 - Posted: 4 Aug 2017, 12:55:20 UTC

I stand corrected... these "yh" WUs are definitely RAM hoarders.
ID: 86969 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
yhsia
Volunteer moderator
Project developer
Project scientist

Send message
Joined: 21 May 16
Posts: 2
Credit: 97,172
RAC: 0
Message 86973 - Posted: 4 Aug 2017, 20:02:07 UTC

Hi,

I'm the culprit behind the "yh..." jobs!
I apologize if it's causing any issues, I have set rsc_memory_bound to be 2gb, but I will set it higher in the future to make sure I don't top out anyone's computers.

These jobs are larger symmetrical proteins, we are testing a computational method to only "fold" a portion of the larger structure.
Even though we only modify a portion, there are just so many atoms there that it seems to eat up a lot of memory.

Thanks for your precious resources though!
Please do let us/me know if anything we do is causing problems.
ID: 86973 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
LarryMajor

Send message
Joined: 1 Apr 16
Posts: 22
Credit: 31,533,212
RAC: 1
Message 86974 - Posted: 4 Aug 2017, 23:37:30 UTC - in response to Message 86973.  

As others have mentioned, some of us have enough memory to run 2Gb jobs, and will gladly do it. If it works better for you guys, it might be worth designing a way for us to request such jobs.
ID: 86974 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile Chilean
Avatar

Send message
Joined: 16 Oct 05
Posts: 711
Credit: 26,669,447
RAC: 0
Message 86975 - Posted: 5 Aug 2017, 0:27:19 UTC

I have no problem running high-memory WUs :)
ID: 86975 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Profile [VENETO] boboviz

Send message
Joined: 1 Dec 05
Posts: 1686
Credit: 6,629,809
RAC: 98
Message 87014 - Posted: 8 Aug 2017, 16:05:14 UTC - in response to Message 86948.  

There is no need to introduce a button for tasks with high memory usage. BOINC server already handles this out of the box. The server sends only such tasks to a host that have rsc_memory_bound less than the memory limit set in host's/user's computing preferences. If user doesn't want memory filled with tasks all he or she needs to do is lower the memory limit in computing preferences.


I continue to prefer the idea of button in profile's page...
ID: 87014 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
Jim1348

Send message
Joined: 19 Jan 06
Posts: 881
Credit: 52,257,545
RAC: 2
Message 87015 - Posted: 8 Aug 2017, 17:32:45 UTC - in response to Message 87014.  
Last modified: 8 Aug 2017, 17:49:29 UTC

There is no need to introduce a button for tasks with high memory usage. BOINC server already handles this out of the box. The server sends only such tasks to a host that have rsc_memory_bound less than the memory limit set in host's/user's computing preferences. If user doesn't want memory filled with tasks all he or she needs to do is lower the memory limit in computing preferences.


I continue to prefer the idea of button in profile's page...


I think the profile page is a much better place for it too. Lowering the memory limit in computing preferences is a very clumsy way to do it, and most people would never think of it. Furthermore, it would apply to all projects you run, not just Rosetta.

I am all for using more memory too if some group of tasks can be run more efficiently that way. 3 GB would work for me. And I could do more if necessary by using an app_config.xml to limit the number run concurrently.
ID: 87015 · Rating: 0 · rate: Rate + / Rate - Report as offensive    Reply Quote
1 · 2 · Next

Message boards : Number crunching : Larger Memory Models



©2023 University of Washington
https://www.bakerlab.org