Posts by Stephen "Heretic"

1) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93867)
Posted 8 Apr 2020 by Stephen "Heretic"
Post:
8G RAM? Well, that means it can only be run in x64 systems. Ok, bye bye Rosetta.
You need up to 1.3GB RAM per Task you run.
So even a system with less than 4GB can run 2 Tasks.


. . If you have absolutely nothing else happening you could get away with 4GB, if you have only 2GB, rotsa ruck!

Stephen

. .
2) Message boards : Number crunching : Discussion on increasing the default run time (Message 93796)
Posted 8 Apr 2020 by Stephen "Heretic"
Post:
I'm getting 18-20 hour runs but F@H it's only 4 hours.


. . Different projects run different apps. It is not unusual for their task runtimes to differ greatly from one another. I have not tried Folding at Home but I suspect their apps/tasks require less time to do their thing. In R@H there is a preference setting for target run time and minimum run time, with v4.12 the default target is 8 hours, Rosetta Mini has a different default it seems. If you want to spend less time on each task you can reduce those settings. R@H creates multiple models called Decoys for each task, the run time you set will affect how many models are created when you run the task. I hope that helps.

Stephen

. .
3) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93794)
Posted 8 Apr 2020 by Stephen "Heretic"
Post:
A Windows XP pc connected to internet? A Pentium 4? Yeah.... well.... the problem seems self explanatory, too old...
Windows XP is horribly unsecure, at least switch to Linux.


Well. I'm currently living at my dad's place and this is his PC, the only one I can have. It still can run WUs from WCG and Asteroid@Home. The problem is not how powerful the PC is. It's why current Rosetta WUs don't work with it? Compatible issue? A month ago there was no problem, even my older PC, a PIII/WinXP, run Rosetta WUs pretty well.


. . They have revised the app from 4.07/4.08 to 4.12. This new version asks a bit more from the hardware and seems to be a bit of a memory hog, see the thread on use of memory and Rosetta. I have an i5 with 8GB ram and I have had problems getting it to run reliably. But there may be another cause.

Stephen

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4) Message boards : Number crunching : How might memory effect R@h processing? (Message 93616)
Posted 6 Apr 2020 by Stephen "Heretic"
Post:
The Rosetta tasks seem to run best with 2 GB per task, plus more for the CPU portion of any GPU task, plus more for the operating system. For 8 GB, two Rosetta tasks running at once is about the limit. If you have enough virtual cores, 16 GB should raise the limit to about 6 tasks.
This assumes that you don't let any BOINC tasks stay in memory while they are not running. Expect lower numbers if you do.
Filling both slots with the same model of memory board gives a little more speed than mismatched memory boards. You might also check if you can get faster memory boards that are compatible with your computer.
Some models of computers are compatible with memory boards that contain more memory.
Back when I first started with BOINC, I used this site to find compatible types of memory:

https://www.crucial.com/store/systemscanner

I now order any new computers with the largest and fastest memories that are compatible with that model.


. . This is an off the rack bargain package. At the moment I have upped the memory reserves to 85% when in use and 95% when idle, and I have disabled 'leave non-GPU tasks in memory when suspended" though I am not sure it would be causing problems. I will trial these settings and see if it will play nice.

. . I ran that link and it identifies the MoBo as an Akoya P5110D (H110) chipset. It says that it will support up to 16GB memory at up to DDR4-4000. I find it hard to believe this old MoBo could support memory that fast, but it is recommending a confusing array of memory stick options that has my mind reeling. The sad thing is they must all be USA prices, when I look up similar RAM locally it is double the prices quoted. But I would probably settle for a 16GB kit at DDR4-3000, most of that is backwards compatible with DDR4-2666 so I should be covered, I am not so sure it would support DDR4-3200.

. . Thanks for that link. it seems to have answered some questions.

Stephen

{edit} OK it is running AOK with those settings but I had to set BOINC to use 3 cores to get the second 64 bit task to run. This is not a problem to me as long as it does not crash again :) I ran Process Explorer again and system memory commit has increased to 6GB (from 5.5) but memory physically used is still at 3.4/3.5GB. The second Rosetta task is only using half the memory of the first but there is still plenty of head room within the reserved memory for it to increase. Fingers crossed ...
:)
{/edit}
. .
5) Message boards : Number crunching : How might memory effect R@h processing? (Message 93613)
Posted 6 Apr 2020 by Stephen "Heretic"
Post:
So in the end, with 32Gb Ram were you able to support all 22 tasks it was trying to run? Or did have to restrict it to any particular number?

I knocked it down to 16 x86_64 cpu tasks so I could run the three gpu tasks. If I tried to run more, I knocked gpu tasks offline with out of memory-postponed messages. That was with use 90% of memory while idle, 85% while active preferences. Was consuming a little shy of 30GB. The host is my daily driver.


. . So on a pro rata basis 8GB should suffice to run just 2 x x86_64 tasks and one GPU task with 90% available even when active.

Stephen

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6) Message boards : Number crunching : How might memory effect R@h processing? (Message 93612)
Posted 6 Apr 2020 by Stephen "Heretic"
Post:
Some of the ram merchants have a ram tester that will recommend the highest level of ram that a MB will support.
If you don't have a lot of cpu cores/threads running Rosetti@Home you should be able to run multiples of the task even if it is running up near 2GB per task on a 16GB ram MB. Lately mine have all been a lot smaller.
Tom


. . I tried CPUZ but it only shows what is installed not what is supported.

Stephen

:(
7) Message boards : Number crunching : How might memory effect R@h processing? (Message 93610)
Posted 6 Apr 2020 by Stephen "Heretic"
Post:
Task Manager, Processes tab, Memory column.
It can vary by several hundred MB depending on where in the Task it is at.
Although Process Explorer is probably better as it shows how much is also reserved, but not using at the time- it's values are higher than those shown in Task Manager.
A Task using 730MB in Task Manager shows as 760MB Private/ 783MB Working Set in Process Explorer.

It doesn't support 16GB DIMMs?
. . It is an old cheapy MSI MoBo. I have very little info but I am pretty sure when I bought it the max was 16GB.
Check the motherboard manual, it should list what capacity & speed DIMMs are supported.


, , With process manager is it the greater of the 2 values or the sum of the 2 values that is the memory rquirement?

Stephen

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8) Message boards : Number crunching : How might memory effect R@h processing? (Message 93608)
Posted 6 Apr 2020 by Stephen "Heretic"
Post:
Is the motherboard so old that it has a northbridge chipset?
That statement was probably true at the time since two channels of the highest density RAM DIMMS at the time was probably 8GB. Now RAM density is much higher per stick with 8GB and 16GB dies and dual rank DIMMS. I don't see how the motherboard could have any limitation on how much memory can be installed other than still only two channels. The limitation would be in the cpu.



. . It is a Medion computer, it has an MSI MoBo with no designation so I cannot get specs for it, it came with a booklet which basically said "congratulations on buying this computer" and little else (not sure where even that is now) but if I remember correctly the largest memory it supports is 8GB. I remember thinking 16GB should be enough if I have to expand it. But since it is shaping up that memory size is not the actual core problem then it is a moot point. Going on figures that others have posted I should not need more than 2GB each both for the GPU task and each of 2 CPU tasks so 8GB should be killing it, but that is not the case. After digging around I found Process Explorer just before getting Grant's reply and it showed the system Ram as 3.2GB physically in use and 5.4GB committed (not sure about that distinction but I presume it means that 5.4GB is reserved by current apps). E@H shows as 899MB private and 520MB as whatever. The Rosetta task was much lower at 289 Mb and 234 MB. But to me that says that the problem is NOT that 8GB is insufficient.

Stephen

:(
9) Message boards : Number crunching : How might memory effect R@h processing? (Message 93584)
Posted 6 Apr 2020 by Stephen "Heretic"
Post:
I would love to know just how much ram is needed to keep 2 64 bit Rosetta tasks happy and still support the GPU.

On my system, of 2 Tasks being processed by Rosetta v4.12 windows_x86_64, one is using 750MB of RAM, the other 320MB of RAM.

. . Well at those levels I should be AOK as is, the E@H tasks do not require more than 2GB of system ram so there is 5 GB or more left for Rosetta. But it aint happening. How are you seeing how much system ram each task is using?

It's similar to CPU & GPU work on Seti- there are no CPU or GPU tasks, just tasks. Same with the Rosetta v4.12 windows_intelx86 and Rosetta v4.12 windows_x86_64 applications. The Task is allocated to the Application when it is downloaded.

. . Thanks Grant, but I did know that.

The amount of required RAM depends on the Task, not the application being used.

. . That may be so but it does not fit the pattern I am seeing, so if it is not a memory insufficiency then there is something about the 64 bit app that does NOT like my machine. I need a way to preclude the 64 bit app from running to confirm this over a larger sample of tasks.

This MoBo only has 2 memory slots so I cannot go past 16GB even if I decide to invest more dollars in this project.
It doesn't support 16GB DIMMs?

. . It is an old cheapy MSI MoBo. I have very little info but I am pretty sure when I bought it the max was 16GB.

Stephen

:(
10) Message boards : Number crunching : How might memory effect R@h processing? (Message 93581)
Posted 5 Apr 2020 by Stephen "Heretic"
Post:
I froze the computer up solid through 3 reboots once I added Rosetta. Every time that BOINC started the computer froze with the disk access light solid. I didn't realize that the 22 cpu tasks I ran for SETI in %cpu usage was going to try and run 22 Rosetta tasks with just 16GB of memory installed.
I finally was able to stop BOINC from loading so I could manually edit the global and override preferences files to knock the number of cpu threads down to a value where the Rosetta startup wouldn't consume all my memory. I eventually stole memory from another SETI mothballed computer to add another 16GB to the computer I was running Rosetta on.


. . That is exactly the problem I have been suffering. I would like to run 2 x Rosetta tasks on my i5-6400 and support the GTX1050 running E@H but I only have 8 GB Ram. It is OK with the 32 bit tasks, I have 2 CPU cores committed to Rosetta and it mainly runs just one task, but sometimes there must be enough memory free and it will run 2. The good thing is that when memory demands increase it simply suspends one of the running Rosetta tasks and keeps on ticking, no harm, no foul. But when I have 64 bit tasks it goes to hell in a handbasket. At the moment I have it running OK by suspending the other 64bit Rosetta tasks so that they do NOT attempt to run. It works just fine like that but I have to check the machine more often than I should need to. I would love to know just how much ram is needed to keep 2 64 bit Rosetta tasks happy and still support the GPU. This MoBo only has 2 memory slots so I cannot go past 16GB even if I decide to invest more dollars in this project. I never had this problem running S@H. It ran 3 + 1 as smooth as silk. So in the end, with 32Gb Ram were you able to support all 22 tasks it was trying to run? Or did have to restrict it to any particular number?

Stephen

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11) Message boards : Number crunching : How might memory effect R@h processing? (Message 93454)
Posted 5 Apr 2020 by Stephen "Heretic"
Post:
. . Thanks Grant but I did know that. This system is using a low end MSI MoB with only 2 memory slots, to be honest I would have to do research to even be sure it can do dual channel mode, though I expect it does. But if I have to replace the one stick it came with I would go all out and get a pair.

Stephen

:)
12) Message boards : Number crunching : How might memory effect R@h processing? (Message 93450)
Posted 5 Apr 2020 by Stephen "Heretic"
Post:
You’d better run memtest86+ on it. If it’s overclocked then reset to factory defaults.
I had one machine that did that last week. Never had a problem with it before. I ran memtest86+ on it. Narrowed it down to a pair of memory sticks (the i7 in question had 4 x 8GB sticks). I’ve since replaced all 4 sticks and sent the dud pair back under warranty.


. . I never overclock, I'm not that adventurous. But it sounds like a memtest session might be a good idea. If it fails I might have to fork out some dollars for a pair of 8GB sticks, it is running just one x 8GB at the moment.

. . Thanks

Stephen

. .
13) Message boards : Number crunching : Discussion on increasing the default run time (Message 93449)
Posted 5 Apr 2020 by Stephen "Heretic"
Post:
IIRC it has something to do with looking at 10 million of them, with only about 10 or 100 really worth studying further. MOST of the are decoys. i.e. not the solution you are looking for
.


. . OK, thanks for that ...

Stephen

:)
14) Message boards : Number crunching : How might memory effect R@h processing? (Message 93444)
Posted 5 Apr 2020 by Stephen "Heretic"
Post:
. . I finally have some completed tasks and I delved into the result files for information.

. . The first two results had the following errors ...

    - Unhandled Exception Record -
    Reason: Access Violation (0xc0000005) at address 0x019F2BE0 write attempt to address 0x017D7EC9

    - Unhandled Exception Record -
    Reason: Access Violation (0xc0000005) at address 0x01AC2BE0 write attempt to address 0x017D7EC9



. . While different source addresses both were to the same destination address. Both ran debug twice but I cannot make sense of the results, I am not a programmer. Anyone able to suggest what the cause might be? Do I need to fix anything, should I be worried by this? The third completed task did not have any errors.

Stephen

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15) Message boards : Number crunching : Discussion on increasing the default run time (Message 93442)
Posted 5 Apr 2020 by Stephen "Heretic"
Post:
Is there any preferred or required number of models that need to be run for each task?


Required, one. That's it. If it takes more than a 2 hour preferred runtime to complete one model, then that is all that it will do. Each machine is different. Each protein is different. Each work unit could be used for millions of models, so the runtime preference is basically just a round number to try and break things up into a digestible size.


. . Just out of curiosity can you offer any reason why they call the models 'decoys'? It seems a strange term to use. I ask because I finally have some completed tasks and went looking for info in the result files.

Stephen

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16) Message boards : Number crunching : Discussion on increasing the default run time (Message 93331)
Posted 4 Apr 2020 by Stephen "Heretic"
Post:
It is just a target. If your target is 8 hours, and models each take 90 minutes, the 5th model will be completed at 7.5 hours of CPU time. At that point, one reasonably predicts running another model will take you to 9 hours, stopping now only gets you to the 7.5 hours. Neither one is an exact match. But when the prediction exceeds the preference, that is when the next model is not attempted, and the WU is marked completed and reported back, with all of the models completed so far.


. . Thank you, now I understand what the target is about. Is there any preferred or required number of models that need to be run for each task? And is there any metric to know how long each model is taking on a particular host? One thing I have noted by going over the limited information available for my host is that the tasks that seem to run OK are using the 32 bit app, the 3 tasks that have failed (spectacularly) were all for the 64 bit app. Do you know of anything I might have done to cause an issue with the 64 bit app? Grant indicated that RAM is a major factor in running Rosetta tasks, does the 64 bit app significantly increase the demand on RAM? What are the ram requirements per task for both the 32 bit app and the 64 bit app? Does the 64 bit app increase productivity to any appreciable degree or improve the quality of the modelling? Sorry to barrage you with so many questions but I am starting from a position of knowing nothing about this project.

. . Thanks for any help or info you can provide.

Stephen

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17) Message boards : Number crunching : Discussion on increasing the default run time (Message 93320)
Posted 4 Apr 2020 by Stephen "Heretic"
Post:
The length of time a Rosetta Task runs for is fixed (the default is 8 hours but you can select other target Runtimes in your Rosetta project settings).
Rosetta basically tries & whole bunch of different scenarios on the data. Some may run in to a dead end- and end early. Others may go in indefinitely- never ending. So the target Runtime is set & that is how long a Task will run for (if there is an issue with it & things get stuck, the Watchdog timer will kill the Task off, but you will still get Credit for work done. Unless of course it choked up right at the start of processing).


OK, so the target time limits the run length of the task, but how is that affected by or interact with the minimum target setting?

Having "Use at most xx% of the CPUs" at anything less ant 100% and running multiple projects, due to the CPU usage restriction, Resource share settings, cache settings & any other app_config.xml project specific limitations along with any locally set preferences that override web based ones you may have made will result in unexpected behaviour.


. . Actually I am finding just the opposite, with % CPU numbers running at 50% (2 cores) one task is running just fine (has just completed AOK and a second one has started) but when I increased CPUs to 75% (3 cores) all hell broke loose, it crashed BOINC totally and really screwed the pooch, so I dread to think what would happen if I tried running at 100%. I would like to understand what governs resource usage in this app (v4.12) so I am can gt it to play well with E@H which I intend to keep running. Apart from CPU support for the GPU app there is no conflict because E@H is GPU app only and Rosetta is CPU app only.
18) Message boards : Number crunching : Discussion on increasing the default run time (Message 93309)
Posted 3 Apr 2020 by Stephen "Heretic"
Post:
Right. You are not impacted by the proposed change to default run time, because you are not using the default. And you are not impacted by the proposed change to minimum runtime, because you are over the proposed new minimum runtime.

. . Hi,

. . I am a newbie refugee from S@H and was hoping someone could explain the function/purpose/usage of target times?

. . I am at present running 2 cores of an i5 with default target times. These settings are only allowing one task to run. I originally only committed one core and one task was running AOK, but after trying 2 cores which made no difference then 3 cores which allowed a second task to run but let loose the dogs of war and sent everything into meltdown, when I returned to the original committment of one core the initial task remained in the waiting to run state until I commit a second core. What is the secret to making things play nice. With the current mode the CPU usage is very low. Also what memory resources are required and how is it best to manage these resources?

Stephen

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19) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93169)
Posted 3 Apr 2020 by Stephen "Heretic"
Post:
. . OK, I am totally new to this project. I started cautiously giving it one core of my i5-6400 with the other 3 cores idle as backup and support for E@H on the GPU. One task ran and was looking good, pretty much on target (8 hours) after 6 hours runtime with CPU utilisation remaining under 50% on all 4 cores. To try and improve CPU usage I increased it to 2 cores but it remained at one task running. I then increased commitment to 3 cores and it started a 2nd task, but soon crashed BOINC requiring me to go to task manager to kill all Rosetta functions and E@H before I could get BOINC to launch again. I reduced CPU commitment back to 1 core and left it running, but upon returning to this machine about 8 hours later it had crashed the boinc-client several times and despite trying to kill off still active app components I could not get BOINC to restart, so I had to reboot the machine. I suspended the idle Rosetta tasks but now the one running task has gone to 'waiting to run". This machine has 8GB RAM. If I cannot get Rosetta to play nice with E@H it may have to go.

. . I increased CPU commitment back to 2 cores and the stalled task has resumed, but I am now waiting for the other shoe to drop. Will it crash BOINC yet again?

Stephen

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20) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 93081)
Posted 2 Apr 2020 by Stephen "Heretic"
Post:
Hello, I have just joined this project but it seems there is no work to do at the moment. Is this a common state of affairs or have I struck a bad moment to join??
Work being done has increased by 500% over the last 2 and a bit weeks, so there's not much work available as demand is far exceeding supply.
More work is meant to be coming, but apparently it takes quite a while to prepare it for release, so it will take a while before work production comes close to matching the present demand.


. . I'm guessing fellow refugees from S@H ... oh well, I'll just have to be patient ...

Stephen

:(


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