Beta Testing Autodock Enhancements

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Profile Erkan Yilmaz
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Message 1969 - Posted: 13 Dec 2009, 18:22:47 UTC
Last modified: 13 Dec 2009, 18:23:10 UTC

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
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Profile Jack Shultz
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Message 1974 - Posted: 14 Dec 2009, 19:32:08 UTC - in response to Message 1969.  

it should extract the ligand.mol2 from this step

18:12:05 (3816): wrapper: running 7za.exe (e ligand.mol2.7z)


You can pause all your work, exit the boinc manager and then run this in the command line from the BOINC program directory ./boinc --exit_after_finish

then open the manager, check the properties on an autodock workunit to detmine which slot number it is occupying. Unpause this autodock workunit

once it completes it should make the entries in the manager go blank. If you look at the slot directory to determine which files have been generate. If you look with a detailed view of the files, you can sort them by date created.

Do you see a ligand.mol2 file? This tells us where the failure was. Maybe it failed to extract a file from the 7z maybe the file was not in the 7z to begin with.


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Profile Erkan Yilmaz
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Message 1975 - Posted: 14 Dec 2009, 22:00:17 UTC

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?
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Profile Erkan Yilmaz
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Message 1976 - Posted: 14 Dec 2009, 23:02:17 UTC
Last modified: 14 Dec 2009, 23:42:48 UTC

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
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Profile Jack Shultz
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Message 1977 - Posted: 14 Dec 2009, 23:57:33 UTC - in response to Message 1976.  

I see, it was just a corrupted input file
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Profile Erkan Yilmaz
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Message 1980 - Posted: 15 Dec 2009, 18:09:36 UTC - in response to Message 1977.  

Thanks for looking into this, see you
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Message 1984 - Posted: 16 Dec 2009, 5:27:49 UTC

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
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Message 1985 - Posted: 16 Dec 2009, 23:44:44 UTC - in response to Message 1984.  

yup, I know this beta version is going to blow up several times. Testing screen savers.
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Message 1986 - Posted: 17 Dec 2009, 5:01:26 UTC - in response to Message 1985.  

On my end autodock_mgl_beta v 104 works. Please report if you have issues. It is only going to the Developer Team
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Profile Erkan Yilmaz
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Message 1987 - Posted: 17 Dec 2009, 6:19:33 UTC

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
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Message 1989 - Posted: 17 Dec 2009, 8:48:32 UTC

Yes !
Good job ;)
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Message boards : Number crunching : Beta Testing Autodock Enhancements


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