Upload, Download and WU Errors

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Profile [AF>Libristes] Dudumomo

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Message 594 - Posted: 13 Jun 2009, 2:18:23 UTC - in response to Message 540.  

All my WU went into error :
example, task 620736 :
<core_client_version>6.4.5</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)
</message>
<stderr_txt>
wrapper: starting
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 66666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 66666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666666
TASK::parse(): unexpected text 66666666666
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/unzip_0.200_x86_64-pc-linux-gnu (-qq -n gromacs.zip)
wrapper: running gromacs/bin/pdb2gmx_d.exe (-ff amber03 -water tip3p)
gromacs/bin/pdb2gmx_d.exe: relocation error: ./libc.so.6: symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference
app exit status: 0x7f00
called boinc_finish

</stderr_txt>
]]>
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Message 595 - Posted: 13 Jun 2009, 13:30:34 UTC

Still the same, here some more messages from the client:
Sa 13 Jun 2009 15:05:37 CEST	DrugDiscovery	Sending scheduler request: To fetch work.  Requesting 4453 seconds of work, reporting 0 completed tasks
Sa 13 Jun 2009 15:05:42 CEST	DrugDiscovery	Scheduler request completed: got 1 new tasks
Sa 13 Jun 2009 15:05:44 CEST	DrugDiscovery	Started download of fzd2.pdb.txt
Sa 13 Jun 2009 15:05:44 CEST	DrugDiscovery	Started download of gromacs_run7.txt
Sa 13 Jun 2009 15:05:46 CEST	DrugDiscovery	Finished download of gromacs_run7.txt
Sa 13 Jun 2009 15:05:46 CEST	DrugDiscovery	Started download of em.mdp.txt
Sa 13 Jun 2009 15:05:47 CEST	DrugDiscovery	Finished download of fzd2.pdb.txt
Sa 13 Jun 2009 15:05:47 CEST	DrugDiscovery	Finished download of em.mdp.txt
Sa 13 Jun 2009 15:05:47 CEST	DrugDiscovery	Started download of pr.mdp.txt
Sa 13 Jun 2009 15:05:47 CEST	DrugDiscovery	Started download of run.mdp.txt
Sa 13 Jun 2009 15:05:49 CEST	DrugDiscovery	Finished download of pr.mdp.txt
Sa 13 Jun 2009 15:05:49 CEST	DrugDiscovery	Finished download of run.mdp.txt
Sa 13 Jun 2009 15:05:52 CEST	DrugDiscovery	Sending scheduler request: To fetch work.  Requesting 2197 seconds of work, reporting 0 completed tasks
Sa 13 Jun 2009 15:05:57 CEST	DrugDiscovery	Scheduler request completed: got 1 new tasks
Sa 13 Jun 2009 15:26:42 CEST	DrugDiscovery	Starting run_1244238507989108456_2
Sa 13 Jun 2009 15:26:42 CEST	DrugDiscovery	Starting task run_1244238507989108456_2 using gromacs version 205
Sa 13 Jun 2009 15:26:44 CEST	DrugDiscovery	[app_msg_send] sent heartbeat to run_1244238507989108456_2
Sa 13 Jun 2009 15:26:52 CEST	DrugDiscovery	[error] Can't rename output file run_1244238507989108456_2_0 to projects/boinc.drugdiscoveryathome.com/run_1244238507989108456_2_0: Error -1
Sa 13 Jun 2009 15:26:52 CEST	DrugDiscovery	Computation for task run_1244238507989108456_2 finished
Sa 13 Jun 2009 15:26:52 CEST	DrugDiscovery	Starting run_1244238506498085176_1
Sa 13 Jun 2009 15:26:52 CEST	DrugDiscovery	Starting task run_1244238506498085176_1 using gromacs version 205
Sa 13 Jun 2009 15:26:52 CEST	DrugDiscovery	[app_msg_send] sent heartbeat to run_1244238506498085176_1
Sa 13 Jun 2009 15:26:53 CEST	DrugDiscovery	[app_msg_send] sent heartbeat to run_1244238506498085176_1
Sa 13 Jun 2009 15:26:55 CEST	DrugDiscovery	[app_msg_send] sent heartbeat to run_1244238506498085176_1
Sa 13 Jun 2009 15:27:01 CEST	DrugDiscovery	[error] Can't rename output file run_1244238506498085176_1_0 to projects/boinc.drugdiscoveryathome.com/run_1244238506498085176_1_0: Error -1
Sa 13 Jun 2009 15:27:01 CEST	DrugDiscovery	Computation for task run_1244238506498085176_1 finished
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Message 596 - Posted: 13 Jun 2009, 14:08:08 UTC - in response to Message 594.  

All my WU went into error

Same here, as told in this thread.
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Profile [AF>HFR>RR] Jim PROFIT

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Message 597 - Posted: 13 Jun 2009, 14:35:06 UTC - in response to Message 595.  

Same here for me.
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Profile [AF>Libristes] Pascal94
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Message 600 - Posted: 14 Jun 2009, 12:04:21 UTC - in response to Message 597.  
Last modified: 14 Jun 2009, 12:06:54 UTC

Runing Ubuntu 9.04 x64, using Gromacs 2.05 application:

<core_client_version>6.6.36</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)
</message>
<stderr_txt>
wrapper: starting
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 66666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 66666666666
TASK::parse(): unexpected text 6666666666
TASK::parse(): unexpected text 6666666666666
TASK::parse(): unexpected text 66666666666
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/unzip_0.200_x86_64-pc-linux-gnu (-qq -n gromacs.zip)
wrapper: running gromacs/bin/pdb2gmx_d.exe (-ff amber03 -water tip3p)
gromacs/bin/pdb2gmx_d.exe: relocation error: ./libc.so.6: symbol _dl_tls_get_addr_soft, version GLIBC_PRIVATE not defined in file ld-linux-x86-64.so.2 with link time reference
app exit status: 0x7f00
called boinc_finish

</stderr_txt>

all my WUs finished erroring, except this one.
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Message 607 - Posted: 15 Jun 2009, 4:07:32 UTC
Last modified: 15 Jun 2009, 4:31:53 UTC

a lot of my 1245 wu are erroring...

error output file...

6/15/2009 12:26:29 AM DrugDiscovery [error] Can't rename output file run_1245007733228152068_0_0 to projects/boinc.drugdiscoveryathome.com/run_1245007733228152068_0_0: Error 2


none of the autodock 3b7e have run yet on my pc..
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Message 608 - Posted: 15 Jun 2009, 4:40:47 UTC

6/15/2009 12:38:44 AM DrugDiscovery [error] Can't rename output file 3b7e_25630_ChemDiv_0814-0115_1245021804_1_0 to projects/boinc.drugdiscoveryathome.com/3b7e_25630_ChemDiv_0814-0115_1245021804_1_0: Error 2

output errors.....
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Profile Tim Turner
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Message 609 - Posted: 15 Jun 2009, 4:50:18 UTC - in response to Message 608.  

<core_client_version>6.6.31</core_client_version>
<![CDATA[
<message>
- exit code 195 (0xc3)
</message>
<stderr_txt>
wrapper: starting
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/unzip_1.011_windows_intelx86.exe (-qq -o "./MGLTools*.zip" -d ".")
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/7za_1.023_windows_intelx86.exe (e ligand.mol2.7z)
wrapper: running ./Python25/python.exe (make_sitecustomize.py ".")
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/Support/sitecustomize.py")
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py" -l ligand.mol2 -o ligand.pdbqt)
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py" -U nphs_lps_waters -r receptor.pdb -o receptor.pdbqt)
close failed: [Errno 9] Bad file descriptor
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py" -r receptor.pdbqt -g receptor_rigid.pdbqt -x receptor_flex.pdbqt -s TRP73_HIS70_GLU68)
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py" -l ligand.pdbqt -r receptor_rigid.pdbqt -p custom_parameter_file=1 -p parameter_file=AD4_parameters.dat -p ligand_types="A C HD N NA OA SA")
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py" -l ligand.pdbqt -r receptor_rigid.pdbqt -p compute_unbound_extended_flag=0 -p ga_run=1 -p flexres=receptor_flex.pdbqt)
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/autogrid_1.011_windows_intelx86.exe (-p receptor_rigid.gpf -l out.glg)
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/autodock_1.011_windows_intelx86.exe (-p ligand_receptor_rigid.dpf -l out.dlg)
app exit status: 0xff
called boinc_finish

</stderr_txt>
]]>

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Message 610 - Posted: 15 Jun 2009, 4:57:10 UTC - in response to Message 609.  
Last modified: 15 Jun 2009, 4:59:49 UTC

this one finished.....

so it seems that some will fail and others will succeed.


LOL

gcq#36: "All Work and No Play Makes Jack a Dull Boy" (The Shining)

from a run_1245....
Tim Turner
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Profile Tim Turner
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Message 611 - Posted: 15 Jun 2009, 5:07:00 UTC - in response to Message 610.  

oh yeah, the quota limit is at like 120 something, can you increase it please...
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Message 612 - Posted: 15 Jun 2009, 9:30:13 UTC

I've been getting a lot of Errors too lately, but I discovered some if not all of them are directly linked to running the AQUA CUDA v3.26 Wu's. Running AQUA CUDA v3.24 Wu's which are no longer being sent out but I still have some to run doesn't Error the Drug Project's Wu's.

I Discovered this by noticing only the Box's I have that were running the AQUA v3.26 Wu's were getting Errors and not the ones that were running the AQUA v3.24 Wu's. I even Stopped the AQUA v3.26 Wu from running and on 1 Box & the Error's for the Drug Projects Wu weren't there anymore. Turned the AQUA v3.26 Wu back on & the Errors started to pop back up again on that Box.
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Message 614 - Posted: 15 Jun 2009, 20:23:27 UTC
Last modified: 15 Jun 2009, 20:23:47 UTC

A lot of that errors:
<core_client_version>6.6.31</core_client_version>
<![CDATA[
<message>
- exit code 195 (0xc3)
</message>
<stderr_txt>
wrapper: starting
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/unzip_1.011_windows_intelx86.exe (-qq -o "./MGLTools*.zip" -d ".")
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/7za_1.023_windows_intelx86.exe (e ligand.mol2.7z)
wrapper: running ./Python25/python.exe (make_sitecustomize.py ".")
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/Support/sitecustomize.py")
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_ligand4.py" -l ligand.mol2 -o ligand.pdbqt)
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_receptor4.py" -U nphs_lps_waters -r receptor.pdb -o receptor.pdbqt)
close failed: [Errno 9] Bad file descriptor
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_flexreceptor4.py" -r receptor.pdbqt -g receptor_rigid.pdbqt -x receptor_flex.pdbqt -s TRP73_HIS70_GLU68)
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_gpf4.py" -l ligand.pdbqt -r receptor_rigid.pdbqt -p custom_parameter_file=1 -p parameter_file=AD4_parameters.dat -p ligand_types="A C HD N NA OA SA")
wrapper: running ./Python25/python.exe ("./MGLToolsPckgs/AutoDockTools/Utilities24/prepare_dpf4.py" -l ligand.pdbqt -r receptor_rigid.pdbqt -p compute_unbound_extended_flag=0 -p ga_run=1 -p flexres=receptor_flex.pdbqt)
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/autogrid_1.011_windows_intelx86.exe (-p receptor_rigid.gpf -l out.glg)
wrapper: running ../../projects/boinc.drugdiscoveryathome.com/autodock_1.011_windows_intelx86.exe (-p ligand_receptor_rigid.dpf -l out.dlg)
app exit status: 0xff
called boinc_finish

</stderr_txt>
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Message 617 - Posted: 16 Jun 2009, 8:00:57 UTC

Another fresh errors:

16.06.2009 11:38:47 DrugDiscovery Sending scheduler request: To fetch work.
16.06.2009 11:38:47 DrugDiscovery Requesting new tasks
16.06.2009 11:38:52 DrugDiscovery Scheduler request completed: got 2 new tasks
16.06.2009 11:38:54 DrugDiscovery Started download of nodelete_34174_ChemDiv_8013-6574.7z
16.06.2009 11:38:54 DrugDiscovery Started download of fzd8min_renum_SS.pdb
16.06.2009 11:38:56 DrugDiscovery Finished download of nodelete_34174_ChemDiv_8013-6574.7z
16.06.2009 11:38:56 DrugDiscovery Started download of pal_wnt_bind3.txt
16.06.2009 11:38:57 DrugDiscovery Finished download of pal_wnt_bind3.txt
16.06.2009 11:38:57 DrugDiscovery Started download of nodelete_33806_ChemDiv_8016-7610.7z
16.06.2009 11:38:59 DrugDiscovery Finished download of nodelete_33806_ChemDiv_8016-7610.7z
16.06.2009 11:39:22 DrugDiscovery Temporarily failed download of fzd8min_renum_SS.pdb: HTTP error
16.06.2009 11:39:22 DrugDiscovery Backing off 1 min 0 sec on download of fzd8min_renum_SS.pdb
16.06.2009 11:40:23 DrugDiscovery [error] File fzd8min_renum_SS.pdb has wrong size: expected 315243, got 310665
16.06.2009 11:40:23 DrugDiscovery Started download of fzd8min_renum_SS.pdb
16.06.2009 11:40:25 DrugDiscovery Finished download of fzd8min_renum_SS.pdb
16.06.2009 11:40:25 DrugDiscovery [error] MD5 check failed for fzd8min_renum_SS.pdb
16.06.2009 11:40:25 DrugDiscovery [error] expected 1f5b313bb6e1223330e42419da68dd8a, got b8dbf8df68e1e620fce265e3ec1e63c4
16.06.2009 11:40:25 DrugDiscovery [error] Checksum or signature error for fzd8min_renum_SS.pdb
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Message 623 - Posted: 16 Jun 2009, 18:22:40 UTC

All the errors i've gotten are the Can't rename output errors.

6/16/2009 9:18:55 AM DrugDiscovery [error] Can't rename output file 3b7e_32987_ChemDiv_8015-1467_1245022149_5_0 to projects/boinc.drugdiscoveryathome.com/3b7e_32987_ChemDiv_8015-1467_1245022149_5_0: Error 2

But I see that they are being credited.
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Message 648 - Posted: 21 Jun 2009, 8:04:20 UTC

Наблюдаются классические для данного проекта ошибки. ОС: Linux Kubuntu 9.04 amd64. Свободного места на диске - 6 Гб.


Вск 21 Июн 2009 15:53:14|DrugDiscovery|Starting v2_flex3_fzd8min_23885_ChemDiv_000A-0051_1245432370_1
Вск 21 Июн 2009 15:53:14|DrugDiscovery|Starting task v2_flex3_fzd8min_23885_ChemDiv_000A-0051_1245432370_1 using autodock_mgl version 502
Вск 21 Июн 2009 15:53:23|DrugDiscovery|[error] Can't rename output file v2_flex3_fzd8min_23884_ChemDiv_1863-1069_1245432370_0_0
Вск 21 Июн 2009 15:53:23|DrugDiscovery|Computation for task v2_flex3_fzd8min_23884_ChemDiv_1863-1069_1245432370_0 finished
Вск 21 Июн 2009 15:53:23|DrugDiscovery|Starting v2_flex3_fzd8min_23888_ChemDiv_5339-0122_1245432370_0
Вск 21 Июн 2009 15:53:23|DrugDiscovery|Starting task v2_flex3_fzd8min_23888_ChemDiv_5339-0122_1245432370_0 using autodock_mgl version 502
Вск 21 Июн 2009 15:53:45|DrugDiscovery|[error] Can't rename output file v2_flex3_fzd8min_23885_ChemDiv_000A-0051_1245432370_1_0
Вск 21 Июн 2009 15:53:45|DrugDiscovery|Computation for task v2_flex3_fzd8min_23885_ChemDiv_000A-0051_1245432370_1 finished
Вск 21 Июн 2009 15:53:45|DrugDiscovery|Starting v2_flex3_fzd8min_23889_ChemDiv_5754-2997_1245432370_1
Вск 21 Июн 2009 15:53:46|DrugDiscovery|Starting task v2_flex3_fzd8min_23889_ChemDiv_5754-2997_1245432370_1 using autodock_mgl version 502
Вск 21 Июн 2009 15:53:53|DrugDiscovery|[error] Can't rename output file v2_flex3_fzd8min_23888_ChemDiv_5339-0122_1245432370_0_0
Вск 21 Июн 2009 15:53:53|DrugDiscovery|Computation for task v2_flex3_fzd8min_23888_ChemDiv_5339-0122_1245432370_0 finished
Вск 21 Июн 2009 15:54:16|DrugDiscovery|[error] Can't rename output file v2_flex3_fzd8min_23889_ChemDiv_5754-2997_1245432370_1_0
Вск 21 Июн 2009 15:54:16|DrugDiscovery|Computation for task v2_flex3_fzd8min_23889_ChemDiv_5754-2997_1245432370_1 finished
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Message 679 - Posted: 24 Jun 2009, 18:12:07 UTC
Last modified: 24 Jun 2009, 18:21:31 UTC

49 tasks download failed (host ID 60).
Examples
fzd8min_23934_ChemDiv_5989-2720_1245862987_0
v2_flex3_fzd8min_23925_ChemDiv_000A-0179_1245851994_4

<![CDATA[
<message>
WU download error: couldn't get input files:
<file_xfer_error>
<file_name>summary_job.txt</file_name>
<error_code>-200</error_code>
</file_xfer_error>
</message>
]]>

New balls, please:-).

EDIT: adding msgs
24/06/2009 20:04:08 DrugDiscovery Finished download of autodock_mgl_1.024_windows_intelx86.exe
24/06/2009 20:04:08 DrugDiscovery Started download of nodelete_23948_ChemDiv_000A-0564.7z
24/06/2009 20:04:11 DrugDiscovery Finished download of nodelete_23948_ChemDiv_000A-0564.7z
24/06/2009 20:04:11 DrugDiscovery Started download of fzd8min_renum_SS.pdb
24/06/2009 20:04:22 DrugDiscovery Finished download of fzd8min_renum_SS.pdb
24/06/2009 20:04:22 DrugDiscovery Started download of summary_job.txt
24/06/2009 20:04:24 DrugDiscovery Incomplete read of 3123.000000 < 5KB for summary_job.txt - truncating
24/06/2009 20:04:24 DrugDiscovery Finished download of summary_job.txt
24/06/2009 20:04:24 DrugDiscovery Started download of nodelete_23925_ChemDiv_000A-0179.7z
24/06/2009 20:04:24 DrugDiscovery [error] Checksum or signature error for summary_job.txt
24/06/2009 20:04:26 DrugDiscovery Finished download of 7za_1.024_windows_intelx86.exe
24/06/2009 20:04:26 DrugDiscovery Finished download of nodelete_23925_ChemDiv_000A-0179.7z
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Message 681 - Posted: 25 Jun 2009, 15:42:59 UTC
Last modified: 25 Jun 2009, 15:52:45 UTC

Been seeing a few of these tasks, where the quorum is 3, two copies are returned and granted credit alright, but a third task times out and the WU status shows as "Completed, can't validate"

Not familiar enough with the backend of BOINC to know if this would cause issues with extracting job data later on or not, but thought I would bring it up here just in case. Though it might just be because you cancelled the rest of the batch ? "Divine Intervention ?"

examples:
203678, 204309, 204311, 204312, 204313

other than that I'm just getting the same errors in abundance as everyone else :P
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Message 686 - Posted: 27 Jun 2009, 10:23:14 UTC

Why is the differens from the CPU-Time by autodock with mgltools scripts so great? My cpu 2,021.05sec the two other´s take around 200sec.
For Example Workunit id: 216477
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Message 688 - Posted: 27 Jun 2009, 15:17:43 UTC - in response to Message 687.  
Last modified: 27 Jun 2009, 15:19:16 UTC

Well the only obvious difference is the other wingman have a CUDA GPU.

So my guess is the WU ran on them, based on the performance jump you see between CPU and GPU apps elsewhere on the same work.

My initial guess as well, but for that the testing of the CUDA app was with the Gromacs application. We don't have an Autodock CUDA application yet. Seeing how quick Autodock (even those with MGL Tools) runs on the CPU, it's not worth making an application for the GPU either.

Besides, if you checked the application version used, for all it was 1.24 ... something of an impossibility for BOINC to use the same application on two different architectures.

As for why they did it then, I haven't got an answer. Could be their amount of CPUs giving a thwarted view. Unless they built their own CUDA app, but it isn't that easy either. I am still very much stuck in making the ATI app.
Jord

'Cause you seem like an orchard of mines, Just take one step at a time.
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Message 700 - Posted: 30 Jun 2009, 17:07:11 UTC - in response to Message 689.  

new set, some work & complete, others error out....about 1:50 into the wu on Q6600.
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