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Profile Tim Turner
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Message 2502 - Posted: 10 Nov 2010, 21:51:33 UTC

All issues, errors and related dealing with Cuda OpenCL.
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Message 2504 - Posted: 11 Nov 2010, 18:18:58 UTC - in response to Message 2502.  

Please tell about requirements for OPENCL GPU application.
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Message 2506 - Posted: 11 Nov 2010, 21:24:46 UTC - in response to Message 2504.  

I'm in the process of getting those from jack.

I think all that you need is the latest driver. don't quote though.
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Message 2537 - Posted: 21 Nov 2010, 20:43:51 UTC - in response to Message 2506.  

We may need some help figuring this one out...

Basically, the ati & cuda app are one in the same, they just need different plan classes...

right now, i can't get the opencl app to run on my gtx 260...

although, i was just able to get it to run on my 9400 gt with no problems.

so right now, i'm rolling back my driver on the gtx 260 to see if that is the issue..

if not, i will need a couple of volunteers to see if they can get this app to run...

and also if anyone with a gtx 260 model 216 core and the standard 192 would be willinly to test the app, please just post...
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Message 2538 - Posted: 21 Nov 2010, 21:01:27 UTC - in response to Message 2537.  

oh yes... Bingo!!!!!!!!


it turns out that the app doesn't like driver 260.99...


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Message 2539 - Posted: 21 Nov 2010, 21:39:49 UTC - in response to Message 2538.  
Last modified: 21 Nov 2010, 21:56:27 UTC

jack sent out a mini-batch of about 50. if your special, POST!

driver should be around 258.96, lower drivers may work or may not work, please do a little experimenting please.. help us out...
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Message 2540 - Posted: 21 Nov 2010, 23:21:22 UTC - in response to Message 2539.  

Testing one now on a GTX 460 768mb.
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Message 2543 - Posted: 22 Nov 2010, 3:56:11 UTC

Was at 99% then disappeared with a computation error????

Messages tab in Boinc says work unit completed.

Oh well.........try one more.
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Message 2544 - Posted: 22 Nov 2010, 10:51:06 UTC

Hi,

looks like I got the same error on this WU crunched on this host.

Below stderr out transcript for your convenience:

<core_client_version>6.10.58</core_client_version>
<![CDATA[
<message>
- exit code 195 (0xc3)
</message>
<stderr_txt>
wrapper: starting
23:48:45 (7156): wrapper: running mdrun.exe (-v -x -c -o -e -cpi md.cpt -cpt 1 -deffnm md --device 0)
:-) G R O M A C S (-:

Groningen Machine for Chemical Simulation

:-) VERSION 4.0.99_development_20090421 (-:


Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2008, The GROMACS development team,
check out http://www.gromacs.org for more information.

This program is free software; you can redistribute it and/or
modify it under the terms of the GNU General Public License
as published by the Free Software Foundation; either version 2
of the License, or (at your option) any later version.

:-) mdrun.exe (-:

Option Filename Type Description
------------------------------------------------------------
-s md.tpr Input Run input file: tpr tpb tpa
-o md.trr Output Full precision trajectory: trr trj cpt
-x md.xtc Output, Opt! Compressed trajectory (portable xdr format)
-cpi md.cpt Input, Opt! Checkpoint file
-cpo md.cpt Output, Opt. Checkpoint file
-c md.gro Output Structure file: gro g96 pdb
-e md.edr Output Energy file: edr ene
-g md.log Output Log file
-dgdl md.xvg Output, Opt. xvgr/xmgr file
-field md.xvg Output, Opt. xvgr/xmgr file
-table md.xvg Input, Opt. xvgr/xmgr file
-tablep md.xvg Input, Opt. xvgr/xmgr file
-tableb md.xvg Input, Opt. xvgr/xmgr file
-rerun md.xtc Input, Opt. Trajectory: xtc trr trj gro g96 pdb cpt
-tpi md.xvg Output, Opt. xvgr/xmgr file
-tpid md.xvg Output, Opt. xvgr/xmgr file
-ei md.edi Input, Opt. ED sampling input
-eo md.edo Output, Opt. ED sampling output
-j md.gct Input, Opt. General coupling stuff
-jo md.gct Output, Opt. General coupling stuff
-ffout md.xvg Output, Opt. xvgr/xmgr file
-devout md.xvg Output, Opt. xvgr/xmgr file
-runav md.xvg Output, Opt. xvgr/xmgr file
-px md.xvg Output, Opt. xvgr/xmgr file
-pf md.xvg Output, Opt. xvgr/xmgr file
-mtx md.mtx Output, Opt. Hessian matrix
-dn md.ndx Output, Opt. Index file

Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 19 Set the nicelevel
-deffnm string md Set the default filename for all file options
-[no]xvgr bool yes Add specific codes (legends etc.) in the output
xvg files for the xmgrace program
-device int 0 Select the CUDA device (default m=0)
-[no]pd bool no Use particle decompostion
-dd vector 0 0 0 Domain decomposition grid, 0 is optimize
-npme int -1 Number of separate nodes to be used for PME, -1
is guess
-ddorder enum interleave DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool yes Check for all bonded interactions with DD
-rdd real 0 The maximum distance for bonded interactions with
DD (nm), 0 is determine from initial coordinates
-rcon real 0 Maximum distance for P-LINCS (nm), 0 is estimate
-dlb enum auto Dynamic load balancing (with DD): auto, no or yes
-dds real 0.8 Minimum allowed dlb scaling of the DD cell size
-[no]sum bool yes Sum the energies at every step
-[no]v bool yes Be loud and noisy
-[no]compact bool yes Write a compact log file
-[no]seppot bool no Write separate V and dVdl terms for each
interaction type and node to the log file(s)
-pforce real -1 Print all forces larger than this (kJ/mol nm)
-[no]reprod bool no Try to avoid optimizations that affect binary
reproducibility
-cpt real 1 Checkpoint interval (minutes)
-[no]append bool no Append to previous output files when continuing
from checkpoint
-[no]addpart bool yes Add the simulation part number to all output
files when continuing from checkpoint
-maxh real -1 Terminate after 0.99 times this time (hours)
-multi int 0 Do multiple simulations in parallel
-replex int 0 Attempt replica exchange every # steps
-reseed int -1 Seed for replica exchange, -1 is generate a seed
-[no]glas bool no Do glass simulation with special long range
corrections
-[no]ionize bool no Do a simulation including the effect of an X-Ray
bombardment on your system

Getting Loaded...
Reading file md.tpr, VERSION 4.0.5 (single precision)
Note: tpx file_version 58, software version 59
Loaded with Money

starting mdrun 'Protein in water'
50000 steps, 100.0 ps.

Writing final coordinates.

Parallel run - timing based on wallclock.

NODE (s) Real (s) (%)
Time: 24207.000 24207.000 100.0
6h43:27
(Mnbf/s) (MFlops) (ns/day) (hour/ns)
Performance: 0.000 0.000 0.357 67.240

gcq#0: Thanx for Using GROMACS - Have a Nice Day

06:33:00 (7156): wrapper: running 7za.exe (a -y out.7z Ligand.acpypi.7z *.log *.tpr *.gro *.mdp *.edr *.cpt job.xml *.xtc *.top *.itp --device 0)
app exit status: 0x7
06:33:01 (7156): called boinc_finish


**********
**********

Memory Leaks Detected!!!

Memory Statistics:
0 bytes in 0 Free Blocks.
894 bytes in 5 Normal Blocks.
592 bytes in 3 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 7135 bytes.
Total allocations: 97755374 bytes.

Dumping objects ->
{23938} normal block at 0x01FF1718, 143 bytes long.
Data: <a -y out.7z Liga> 61 20 2D 79 20 6F 75 74 2E 37 7A 20 4C 69 67 61
{72} normal block at 0x01FF16A0, 71 bytes long.
Data: <-v -x -c -o -e -> 2D 76 20 2D 78 20 2D 63 20 2D 6F 20 2D 65 20 2D
{68} normal block at 0x01FF4800, 672 bytes long.
Data: < mdrun.ex> 00 00 00 00 CD CD CD CD 6D 64 72 75 6E 2E 65 78
c:\documents and settings\jshultz\my documents\visual studio 2008\projects\boinc\api\boinc_api.cpp(196) : {61} normal block at 0x01FF1610, 4 bytes long.
Data: < ' > 00 00 27 00
{57} normal block at 0x01FF1598, 4 bytes long.
Data: < 2 > E8 32 FF 01
Object dump complete.


</stderr_txt>
]]>

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Message 2545 - Posted: 22 Nov 2010, 11:49:35 UTC
Last modified: 22 Nov 2010, 12:39:57 UTC

host ID 169 (Win XP x64, GTX260 65nm rev A.2, driver 258.96) first 17 minutes no GPU load and no progress, then cca 36% GPU load. After 20 minutes 1.36% done.

prewiev 1
prewiev 2

after 72 minutes 17.07 % progress
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zombie67 [MM]
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Message 2547 - Posted: 22 Nov 2010, 16:06:50 UTC

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Message 2549 - Posted: 22 Nov 2010, 16:15:17 UTC - in response to Message 2547.  

It looks like these run to completion and then compute error at the end....

Jack, will have to look at these for analysis...


good news is, they run, bad news, something at the end is causing the compute error.

we're so close, i can touch molecules!!!!! LOL!
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Message 2550 - Posted: 22 Nov 2010, 17:21:57 UTC - in response to Message 2545.  
Last modified: 22 Nov 2010, 17:47:10 UTC

Task errored out at the end after 20,270s.
http://boinc.drugdiscoveryathome.com/result.php?resultid=2784722
What about other 4 tasks at GTX260 buffer and one task at 9600GT buffer? Delete or crunch on? I have suspended these tasks for now.
EDIT: Swan_Sync=0 has been set
<core_client_version>6.10.58</core_client_version>
<![CDATA[
<message>
 - exit code 195 (0xc3)
</message>
<stderr_txt>
wrapper: starting
12:27:34 (5848): wrapper: running mdrun.exe (-v -x -c -o -e -cpi md.cpt -cpt 1 -deffnm md --device 0)
                         :-)  G  R  O  M  A  C  S  (-:

                   Groningen Machine for Chemical Simulation

                 :-)  VERSION 4.0.99_development_20090421  (-:


      Written by David van der Spoel, Erik Lindahl, Berk Hess, and others.
       Copyright (c) 1991-2000, University of Groningen, The Netherlands.
             Copyright (c) 2001-2008, The GROMACS development team,
            check out http://www.gromacs.org for more information.

         This program is free software; you can redistribute it and/or
          modify it under the terms of the GNU General Public License
         as published by the Free Software Foundation; either version 2
             of the License, or (at your option) any later version.

                              :-)  mdrun.exe  (-:

Option     Filename  Type         Description
------------------------------------------------------------
  -s         md.tpr  Input        Run input file: tpr tpb tpa
  -o         md.trr  Output       Full precision trajectory: trr trj cpt
  -x         md.xtc  Output, Opt! Compressed trajectory (portable xdr format)
-cpi         md.cpt  Input, Opt!  Checkpoint file
-cpo         md.cpt  Output, Opt. Checkpoint file
  -c         md.gro  Output       Structure file: gro g96 pdb
  -e         md.edr  Output       Energy file: edr ene
  -g         md.log  Output       Log file
-dgdl        md.xvg  Output, Opt. xvgr/xmgr file
-field       md.xvg  Output, Opt. xvgr/xmgr file
-table       md.xvg  Input, Opt.  xvgr/xmgr file
-tablep      md.xvg  Input, Opt.  xvgr/xmgr file
-tableb      md.xvg  Input, Opt.  xvgr/xmgr file
-rerun       md.xtc  Input, Opt.  Trajectory: xtc trr trj gro g96 pdb cpt
-tpi         md.xvg  Output, Opt. xvgr/xmgr file
-tpid        md.xvg  Output, Opt. xvgr/xmgr file
 -ei         md.edi  Input, Opt.  ED sampling input
 -eo         md.edo  Output, Opt. ED sampling output
  -j         md.gct  Input, Opt.  General coupling stuff
 -jo         md.gct  Output, Opt. General coupling stuff
-ffout       md.xvg  Output, Opt. xvgr/xmgr file
-devout      md.xvg  Output, Opt. xvgr/xmgr file
-runav       md.xvg  Output, Opt. xvgr/xmgr file
 -px         md.xvg  Output, Opt. xvgr/xmgr file
 -pf         md.xvg  Output, Opt. xvgr/xmgr file
-mtx         md.mtx  Output, Opt. Hessian matrix
 -dn         md.ndx  Output, Opt. Index file

Option       Type   Value   Description
------------------------------------------------------
-[no]h       bool   no      Print help info and quit
-nice        int    19      Set the nicelevel
-deffnm      string md      Set the default filename for all file options
-[no]xvgr    bool   yes     Add specific codes (legends etc.) in the output
                            xvg files for the xmgrace program
-device      int    0       Select the CUDA device (default m=0)
-[no]pd      bool   no      Use particle decompostion
-dd          vector 0 0 0   Domain decomposition grid, 0 is optimize
-npme        int    -1      Number of separate nodes to be used for PME, -1
                            is guess
-ddorder     enum   interleave  DD node order: interleave, pp_pme or cartesian
-[no]ddcheck bool   yes     Check for all bonded interactions with DD
-rdd         real   0       The maximum distance for bonded interactions with
                            DD (nm), 0 is determine from initial coordinates
-rcon        real   0       Maximum distance for P-LINCS (nm), 0 is estimate
-dlb         enum   auto    Dynamic load balancing (with DD): auto, no or yes
-dds         real   0.8     Minimum allowed dlb scaling of the DD cell size
-[no]sum     bool   yes     Sum the energies at every step
-[no]v       bool   yes     Be loud and noisy
-[no]compact bool   yes     Write a compact log file
-[no]seppot  bool   no      Write separate V and dVdl terms for each
                            interaction type and node to the log file(s)
-pforce      real   -1      Print all forces larger than this (kJ/mol nm)
-[no]reprod  bool   no      Try to avoid optimizations that affect binary
                            reproducibility
-cpt         real   1       Checkpoint interval (minutes)
-[no]append  bool   no      Append to previous output files when continuing
                            from checkpoint
-[no]addpart bool   yes     Add the simulation part number to all output
                            files when continuing from checkpoint
-maxh        real   -1      Terminate after 0.99 times this time (hours)
-multi       int    0       Do multiple simulations in parallel
-replex      int    0       Attempt replica exchange every # steps
-reseed      int    -1      Seed for replica exchange, -1 is generate a seed
-[no]glas    bool   no      Do glass simulation with special long range
                            corrections
-[no]ionize  bool   no      Do a simulation including the effect of an X-Ray
                            bombardment on your system

Getting Loaded...
Reading file md.tpr, VERSION 4.0.5 (single precision)
Note: tpx file_version 58, software version 59
Loaded with Money

starting mdrun 'Protein in water'
50000 steps,    100.0 ps.

Writing final coordinates.

	Parallel run - timing based on wallclock.

               NODE (s)   Real (s)      (%)
       Time:  19399.000  19399.000    100.0
                       5h23:19
               (Mnbf/s)   (MFlops)   (ns/day)  (hour/ns)
Performance:      0.000      0.001      0.445     53.885

gcq#0: Thanx for Using GROMACS - Have a Nice Day

18:05:21 (5848): wrapper: running 7za.exe (a -y out.7z Ligand.acpypi.7z *.log *.tpr *.gro *.mdp *.edr *.cpt job.xml *.xtc *.top *.itp --device 0)
app exit status: 0x7
18:05:23 (5848): called boinc_finish


**********
**********

Memory Leaks Detected!!!

Memory Statistics:
0 bytes in 0 Free Blocks.
1062 bytes in 7 Normal Blocks.
592 bytes in 3 CRT Blocks.
0 bytes in 0 Ignore Blocks.
0 bytes in 0 Client Blocks.
Largest number used: 7303 bytes.
Total allocations: 77222294 bytes.

Dumping objects ->
{18926} normal block at 0x01D96360, 143 bytes long.
 Data: <a -y out.7z Liga> 61 20 2D 79 20 6F 75 74 2E 37 7A 20 4C 69 67 61 
{73} normal block at 0x01D92E60, 71 bytes long.
 Data: <-v -x -c -o -e -> 2D 76 20 2D 78 20 2D 63 20 2D 6F 20 2D 65 20 2D 
{69} normal block at 0x01D95DC0, 672 bytes long.
 Data: <        mdrun.ex> 00 00 00 00 CD CD CD CD 6D 64 72 75 6E 2E 65 78 
{62} normal block at 0x01D92D80, 84 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
c:\documents and settings\jshultz\my documents\visual studio 2008\projects\boinc\api\boinc_api.cpp(196) : {61} normal block at 0x01D92D50, 4 bytes long.
 Data: <    > 00 00 EF 01 
..\lib\parse.cpp(153) : {60} normal block at 0x01D92CD0, 84 bytes long.
 Data: <<project_prefere> 3C 70 72 6F 6A 65 63 74 5F 70 72 65 66 65 72 65 
{53} normal block at 0x01D92C58, 4 bytes long.
 Data: <(G  > 28 47 D9 01 
Object dump complete.


</stderr_txt>
]]>
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Message 2559 - Posted: 23 Nov 2010, 18:37:55 UTC
Last modified: 23 Nov 2010, 18:40:44 UTC

For me it's 68,783.31 sec for nothing 717861 (MDRUN CUDA OPENCL v0.03) on my E8400 under W$ 32 bits and with a NVIDIA Quadro FX 580 (511MB) driver: 25957.

I stop the tests.
"Libre de penser... pensez Libre" =8?()>
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Message 2560 - Posted: 23 Nov 2010, 19:01:26 UTC - in response to Message 2559.  

yes, all of these first 50 error out at the end for some reason....

we hope to solve this before we release the next batch...

but believe me, it better that we tried this instead of waiting another week... no need in delaying further progress...

anyone who has any left, you may abort them...
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Message 2564 - Posted: 25 Nov 2010, 6:28:41 UTC

As I can remember a similar issue occured one year or more ago - the gromacs part had finished but any problem was with zipping.
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Message 2565 - Posted: 25 Nov 2010, 15:09:55 UTC - in response to Message 2564.  

As I can remember a similar issue occured one year or more ago - the gromacs part had finished but any problem was with zipping.


yea, i remember too, don't know if that the issue here or not...

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Message 2570 - Posted: 26 Nov 2010, 19:01:45 UTC - in response to Message 2565.  
Last modified: 26 Nov 2010, 19:03:01 UTC

we've sent a message to our developer about the exit code -195.... hopefully he might come up with a solution for it..
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Message 2620 - Posted: 24 Jan 2011, 7:58:02 UTC - in response to Message 2570.  

Do you know if any of the DD@H CUDA or OpenCL apps have problems with the newer Fermi-based Nvidia cards, such as my GTS 450?
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Message 2622 - Posted: 26 Jan 2011, 2:06:09 UTC - in response to Message 2620.  

we had volunteers test the app on their cards... it's the driver versions that are giving use trouble....
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