Supporting SARS-COV2 related research

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rituarora
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Message 247 - Posted: 5 Apr 2020, 1:44:19 UTC - in response to Message 243.  

Greetings,

Just wanted to confirm that we checked the input data for the jobs and the file was indeed corrupted, and hence, the application could not read it.

Thanks,
BOINC@TACC Team

Greetings,

Thanks for reporting the errors with the jobs. It seems like the data file "5r80_apo.pdbqt" either got corrupted or was missing from the submitted job, and due to this the jobs clocked 0 CPU time. Sorry about this. We will check the logs at our end to see what all might have gone wrong with the data.

Best Regards,
The BOINC@TACC Team

I see two strange things in my tasks:

first the tasks are reported with 0.00 CPU time and the log looks also not really convincing with all the errors:

2020-04-04 11:01:02 (2168): Guest Log: Error: could not open "5r80_apo.pdbqt" for reading.

However the WUs are validated which might be the case because I was always my own wingman. So I have just aborted half of my WUs to get it validated by another computer.

Greetings Marcus.
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xRXT2toIGA
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Message 248 - Posted: 5 Apr 2020, 1:45:56 UTC - in response to Message 246.  

Hello,

Thank you for this information. We have seen that some volunteers mentioned that they were able to successfully process jobs while running VirtualBox 6.1.4. However, we have also noticed that some volunteers may experience problems with this due to their operating system such as those running Ubuntu 16.04.
We are looking forward to processing thousands of jobs in the next few days.


Sincerely,
the BOINC@TACC development team
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Henk Haneveld

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Message 251 - Posted: 5 Apr 2020, 17:28:17 UTC
Last modified: 5 Apr 2020, 17:28:58 UTC

Hello Admin,

Altough you have send out several thousands of results I have got only a few.
After some checking I found that some users have got a large numbers of results in their queue.

May I suggest that you implement the max work in progress parameter.
It will give all users a fair change on work and it will lead to a faster turnaround time of work you send out.
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rituarora
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Message 252 - Posted: 5 Apr 2020, 19:37:08 UTC - in response to Message 251.  

Hello Henk,

That is an excellent idea - thanks for mentioning this! We will soon go through the documentation for project options to implement this - perhaps we can limit per BOINC client tasks to 100 (with validation turned on) and see how it goes. There are several thousand jobs that will be submitted in the next few hours. Hopefully, some of them could find their way to your computer/s too.

Best Regards,
The BOINC@TACC Team

Hello Admin,

Altough you have send out several thousands of results I have got only a few.
After some checking I found that some users have got a large numbers of results in their queue.

May I suggest that you implement the max work in progress parameter.
It will give all users a fair change on work and it will lead to a faster turnaround time of work you send out.
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rituarora
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Message 263 - Posted: 6 Apr 2020, 18:44:26 UTC

Thanks to all the volunteers who have helped over the last one week! The researchers using BOINC@TACC have already completed scoring several thousand combinations of receptors and ligands. There are millions of such comparisons that still need to be done. Therefore, wanted to post a quick note to request for your continued support. Additionally, also wanted to mention that some of the initially submitted jobs ended in errors due to input file corruption. We apologize if those erroneous jobs ended on your computers!

Best Regards,
The BOINC@TACC Team
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Message 264 - Posted: 6 Apr 2020, 19:30:39 UTC - in response to Message 263.  

Thanks to all the volunteers who have helped over the last one week! The researchers using BOINC@TACC have already completed scoring several thousand combinations of receptors and ligands. There are millions of such comparisons that still need to be done. Therefore, wanted to post a quick note to request for your continued support. Additionally, also wanted to mention that some of the initially submitted jobs ended in errors due to input file corruption. We apologize if those erroneous jobs ended on your computers!

Best Regards,
The BOINC@TACC Team


Fantastic news. It would be great if statistics export was enabled. I am sure more users would be willing to contribute then.
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xRXT2toIGA
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Message 268 - Posted: 7 Apr 2020, 0:57:37 UTC - in response to Message 264.  
Last modified: 7 Apr 2020, 1:28:53 UTC

Hello,

Thank you all for your continued interest in BOINC@TACC. We have contacted boinctstats regarding adding statistics from those volunteers who agree to show their real username and agree to exporting statistics. Please be assured that your current credit is stored in BOINC@TACC, even if the statistics are not yet being exported.
We will update you all once we receive an answer.

Sincerely,
the BOINC@TACC development team
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Henk Haneveld

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Message 271 - Posted: 7 Apr 2020, 9:22:15 UTC

Admin, I noticed that the project executes a project server call every minute. Why?

I can not find a usefull reason for it. You create a high load on your server without any gain.
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Message 273 - Posted: 7 Apr 2020, 16:20:03 UTC - in response to Message 252.  

Hello Henk,

That is an excellent idea - thanks for mentioning this! We will soon go through the documentation for project options to implement this - perhaps we can limit per BOINC client tasks to 100 (with validation turned on) and see how it goes. There are several thousand jobs that will be submitted in the next few hours. Hopefully, some of them could find their way to your computer/s too.

Best Regards,
The BOINC@TACC Team

Hello Admin,

Altough you have send out several thousands of results I have got only a few.
After some checking I found that some users have got a large numbers of results in their queue.

May I suggest that you implement the max work in progress parameter.
It will give all users a fair change on work and it will lead to a faster turnaround time of work you send out.

Please don't limit work. You ask for volunteers and then when they show up you want to limit the work. Why? I'm getting aggravated at projects that constantly ask for volunteers but can't support the demand. The way to prolong research is to limit the work. Let it flow. I have one machine with 128 threads and anticipate getting another with 256 threads. If you limit it to 100 per boinc client then I'm out. Like I suggested to a few other projects, "Welcome to the big leagues..."
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xRXT2toIGA
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Message 274 - Posted: 7 Apr 2020, 18:55:07 UTC - in response to Message 273.  

Hello,

As there will be a constant flow of work for the next few weeks, if a host is done with processing a set of jobs, the host can always fetch additional work-units. There will be several thousand jobs submitted daily for the next few days.
We will watch the job turn around time with the current setting, and we can always adjust the settings for limiting the number of work-units on a computer at a given point in time. As of now, each host will be able to have 256 active tasks from the queue at any instance of time. If they finish processing for example128 tasks, they can always get additional 128 tasks from the queue. Any volunteer can continue requesting jobs from the queue once they finish processing jobs and stay below the limit.

Sincerely,
the BOINC@TACC development team
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rituarora
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Message 276 - Posted: 7 Apr 2020, 19:09:32 UTC - in response to Message 271.  

Hello Henk,

We had changed this number to check the status of a job every 10 minutes so that, if needed, the in-progress jobs can be canceled. As per the current job-size, we are estimating that each job should take roughly 8-10 minutes to complete depending upon the processor. However, if a job is erroneous (like it happened with some of the previous jobs due to a corrupt input file), the application would stall. Therefore, we thought of polling the clients to check the status.

If you or others have suggestions on alternative ways to handle this, please do let us know - we will be very grateful for any suggestions.

Thanks,
The BOINC@TACC Team



Admin, I noticed that the project executes a project server call every minute. Why?

I can not find a usefull reason for it. You create a high load on your server without any gain.
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rituarora
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Message 277 - Posted: 7 Apr 2020, 19:12:22 UTC - in response to Message 270.  

Hello Greg,

We have contacted some colleagues to post the news about the project on their network. We will post a news on the project website too. If you know of any networks/forums that we can access to post the news, could you please let us know?

Thanks,
The BOINC@TACC Team

Not sure how else you can get the word out to the BOINC community about your COVID research, but now that your up and running, it might be worth getting a blurb on BOINC web or publishing something on your webpage.

Get the news out that you are doing COVID research and watch the computers come flooding in.
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Message 279 - Posted: 7 Apr 2020, 19:23:54 UTC - in response to Message 274.  

Hello,

As there will be a constant flow of work for the next few weeks, if a host is done with processing a set of jobs, the host can always fetch additional work-units. There will be several thousand jobs submitted daily for the next few days.
We will watch the job turn around time with the current setting, and we can always adjust the settings for limiting the number of work-units on a computer at a given point in time. As of now, each host will be able to have 256 active tasks from the queue at any instance of time. If they finish processing for example128 tasks, they can always get additional 128 tasks from the queue. Any volunteer can continue requesting jobs from the queue once they finish processing jobs and stay below the limit.

Sincerely,
the BOINC@TACC development team

Several thousand jobs a day is not that many jobs especially considering they only run 8 to 10 minutes. On my 128 thread machine, that is 768 jobs per hour at 10 minutes each. I could do 10,000 jobs in 13 to 14 hours and that is only one contributor using one machine. How much science is actually getting done at that rate? There are projects out there doing 500,000 to 1,000,000 jobs per day and their projects are years long.
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rituarora
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Message 282 - Posted: 7 Apr 2020, 21:13:02 UTC - in response to Message 279.  

Thanks, that is great to know. We can easily increase the volume of jobs submitted per day by a factor of 4 or 5. However, as the overall turnaround time has been slow so far, we are also using additional resources not connected to BOINC@TACC. We can increase the volume of jobs for BOINC@TACC for the next few days and test the turnaround time again.

Best Regards,
The BOINC@TACC Team


Hello,

As there will be a constant flow of work for the next few weeks, if a host is done with processing a set of jobs, the host can always fetch additional work-units. There will be several thousand jobs submitted daily for the next few days.
We will watch the job turn around time with the current setting, and we can always adjust the settings for limiting the number of work-units on a computer at a given point in time. As of now, each host will be able to have 256 active tasks from the queue at any instance of time. If they finish processing for example128 tasks, they can always get additional 128 tasks from the queue. Any volunteer can continue requesting jobs from the queue once they finish processing jobs and stay below the limit.

Sincerely,
the BOINC@TACC development team

Several thousand jobs a day is not that many jobs especially considering they only run 8 to 10 minutes. On my 128 thread machine, that is 768 jobs per hour at 10 minutes each. I could do 10,000 jobs in 13 to 14 hours and that is only one contributor using one machine. How much science is actually getting done at that rate? There are projects out there doing 500,000 to 1,000,000 jobs per day and their projects are years long.
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rituarora
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Message 283 - Posted: 7 Apr 2020, 21:16:07 UTC - in response to Message 275.  

Thanks, noted the issue and we have it on our priority list. We will post an update once we know the underlying cause. At least one volunteer has confirmed that the jobs are getting processed just fine on their end with VirtualBox 6.1.4.




Team Members,

Just got my first 4 tasks from you guys and 3 errored out and 1 I aborted another due to a technical problem.

If you want us to complete tasks properly, you should ensure that they run on VBOX 6.1.4 before you release them. If you can't make it work with 6.1.4 then I guess I will have to leave the project since all my other projects work fine on 6.1.4, which would be a shame.

I will go look for a technical board to continue this topic in its specifics.
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Message boards : News : Supporting SARS-COV2 related research