Problems and Technical Issues with Rosetta@home

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Jean-David Beyer

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Message 103787 - Posted: 9 Dec 2021, 19:12:32 UTC - in response to Message 103785.  


Something different...I have been getting some 4.2 stuff and now I am back to Python.
Anyone figure out the scheduler routine yet?
If I was to up the cores in the app_config (project_max_concurrent) to 3 or 4, would I get all Python or a blend of 4.2 and Python?


I have the following in my app_config file:

[/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]$ cat app_config.xml
<app_config>
<project_max_concurrent>3</project_max_concurrent>
</app_config>

and the boinc-cllient runs up to three of these work units at a time. I am getting plenty of work units. I have a 16-core machine but the boinc-client is instructed to run no more than 8 Boinc tasks at a time. The various app_config.xml files allow up to 4 ClimatePrediction tasks at a time, 5 WCG at a time, three Rosetta at a time, and 2 Universe tasks at a time -- though the priority of the Universe tasks is so low that they hardly ever run, and then only one at a time.
Currently I have these Rosetta tasks on my machine and none of them are running.

3443919 Dec  9 13:09 fcgr3a_site1_5mn2_3h_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_7ts1jp9r.zip
3453466 Dec  9 13:09 fcgr3a_site1_5mn2_3h_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_9zi4uu3j.zip
2646638 Dec  9 13:09 her2_site4_3h_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_0ic4nn1s.zip
2544075 Dec  9 13:09 her2_site4_3h_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_6kw0cf1j.zip
2804583 Dec  9 13:09 niv_site3_6vy5_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_2fs1jz6r.zip
2585084 Dec  9 13:09 niv_site3_6vy6_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_2cm7fe4w.zip
2748992 Dec  9 13:09 niv_site3_6vy6_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_2jg7fo9z.zip
2640314 Dec  9 13:09 niv_site3_6vy6_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_7jp7ej6d.zip
2575060 Dec  9 13:09 niv_site3_6vy6_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_8yo1qr6j.zip


This is when I have been receiving work units for Rosetta:

Tue 07 Dec 2021 03:10:29 PM EST | Rosetta@home | Sending scheduler request: To fetch work.
Tue 07 Dec 2021 03:10:29 PM EST | Rosetta@home | Requesting new tasks for CPU
Tue 07 Dec 2021 03:10:33 PM EST | Rosetta@home | Scheduler request completed: got 9 new tasks
Wed 08 Dec 2021 12:30:55 AM EST | Rosetta@home | Sending scheduler request: To fetch work.
Wed 08 Dec 2021 12:30:55 AM EST | Rosetta@home | Requesting new tasks for CPU
Wed 08 Dec 2021 12:30:59 AM EST | Rosetta@home | Scheduler request completed: got 8 new tasks
Wed 08 Dec 2021 09:52:40 AM EST | Rosetta@home | Sending scheduler request: To fetch work.
Wed 08 Dec 2021 09:52:40 AM EST | Rosetta@home | Reporting 2 completed tasks
Wed 08 Dec 2021 09:52:40 AM EST | Rosetta@home | Requesting new tasks for CPU
Wed 08 Dec 2021 09:52:42 AM EST | Rosetta@home | Scheduler request completed: got 8 new tasks
Wed 08 Dec 2021 10:55:08 PM EST | Rosetta@home | Sending scheduler request: To fetch work.
Wed 08 Dec 2021 10:55:08 PM EST | Rosetta@home | Reporting 3 completed tasks
Wed 08 Dec 2021 10:55:08 PM EST | Rosetta@home | Requesting new tasks for CPU
Wed 08 Dec 2021 10:55:16 PM EST | Rosetta@home | Scheduler request completed: got 9 new tasks


I do not know about python tasks because I do not get them because I cannot run them.
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Profile Greg_BE
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Message 103788 - Posted: 9 Dec 2021, 23:10:02 UTC - in response to Message 103786.  

Something different...I have been getting some 4.2 stuff and now I am back to Python.
Anyone figure out the scheduler routine yet?
If I was to up the cores in the app_config (project_max_concurrent) to 3 or 4, would I get all Python or a blend of 4.2 and Python?

It seems to be a random mix of whatever of available, rather than a schedule. I suspect that it is whatever they are currently teaching their students to create workunits for.



I think you missed out at what I am asking.
I get both 4.2 and Python.
However, I had to limit RAH to 2 tasks at a time because while 4.2 runs just fine and takes very little memory and processes very fast, Python is a memory hog and if it runs 3 it kills my other projects ability to run seamlessly.

So I was wondering if anyone has seen a pattern from the two schedulers, does it do 4.2 for a time and then go back to Python or does it also go 1:1 or whatever with python and 4.2 at the same time? Or is it just a random mix of the two?
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Profile Greg_BE
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Message 103789 - Posted: 9 Dec 2021, 23:14:41 UTC - in response to Message 103787.  
Last modified: 9 Dec 2021, 23:15:12 UTC


Something different...I have been getting some 4.2 stuff and now I am back to Python.
Anyone figure out the scheduler routine yet?
If I was to up the cores in the app_config (project_max_concurrent) to 3 or 4, would I get all Python or a blend of 4.2 and Python?


I have the following in my app_config file:

[/var/lib/boinc/projects/boinc.bakerlab.org_rosetta]$ cat app_config.xml
<app_config>
<project_max_concurrent>3</project_max_concurrent>
</app_config>

and the boinc-cllient runs up to three of these work units at a time. I am getting plenty of work units. I have a 16-core machine but the boinc-client is instructed to run no more than 8 Boinc tasks at a time. The various app_config.xml files allow up to 4 ClimatePrediction tasks at a time, 5 WCG at a time, three Rosetta at a time, and 2 Universe tasks at a time -- though the priority of the Universe tasks is so low that they hardly ever run, and then only one at a time.
Currently I have these Rosetta tasks on my machine and none of them are running.

3443919 Dec  9 13:09 fcgr3a_site1_5mn2_3h_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_7ts1jp9r.zip
3453466 Dec  9 13:09 fcgr3a_site1_5mn2_3h_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_9zi4uu3j.zip
2646638 Dec  9 13:09 her2_site4_3h_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_0ic4nn1s.zip
2544075 Dec  9 13:09 her2_site4_3h_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_6kw0cf1j.zip
2804583 Dec  9 13:09 niv_site3_6vy5_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_2fs1jz6r.zip
2585084 Dec  9 13:09 niv_site3_6vy6_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_2cm7fe4w.zip
2748992 Dec  9 13:09 niv_site3_6vy6_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_2jg7fo9z.zip
2640314 Dec  9 13:09 niv_site3_6vy6_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_7jp7ej6d.zip
2575060 Dec  9 13:09 niv_site3_6vy6_jhr_ggraft_1_SAVE_ALL_OUT_IGNORE_THE_REST_8yo1qr6j.zip


This is when I have been receiving work units for Rosetta:

Tue 07 Dec 2021 03:10:29 PM EST | Rosetta@home | Sending scheduler request: To fetch work.
Tue 07 Dec 2021 03:10:29 PM EST | Rosetta@home | Requesting new tasks for CPU
Tue 07 Dec 2021 03:10:33 PM EST | Rosetta@home | Scheduler request completed: got 9 new tasks
Wed 08 Dec 2021 12:30:55 AM EST | Rosetta@home | Sending scheduler request: To fetch work.
Wed 08 Dec 2021 12:30:55 AM EST | Rosetta@home | Requesting new tasks for CPU
Wed 08 Dec 2021 12:30:59 AM EST | Rosetta@home | Scheduler request completed: got 8 new tasks
Wed 08 Dec 2021 09:52:40 AM EST | Rosetta@home | Sending scheduler request: To fetch work.
Wed 08 Dec 2021 09:52:40 AM EST | Rosetta@home | Reporting 2 completed tasks
Wed 08 Dec 2021 09:52:40 AM EST | Rosetta@home | Requesting new tasks for CPU
Wed 08 Dec 2021 09:52:42 AM EST | Rosetta@home | Scheduler request completed: got 8 new tasks
Wed 08 Dec 2021 10:55:08 PM EST | Rosetta@home | Sending scheduler request: To fetch work.
Wed 08 Dec 2021 10:55:08 PM EST | Rosetta@home | Reporting 3 completed tasks
Wed 08 Dec 2021 10:55:08 PM EST | Rosetta@home | Requesting new tasks for CPU
Wed 08 Dec 2021 10:55:16 PM EST | Rosetta@home | Scheduler request completed: got 9 new tasks


I do not know about python tasks because I do not get them because I cannot run them.



Before I got interested in python I let RAH take whatever it wanted.
Then when I got into Python and letting it do its thing, then it was 3 tasks and taking up over half the memory and stalling other tasks. Then I took your project_concurrent and limited it to 2. But I see "name" does not affect anything. Project is project. So RAH is limited to 2 tasks no matter which application is running. I am afraid to release it, because then Python will take over. Unless that was a matter of RAH debt when 4.2 ran out. All I know is that Python x3 is a system killer unless I buy some new memory sticks. Then we are talking an absurd amount of memory to keep BOINC running the way I like it to run or dropping Python which seems crazy after complaining about not getting it for so long.

Why can't you run Python? I forgot.
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.clair.

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Message 103790 - Posted: 10 Dec 2021, 2:19:44 UTC - in response to Message 103789.  
Last modified: 10 Dec 2021, 2:34:05 UTC

All I know is that Python is a system killer unless I buy some new memory sticks.

I don't know what motherboard you have, but don't scimp on it, you may have to max out what the board can take.
................
Recently because of going to some dodgy website an downloading a new version of boinc mangler 7,16.20 that had `virtual pox` in with it. {its not had VB before}
I get my computer infected with pythons in cages, and they are horrible big things that realy take over the poor thing.
I decided to upgrade one my systems from 32GB to 128GB {not its max}
it`s `only` a twin xeon E5 2697 48 thread 128GB of ram and they can realy stuff it. even if actual memory use is 50GB and only run 16 at a time. it'll run plenty more R4.20, [ and other work]
further up this thread I had problems with another system getting daft disk space messages that I now ignore, {and I had just upped that from 16 to 32 GB}
now even this one gets them,
Just now, rosetta is using 77GB of disk space and it has 246GB more free available for boinc to use.
.............
09-Dec-2021 06:40:46 [Rosetta@home] Rosetta needs 1907.35MB more disk space. You currently have 0.00 MB available and it needs 1907.35 MB.
09-Dec-2021 06:40:46 [Rosetta@home] rosetta python projects needs 19073.49MB more disk space. You currently have 0.00 MB available and it needs 19073.49 MB
............
crazy stuff I don't bother about any more
And I have rosetta set to a zero resource share on that system to try and limit what funky stuff it can do
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Message 103791 - Posted: 10 Dec 2021, 2:31:19 UTC - in response to Message 103763.  

Looks like another batch of 4.2 work is available.

NKG2D, EPHA2 and BCMA. Reading on all those 3, I guess this work could be cancer-related (I'm assuming this was sent back by the same person/team and that they are all related). Or not at all.

Looks like there are an extra 1.4 million queued tasks when compared to this morning's 2.2 million Pythons.

Yes, but all seem limited to 100 decoys before stopping short, so only running between 1 & 2hrs here.

They won't last long at all

I did get a few Robetta tasks that ran the full 8hrs but it looks like all Rosetta 4.20 tasks have been downloaded now.
Won't be long before I'm back running WCG

My resource share is set to Rosetta 29 - WCG 1 but my RAC is 6.5k to 19.6k atm... <sigh>
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Jean-David Beyer

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Message 103792 - Posted: 10 Dec 2021, 4:11:11 UTC - in response to Message 103789.  

Why can't you run Python? I forgot.


I do not have VirtualBox, so I cannot run them.
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Profile Greg_BE
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Message 103793 - Posted: 10 Dec 2021, 7:01:12 UTC - in response to Message 103792.  

Why can't you run Python? I forgot.


I do not have VirtualBox, so I cannot run them.



Do you want to run them?
Then download virtual box 5 not 6.
And enable the option to get them on your profile on this page: https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=5958977 (Thats your windows machine)
But they are memory hogs (can only do 3 tasks) plus the VDI is 9 gigs.
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Message 103795 - Posted: 10 Dec 2021, 11:53:53 UTC - in response to Message 103793.  

Why can't you run Python? I forgot.


I do not have VirtualBox, so I cannot run them.



Do you want to run them?
Then download virtual box 5 not 6.
And enable the option to get them on your profile on this page: https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=5958977 (Thats your windows machine)
But they are memory hogs (can only do 3 tasks) plus the VDI is 9 gigs.



Each Python requires 7629.39 MB of physical memory and an additional 101 to 103 MB of Virtual Memory.
Which is why I put the restriction in place so other tasks from other projects could run.
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Jean-David Beyer

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Message 103796 - Posted: 10 Dec 2021, 16:27:08 UTC - in response to Message 103793.  


I do not have VirtualBox, so I cannot run them.

Do you want to run them?
Then download virtual box 5 not 6.
And enable the option to get them on your profile on this page: https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=5958977 (Thats your windows machine)
But they are memory hogs (can only do 3 tasks) plus the VDI is 9 gigs.


While I have python, I do not want to bother installing and running VirtualBox on my machine; it has enough to do already.
[/usr/bin]$ ls -l python*
lrwxrwxrwx. 1 root root    9 Aug 11 06:22 python2 -> python2.7
-rwxr-xr-x. 1 root root 8016 Aug 11 06:22 python2.7
lrwxrwxrwx. 1 root root   25 Oct 26  2020 python3 -> /etc/alternatives/python3
lrwxrwxrwx. 1 root root   31 Aug 11 06:56 python3.6 -> /usr/libexec/platform-python3.6
lrwxrwxrwx. 1 root root   32 Aug 11 06:56 python3.6m -> /usr/libexec/platform-python3.6m

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Message 103798 - Posted: 10 Dec 2021, 20:07:47 UTC
Last modified: 10 Dec 2021, 20:08:06 UTC

And more work was added to the queue.
From 2.2 million to 6 million tasks.
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Message 103800 - Posted: 10 Dec 2021, 21:05:51 UTC - in response to Message 103798.  

And more work was added to the queue.
From 2.2 million to 6 million tasks.
many of these are completing in 1 hour or so, not the 8 hr Target CPU time. So they won't last long at all if most of them are like these initial ones.
Grant
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Message 103802 - Posted: 10 Dec 2021, 23:05:26 UTC - in response to Message 103796.  


I do not have VirtualBox, so I cannot run them.

Do you want to run them?
Then download virtual box 5 not 6.
And enable the option to get them on your profile on this page: https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=5958977 (Thats your windows machine)
But they are memory hogs (can only do 3 tasks) plus the VDI is 9 gigs.


While I have python, I do not want to bother installing and running VirtualBox on my machine; it has enough to do already.
[/usr/bin]$ ls -l python*
lrwxrwxrwx. 1 root root    9 Aug 11 06:22 python2 -> python2.7
-rwxr-xr-x. 1 root root 8016 Aug 11 06:22 python2.7
lrwxrwxrwx. 1 root root   25 Oct 26  2020 python3 -> /etc/alternatives/python3
lrwxrwxrwx. 1 root root   31 Aug 11 06:56 python3.6 -> /usr/libexec/platform-python3.6
lrwxrwxrwx. 1 root root   32 Aug 11 06:56 python3.6m -> /usr/libexec/platform-python3.6m



Well you can exclude them if you don't want to have them. Same page allows you to opt out.
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Jean-David Beyer

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Message 103803 - Posted: 11 Dec 2021, 1:36:55 UTC - in response to Message 103802.  

While I have python, I do not want to bother installing and running VirtualBox on my machine; it has enough to do already.

[/usr/bin]$ ls -l python*
lrwxrwxrwx. 1 root root 9 Aug 11 06:22 python2 -> python2.7
-rwxr-xr-x. 1 root root 8016 Aug 11 06:22 python2.7
lrwxrwxrwx. 1 root root 25 Oct 26 2020 python3 -> /etc/alternatives/python3
lrwxrwxrwx. 1 root root 31 Aug 11 06:56 python3.6 -> /usr/libexec/platform-python3.6
lrwxrwxrwx. 1 root root 32 Aug 11 06:56 python3.6m -> /usr/libexec/platform-python3.6m

Well you can exclude them if you don't want to have them. Same page allows you to opt out.


To what page do you refer?

OTOH, for some reason, I do not get any, though I do get the messages

Fri 10 Dec 2021 10:30:09 AM EST | Rosetta@home | Message from server: VirtualBox is not installed <---<<<
Fri 10 Dec 2021 10:30:09 AM EST | Rosetta@home | Project requested delay of 31 seconds
Fri 10 Dec 2021 12:26:12 PM EST | Rosetta@home | Sending scheduler request: To fetch work.
Fri 10 Dec 2021 12:26:12 PM EST | Rosetta@home | Requesting new tasks for CPU
Fri 10 Dec 2021 12:26:15 PM EST | Rosetta@home | Scheduler request completed: got 9 new tasks

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Profile Grant (SSSF)

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Message 103805 - Posted: 11 Dec 2021, 1:47:05 UTC - in response to Message 103803.  

To what page do you refer?
The options on the page mentioned aren't there because you don't have VirtualBox installed.



OTOH, for some reason, I do not get any, though I do get the messages
Just as the message says- because you don't have VirtualBox installed, you won't get any.

If you want to do Python Tasks, you must install VirtualBox. If you don't want to do them, or just don't want to install VirtualBox, then don't.
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Message 103808 - Posted: 11 Dec 2021, 9:41:31 UTC - in response to Message 103805.  

To what page do you refer?
The options on the page mentioned aren't there because you don't have VirtualBox installed.



OTOH, for some reason, I do not get any, though I do get the messages
Just as the message says- because you don't have VirtualBox installed, you won't get any.

If you want to do Python Tasks, you must install VirtualBox. If you don't want to do them, or just don't want to install VirtualBox, then don't.



Thanks for the assist.
I forgot that non Vbox users can't see the tasks.
But then again, why should they get the error saying Vbox is not installed?
IF they were smart, then when they detect that Vbox is not installed, just ignore sending any messages to the system. Would save this kind of confusion.
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Message 103811 - Posted: 11 Dec 2021, 12:49:30 UTC - in response to Message 103791.  

Looks like another batch of 4.2 work is available.

NKG2D, EPHA2 and BCMA. Reading on all those 3, I guess this work could be cancer-related (I'm assuming this was sent back by the same person/team and that they are all related). Or not at all.

Looks like there are an extra 1.4 million queued tasks when compared to this morning's 2.2 million Pythons.

Yes, but all seem limited to 100 decoys before stopping short, so only running between 1 & 2hrs here.

They won't last long at all

I did get a few Robetta tasks that ran the full 8hrs but it looks like all Rosetta 4.20 tasks have been downloaded now.
Won't be long before I'm back running WCG

My resource share is set to Rosetta 29 - WCG 1 but my RAC is 6.5k to 19.6k atm... <sigh>



Sid - not all of that millions is for us. I randomly sampled some of the jobs and found some with RoseTTAFold which is the neural network. There is no way on that page to isolate those from the rest without clicking on each one.

Like this group: Potassium-transporting ATPase alpha chain 2 11 That is all for RoseTTaFold.
And so on.
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Message 103816 - Posted: 12 Dec 2021, 17:41:25 UTC - in response to Message 103800.  

And more work was added to the queue.
From 2.2 million to 6 million tasks.
many of these are completing in 1 hour or so, not the 8 hr Target CPU time. So they won't last long at all if most of them are like these initial ones.


Some of my tasks are running beyond the 100 decoy mark.
For example, this one.
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Message 103817 - Posted: 12 Dec 2021, 20:06:44 UTC - in response to Message 103816.  

And more work was added to the queue.
From 2.2 million to 6 million tasks.
many of these are completing in 1 hour or so, not the 8 hr Target CPU time. So they won't last long at all if most of them are like these initial ones.


Some of my tasks are running beyond the 100 decoy mark.
For example, this one.


Try this one ....198
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Message 103822 - Posted: 14 Dec 2021, 13:05:40 UTC

I have encountered some virtualbox tasks that takes over a day to run. When task takes over a day to run, I thought that it is stuck in some way and aborted the task. Other thought is that there is some problem in my environment.

Does virtualbox tasks usually take over a day to run? Is there some problem in my environment?



One longlasting task is as follows:

Task 1453463295
Name aagb-mALA_pp-mHPR-mACPenC13T-B3PHE_1_2611271_1_0
Workunit 1297021861
Created 8 Dec 2021, 21:03:21 UTC
Sent 9 Dec 2021, 13:51:23 UTC
Report deadline 12 Dec 2021, 13:51:23 UTC
Received 11 Dec 2021, 12:36:28 UTC
Server state Over
Outcome Computation error
Client state Aborted by user
Exit status 203 (0x000000CB) EXIT_ABORTED_VIA_GUI
Computer ID 2401895
Run time 1 days 2 hours 45 min 39 sec
CPU time 25 min 55 sec
Validate state Invalid
Credit 14.00
Device peak FLOPS 4.90 GFLOPS
Application version rosetta python projects v1.03 (vbox64)
x86_64-pc-linux-gnu
Peak working set size 1,185.08 MB
Peak swap size 2,565.54 MB
Peak disk usage 7,979.68 MB


Computer:

IP address Show IP address
Domain name huono3-desktop
Local Standard Time UTC +2 hours
Created 17 Nov 2015, 17:05:25 UTC
Total credit 4,147,395
Average credit 262.50
Cross project credit BOINCstats.com Free-DC
CPU type GenuineIntel
Intel(R) Pentium(R) CPU G3258 @ 3.20GHz [Family 6 Model 60 Stepping 3]
Number of processors 2
Coprocessors ---
Operating System Linux Ubuntu
Ubuntu 20.04.3 LTS [5.4.0-91-generic|libc 2.31 (Ubuntu GLIBC 2.31-0ubuntu9.2)]
BOINC version 7.16.6
Memory 7639 MB
Cache 3072 KB
Swap space 3905 MB
Total disk space 106.16 GB
Free Disk Space 83.67 GB
Measured floating point speed 4895.56 million ops/sec
Measured integer speed 111568.63 million ops/sec
Average upload rate 160.08 KB/sec
Average download rate 2790.46 KB/sec
Average turnaround time 2.77 days
Application details Show
Tasks 27
Number of times client has contacted server 5500
Last time contacted server 14 Dec 2021, 12:32:40 UTC
Fraction of time BOINC is running 83.79%
While BOINC is running, fraction of time computing is allowed 100.00%
While is BOINC running, fraction of time GPU computing is allowed 100.00%
Task duration correction factor 1

virtual box version: 6.1.26
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Jim1348

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Message 103823 - Posted: 14 Dec 2021, 15:04:12 UTC - in response to Message 103822.  

I have encountered some virtualbox tasks that takes over a day to run. When task takes over a day to run, I thought that it is stuck in some way and aborted the task. Other thought is that there is some problem in my environment.

Does virtualbox tasks usually take over a day to run? Is there some problem in my environment?

There are a few "0 CPU" tasks. Just check the CPU usage. If it is very low, abort that task.
I use BoincTasks to check that easily, but you can look at the CPU runtime in BOINC manager as well.
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