Posts by Erkan Yilmaz

21) Message boards : Number crunching : screen saver (Message 2018)
Posted 26 Dec 2009 by Profile Erkan Yilmaz
Post:
Thanks, I understand

I think the behaviour might arise from something specific on this OS:
- I have limited downloads to 2 tasks (one of my debug settings)
- running other projects
- boincmanager (win version)
- slow HD
- ...

My boincmanager under win hung (showed "communicating with boinc"-msg when I wanted to do some action in boincmanager) and so I either had to wait until these downloads would finish.
e.g. atm I just have 10 beta DD@H-WUs and all is fine

e.g. under linux64 I didn't have such a problem. The settings there were: no download limit, was working in memory only + had no other projects running.
22) Message boards : Number crunching : screen saver (Message 2016)
Posted 25 Dec 2009 by Profile Erkan Yilmaz
Post:
Not sure, if this is related to the mentioned changes, but:
under win7-64 with this host and boinc 6.10.17:
boincmanager got under very heavy load

I guess it was because I had many "autodock with mgl beta test v1.10"-WUs in download queue. Can the amount of WUs being sent out reduced or limited per a certain time interval?

The only solution left was:
detach DD@H and reattach, which caused all WUs being lost in nirvana
23) Message boards : Number crunching : process exited with code 195 (0xc3, -61) for autodock with mgltools scripts v5.11 (Message 2009)
Posted 25 Dec 2009 by Profile Erkan Yilmaz
Post:
Also with these WUs:
http://boinc.drugdiscoveryathome.com/result.php?resultid=1398964
http://boinc.drugdiscoveryathome.com/result.php?resultid=1398647
http://boinc.drugdiscoveryathome.com/result.php?resultid=1396748

The behaviour seems to happen also under Windows.
24) Message boards : Number crunching : process exited with code 195 (0xc3, -61) for autodock with mgltools scripts v5.11 (Message 2008)
Posted 25 Dec 2009 by Profile Erkan Yilmaz
Post:
from the many WUs since yesterday these 2 had errors. As I see also the other crunchers had errors:
http://boinc.drugdiscoveryathome.com/result.php?resultid=1384440
http://boinc.drugdiscoveryathome.com/result.php?resultid=1398647

boinc 6.10.17 on linux64, this host


<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)
</message>
<stderr_txt>
wrapper: starting
00:48:17 (22966): wrapper: running ../../projects/boinc.drugdiscoveryathome.com/unzip_1.401_x86_64-pc-linux-gnu (-qq -o "./MGLTools*.zip" -d ".")
00:48:19 (22966): wrapper: running 7za.exe (e ligand.mol2.7z)
00:48:20 (22966): wrapper: running ./Python25/python.exe (make_sitecustomize.py ".")
00:48:21 (22966): wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/Support/sitecustomize.py")
00:48:22 (22966): wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py" -l ligand.mol2 -o ligand.pdbqt)
Traceback (most recent call last):
File "./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line 155, in <module>
mol = mols[0]
File "/home/grml/Desktop/BOINC/slots/3/Python25/Lib/UserList.py", line 28, in __getitem__
def __getitem__(self, i): return self.data[i]
IndexError: list index out of range
app exit status: 0x100
00:48:23 (22966): called boinc_finish

</stderr_txt>
]]>
25) Message boards : Organization : Different languages translation (Message 2002)
Posted 21 Dec 2009 by Profile Erkan Yilmaz
Post:
Thanks also. If you need further pages translated, ring the bell :-)
26) Message boards : Number crunching : screen saver (Message 1998)
Posted 19 Dec 2009 by Profile Erkan Yilmaz
Post:
>I wonder if I should credit them in the logo or somewhere else in the screen saver.
How would you like others to value your work? :-)

Besides: the source code was published under: GNU Lesser General Public License
-> so the conditions there apply

If I remember correct (someone needs to look these up please, I am no lawyer):
- the screensaver you will create must also be LGPL (or GPL)
- if using in conjunction in another program the other program must also be released under LGPL or compatible one
- you must make available source code

I guess when talking directly with the screen saver creators they can also unrestrict some of the conditions, could be worth sending an email.

>I released some screen saver workunits for the mdrun_beta windows platform. Please report on how it runs
got no WUs yet, server seems down
Message from server: Project is temporarily shut down for maintenance
27) Message boards : Number crunching : Progress bar (Message 1997)
Posted 18 Dec 2009 by Profile Erkan Yilmaz
Post:
960% -> 1920% -> 3840% -> 97.959%

mdrun beta test v2.01
host: debian64, quad

but: the WUs calculated with sucess :-)
28) Message boards : Cafe : Pondering my future... (Message 1996)
Posted 18 Dec 2009 by Profile Erkan Yilmaz
Post:
How was it? Alright? First days may be always stressy.
29) Message boards : Number crunching : screen saver (Message 1988)
Posted 17 Dec 2009 by Profile Erkan Yilmaz
Post:
Great, thanks for the effort Jack.

I guess these are known already?
1. Percentage complete stays at 0% (also when I manually open the graphics in tab "Resources"), also no 2d graphs for min.energy, RMSD
2. The news ticker at bottom of page does not scroll smooth to left side (is this dependent on cpuload?)
3. logo.jpg looks blurry and doesn't scale good when resizing the graphics tab. Can there be used another resolution or a better/scalable file format?
4. could there be some explanation text for the protein, ligand, complex tabs? Or a link that leads to a special web page (for getting further info on topic). I mean for a newbie it could look like this: "Ah, screensaver/graphics tab works and there is something moving." After 1 minute: "Ok, but what is this exactly? RMSD (=Root mean square deviation), VDW, CPK"


Could you elaborate more what should be paid attention to?
1. calculation works? in different scenarios
2. see more test cases at Screensaver tests
3. ...


nothing more checked so far
info: I have disabled screensaver on my OS, but tried with windows screensaver preview
host: win7 ultimate64, quad
WUs: autodock with mgl beta test v1.04
30) Message boards : Number crunching : Beta Testing Autodock Enhancements (Message 1987)
Posted 17 Dec 2009 by Profile Erkan Yilmaz
Post:
So far 7 WUs of "autodock with mgl beta test v1.04" were successful
same host/os as above

screensaver issues will be reported here
31) Message boards : Number crunching : Beta Testing Autodock Enhancements (Message 1984)
Posted 16 Dec 2009 by Profile Erkan Yilmaz
Post:
all "autodock with mgl beta test v1.01" WUs I got, had "Error while computing"
e.g. see this WU

progress bar moves until 1.818% and then computation error happens

<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
- exit code 195 (0xc3)
</message>
<stderr_txt>
wrapper: starting
05:13:48 (2404): wrapper: running ../../projects/boinc.drugdiscoveryathome.com/unzip_1.01_windows_intelx86.exe (-qq -o "./MGLTools*.zip" -d ".")
05:14:02 (2404): wrapper: running 7za.exe (e ligand.mol2.7z)
05:14:03 (2404): wrapper: running ./Python25/python.exe (make_sitecustomize.py ".")
app exit status: 0xc000012f
05:14:04 (2404): called boinc_finish

dir output while WU is running:
16.12.2009 04:48 1.280.000 7za.exe
16.12.2009 04:48 10.564 AD4_parameters.dat
16.12.2009 05:22 104 autodock
16.12.2009 05:22 113 autodock_mgl_beta_1.01_windows_intelx86.exe
16.12.2009 05:22 104 autogrid
16.12.2009 05:23 423 boinc_task_state.xml
16.12.2009 04:48 591.360 cygblas.dll
16.12.2009 04:48 5.003.776 cyglapack.dll
16.12.2009 04:49 1.872.884 cygwin1.dll
16.12.2009 02:57 821.248 graphics_app
16.12.2009 02:05 66.708 Helvetica.txf
16.12.2009 05:22 4.427 init_data.xml
16.12.2009 04:49 2.887 job.xml
24.11.2009 23:28 4.697 ligand.mol2
16.12.2009 04:49 1.079 ligand.mol2.7z
16.12.2009 02:05 32.076 ligand.psf
16.12.2009 02:50 10.443 logo.jpg
16.12.2009 04:48 743 make_sitecustomize.py
16.07.2008 02:52 <DIR> MGLToolsPckgs
16.12.2009 04:49 21.954.836 MGLToolsPckgs.zip
16.12.2009 02:05 19.755 minenergy.pdb
16.12.2009 02:05 9.969 minrmsd.pdb
16.12.2009 02:05 1.450 minus.jpg
16.12.2009 04:48 348.160 MSVCR71.DLL
16.12.2009 02:05 1.652 plus.jpg
18.07.2008 02:19 <DIR> Python25
16.12.2009 05:22 105 python25.dll
16.12.2009 02:05 875 readme.txt
16.12.2009 04:49 315.243 receptor.pdb
16.12.2009 02:05 875.345 receptor.psf
16.12.2009 02:05 2.223 rotate_left.jpg
16.12.2009 02:05 1.812 rotate_right.jpg
16.12.2009 02:05 6.349 screenenergy.pdb
16.12.2009 02:05 21.119 screenenergy.psf
16.12.2009 02:05 9.786 screenrmsd.pdb
16.12.2009 02:05 32.650 screenrmsd.psf
02.05.2009 17:40 14.828 site.py
16.12.2009 05:23 3.247 stderr.txt
16.12.2009 05:22 101 unzip
16.12.2009 05:23 13 wrapper_checkpoint.txt
16.12.2009 05:22 99 zip


host: win7 64 ultimate
boinc: 6.10.17
32) Message boards : Number crunching : Beta Testing Autodock Enhancements (Message 1980)
Posted 15 Dec 2009 by Profile Erkan Yilmaz
Post:
Thanks for looking into this, see you
33) Message boards : Number crunching : Beta Testing Autodock Enhancements (Message 1976)
Posted 14 Dec 2009 by Profile Erkan Yilmaz
Post:
made a short break in my calcs

so, this wu running: autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000030_ts_1260830288290608000_0
(yesterday was: autodock_ga_run_10_bt_fzd8min_renum_SS.pdb_lig_omega_000837_ts_1260674979252506000_5)

in the slots dir I have the file you mention (dir output is while calculation is in progress)

14.12.2009 22:56 <DIR> .
14.12.2009 22:56 <DIR> ..
07.11.2009 17:02 1.280.000 7za.exe
07.11.2009 17:02 10.564 AD4_parameters.dat
14.12.2009 22:46 105 autodock
14.12.2009 22:46 109 autodock_mgl_1.055_windows_intelx86.exe
14.12.2009 22:46 105 autogrid
14.12.2009 22:46 0 boinc_lockfile
14.12.2009 22:47 401 boinc_task_state.xml
07.11.2009 17:02 591.360 cygblas.dll
07.11.2009 17:02 5.003.776 cyglapack.dll
01.12.2009 13:40 1.872.884 cygwin1.dll
14.12.2009 22:54 4.419 init_data.xml
14.12.2009 22:38 2.887 job.xml
24.11.2009 23:32 3.889 ligand.mol2
14.12.2009 22:38 989 ligand.mol2.7z
14.12.2009 22:46 2.544 ligand.pdbqt
14.12.2009 22:46 3.171 ligand_receptor.dpf
07.11.2009 17:02 743 make_sitecustomize.py
16.07.2008 02:52 <DIR> MGLToolsPckgs
07.11.2009 17:03 21.500.322 MGLToolsPckgs.zip
07.11.2009 17:02 348.160 MSVCR71.DLL
14.12.2009 22:54 70.814 out.dlg
14.12.2009 22:47 363.242 out.glg
18.07.2008 02:19 <DIR> Python25
07.11.2009 17:02 2.117.632 python25.dll
14.12.2009 22:47 563.642 receptor.A.map
14.12.2009 22:47 563.790 receptor.C.map
14.12.2009 22:47 413.681 receptor.d.map
14.12.2009 22:47 469.426 receptor.e.map
14.12.2009 22:46 1.235 receptor.gpf
14.12.2009 22:47 496.020 receptor.HD.map
14.12.2009 22:47 1.824 receptor.maps.fld
14.12.2009 22:47 44 receptor.maps.xyz
14.12.2009 22:47 547.475 receptor.N.map
14.12.2009 22:47 547.981 receptor.NA.map
14.12.2009 22:47 541.459 receptor.OA.map
14.12.2009 22:38 315.243 receptor.pdb
14.12.2009 22:46 193.295 receptor.pdbqt
14.12.2009 22:47 568.712 receptor.SA.map
02.05.2009 17:40 14.828 site.py
14.12.2009 22:47 102 stderr
14.12.2009 22:54 4.169 stderr.txt
14.12.2009 22:46 0 stdout
14.12.2009 22:46 102 unzip
14.12.2009 22:47 13 wrapper_checkpoint.txt
14.12.2009 22:46 100 zip



Edit: WU finished with status: Success
34) Message boards : Number crunching : Beta Testing Autodock Enhancements (Message 1975)
Posted 14 Dec 2009 by Profile Erkan Yilmaz
Post:
When I get one such WU, I will try again. O rcan you resend me specifically the same WU?

Please remember: two other WUs of this app-type worked
Perhaps you can see in the database some more info?
35) Message boards : Number crunching : Beta Testing Autodock Enhancements (Message 1969)
Posted 13 Dec 2009 by Profile Erkan Yilmaz
Post:
had 2 successful WUs yesterday of "autodock with mgltools scripts v1.55"
but today this one failed on win7-64:

<message>
- exit code 195 (0xc3)
</message>

as I see also on other pcs:
xp32, vista32, Windows Server 2008-64




<core_client_version>6.10.17</core_client_version>
<![CDATA[
<message>
- exit code 195 (0xc3)
</message>
<stderr_txt>
wrapper: starting
18:11:50 (3816): wrapper: running ../../projects/boinc.drugdiscoveryathome.com/unzip_1.054_windows_intelx86.exe (-qq -o "./MGLTools*.zip" -d ".")
18:12:05 (3816): wrapper: running 7za.exe (e ligand.mol2.7z)
18:12:06 (3816): wrapper: running ./Python25/python.exe (make_sitecustomize.py ".")
18:12:07 (3816): wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/Support/sitecustomize.py")
18:12:08 (3816): wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py" -l ligand.mol2 -o ligand.pdbqt)
Traceback (most recent call last):
File "./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py", line 153, in <module>
mols = Read(ligand_filename)
File ".\MGLToolsPckgs\MolKit\__init__.py", line 21, in Read
raise AssertionError , "%s does't exist" %filename
AssertionError: ligand.mol2 does't exist
app exit status: 0x1
18:12:10 (3816): called boinc_finish
36) Message boards : Cafe : Radio Stations (Message 1968)
Posted 13 Dec 2009 by Profile Erkan Yilmaz
Post:
listening just now to this station
37) Message boards : Number crunching : Progress bar (Message 1960)
Posted 12 Dec 2009 by Profile Erkan Yilmaz
Post:
Hello Jaxis,

as I see Jack canceled same app on
win7 32bit, boinc 6.10.18

As I see you are getting also higher version number WUs, so it doesn't hurt to let these 14 still there, until Jack says something.

for all: these are the 14 WUs


Re: mdrun beta test 7.04

14 wu's sent to me 12 Dec 2009 0:41:06 UTC
But the Time reported or deadline is 15 Nov 2009 6:00:00 UTC.
Perhaps this is my problem as to why they keep running without completing?

I hate to abort anything without permission. A couple of wu's have run for over two hours now.












38) Message boards : Number crunching : Progress bar (Message 1959)
Posted 12 Dec 2009 by Profile Erkan Yilmaz
Post:
about the progress bar:

Behaviour now is:
still stays at 0%
and then at end jumps to 97.959% and then WU finished immediately

could have been also like this earlier, since I only just now watched the WU operate

app: mdrun beta test v7.07
OS: win7 64 RC
just finished some WUs with outcome Success :-)
39) Message boards : Organization : Different languages translation (Message 1956)
Posted 11 Dec 2009 by Profile Erkan Yilmaz
Post:
German transformation:
DrugDiscovery@Home - ist ein Projekt, welches nach dem Prinzip des verteilten Rechnens funktioniert, sprich die Leistung von weltweit verteilten PCs wird genutzt. Die Rechenzeit wird freundlicherweise von Freiwilligen auf der ganzen Welt bereitgestellt, die einen Einfluss ausüben wollen auf die Entdeckung von neuen Pharmaka in den Bereichen Stammzellbiologie für Alterung und Krebsforschung.

Unser wichtigstes Forschungsinteresse ist die Entwicklung von neuen Behandlungen für Alterung und Krebs durch die Regulierung adulter Stammzellen. Unser Projekt wird durch eine Online-Community von Freiwilligen unterstützt, die ihre Rechenkraft spenden, um bei der Modellierung von Pharmaka-Interaktionen mitzuhelfen.
Jeder kann am Projekt teilnehmen, indem man sich registriert und eine Software herunterlädt, um automatische Analysen durchzuführen.
Eines der Vorteile des Projektes ist das Ziel für Translationale Forschung, was wir vom frühen Pharmaka-Findungsprozess bis zu den letzten Phasen der Pharmaka-Entwicklung managen wollen. Die multiple Zusammenarbeit mit Pharmaforschungsinstituten und Pharmaunternehmen wird genutzt, um solche Gemeinschaftsproduktionen bei der Erstellung neuer Pharmaka so effektiv wie nur möglich zu gestalten.
Unser Projekt benutzt die BOINC-Software, die hier heruntergeladen werden kann. Als Basis-Applikationen nutzen wir Software für Virtual Screening und koppeln dies mit der Weiterentwicklung anhand Moleküldynamik-Software. Aber unser Ziel ist es, so weit wie möglich in silico Pharmaka-Design-Software auf unsere Plattform zu bringen, zur effektiven Entdeckung von Pharmaka und Vorhersage von Eigenschaften kleiner Moleküle.
Diese Anwendungen werden zur Verfeinerung von 3D-Strukturen von offline modellierten Bio-Targets und in silico strukturbasiertem Pharmaka-Design benutzt. Unser Projekt ist gemeinnützig unter dem Aspekt, dass wir mit Projektgründern keine Gewinne teilen und Information über jegliche Zusammenarbeit wird soweit wie möglich an unsere freiwilligen Helfer offengelegt.


suggestions:
...for English text:
1.
is: which want to
could be: who want to
2.
is: BOINC softwer
could be: BOINC software

...general:
1. how about linking some of the technical terms with some info page (Wikipedia, ...) ?


question:
1. could this German text now also be used in this wiki?
http://www.rechenkraft.net/wiki/index.php?title=DrugDiscovery%40Home
I am asking since it is just a mere transformation into German

2. Could you give permission to use this image on the wiki also?
http://www.rechenkraft.net/wiki/index.php?title=Bild:DrugDiscoverylogo.png


Thanks for your time + all have nice dreams!
40) Message boards : Number crunching : Progress bar (Message 1926)
Posted 6 Dec 2009 by Profile Erkan Yilmaz
Post:
progress bar not working :-(

mdrun v7.28
windows 64bit RC
boinc 6.10.17


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