Rosetta 4.1+ and 4.2+

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bkil
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Message 94052 - Posted: 10 Apr 2020, 10:20:02 UTC - in response to Message 93364.  
Last modified: 10 Apr 2020, 10:20:13 UTC

You may try disabling i686 apps as mentioned here to get it up and running: https://boinc.bakerlab.org/rosetta/forum_thread.php?id=13727&postid=94049#94049
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Michael E.

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Message 94091 - Posted: 10 Apr 2020, 18:31:14 UTC

I am running Windows 10, BOINC 7.14.2 (x86), with Rosetta preferences at 1 day 12 hours.

The Rosetta 4.12 tasks downloaded initially said they would execute in 6 hours but it is taking much longer.

How much longer than the Deadline time is allowed? Sorry but I had to abort several of these.

The Elapsed time seems to reset on some of these tasks. One task completed (1143119307.) and others had to be aborted.

I just downloaded some Rosetta Mini v3.78 tasks and will see how those go.

How can I help? I am a retired software writing/support guy who knows what native code means :-).

Mike
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Message 94096 - Posted: 10 Apr 2020, 19:03:43 UTC - in response to Message 94091.  

As you first get started, BOINC Manager really hasn't had a chance to see the tasks run, and so the estimate to completion will not be very good. If you set to 36 hours, they will probably take about that long. No worries on deleting the extras, there are other machines clamoring for work. Don't count on any slack on the deadlines.

The Elapsed time seems to reset on some of these tasks

Do you have the box checked to leave tasks in memory while suspended?
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Message 94106 - Posted: 10 Apr 2020, 20:29:56 UTC - in response to Message 94096.  

Mod.Sense asked:"Do you have the box checked to leave tasks in memory while suspended?"

On both local PCs, this is is checked/on: BOINC > Advanced View > Options > Computing Preferences > Disk and Memory > Leave non-GPU tasks in memory while suspended

On the web pref's, it was unchecked so I checked it. I usually use the local pref's only.

To minimize disk writes, I set the BOINC > Advanced View > Options > Computing Preferences > Computing > Request tasks to checkpoint at most every 300 seconds

The two PCs both had similar unexpectedly low elapsed time for a short time after they had been processing for a while. They both returned one task so far.

Mike
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Message 94118 - Posted: 10 Apr 2020, 21:49:46 UTC - in response to Message 94106.  

Mod.Sense asked:"Do you have the box checked to leave tasks in memory while suspended?"

On both local PCs, this is is checked/on: BOINC > Advanced View > Options > Computing Preferences > Disk and Memory > Leave non-GPU tasks in memory while suspended
If you're going to have that checked, you might want to increase the amount of memory available to BOINC to avoid out of memory problems (it should make use of page file/virtual memory, but why risk it?).
   Memory
          When computer is in use, use at most 95 %
      When computer is not in use, use at most 95 %
                   Page/swap file: use at most 75 %


On the web pref's, it was unchecked so I checked it. I usually use the local pref's only.
Local preferences do override the web based ones.


To minimize disk writes, I set the BOINC > Advanced View > Options > Computing Preferences > Computing > Request tasks to checkpoint at most every 300 seconds
Unnecessary, and will make missing a checkpoint much more likely.
With it set to 60 seconds, it doesn't mean it will checkpoint then- it will just ask the application to checkpoint, if it can. If it can, it will. If it can't, it won't.

And as for minimising disk writes, that too is unnecessary (unless you are running it on a thumb drive),
Even though Rosetta does hammer the disk compared to other projects (and other workloads), the fact is the total amount of writes it does is bugger all of what the drive is capable of dealing with before it eventually dies, in 20 or more years time with much, much heavier use than even Rosetta does with it.
And even then, as Annandtech showed many years ago, even consumer based SSDs will outlast their specified life expectancy, often by a huge margin. It took them 18 months to kill the last of their consumer SSDs, using loads that far exceed any regular desktop's extreme disk usage (yes they were SLC drives, and more recent flash technologies (MLC, TLC & QLC) have less total writes before they will fail. But the software to reduce write amplification, combined with capacities much larger than the tested drives, means current SSD would probably last longer, even with a heavier load).
The SSD Endurance Experiment
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Michael E.

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Message 94130 - Posted: 11 Apr 2020, 1:33:25 UTC - in response to Message 94118.  

Grant - Way cool! Thanks much for the help.

I changed the Computing Preferences as you suggested to allow disk writes at 60 seconds and increased the memory allowed to 90%. My PCs have 8 and 16 GB respectively.

Are these suggested Preferences written down anywhere? If not, if you could review it, want me to create a PDF-based guide? Send me a message. It needs to be easy to locate as well.

Mike
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Message 94131 - Posted: 11 Apr 2020, 1:58:00 UTC - in response to Message 94130.  
Last modified: 11 Apr 2020, 2:00:03 UTC

Are these suggested Preferences written down anywhere? If not, if you could review it, want me to create a PDF-based guide? Send me a message. It needs to be easy to locate as well.
I've just been copying & pasting as people post their questions/issues, although having them somewhere ready to go would speed things up.
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Message 94140 - Posted: 11 Apr 2020, 6:20:36 UTC - in response to Message 93849.  

The 64-Bit app for Linux works fine with my machine, i think the 32 bit app for Linux has a bug.
Perhaps the Rosetta Admins should think about removing 32-bit apps for x86 cpu's. Machines run 32 bit must be really old with low speed cpu's.
It makes no sense running this machines for Boinc.

Microsoft Windows (98 or later) running on an Intel x86-compatible CPU 4.12 1 Apr 2020, 0:32:45 UTC 76,058 GigaFLOPS
yes,delete all of them )
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James W

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Message 94156 - Posted: 11 Apr 2020, 13:42:14 UTC - in response to Message 94140.  

Microsoft Windows (98 or later) running on an Intel x86-compatible CPU 4.12 1 Apr 2020, 0:32:45 UTC 76,058 GigaFLOPS
(yes,delete all of them)

Just a touch of irony here??
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Message 94167 - Posted: 11 Apr 2020, 17:58:50 UTC - in response to Message 94156.  
Last modified: 11 Apr 2020, 18:00:20 UTC

Microsoft Windows (98 or later) running on an Intel x86-compatible CPU 4.12 1 Apr 2020, 0:32:45 UTC 76,058 GigaFLOPS
(yes,delete all of them)

Just a touch of irony here??

exactly,man offered to drop 50% performance in this project)
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Message 94171 - Posted: 11 Apr 2020, 18:57:57 UTC - in response to Message 94167.  
Last modified: 11 Apr 2020, 19:00:41 UTC

Microsoft Windows (98 or later) running on an Intel x86-compatible CPU 4.12 1 Apr 2020, 0:32:45 UTC 76,058 GigaFLOPS

exactly,man offered to drop 50% performance in this project

The current power on R@H is 22,776.39 TeraFLOPS:
1 - is not 50%
2 - is not a big problem.
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Message 94177 - Posted: 11 Apr 2020, 20:50:44 UTC - in response to Message 94171.  
Last modified: 11 Apr 2020, 20:51:32 UTC

The current power on R@H is 22,776.39 TeraFLOPS

My fault.
There are different values:
from home page: TeraFLOPS estimate: 1792.376
from cpu list: 22,776.39 TeraFLOPS
from BoincStats: 356.004 TeraFLOPS

Despite this discrepacy, the 32 bit systems are marginal
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Message 94183 - Posted: 11 Apr 2020, 22:28:49 UTC - in response to Message 94177.  
Last modified: 11 Apr 2020, 22:31:21 UTC

Despite this discrepacy, the 32 bit systems are marginal
How can you tell? The numbers of FLOPs are for the applications, it doesn't show the type of system (32bit or 64bit) that was running the application.
Even so, one third of the current compute performance is not insignificant.
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Message 94185 - Posted: 12 Apr 2020, 0:15:22 UTC - in response to Message 93928.  

Perhaps the Rosetta Admins should think about removing 32-bit apps for x86 cpu's.
Why? They're no slower than the equivalent 64bit application.

The Projekt developers have to support two more App-Versions not really needed anymore.
My point exactly. There is no need for the 64bit applications, so why produce them?

Haven't you noticed that some operating systems are planning to drop support for 32-bit apps?

Do you want Rosetta to be incompatible with new versions of those operating systems?
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Message 94186 - Posted: 12 Apr 2020, 0:22:12 UTC

I got an error I've never seen before.

ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF

https://boinc.bakerlab.org/rosetta/result.php?resultid=1146962553

Does this mean an error built into the workunit?

Rosetta 4.12

BOINC 7.16.5

Returning it got my first 4.15 task on Rosetta, though.
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Message 94189 - Posted: 12 Apr 2020, 0:43:53 UTC - in response to Message 94185.  

Haven't you noticed that some operating systems are planning to drop support for 32-bit apps?
Do you want Rosetta to be incompatible with new versions of those operating systems?
And that is actually a good reason to produce them, unlike the "32bit is old, lets get rid of it" argument for getting rid of 32bit applications- even though they provide a very significant portion of Rosetta's computing power.

The same reason for producing 64bit applications is the same reason to continue with 32bit ones- to make use of the computing resources that are available. As it is, all present 64bit hardware & operating systems can handle 32bit applications- and their performance is on par with the 64bit ones. When support for 32bit applications is eventually dropped, then the need for 64bit becomes considerably greater.
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Message 94190 - Posted: 12 Apr 2020, 0:54:34 UTC - in response to Message 94186.  

I got an error I've never seen before.

ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF

https://boinc.bakerlab.org/rosetta/result.php?resultid=1146962553

Does this mean an error built into the workunit?
That's how i would interpret it; the application doesn't recognise that file type.

It could be the new application was released to process them, but it hasn't been released for Linux on x86 systems at all, nor for Windows 32bit.
And if the servers haven't been configured to allocate the new work type only to the new application a lot of Tasks are going to be trashed.

Hopefully it was just a one off file corruption glitch.
Grant
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Message 94199 - Posted: 12 Apr 2020, 2:24:34 UTC
Last modified: 12 Apr 2020, 3:08:15 UTC

It looks like there's going to be some problems with v 4.15- Estimated completion times are 39min 18sec, that's going to lead to a lot of overfilled caches & Tasks timing out. I can see a lot of work going to waste with this if they run to the default time of 8 hours.

Edit-
Suspended some Tasks to get the v4.15 ones to run, and it's not looking good. Two are presently running, and their current rate of progress has them running for 8 hours. 3 others ended with a Computation Error within 30 seconds. One running on Rosetta v4.12 windows_intelx86 took 42 seconds to die.


Edit-
Looks like a batch of dodgy Tasks.
All 4 of the errors above were the same as robertmiles had,
ERROR: Cannot determine file type. Current supported types are: PDB, CIF, SRLZ, MMTF
ERROR:: Exit from: ......srccoreimport_poseimport_pose.cc line: 380
BOINC:: Error reading and gzipping output datafile: default.out


Problem Tasks
0930dfdd5b7a8dbc439376d35ff43cd0_dock_ens_20_04_15_28_11_localDocking_0_SAVE_ALL_OUT_910048_18_0
4b344669e2c2754038b4438c4e2e5d64_dock_ens_20_04_15_28_14_localDocking_1_SAVE_ALL_OUT_910066_18_0
c31ed6e33409f8d7b8e76abdd93af3a6_dock_ens_20_04_15_28_13_localDocking_0_SAVE_ALL_OUT_910304_18_0
58975f05ec37c073d52b9aa38b7d1b28_dock_ens_20_04_15_28_13_localDocking_1_SAVE_ALL_OUT_910258_26_0

_globalDocking_ Tasks are processing Ok.
Grant
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James W

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Message 94206 - Posted: 12 Apr 2020, 5:33:55 UTC - in response to Message 94199.  

It looks like there's going to be some problems with v 4.15- Estimated completion times are 39min 18sec; that's going to lead to a lot of overfilled caches & Tasks timing out....
The first v4.15 tasks I got were also noted to be in the 39 min. range. However, my BOINC manager revised their completion times to 01:14:54, almost twice as long. Will see if I get same results as you did.
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Message 94212 - Posted: 12 Apr 2020, 6:02:31 UTC - in response to Message 94199.  

Edit-
Suspended some Tasks to get the v4.15 ones to run, and it's not looking good. Two are presently running, and their current rate of progress has them running for 8 hours. 3 others ended with a Computation Error within 30 seconds. One running on Rosetta v4.12 windows_intelx86 took 42 seconds to die.

To be fair, at that rate, they should all complete by deadline...

...yeah, sorry. Had to say it...
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Message boards : Number crunching : Rosetta 4.1+ and 4.2+



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