Problems and Technical Issues with Rosetta@home

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.clair.

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Message 103670 - Posted: 2 Dec 2021, 21:51:18 UTC

Now I`me getting some nuty messages from the server about disk space and python`s greed for everything
ok, its `only` a 250GB disk but boinc mangler is now set to use all disk space possible {untick all disk space limits boxes, not had to do that before}
rosetta is already using 95GB and boinc mangler reports there is still 64GB free for boinc to use.
so the `currently have` bits are wrong
`it needs19073MB` does it realy , well , its already using 95GB of space , so what is it going on about now
o well more silliness to ignor
Just how munch of everything do the pythons want to eat . . . . .
[and I assure you I have not got my MB and GB mixed up]

01/12/2021 11:41:12 Rosetta@home Message from server: rosetta python projects needs 10252.03MB more disk space.You currently have 8821.45 MB available and it needs 19073.49 MB.
01/12/2021 22:06:01 Rosetta@home Message from server: rosetta python projects needs 16191.05MB more disk space.You currently have 2882.43 MB available and it needs 19073.49 MB.
02/12/2021 10:58:53 Rosetta@home Message from server: rosetta python projects needs 8276.39MB more disk space.You currently have 10797.10 MB available and it needs 19073.49 MB.
02/12/2021 11:09:53 Rosetta@home Message from server: rosetta python projects needs 15155.41MB more disk space.You currently have 3918.08 MB available and it needs 19073.49 MB.
02/12/2021 11:32:34 Rosetta@home Message from server: rosetta python projects needs 15828.33MB more disk space.You currently have 3245.16 MB available and it needs 19073.49 MB.
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Message 103673 - Posted: 2 Dec 2021, 23:01:56 UTC - in response to Message 103670.  
Last modified: 2 Dec 2021, 23:05:36 UTC

Now I`me getting some nuty messages from the server about disk space and python`s greed for everything
ok, its `only` a 250GB disk but boinc mangler is now set to use all disk space possible {untick all disk space limits boxes, not had to do that before}
rosetta is already using 95GB and boinc mangler reports there is still 64GB free for boinc to use.
so the `currently have` bits are wrong
`it needs19073MB` does it realy , well , its already using 95GB of space , so what is it going on about now
o well more silliness to ignor
Just how munch of everything do the pythons want to eat . . . . .
[and I assure you I have not got my MB and GB mixed up]

01/12/2021 11:41:12 Rosetta@home Message from server: rosetta python projects needs 10252.03MB more disk space.You currently have 8821.45 MB available and it needs 19073.49 MB.
01/12/2021 22:06:01 Rosetta@home Message from server: rosetta python projects needs 16191.05MB more disk space.You currently have 2882.43 MB available and it needs 19073.49 MB.
02/12/2021 10:58:53 Rosetta@home Message from server: rosetta python projects needs 8276.39MB more disk space.You currently have 10797.10 MB available and it needs 19073.49 MB.
02/12/2021 11:09:53 Rosetta@home Message from server: rosetta python projects needs 15155.41MB more disk space.You currently have 3918.08 MB available and it needs 19073.49 MB.
02/12/2021 11:32:34 Rosetta@home Message from server: rosetta python projects needs 15828.33MB more disk space.You currently have 3245.16 MB available and it needs 19073.49 MB.


Old thread with Grant leading the answers: [url]https://boinc.bakerlab.org/rosetta/forum_thread.php?id=14537[/url}

Short version, which is what I was thinking MIGHT (no guarantees) help, is to reset the project via BOINC manager. Wipe out all the old information and load a fresh copy in.

One other thing to do as well is use your favorite disk cleaner and clean your drive.
I use Wise and it does a good job. In addition to that I use ccleaner. Wise will let you do a deep clean and cleans stuff that ccleaner wont. Then for sure after you have done this all the garbage will be gone and you can do a reset and try to download again.

Those are the simple steps. If after all that it fails, post the errors here again.
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Message 103674 - Posted: 3 Dec 2021, 0:38:43 UTC

I will have a look at a cleanup and see what happens
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Profile Grant (SSSF)

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Message 103675 - Posted: 3 Dec 2021, 4:59:18 UTC - in response to Message 103670.  

Now I`me getting some nuty messages from the server about disk space and python`s greed for everything
ok, its `only` a 250GB disk but boinc mangler is now set to use all disk space possible {untick all disk space limits boxes, not had to do that before}
rosetta is already using 95GB and boinc mangler reports there is still 64GB free for boinc to use.
so the `currently have` bits are wrong
`it needs19073MB` does it realy , well , its already using 95GB of space , so what is it going on about now
o well more silliness to ignor
Just how munch of everything do the pythons want to eat . . . . .
[and I assure you I have not got my MB and GB mixed up]

01/12/2021 11:41:12 Rosetta@home Message from server: rosetta python projects needs 10252.03MB more disk space.You currently have 8821.45 MB available and it needs 19073.49 MB.
01/12/2021 22:06:01 Rosetta@home Message from server: rosetta python projects needs 16191.05MB more disk space.You currently have 2882.43 MB available and it needs 19073.49 MB.
02/12/2021 10:58:53 Rosetta@home Message from server: rosetta python projects needs 8276.39MB more disk space.You currently have 10797.10 MB available and it needs 19073.49 MB.
02/12/2021 11:09:53 Rosetta@home Message from server: rosetta python projects needs 15155.41MB more disk space.You currently have 3918.08 MB available and it needs 19073.49 MB.
02/12/2021 11:32:34 Rosetta@home Message from server: rosetta python projects needs 15828.33MB more disk space.You currently have 3245.16 MB available and it needs 19073.49 MB.
Keep in mind the "Leave at least xx GB free" and "Use no more than xx% of total" settings as well. You might let it use no more than 500GB, thinking that will allow it to use up tp 500GB, but depending on those other settings it may not have that much available to actually use.

And these values are for BOINC- they are for all of your projects, not just Rosetta.
Apparently Einstein@Home has a tendency to eat up huge amounts of disk space in order to do it's work, and that is one of your other projects.
Grant
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Message 103679 - Posted: 3 Dec 2021, 17:41:08 UTC - in response to Message 103675.  

Now I`me getting some nuty messages from the server about disk space and python`s greed for everything
ok, its `only` a 250GB disk but boinc mangler is now set to use all disk space possible {untick all disk space limits boxes, not had to do that before}
rosetta is already using 95GB and boinc mangler reports there is still 64GB free for boinc to use.
so the `currently have` bits are wrong
`it needs19073MB` does it realy , well , its already using 95GB of space , so what is it going on about now
o well more silliness to ignor
Just how munch of everything do the pythons want to eat . . . . .
[and I assure you I have not got my MB and GB mixed up]

01/12/2021 11:41:12 Rosetta@home Message from server: rosetta python projects needs 10252.03MB more disk space.You currently have 8821.45 MB available and it needs 19073.49 MB.
01/12/2021 22:06:01 Rosetta@home Message from server: rosetta python projects needs 16191.05MB more disk space.You currently have 2882.43 MB available and it needs 19073.49 MB.
02/12/2021 10:58:53 Rosetta@home Message from server: rosetta python projects needs 8276.39MB more disk space.You currently have 10797.10 MB available and it needs 19073.49 MB.
02/12/2021 11:09:53 Rosetta@home Message from server: rosetta python projects needs 15155.41MB more disk space.You currently have 3918.08 MB available and it needs 19073.49 MB.
02/12/2021 11:32:34 Rosetta@home Message from server: rosetta python projects needs 15828.33MB more disk space.You currently have 3245.16 MB available and it needs 19073.49 MB.
Keep in mind the "Leave at least xx GB free" and "Use no more than xx% of total" settings as well. You might let it use no more than 500GB, thinking that will allow it to use up tp 500GB, but depending on those other settings it may not have that much available to actually use.

And these values are for BOINC- they are for all of your projects, not just Rosetta.
Apparently Einstein@Home has a tendency to eat up huge amounts of disk space in order to do it's work, and that is one of your other projects.


I also run Einstein plus ATLAS and I have a way smaller drive than this person does and I don't have this problem.
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Message 103682 - Posted: 3 Dec 2021, 18:06:45 UTC - in response to Message 103679.  

I also run Einstein plus ATLAS and I have a way smaller drive than this person does and I don't have this problem.

I have suggested that he delete all his projects and start over. He obviously has something wrong. It doesn't work.
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Jonathan

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Message 103683 - Posted: 3 Dec 2021, 19:04:09 UTC

Python tasks failing
Error posted inside VM is "Intel MKL FATAL ERROR: Error on loading function mkl_lapack_ps_mc3_dsytrf_l_small."
Stops right after it gives workunit name.

Computer is an old Intel I7-920. I get no cpu usage after hang.
I have removed and reattached project from a December 1 when this first started. I thought maybe it was bad files.

https://boinc.bakerlab.org/rosetta/results.php?hostid=6157362
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Message 103684 - Posted: 3 Dec 2021, 19:53:33 UTC - in response to Message 103683.  

Python tasks failing

I don't see that you have VirtualBox installed.
https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=6157362

But you are better off with VBox 5.2.44 anyway. Version 6.1 gives "Vm job unmanageable" suspensions.
https://www.virtualbox.org/wiki/Download_Old_Builds_5_2
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Message 103686 - Posted: 3 Dec 2021, 20:09:46 UTC - in response to Message 103684.  

Are you thinking of a different project that shows Virtual Box on the computer details page? I don't see it on either of the computer details for mine, nor on the two I check listed under you.
Virtual Box is working on both my computers but I have been sticking to 6.1 since it is supported by Virtualbox. Support was dropped for the earlier versions. I just don't load up my computers to 100 percent processor usage nor juggle too many concurrent VM tasks. These Python / Rosettas are brutal with creating almost 8 Gb images.

I just can't figure out why the one computer is having problems now as it was working with the previous python related tasks.
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Message 103687 - Posted: 3 Dec 2021, 20:18:55 UTC - in response to Message 103686.  
Last modified: 3 Dec 2021, 20:20:42 UTC

Probably so. I usually see VirtualBox listed on most projects.

The memory requirement for downloading the new pythons is now down to 3 GB, and the amount required to run is less than that.
But the .vdi images in the slots are still large. Maybe they will be reduced eventually.

Have you checked BOINC Manager for memory and disk usage allowed? It may not be enough.
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Message 103688 - Posted: 3 Dec 2021, 21:03:38 UTC - in response to Message 103687.  

It's using Rosetta preferences
RAM set to %75 in use and not in use. So can use 9 out of 12Gb. That seems correct as It has 3 tasks. It doesn't keep non running tasks in memory. that box is unchecked.

I think it is something inside the VM. I kind of got spoiled with the LCH Atlas tasks and being able to see the second and third terminals. One for tasks and one showing TOP
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Message 103689 - Posted: 3 Dec 2021, 21:26:47 UTC - in response to Message 103688.  
Last modified: 3 Dec 2021, 21:40:26 UTC

I kind of got spoiled with the LCH Atlas tasks and being able to see the second and third terminals. One for tasks and one showing TOP

While the VBox version won't affect your ability to download, LHC is the only project that uses VBox 6.1 without the suspensions, from what I have seen at any rate.
That is apparently because they use a different wrapper, which I think they compile themselves. At least it is different.

But that is why I went to Win10. It allows the use of VBox 5.2.44, whereas Ubuntu 20.04.3 allows only 6.1.
I haven't had a suspension yet in Win10, though it has been running only a day. But I would normally get several in that time with VBox 6.1.

Unfortunately, it does not solve the "0 CPU" error, where a work unit uses very little (less than 1%) CPU power, and goes on forever, or else times out.
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Message 103692 - Posted: 4 Dec 2021, 0:17:40 UTC - in response to Message 103684.  

Python tasks failing

I don't see that you have VirtualBox installed.
https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=6157362

But you are better off with VBox 5.2.44 anyway. Version 6.1 gives "Vm job unmanageable" suspensions.
https://www.virtualbox.org/wiki/Download_Old_Builds_5_2


I have 6.x and never have this issue with LHC but about half have these issues at Rosetta.. Plenty of place and memory. Rosetta has never had an efficient app.
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Message 103694 - Posted: 4 Dec 2021, 0:26:45 UTC - in response to Message 103692.  

Python tasks failing

I don't see that you have VirtualBox installed.
https://boinc.bakerlab.org/rosetta/show_host_detail.php?hostid=6157362

But you are better off with VBox 5.2.44 anyway. Version 6.1 gives "Vm job unmanageable" suspensions.
https://www.virtualbox.org/wiki/Download_Old_Builds_5_2


I have 6.x and never have this issue with LHC but about half have these issues at Rosetta.. Plenty of place and memory. Rosetta has never had an efficient app.



I run LHC ATLAS and I had to downgrade to run RAH Python.
Python is new to RAH style of computing on PC's.
I've been with this project since almost the beginning and they have never deviated from their base program.
They always have bugs, that's a given. We saw that here, quite a few things went wrong before they got a stable working project.
It's been the same with some of the projects they put out on normal Rosetta.
It's just one of those things that we have to deal with.

As far as the two versions of Vbox, I don't see any difference in the way ATLAS runs on 6 or on 5.
So I will just stick with 5 until a newer version of 6 comes out that may make the errors go away or maybe not.
But it really doesn't seem to make any difference on any of the other 2 Vbox projects I run.
So just down grade to 5 if you want to run Python.
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Message 103695 - Posted: 4 Dec 2021, 0:35:20 UTC - in response to Message 103683.  

Python tasks failing
Error posted inside VM is "Intel MKL FATAL ERROR: Error on loading function mkl_lapack_ps_mc3_dsytrf_l_small."
Stops right after it gives workunit name.

Computer is an old Intel I7-920. I get no cpu usage after hang.
I have removed and reattached project from a December 1 when this first started. I thought maybe it was bad files.

https://boinc.bakerlab.org/rosetta/results.php?hostid=6157362



You might want to research that error. I found quite a few things about it, but it way over my head to understand.
It's quite technical stuff that comes back in the search results.
https://www.google.com/search?client=firefox-b-d&q=%22Intel+MKL+FATAL+ERROR%3A+Error+on+loading+function+mkl_lapack_ps_mc3_dsytrf_l_small
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Message 103696 - Posted: 4 Dec 2021, 1:21:26 UTC
Last modified: 4 Dec 2021, 1:47:57 UTC

At the moment the only projects I am running on that computer are Moo on the gpu and rosetta on cpu
I have not had many disk space messages today though some rosetta 42 work has found its way here, wich eased the problem
I decided not to install any more programs to deleat the disk junk coz they would take up more space on the disk :)
though I know I can uninstall them later
So after the usual microwsoft `disk cleanup` and system files I had a good uninstall of everything I don't need, had a play with the digital chainsaw
and deleted everything that don't have to be on the disk including everything from documents and download folders. that got me 12GB back
even that did`nt get rid of the "disk space" message , though the demands where less.
the thing that finaly shut it up was reducing the virtual memory size on the disk coz it was holding 39GB to ransom and not using it , my account page still shows it as - Swap space 32784.33 MB
its got 32GB ram in it and windows automatically creates a page file 1 1/2 times the size of fitted RAM, give or take a bit
{having remembered the fun I had with win98se all those years ago with running out of memory when it only had 756MB in it to start with}
But you dident need gigabites of memory just to boot the thing back then.
so having read up on how its done these days and chopped it down to a tenth of what it was using
and now have 106GB free disk space even with several greedy python tasks running
I will just have to keep an eye on it and see what happens
.................
Just been to check on it
it last had a disk space moan ten hours ago so that seems to be it for now
Einstein does use the most disk space at 330MB [suspended]
Rosetta [we will all have much the same] is using 49GB
So , yes , rosetta is the disk hog
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Message 103697 - Posted: 4 Dec 2021, 10:15:10 UTC - in response to Message 103696.  

At the moment the only projects I am running on that computer are Moo on the gpu and rosetta on cpu
I have not had many disk space messages today though some rosetta 42 work has found its way here, wich eased the problem
I decided not to install any more programs to deleat the disk junk coz they would take up more space on the disk :)
though I know I can uninstall them later
So after the usual microwsoft `disk cleanup` and system files I had a good uninstall of everything I don't need, had a play with the digital chainsaw
and deleted everything that don't have to be on the disk including everything from documents and download folders. that got me 12GB back
even that did`nt get rid of the "disk space" message , though the demands where less.
the thing that finaly shut it up was reducing the virtual memory size on the disk coz it was holding 39GB to ransom and not using it , my account page still shows it as - Swap space 32784.33 MB
its got 32GB ram in it and windows automatically creates a page file 1 1/2 times the size of fitted RAM, give or take a bit
{having remembered the fun I had with win98se all those years ago with running out of memory when it only had 756MB in it to start with}
But you dident need gigabites of memory just to boot the thing back then.
so having read up on how its done these days and chopped it down to a tenth of what it was using
and now have 106GB free disk space even with several greedy python tasks running
I will just have to keep an eye on it and see what happens
.................
Just been to check on it
it last had a disk space moan ten hours ago so that seems to be it for now
Einstein does use the most disk space at 330MB [suspended]
Rosetta [we will all have much the same] is using 49GB
So , yes , rosetta is the disk hog


That's interesting...I had a look at my RAH folder and its 30.7 GB in size and in compressed form it is 13.7 (size on disk) 5,316 files and 424 folders. I have a smaller drive than you and yet I don't get errors and I am running 7 BOINC projects and FAH plus Facebook and Firefox with many tabs and I don't get a disk space error.

I am beginning to think RAH is having issues with Win7. I use Win 10.
Just a thought.
Which one of your systems is having issues?
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Message 103698 - Posted: 4 Dec 2021, 11:55:36 UTC - in response to Message 103695.  

I aborted all the newer python jobs that started with 'aa'. I got a single 'boinc_cages_IL' job so I kept that one. That one runs fine. I set the computer to not receive VM jobs from Rosetta.
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Message 103699 - Posted: 4 Dec 2021, 12:56:28 UTC

Its windblows 7, opteron16 that has gone funky
I thort I had it fixed, but today its back on python only work ,
11 at once and it is getting the disk space moan again, except even after all that clear out, its got worse !!!??

04/12/2021 10:50:17 | Rosetta@home | Message from server: rosetta python projects needs 16200.20MB more disk space. You currently have 2873.28 MB available and it needs 19073.49 MB.
04/12/2021 12:19:11 | Rosetta@home | Message from server: rosetta python projects needs 16255.39MB more disk space. You currently have 2818.09 MB available and it needs 19073.49 MB.

right now, as far as the OS on drive C, its got 91GB of disk space free
even with the 11 pythons running
so just for interest I have set it off on a full 5 pass disk check to see if it finds anything
funny old world . . . .
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Message 103700 - Posted: 4 Dec 2021, 14:29:04 UTC

Now my pcs have "got 0 new tasks" of python wus, but in the queue there are over 5000 wus...
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Message boards : Number crunching : Problems and Technical Issues with Rosetta@home



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