Posts by Michael H.W. Weber
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1) Message boards : Number crunching : NO new work. (Message 2841)
Posted 9 Dec 2016 by Profile Michael H.W. Weber
I noticed that the project name has changed in my local BOINC manager but not on the website. Moreover, although the team name is correctly indicated in my project's web account, in the local BOINC manager no team is shown at all.
What is happening?

Michael.
2) Message boards : News : Database change (Message 2807)
Posted 3 Dec 2016 by Profile Michael H.W. Weber
Although the team name is correctly indicated in my account, in the local BOINC manager no team is shown.
Also, the project name has changed in BOINC but not on the website.
What is going on?

Michael.
3) Message boards : Science : what is difference from this project and one on world community grid (Message 2288)
Posted 22 Apr 2015 by Profile Michael H.W. Weber
Thank you for the feedback. ;-)

Michael.
4) Message boards : Science : what is difference from this project and one on world community grid (Message 2285)
Posted 20 Apr 2015 by Profile Michael H.W. Weber
Any comments, please?

Michael.
5) Message boards : Number crunching : Crediting system inconsistent? (Message 2267)
Posted 11 Apr 2015 by Profile Michael H.W. Weber
p.s.: Derzeit sind die Credits sviw. linear von den Torsions abhaengig, sie sollten aber etwa kubisch davon abhaengig sein. Zudem sind sie noch bei 100 gedeckelt und der Einfluss der Rezeptoren wird ueberhaupt nicht beruecksichtigt. Die Laufzeitschaetzung ist derzeit eine Konstante. Beides ist in Arbeit und es wird im naechsten Batch sehr viel besser. Siw. sind die entsprechenden Funktionen bereits im WU-Generator eingebaut, sie wirken aber natuerlich erst, wenn neue WUs generiert werden. Moeglicherweise wird es dann noch etwas Feintuning brauchen, aber besser als jetzt duerfte auch der erste Wurf bereits werden.

Gut. Danke für Die Infos, Volker.
Insbesondere eine Aufhebung der Deckelung bei 100 sollte wohl flugs implementierbar sein - das ist schon arg auffällig, wenn ich mir überlege, dass beispielsweise der Rechenaufwand meiner aktuell in Berechnung befindlichen 12,5 Std. WU am Ende dann bestenfalls mit ganzen 100 Punkten korreliert wird. LOL. Na, wat soll's...

Michael.
6) Message boards : Science : Future possibilities (Message 2264)
Posted 11 Apr 2015 by Profile Michael H.W. Weber
For bacteria, at least to my point of view, the most promising drug compounds are those that act by destroying the organism's cell walls. Bacteriophages (viruses selectively infecting bacteria, even all those antibiotic-resitant ones) provide a whole battery of genes ecoding functions involved in just doing that. So, they may serve as excellent working examples to copy from.

Michael.

P.S.: Plasmodium is of course a different story.
7) Message boards : Science : what is difference from this project and one on world community grid (Message 2263)
Posted 11 Apr 2015 by Profile Michael H.W. Weber
The main advantage we have over the GFAM project is that we KNOW that the compounds we're using already work against malaria. If we figure out which protein they inhibit, then that will open up whole fields of research...

...yes, it certainly would, but:

The main disadvantage is that we will never be able to cover the whole proteome. Some proteins are naturally disordered, and will remain opaque to crystallography or modelling. But we'll give it our best shot. We've already got structures (X-ray or models) for 1426 of the 5,363 proteins (26%), and we'll continue to do modelling of the more difficult proteins.

Of these 1426 protein structures you mentioned, how many were experimentally determined (x-ray, NMR) and how many were (just) computer models (which makes docking difficult / unreliable)?
And regarding the computer models, who modeled these (your group and/or public database ressources?) and with which algorithms / software?
And of these models, how many are based on homology modeling and how many on de novo / ab initio modeling?

Michael.
8) Message boards : Number crunching : WU validation (Message 2262)
Posted 11 Apr 2015 by Profile Michael H.W. Weber
Could someone please explain to me how exactly the incoming results are validated? I mean, these are not like prime number which could be directly compared, so I am a bit curious about the mechanism employed for this problem.

Michael.
9) Message boards : Number crunching : Crediting system inconsistent? (Message 2261)
Posted 11 Apr 2015 by Profile Michael H.W. Weber
...and let me add beforehand: Credits are of minor importance to me. I was just wondering what's the reason for this observation which I made when checking proper completion of one of my (very long running) WUs.

Michael.
10) Message boards : Number crunching : Crediting system inconsistent? (Message 2260)
Posted 11 Apr 2015 by Profile Michael H.W. Weber
In the following stats excerpt of one of my machines (identical hardware for all data shown) you can see that, among other things, same credits are given for WUs that vastly differ in runtime.

Gültig tasks for computer 73852 Task anklicken für Einzelheiten Zeige Namen Arbeitspaket anklicken für Einzelheiten Gesendet Meldezeit oder Ablaufdatum Erklärung Status Laufzeit (sek) CPU Zeit (sek) Punkte Anwendung 28686663 24979572 10 Apr 2015, 6:27:31 UTC 11 Apr 2015, 0:24:03 UTC Fertig und Bestätigt 191.96 183.83 15.00 Autodock Vina v1.01 28686664 24979574 10 Apr 2015, 6:27:31 UTC 10 Apr 2015, 15:16:11 UTC Fertig und Bestätigt 262.49 236.90 15.00 Autodock Vina v1.01 28212286 23823093 1 Apr 2015, 3:52:05 UTC 7 Apr 2015, 15:55:27 UTC Fertig und Bestätigt 7,962.97 6,242.71 53.00 Autodock Vina v1.01 28212287 23823181 1 Apr 2015, 3:52:05 UTC 7 Apr 2015, 13:52:54 UTC Fertig und Bestätigt 3,986.80 3,947.89 53.00 Autodock Vina v1.01 28209205 23780657 1 Apr 2015, 1:59:49 UTC 7 Apr 2015, 12:46:27 UTC Fertig und Bestätigt 99.50 94.65 15.00 Autodock Vina v1.01 28206849 23745313 1 Apr 2015, 0:27:34 UTC 7 Apr 2015, 15:40:10 UTC Fertig und Bestätigt 34,877.77 33,683.33 100.00 Autodock Vina v1.01 28206865 23745306 1 Apr 2015, 0:27:34 UTC 7 Apr 2015, 12:44:47 UTC Fertig und Bestätigt 24,447.25 24,204.30 100.00 Autodock Vina v1.01 28205789 23734008 31 Mar 2015, 23:56:46 UTC 7 Apr 2015, 5:59:59 UTC Fertig und Bestätigt 329.71 319.54 13.00 Autodock Vina v1.01 28205782 23733999 31 Mar 2015, 23:56:45 UTC 7 Apr 2015, 5:52:10 UTC Fertig und Bestätigt 210.29 200.91 13.00 Autodock Vina v1.01

Of course, I am not firm with the way credits are granted by this project, but I think the data shown above suggest that credits are apparently not given proportionally to the computational input.

Michael.
11) Message boards : Number crunching : Wu last 3 hours instead of 14 min. (Message 2258)
Posted 11 Apr 2015 by Profile Michael H.W. Weber
This is nothing unusual:
8:31:10 for WU vina_363777_83604_25p_2 still taking CPU time.
Both on an AMD Phenom II 955BE.

These long runners do complete and validate as detailed below:

11.04.2015 12:06:47 | FiND@Home | Computation for task vina_363777_83604_25p_2 finished 11.04.2015 12:06:49 | FiND@Home | Started upload of vina_363777_83604_25p_2_0 11.04.2015 12:06:50 | FiND@Home | Finished upload of vina_363777_83604_25p_2_0 11.04.2015 12:06:54 | FiND@Home | Sending scheduler request: To report completed tasks. 11.04.2015 12:06:54 | FiND@Home | Reporting 1 completed tasks

...and the WU validated: http://findah.ucd.ie/workunit.php?wuid=25200240

Paket 25200240 Michael H.W. Weber · Abmelden Name vina_363777_83604_25p Anwendung Autodock Vina erstellt 27 Mar 2015, 16:09:09 UTC autorisiertes Ergebnis 28690580 gewährte Punkte 100.00 Mindestanzahl 1 Anfängliche Kopien 1 max # von Fehler/Gesamt/Erfolg Aufgaben 1, 5, 1 Aufgabe anklicken für Einzelheiten Computer Gesendet Meldezeit oder Ablaufdatum Erklärung Status Laufzeit (sek) CPU Zeit (sek) Punkte Anwendung 26307236 44459 27 Mar 2015, 16:09:30 UTC 3 Apr 2015, 16:10:17 UTC Nicht vor Ablaufdatum gestartet - abgebrochen 0.00 0.00 --- Autodock Vina v1.01 28333868 58533 3 Apr 2015, 16:09:39 UTC 10 Apr 2015, 16:09:39 UTC Zeitüberschreitung - keine Antwort 0.00 0.00 --- Autodock Vina v1.01 28690580 73852 10 Apr 2015, 16:09:50 UTC 11 Apr 2015, 10:06:50 UTC Fertig und Bestätigt 34,965.37 33,620.62 100.00 Autodock Vina v1.01

Michael.
12) Message boards : Number crunching : Wu last 3 hours instead of 14 min. (Message 2257)
Posted 11 Apr 2015 by Profile Michael H.W. Weber
The wu I mentioned elsewhere, vina_361594_83593_25p_1, is still running here. It has now used 203:20:15 of crunch time. Still using CPU, but I've no way of seeing what, if anything it is doing/acheiving.

Please cancel this WU. They should not run for more than 2-3 hours - tops.

On what system?

This is nothing unusual:
8:31:10 for WU vina_363777_83604_25p_2 still taking CPU time.
6:39:06 for WU vina_363777_83622_25p_2 still taking CPU time.
Both on an AMD Phenom II 955BE.

There is probably something wrong with that ligand file - we'll look into it and remove it from our lists.

...there seems to be a lot wrong with a lot of ligand files then.

Michael.
13) Message boards : Number crunching : Latest workunits have bad runtime esrimates (Message 2178)
Posted 29 Mar 2015 by Profile Michael H.W. Weber
The problem with the currently heavily underestimated runtimes (>9 hrs on an AMD 955BE Qudcore) is that the clients are soaking up WUs which they can't finish in time. Better ad hoc increase that runtime estimate by introducing at least a factor of 10 if you do not know how to properly estimate/determine it. This way the machines will load less and if kept online, WUs will reload in time.

The long runners do not appear to be generally faulty, however. I just keep'em running.

An issue with the very short runtimes on the other hand is that they might cause server problems. For a while we had some tasks at our RNA World project which ran only a few seconds. They were all fine with good results but the massive server requests finally made us bundle them up to result in longer WUs to stabilize our the server infrastructure. Or send them out selectively to ARM systems.

Michael.
14) Message boards : Number crunching : Error after 2 seconds of runtime: Syntax error in ligand file (Message 2177)
Posted 29 Mar 2015 by Profile Michael H.W. Weber
It's not a faulty application call, it's a faulty ligand ;)

It's a faulty application call because the ligand used as input in the call is ill-defined. ;-)

Michael.
15) Message boards : Number crunching : Error after 2 seconds of runtime: Syntax error in ligand file (Message 2086)
Posted 8 Mar 2015 by Profile Michael H.W. Weber
The 32,947 remaining tasks are all valid, otherwise, they would have been in my failed folder :)

Well, then these do contain a different ligand definition.

What do you mean by "faulty application call"?

Just take a look at my error log posted above. It says:

...Parse error on line 12 in file "ligand": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive...

Michael.
16) Message boards : Number crunching : Error after 2 seconds of runtime: Syntax error in ligand file (Message 2082)
Posted 6 Mar 2015 by Profile Michael H.W. Weber
It actually makes no sense to wait for these tasks to return, because they all must be invalid due to a faulty application call. Hence, the whole batch should rather be cancelled on the server side ASAP.

Michael.
17) Message boards : Number crunching : Error after 2 seconds of runtime: Syntax error in ligand file (Message 2079)
Posted 6 Mar 2015 by Profile Michael H.W. Weber
I have a machine running for FIND@Home since yesterday. So far it received only a single WU which failed with an error after 2 seconds of total runtime.

According to my inspection of the error log, the source of this error appears to reside in a syntax error in the ligand file submitted during the Autodock VINA docking call. Please correct this and be a bit more careful when generating future WUs.

Michael.

Log:

Name vina_305826_82880_14p2flexre_1 Arbeitspaket 20012230 Erstellt 6 Mar 2015, 6:04:19 UTC Gesendet 6 Mar 2015, 6:04:24 UTC Ablaufdatum 13 Mar 2015, 6:04:24 UTC Empfangen 6 Mar 2015, 6:05:00 UTC Serverstatus Abgeschlossen Resultat Berechnungsfehler Clientstatus Berechnungsfehler Endstatus 1 (0x1) Unknown error number Computer ID 73726 Laufzeit 2 sek. CPU Zeit Prüfungsstatus Ungültig Punkte 0.00 Device peak FLOPS 4.08 GFLOPS Anwendungsversion Autodock Vina v1.01 Peak disk usage 0.23 MB Stderr Ausgabe <core_client_version>7.4.36</core_client_version> <![CDATA[ <message> Incorrect function. (0x1) - exit code 1 (0x1) </message> <stderr_txt> Receptor name: PFL1920c_2 Ligand name: CHEMBL211446_0 Parse error on line 12 in file "ligand": ATOM syntax incorrect: "Si" is not a valid AutoDock type. Note that AutoDock atom types are case-sensitive. 07:03:48 (6080): called boinc_finish(1) </stderr_txt> ]]>


Computer ID:

Computer 73726 Michael H.W. Weber · Abmelden Informationen zum Computer IP Adresse Zeige IP-Adresse Domäne i5 Ortszeit GMT +1 Stunden Erstellt 5 Mar 2015, 8:26:38 UTC Gesamtguthaben 0 Durchschnittliche Punkte 0.00 Projektübergreifende Punkte BOINCstats.com Free-DC CPU Typ GenuineIntel Intel(R) Core(TM) i5-2500K CPU @ 3.30GHz [Family 6 Model 42 Stepping 7] Anzahl der Prozessoren 4 Koprozessor AMD Hawaii (4096MB) OpenCL: 2.0 Betriebssystem Microsoft Windows 7 Ultimate x64 Edition, Service Pack 1, (06.01.7601.00) BOINC Version 7.4.36 Arbeitsspeicher 8175.42 MB CPU Cache 256 KB Auslagerungsdatei 16349.03 MB gesamter Festplattenspeicher 128 GB freier Festplattenspeicher 56.74 GB ermittelte Geschwindigkeit für Gleitkommazahlen 4075.55 Millionen Operationen/Sek ermittelte Geschwindigkeit für ganze Zahlen 11150.83 Millionen Operationen/Sek mittlere Uploadgeschwindigkeit 138.62 KB/sek mittlere Downloadgeschwindigkeit 1405.78 KB/sek mittlere Taskdauer 0 Tage Anwendungsdetails Zeige Aufgaben 1 Anzahl der Verbindungen zum Server 28 letztmaliger Kontakt mit Server 6 Mar 2015, 11:15:45 UTC % der Gesamtlaufzeit von BOINC 80.80% Während BOINC läuft, besteht % der Zeit eine Internetverbindung 100.00% Während BOINC läuft, sind in % der Zeit Berechnungen erlaubt 99.99% While BOINC running, % of time GPU work is allowed 99.99% Korrekturfaktor der Taskdauer 1




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