Posts by robertmiles

1) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 102615)
Posted 5 days ago by Profile robertmiles
Post:
Prophylaxis, treatment with probenecid inhibits 'virus replication' in COVID-19, flu, RSV

https://www.healio.com/news/rheumatology/20210910/prophylaxis-treatment-with-probenecid-inhibits-virus-replication-in-covid19-flu-rsv?utm_source=selligent&utm_medium=email&utm_campaign=news&M_BT=6620114329042
2) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102606)
Posted 5 days ago by Profile robertmiles
Post:
[snip]

ERROR: [ERROR] Unable to open constraints file: m_ems_3hC_506_000000211_0001_43_58_H_._HHH_b2_02864_0001_1_0001.MSAcst

What to do?

That's the important line of the error messages.

That usually means that one of the input files for the task was not downloaded correctly.

Lately, that has often been because the file was not in the correct place on the server. If so, you can't do much other than wait for a better task.

If anyone else who gets a task from the same workunit and has it fail the same way, you'll get a little bit of credit for trying to run the task.
3) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102587)
Posted 9 days ago by Profile robertmiles
Post:
[snip]

When my devices complete a task, they seem to prefer downloading WCG tasks over Rosetta ones. I do NOT have a bunch of tasks piled up. With my current settings BOINC only downloads new tasks if the current ones are almost complete.

WCG usually has more tasks available. Lately, Rosetta usually doesn't.
4) Message boards : Rosetta@home Science : More metal-binding proteins? (Message 102561)
Posted 11 days ago by Profile robertmiles
Post:
At least one is nickel-binding.
5) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 102553)
Posted 11 days ago by Profile robertmiles
Post:
[snip]

Who knew proteins were so uncomplicated that they could accidentally bind to all manner of other proteins? There was me thinking it was pretty hard binding tightly to one.
I think "mini" is a relative concept here.
And I'm sure toxicity is a subject that's come up before.

I'd say that it's hard to find something that will bind tightly to a SPECIFIC protein. However, there's quite a large number of types of proteins in the human body. Toxicology tests are needed to make sure that the substance being tested will not also binding tightly enough to any of these other proteins to cause problems.
6) Message boards : Rosetta@home Science : Structure prediction of zinc-binding proteins (Message 102543)
Posted 14 days ago by Profile robertmiles
Post:
Is protein-bound zinc involved?

Scientists reveal the secrets behind ant teeth super strength

https://www.msn.com/en-us/news/technology/scientists-reveal-the-secrets-behind-ant-teeth-super-strength/ar-AAO4JCk?ocid=NL_ENUS_A1_20210905_12_2
7) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102542)
Posted 15 days ago by Profile robertmiles
Post:
Been getting lots of errors recently:

degrader_site_5nvx_jhr_bcov3_SAVE_ALL_OUT_IGNORE_THE_REST_1co8fa9r_1729406_12_1
[code]<core_client_version>7.16.11</core_client_version>

[snip]

I've been seeing a lot of those lately, all in tasks with _5nvx_ in their names. Does that mean that whoever created that group of workunits needs to pay more attention in class?
8) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102473)
Posted 24 days ago by Profile robertmiles
Post:
Hi, for me, for a setting time of 12h , some of them just run in 8h !

Typical if it finishes its list of possible decoys in 8 hours.

Also expected if at the end of a decoy it calculates the time expected to do one more decoy and it would put the total time too far past the time you set.
9) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102472)
Posted 24 days ago by Profile robertmiles
Post:
[snip]

Thannk you, this is super helpful and I will do so.
I don't think some of these tasks are going to complete in time for the deadline without checkpointing. I'm going to try and keep the client running but they're also using pretty excessive amounts of ram.
I thought the quorum for each task (number of machines to complete) needed to be 1? Or do you mean others, apart from myself, also get this task, in case I don't complete it first?

The usual quorum used to be two, but has often been 1 lately. A quorum of 1 is adequate only for tasks for which some quick method of checking the output of the task is available. If the quorum is 2, the first two sets of task output files returned must agree enough before they are considered validated. If they don't agree enough, one more task is sent out to determine which of the first two tasks is correct enough to be validated. The purpose of the quorum is to check whether the task or tasks returned correct outputs, even if the task did not detect an error. Sometimes, a workunit with an error in its input files will give some credit if other tasks for that same workunit agree on detecting the error.

Usually, the first group of tasks sent out has as many tasks as the quorum, so if the quorum is greater than one, at least one other person will also get a task for that workunit. For each task that goes past its deadline, one more task for that workunit will be sent out. You have a head start on any task sent due to another task reaching its deadline, and therefore some chance of still returning it in time.

If the tasks are using excessive amounts of RAM, you may need to tell BOINC to reduce the number of tasks it is allowed to run at the same time, so that the reduced number will fit in the amount of RAM you have available.

I normally keep my computer running and doing BOINC work day and night, so it can handle tasks that go over 24 hours between checkpoints.
10) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102461)
Posted 25 days ago by Profile robertmiles
Post:
Several of these tasks that are running for twice my set computation time and not checkpointing to boot. I hope I get some sort of credit for these.


Application
Rosetta 4.20
Name
rb_08_23_108315_111529_ab_t000__robetta_cstwt_5.0_FT_IGNORE_THE_REST_06_05_1729195_676

[snip]

Rosetta@Home tasks have sections known as decoys. The decision on whether to end the task normally occurs only at the end of a decoy.

Your very long run time looks like you got at least one task with a very long time per decoy.

I have no information on whether checkpoints are also written only at the ends of decoys. However, if so, this is probably why you also had the long time with no checkpoints.

You might want to read the log file from that task to check whether it completed only one decoy.

Also check if you can read the log files from any other tasks for that workunit. If all of them were that slow, expect to get some credit as long as you either returned it by the deadline, or returned it before the quorum was met.
11) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102416)
Posted 17 Aug 2021 by Profile robertmiles
Post:
I've been getting several batches of Rosetta work, but they all crash immediately they start,

The error message I'm getting is this one - is it only my system or everyone?

17/08/2021 19:47:28 | Rosetta@home | [error] Signature verification failed for database_357d5d93529_n_methyl.zip


I'd like to report it quickly, but I've had several problems with my PC recently and don't want to say something that's only a local problem to me.

I looked at the log files. All the errors appear to be due to a problem with the database file shared by all of the failed tasks.

I'd recommend a reset project to replace all of the shared file, since there doesn't appear to be a way of replacing just one of the shared files.
12) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102374)
Posted 10 Aug 2021 by Profile robertmiles
Post:
Not a new problem. It often and it last many days. Not very serious! :-(
I had to go back to W,C,G.

W.C.G. is now almost out of tasks, so you may need to add another project.
13) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102359)
Posted 7 Aug 2021 by Profile robertmiles
Post:
Finally got my machine to start downloading tasks again (Problem at Boincstats) and now everything it's downloading is failing after a short computation time. Is there a way around this issue?

Errors after very short computation times are usually due to errors in one of the input files. In that case, not much can be done except to have the project staff cancel every task that shares the defective input file. Getting them to notice the need to do do is usually quite difficult.

I saw two of the last batch I got fail quickly, but the other five have been running for an hour. This may mean that they have filtered out some, but not all, of the tasks with defective inputs.
14) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102349)
Posted 7 Aug 2021 by Profile robertmiles
Post:
Are we out of work units? I haven't gotten any in a while.

I have noticed that completing a GPU task tends to restrict your computer from downloading any CPU tasks for a few days.
15) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 102344)
Posted 6 Aug 2021 by Profile robertmiles
Post:
Licensed drug could reduce SARS-CoV-2 infection by up to 70 per cent, reveals study

https://www.eurekalert.org/news-releases/924448
16) Message boards : Rosetta@home Science : More metal-binding proteins? (Message 102343)
Posted 6 Aug 2021 by Profile robertmiles
Post:
Plant-based metal? The mining industry could get a sustainable makeover.

https://grist.org/science/phytomining-nickel-kinabalu-park-malaysia/

Nothing mentioned about whether proteins are involved, but it looks worth checking.
17) Message boards : Number crunching : Problems and Technical Issues with Rosetta@home (Message 102297)
Posted 28 Jul 2021 by Profile robertmiles
Post:
[snip]

It's important to note that in the helical tasks, my 3600 actually appears to be doing more work (more decoys generated), it's just being granted less credits.

If there is actually a bug, do I want it to be fixed? Yes. Do I think it is an issue Rosetta should focus on? No.

Note that not all decoys do the same amount of work, so less credit per decoy is not necessarily meaningful.
18) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 102194)
Posted 9 Jul 2021 by Profile robertmiles
Post:
What The Lambda COVID-19 Variant Means For Us Right Now

https://www.huffpost.com/entry/lambda-covid-19-variant_l_60e71fb6e4b01d28533e6bb3
19) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 102193)
Posted 8 Jul 2021 by Profile robertmiles
Post:
New Vaccine Blocks COVID-19 and Variants, Plus Other Coronaviruses

https://corporate.dukehealth.org/news/new-vaccine-blocks-covid-19-and-variants-plus-other-coronaviruses


Tofacitinib lowers risks for death, respiratory failure in COVID-19 pneumonia

https://www.healio.com/news/rheumatology/20210623/tofacitinib-lowers-risks-for-death-respiratory-failure-in-covid19-pneumonia?utm_source=selligent&utm_medium=email&utm_campaign=news&M_BT=6620114329042


FDA issues EUA for tocilizumab to treat patients hospitalized with COVID-19

https://www.healio.com/news/rheumatology/20210625/fda-issues-eua-for-tocilizumab-to-treat-patients-hospitalized-with-covid19?utm_source=selligent&utm_medium=email&utm_campaign=news&M_BT=6620114329042
20) Message boards : Rosetta@home Science : Interesting starting point for attacking Coronavirus (Message 102101)
Posted 21 Jun 2021 by Profile robertmiles
Post:
Biden Administration Unveils $3.2 Billion Hunt For Pill To Treat COVID-19, Other Viruses

https://www.huffpost.com/entry/covid-19-antiviral-pill-biden_n_60cbf90de4b01af0c26e5662


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