boincmgr with rosetta downloaded lots of data and when I rebooted it seemed to start over

Questions and Answers : Unix/Linux : boincmgr with rosetta downloaded lots of data and when I rebooted it seemed to start over

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Macuilxochitl

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Message 96642 - Posted: 20 May 2020, 3:52:01 UTC

I have a Ryzen 5 1600 AF and 'buntu 20.04 and want to contribute to fighting covid. I downloaded boincmgr and attached myself to https://boinc.bakerlab.org/rosetta/

It downloaded a ton of data, over a GB. I guess for most folks that isn't a big deal, but I have funky DSL far from the CO and only get ~200kbps, and the client kept interrupting itself forcing me to manually restart the transfer many times. Finally, after hours I started crunching data and using my 12 cores, I figured I was good to go.

But I'd installed an updated kernel, so I turned the machine off for the evening, and when I rebooted it started over, trying to download another 500MB of data in the Transfers tab of the client. In the Tasks tab it looks like it wants to download another 16 things. When I go to Properties in the Projects page it says I'm using 1.57 GB (which isn't that big a deal) and I've completed 0 tasks and have 27 failed tasks. In the Projects tab it claims my 'Avg. work done' is 0.09, which doesn't sound impressive.

Is this expected behavior? I don't want to pointlessly squander my limited bandwidth, waste electricity and not get anything done. Now boincmgr's Transfers tab is stalled out at 84% but the Status column reads Download: active. Suspending the project does not allow me to Retry and start downloading again. It eventually times out and waits to retry. I can force it to Retry Now, but I'm still getting a speed of 0.00 KBps. But pinging Google shows I have 0% packet loss. Speedtest shows my connection is working:

speedtest-cli --server 3864 --simple
Ping: 52.206 ms
Download: 1.46 Mbit/s
Upload: 0.88 Mbit/s

I understand there has been a major uptick in folding usage, maybe the problem is on your end. This is very frustrating, is there some other project I can contribute to that works on the coronavirus that is a little less finicky and data-intensive?
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Profile Grant (SSSF)

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Message 96649 - Posted: 20 May 2020, 8:55:22 UTC
Last modified: 20 May 2020, 8:56:56 UTC

Do you have another account here? Because there is no sign of any computers on the account you used to post here, let alone them having got any work, or produced any errors.

When you first join a project (any project) there will be a lot of downloading as not only do you have to get Tasks to process, you also need to get the applications to process them. Different types of Tasks will also require different support files.
However once all of these files have been downloaded, then the actual data files downloaded to process are generally only a few hundred kB- although the result files being sent back can be as much as 30MB (some times more), usually a lot less.

If file transfers tend to be sticky (it says it's uploading/downloading but nothing is actually happening), in the BOINC Manager (Advanced view), Activity, select "Suspend network activity", then re-select "Network activity based on preferences".


It may also be necessary to use a proxy server to work around the problems with your net connection.
Grant
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Message 96662 - Posted: 20 May 2020, 15:05:46 UTC

The BOINC Manager will take care of retrying downloads that get interrupted. BOINC also has settings where you can limit bandwidth usage if you like. "Avg. work done" is over the last 10 days, and during most of those, it sounds like you did no work because you were not attached to the project, so sort of a meaningless number hours after you signup.
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Macuilxochitl

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Message 96683 - Posted: 20 May 2020, 23:33:09 UTC - in response to Message 96649.  

Here is the Properties for my Rosetta@home Project tab.
General
URL
https://boinc.bakerlab.org/rosetta/
User name
Macuilxochitl
Team name
Resource share
100
Scheduler RPC deferred for
01:07:09
Disk usage
1.82 GB
Computer ID
4432863
Suspended via GUI
no
Don't request tasks
no
Host location
default
Tasks completed
9
Tasks failed
57
Credit
User
20,818 total, 55.83 average
Host
588 total, 55.83 average
Scheduling
Scheduling priority
-1.01
Don't request tasks for NVIDIA GPU
Project has no apps for NVIDIA GPU
Last scheduler reply
Wed 20 May 2020 12:27:11 PM PDT

As you can see I'm using 1.82 GB of disk space and it seemed like I downloaded something like that in data. Rosetta is the only project I have attached to boincmgr. It looks like I'm finally cranking through some work. My failed Tasks added another 31 to 57, I'm not sure what is going on there. My username 'Macuilxochitl' appears to be the same as my name on this board. My user ID appears to be 2157465. I've devoted 100% of my resources to https://boinc.bakerlab.org/rosetta

But it looks like my machine is now cranking out work units. I'd kind of wanted to work on COVID 19 for personal reasons, but I'm apparently working on 3-dimensional shapes of proteins, but I guess that is OK. I'll let this unit finish in the next 2-3 hours and see if I have to download another big dollop of data. Also, if I don't, I'll try rebooting and see if I have to start over downloading large amounts.
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Macuilxochitl

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Message 96684 - Posted: 21 May 2020, 4:35:50 UTC - in response to Message 96683.  

Well, rosetta@home took up where it left off after a reboot, I guess everything is ducky. But I've used various boinc clients intermittently over the last 15-20 years and never had this much of a PITA getting it up and running before, the downloads were brutal.
Do you have another account here? Because there is no sign of any computers on the account you used to post here, let alone them having got any work, or produced any errors.

When I hit the 'Your Account' button in the advanced Projects tab it takes me to this web site and my computer is obviously thrashing around, seems like I'm using about 55-60% of my CPUs (according to mpstat) and BOINC seems to really like to gobble RAM, I think its using about 5GB, and my previous session I was up to using a system total of 10GB (a personal record!):
$  ps aux  | awk '{print $6/1024 " MBtt" $11}'  | grep boinc | sort -n
19.6133 MB              /usr/bin/boinc
104.738 MB              /usr/bin/boincmgr
374.59 MB               ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu
403.539 MB              ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu
1016.75 MB              ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu
1018.41 MB              ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu
1019.94 MB              ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu
1142.95 MB              ../../projects/boinc.bakerlab.org_rosetta/rosetta_4.20_x86_64-pc-linux-gnu

boincmgr says I've done 22,899 work and my Avg. work done is 259, whatever that means, but according to the linked "Your account" page I don't seem to be doing much of anything:
Total credit 	0
Recent average credit 	0.00
Computers on this account 	blank
Tasks 	blank

That seems a little weird. I don't care about credit, but I hope my computer time is not going to /dev/null
Should I be concerned?

Anyway, I'm going to shop around for a couple of case fans and see if I can increase the 60% of my processors that are being devoted to folding, I seem to have hit a thermal wall (my CPU is at 80C).
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Profile Grant (SSSF)

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Message 96686 - Posted: 21 May 2020, 7:56:23 UTC - in response to Message 96684.  
Last modified: 21 May 2020, 7:58:47 UTC

Should I be concerned?
Yes, you need to figure out how many accounts you have, and what they are.
The account you are posting here with has no computers doing any work at all (as the linked to Account page shows), you need to log in to the project using the name & email address that you used to attach the computer to Rosetta that is presently processing work.
Grant
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Macuilxochitl

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Message 96689 - Posted: 21 May 2020, 10:18:05 UTC - in response to Message 96686.  

As far as I can tell I registered with rosetta exactly once and the boincmgr links to this account that I'm posting from.

This has been too much of a PITA.

shutdown -h +200

That should shut my machine down after my box is finished with the task I'm working on. and will give the both a reasonable time to upload the results

Then:

Wipe the rosetta project with boincmgr

apt-get purge boinc*

Then I will reinstall boinc and try starting over with a fresh account. If that doesn't work any better than this has, I've download the folding@home deb file and can give it a throw, but I gather than folding is more GPU-centric than boinc and I have a fairly anemic GK208B video card.
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Profile Grant (SSSF)

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Message 96691 - Posted: 21 May 2020, 10:48:01 UTC - in response to Message 96689.  

Then I will reinstall boinc and try starting over with a fresh account.
Or just attach to the project with the account you are using here.
Grant
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Macuilxochitl

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Message 96713 - Posted: 22 May 2020, 0:05:29 UTC - in response to Message 96691.  

Grant, I hate to waste all the time and bandwidth I spent setting this up, it would be helpful if you could tell me exactly how to attach to the project with this account. It isn't obvious to me.

This is what happened when I tried to attach using the key from https://boinc.bakerlab.org/rosetta/home.php:

~$ boinccmd --project_attach https://boinc.bakerlab.org/rosetta MYKEYFROMYOURACCONTPAGE
21-May-2020 16:35:24: GUI RPC error: Already attached to project
Operation failed: already attached to project


So I tried this command:
$  boinccmd --lookup_account https://boinc.bakerlab.org/rosetta MYEMAIL@SOMEWHERE.com MYPASSWORD
status: Success
poll status: operation in progress
account key: SOME_COMPLETELY_DIFFERENT_KEY

$ [i]boinccmd --project_attach https://boinc.bakerlab.org/rosetta SOME_COMPLETELY_DIFFERENT_KEY[/i]
21-May-2020 16:41:13: GUI RPC error: Already attached to project
Operation failed: already attached to project

Great.
$     boinccmd --get_state
======== Projects ========
1) -----------
   name: Rosetta@home
   master URL: https://boinc.bakerlab.org/rosetta/
   user_name: Macuilxochitl
   team_name: 
   resource share: 100.000000
   user_total_credit: 26253.309237
   user_expavg_credit: 560.492141
   host_total_credit: 6023.143093
   host_expavg_credit: 560.492141
   nrpc_failures: 0
   master_fetch_failures: 0
   master fetch pending: no
   scheduler RPC pending: no
   trickle upload pending: no
   attached via Account Manager: no
   ended: no
   suspended via GUI: no
   don't request more work: no
   disk usage: 0.000000
   last RPC: Thu May 21 16:15:31 2020

   project files downloaded: 0.000000
GUI URL:
   name: Message boards
   description: Correspond with other users on the Rosetta@home message boards
   URL: https://boinc.bakerlab.org/rosetta/forum_index.php
GUI URL:
   name: Your account
   description: View your account information
   URL: https://boinc.bakerlab.org/rosetta/home.php
GUI URL:
   name: Your tasks
   description: View the last week or so of computational work
   URL: https://boinc.bakerlab.org/rosetta/results.php?userid=283434
   jobs succeeded: 17
   jobs failed: 58
   elapsed time: 585442.120870
   cross-project ID: b234b0bee793944832bb02a56190d855

======== Applications ========
1) -----------
   name: rosetta
   Project: Rosetta@home

======== Application versions ========
1) -----------
   project: Rosetta@home
   application: rosetta
   platform: x86_64-pc-linux-gnu
   version: 4.20
   estimated GFLOPS: 2.78
   filename: rosetta_4.20_x86_64-pc-linux-gnu

======== Workunits ========
1) -----------
   name: Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_3mi5lf1n_929381_18
   FP estimate: 8.000000e+13
   FP bound: 1.000000e+17
   memory bound: 1716.61 MB
   disk bound: 1716.61 MB
----
======== Tasks ========
1) -----------
   name: Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_3mi5lf1n_929381_18_1
   WU name: Junior_HalfRoid_design6_cart_COVID-19_SAVE_ALL_OUT_IGNORE_THE_REST_3mi5lf1n_929381_18
   project URL: https://boinc.bakerlab.org/rosetta/
   received: Wed May 20 16:46:38 2020
   report deadline: Sat May 23 16:46:38 2020
   ready to report: no
   state: downloaded
   scheduler state: scheduled
   active_task_state: EXECUTING
   app version num: 420
   resources: 1 CPU
   estimated CPU time remaining: 16102.080000
   slot: 4
   PID: 3736
   CPU time at last checkpoint: 15733.360000
   current CPU time: 15874.380000
   fraction done: 0.440900
   swap size: 1350 MB
   working set size: 1208 MB
...
======== Time stats ========
  now: 1590104715.493604
  on_frac: 0.901893
  connected_frac: -1.000000
  cpu_and_network_available_frac: 0.987368
  active_frac: 0.987368
  gpu_active_frac: 0.829332
  client_start_time: Thu May 21 16:14:51 2020

  previous_uptime: 30987.510875
  session_active_duration: 1787.619883
  session_gpu_active_duration: 0.000000
  total_start_time: Mon May 18 16:48:52 2020

  total_duration: 161704.501342
  total_active_duration: 150230.505758
  total_gpu_active_duration: 20.217683

What am I doing wrong?

At least the 'boinccmd --get_state' implies that I'm working on COVID, which was my main goal. But it would be nice to know if the work I am doing is actually being used.
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Profile Grant (SSSF)

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Message 96718 - Posted: 22 May 2020, 7:58:21 UTC - in response to Message 96713.  

What am I doing wrong?
No idea.
I have only ever used the graphical Manager. I left the command line behind a very long time ago.


The other option would be instead of posting here using this present account, log off from the site, and log back on using the account the computer is using (that actually makes more sense, as the other account will have all the history of the work the computer has done, where as this account doesn't have any processing history *slaps self*).
Grant
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Macuilxochitl

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Message 96730 - Posted: 22 May 2020, 18:57:08 UTC - in response to Message 96718.  

I'm probably capable of handling the GUI, what exactly are the instructions I'm supposed to follow?

bonicmgr currently tells me it has a dollop of data ready to report.

https://ibb.co/3NMbpz8

But when I click on 'Your tasks' on the Tasks tab of bonicmgr I it takes me to my default browser with this helpful message:

Unable to handle request
No access


https://ibb.co/f1LxZrf

I still have no idea if my work is being processed or used of if I'm just contributing to making up the 17% deficit of greenhouse gases caused by Covid slowing down the economy.
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Profile Grant (SSSF)

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Message 96739 - Posted: 22 May 2020, 23:05:52 UTC
Last modified: 22 May 2020, 23:07:21 UTC

OK, from what you have posted previously,

$     boinccmd --get_state
======== Projects ========
1) -----------
   name: Rosetta@home
   master URL: https://boinc.bakerlab.org/rosetta/
   user_name: Macuilxochitl
   team_name: 
   resource share: 100.000000
   user_total_credit: 26253.309237
   user_expavg_credit: 560.492141
   host_total_credit: 6023.143093
   host_expavg_credit: 560.492141

GUI URL:
   name: Your tasks
   description: View the last week or so of computational work
   URL: https://boinc.bakerlab.org/rosetta/results.php?userid=283434
   jobs succeeded: 17
   jobs failed: 58
   elapsed time: 585442.120870
   cross-project ID: b234b0bee793944832bb02a56190d855
So work is being done, and it is earning Credit for that computer on that account.

The user ID for that account is
283434

The user ID for the account you are posting with here is
2157465


So it looks like you've had an account for quite some time, for some reason you then created a new account- but your computer is still on the old account. But since you have logged in here with the new account, you can't see the computer. And when you go to check out your account using the BOINC Manager on the computer, you can't- because you are not logged in on that account.

If you click on "Log out" at the top right hand corner of this page, that will log you out from this web site using the new account.
If you then follow Step 2 below, that should allow you to log back in using your original account, the one that has the computer on it.
Forgot your account info?

You might wan to triple check everything before doing it (i just got up & i'm still not quite awake yet; it's been a looooong and tiring week), but it should get you logged in to this website using the account that your computer is on.
Grant
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Macuilxochitl

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Message 96741 - Posted: 23 May 2020, 2:01:56 UTC - in response to Message 96739.  

Alright, thanks, that seemed to work. I'm not sure why I have 2 accounts. When I set up BOINC on this box I tried to log in with the username and password I had on record from 12 years ago, but it rejected my password, so I asked to reset my password, but for some reason it seemed to create a second account, I'm not sure what happened, but now everything seems ducky. At least I have some confidence that my computer work is being used.

I just ordered 3 case fans, so we'll see if I can begin to really do some crunching.
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Message 96742 - Posted: 23 May 2020, 2:26:21 UTC

Glad you got that sorted.
Now you can start hunting down what is going on with the system- it's putting out a lot of errors.
Grant
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Macuilxochitl

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Message 96743 - Posted: 23 May 2020, 5:19:43 UTC - in response to Message 96742.  

I see the errors in the manager, but I wouldn't know where to look for the source. Maybe it is because I am using the proprietary Nvidia (linux) graphics driver? I guess I could try some memtest.

I'm not seeing anything in the GUI Event log that flags my attention. If I were going to guess I'd say maybe the errors I was getting trying to transfer data to and fro given my marginal internet connection is to blame.

I took a cursory look in my home directory but didn't see any log file to examine. Can you suggest where I might look?
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Message 96744 - Posted: 23 May 2020, 6:07:18 UTC - in response to Message 96743.  
Last modified: 23 May 2020, 6:09:43 UTC

Can you suggest where I might look?
Unfortunately Linux error messages see to be on par with old DOS ones- next to useless.
It's very unlikely to be related to the video driver (possible, but very unlikely). And the internet issues are also not likely to be the cause- the files were downloaded OK. While several Tasks crashed & burned straight away, others started processing and then crashed. But it is a possibility.
One or 2 of the errors appear to be related to the Tasks themselves- there are issues with some of the Work Units, but all of the others are dying only on your system.


A quick search shows that "process got signal 11" errors are either a problem with the programme (yet others aren't having the issues you are), or it's a hardware problem.

Since you've got your account sorted out, and hopefully the internet issues sorted out, the usual suggested fix it is to Reset project (on the BONC Manager Project tab).
What it does is clears out all of your local files (data and application) for the project, then re-downloads new copies, then downloads new Tasks to process. Given you have had internet issues, it is possible a file or two is corrupted & is responsible for your high error count.
This should eliminate the Rosetta software/libraries/databases being at fault.

If after doing that the problems still occur, then it's a case of testing RAM, making sure the CPU isn't overheating. possibly even turning off hyperthreading & see how things go- with that number of cores & threads, your present system RAM will result in some memory issues as some Tasks can require as much as 3GB of RAM. You generally need to allow for 1.3GB of RAM per core/thread in use to avoid running in to memory limitation issues. But it shouldn't result in the errors that you are seeing.
It's also worth checking the rails of your power supply- if the voltages are dropping under load, that can also result in "process got signal 11" errors.
Grant
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Message 96775 - Posted: 25 May 2020, 6:10:19 UTC - in response to Message 96744.  

Well, I let my work unit finish and then Reset the project, as suggested. It has been cranking for 3.5 hours and the 'tasks failed' has remained at 82, so maybe that did the trick. I'll keep an eye on it. It could be the rocky upload may have been to blame. I stuck a USB wifi dongle on the machine and used my neighbor's much faster internet connection to download my work, which went quickly without any interruptions, so maybe it was cleaner.

I've got some fans on the way, maybe it will reduce my temps from ~70c, though that doesn't seem excessive. I don't think the RAM is a limiting factor, I've never gone past 10 GB out of 16, but I guess I could stick in another 8 GB at some point if it becomes an issue. I really hope the power supply is not an issue, those suckers are expensive at the moment. Also, maybe a source of error is that my Geforce 730 GT is a refurb I got for $20. But I get the impression that the GPU isn't that important for Rosetta. Still, Nvidia is a crummy choice for Linux, and I get screen weirdness way to often. I wish I could find a cheap AMD processor and use the open source driver, but unfortunately, desktop display adapters are largely a thing of the past. Folks that are not gaming use onboard graphics, which is actual faster than this damn card anyway, and it is hard to find a decent video card for < $80 or so.
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Message 96776 - Posted: 25 May 2020, 6:15:22 UTC - in response to Message 96775.  

AMD processor AMD video card
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Message 96801 - Posted: 27 May 2020, 1:05:51 UTC - in response to Message 96776.  

Man, this simultaneously sucks and blow, not unlike the two case fans I just installed to make boinc work better.

Errors are ongoing, for a minute I thought I was through that, but I'm gone from 82 to 115 since I reset the project without increasing my completed units from 26. And now it looks like my communication with rosetta is mucked up again, the Transfers tab show my Download is pending. Specifically: "Download: pending (project backoff: 00:30...." This is using a wifi dongle and my neighbor's much faster wire, speedtest says: Download: 42.18 Mbit/s

Oh well, at least my new blue LED fan is pretty. Guess I'll try some memtest before I give up on the project. Ah, the download just restarted and mostly went comfortably until it got to the last tiem in the Transfers tabs, then it stopped again, but after a minute it retried and now I'm cranking again. My temps went right back up to 73C. despite the new fans, but it looks like I'm using a greater percent of my CPU according to htop. Ah crap, while I was typing my CPU use dropped off again and now I'm getting: Status: Communication deferred... Oh well. I'll report back after running memtest.
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Macuilxochitl

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Message 96802 - Posted: 27 May 2020, 1:16:42 UTC - in response to Message 96801.  

https://imgur.com/ViVw0CA

Oy.
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Questions and Answers : Unix/Linux : boincmgr with rosetta downloaded lots of data and when I rebooted it seemed to start over



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