ACEMD2 6.12 cuda and 6.13 cuda31 for windows and linux

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Message 19362 - Posted: 9 Nov 2010, 11:59:09 UTC
Last modified: 9 Nov 2010, 14:04:53 UTC

I have just benchmarked 6.12 under Linux on a GTX275 and there is less than 2% difference in time between 6.12 and 6.05.

For Linux, 6.12 also uses less CPU than 6.05 and so it is slower. If you want to get to maximum speed use the environment variable SWAN_SYNC=0. Just set in .bashrc (if you use bash as a shell):
export SWAN_SYNC=0

We have asked Anderson to add a simpler way to set this variable and there will be a specific configuration for it in the boinc client.

Also 6.12 is capable of higher performance but we need all applications to be updated (even the cuda3.2 ones) to start this mode of computing.

Please report here what sort of problems do you have with 6.12. Politely and accurately. We simply don't see any problem on our machines.

gdf
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Message 19371 - Posted: 9 Nov 2010, 16:39:27 UTC - in response to Message 19362.  
Last modified: 9 Nov 2010, 16:41:33 UTC

For Linux, 6.12 also uses less CPU than 6.05 and so it is slower. If you want to get to maximum speed use the environment variable SWAN_SYNC=0. Just set in .bashrc (if you use bash as a shell):
export SWAN_SYNC=0

WTF?
In what GUI do I set this variable?
What is .bashrc?
How will it interact with any other program I'm running?

And please don't use in-talk, I'm a user, not nerd. I hate terminal inputs, but will make them if it's good explained why I should and what I'm doing there and why there is no decent, i.e. GUI, way of doing this.

Edith says:
I've just started a new 6.12, and my GPU is freezing. I think the main task atm is really just organizing my screen.
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For questions about Boinc look in the BOINC-Wiki
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Message 19382 - Posted: 9 Nov 2010, 20:27:48 UTC - in response to Message 19371.  

I've just started a new 6.12, and my GPU is freezing. I think the main task atm is really just organizing my screen.

It's now running since 3:50h and has done 2.888%, if it goes on with that "speed" it will be finished in just under 130h, or nearly 6 days. It may or may not be within the deadline, it's about that time.
With the old app a WU of that type would have been finished in 17h, so this new app increases the crunching time by a whopping factor 8, not as expected the speed.
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Message 19384 - Posted: 9 Nov 2010, 20:39:37 UTC - in response to Message 19382.  

Well, clearly a factor 8 is not a general issue.
What if you update drivers to get the cuda3.1 app.

gdf

I've just started a new 6.12, and my GPU is freezing. I think the main task atm is really just organizing my screen.

It's now running since 3:50h and has done 2.888%, if it goes on with that "speed" it will be finished in just under 130h, or nearly 6 days. It may or may not be within the deadline, it's about that time.
With the old app a WU of that type would have been finished in 17h, so this new app increases the crunching time by a whopping factor 8, not as expected the speed.

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Message 19386 - Posted: 9 Nov 2010, 21:37:49 UTC - in response to Message 19384.  
Last modified: 9 Nov 2010, 21:38:06 UTC

Well, clearly a factor 8 is not a general issue.
What if you update drivers to get the cuda3.1 app.

gdf

I've the highest numbered drivers from the ubuntu repository. The version number is 195.36.24.
I've experimented with my old card and some bricolage in the past and it didn't work at all, I wasn't even able to reinstall the proper one back that came with ubuntu, although as proprietorial. I had to do a complete system reinstall and tedious file backups afterwards with a friend of mine as a helping hand, I don't want to have that experience again.

If you guaranty me that nothing will go wrong, I would try to hand-install some newer stuff, but I need precise instructions, and of course a way to undo everything in case something goes wrong.
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Message 19389 - Posted: 9 Nov 2010, 22:16:09 UTC - in response to Message 19386.  

No, I can't guarantee.
You might want to try with the USB Linux stick without installing anything in your system. (See the join section)
gdf
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Message 19391 - Posted: 9 Nov 2010, 23:04:01 UTC

The 6.12 app has cut 8 to 10 thousand seconds off my GT240 task times in Ubuntu 10.4 with Nvidia driver 260.19.12!

I was about to retire my 240s but I think I will try to get them back into a system now. I there anyway they can be put in the same system with a fermi?
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Message 19408 - Posted: 10 Nov 2010, 10:28:14 UTC - in response to Message 19391.  

Is 6.12 a release app now?
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Message 19410 - Posted: 10 Nov 2010, 11:44:25 UTC - in response to Message 19408.  

Yes, 6.12 is in use:

GT200 cards on Linux can run ACEMD2: GPU molecular dynamics v6.12 (cuda)
Fermi cards on Linux can run ACEMD2: GPU molecular dynamics v6.06 (cuda30)

GT200 cards on Windows can run ACEMD2: GPU molecular dynamics v6.12 (cuda)
Fermi cards on Windows can run ACEMD2: GPU molecular dynamics v6.11 (cuda31)

The test app for Fermi on Linux is ACEMD beta version v6.37 (cuda31)
The test app for Fermi on Linux is ACEMD beta version v6.37 (cuda31)
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Message 19412 - Posted: 10 Nov 2010, 12:49:39 UTC - in response to Message 19410.  

just reattached again ang got 6.11 :( and downgraded drivers and still got 6.11
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Message 19414 - Posted: 10 Nov 2010, 16:11:33 UTC - in response to Message 19412.  
Last modified: 10 Nov 2010, 16:49:25 UTC

For GF200 series cards you need to use an earlier driver (before 25715) to run the 6.12 app for Windows.
197.45 might be the best one.

If you use one of the more recent drivers you will end up running the ACEMD2: GPU molecular dynamics v6.11 (cuda31) app which only works well for Fermi cards.
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Message 19415 - Posted: 10 Nov 2010, 16:54:42 UTC - in response to Message 19414.  

I'll just stay off the project. I aren't going back to an ancient driver just to get the right app.
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Message 19416 - Posted: 10 Nov 2010, 17:45:20 UTC - in response to Message 19415.  

In fact, you shouldn't. The cuda31 app should run on all cards.
Only the cuda app runs on g200 only. That's due to incompatibility of cuda2 with fermi. Nevertheless, the best driver is not the last one but is the last before the change of technology (in this case g200 to fermi) which is the 195 driver.

gdf

I'll just stay off the project. I aren't going back to an ancient driver just to get the right app.

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Message 19417 - Posted: 10 Nov 2010, 18:12:41 UTC - in response to Message 19416.  

In fact, you shouldn't. The cuda31 app should run on all cards.
Only the cuda app runs on g200 only. That's due to incompatibility of cuda2 with fermi. Nevertheless, the best driver is not the last one but is the last before the change of technology (in this case g200 to fermi) which is the 195 driver.

I have the 195 driver running, and I can't see anything even remotely "best" on my machine. The WU is now 25:34h running and still at 17.168%, so another 100h waiting before it will finish if I don't decide to let my GPU crunch something, not just sit idle. 45°C is just idle temperature, with DNetC I get to 70°. The only good thing is that the 4 CPU-WUs all get a whole core, but would rather give one away than waste my GPU time so much.

The 260-drivers are not in a repository, and all I've read about the manual installation of nvidia drivers in different Linux boards is that you have to maintain and babysit your machine very very close, and the possibility to loose the screen completely after a kernel update seems to be a very likely possibility.
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Message 19423 - Posted: 11 Nov 2010, 9:55:47 UTC - in response to Message 19417.  

I have uploaded the new cuda3.1 for Linux to have some further feedbacks from a larger pool of machines. This version will work with the GTX460.

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Message 19424 - Posted: 11 Nov 2010, 11:11:58 UTC - in response to Message 19423.  

For what it's worth, since the upgrade, all the WUs have been erroring out on my Linux box.

I run Ubuntu 10.10 64-bits (2.6.35-22 kernel), Boinc client 6.10.58 (the default one from Brekeley's site - manual install, not from repository), Nvidia 9800 GTX+ GPU with Nvidia drivers 256-53 (manual install, not from repositories).

Should I upgrade/downgrade my Nvidia drivers ?
Should I switch to Boinc 6.12 (which is still not recommended on Berkeley's site) ?

The message in the Boinc Manager I get is :
"GPUGRID Output file 406-KASHIF_HIVPR_n1_unbound_so_ba1-62-100-RND1104_0_0 for task 406-KASHIF_HIVPR_n1_unbound_so_ba1-62-100-RND1104_0 absent"
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Message 19425 - Posted: 11 Nov 2010, 12:48:03 UTC - in response to Message 19424.  
Last modified: 11 Nov 2010, 12:52:21 UTC

I see the problem, new version coming up.

gdf

For what it's worth, since the upgrade, all the WUs have been erroring out on my Linux box.

I run Ubuntu 10.10 64-bits (2.6.35-22 kernel), Boinc client 6.10.58 (the default one from Brekeley's site - manual install, not from repository), Nvidia 9800 GTX+ GPU with Nvidia drivers 256-53 (manual install, not from repositories).

Should I upgrade/downgrade my Nvidia drivers ?
Should I switch to Boinc 6.12 (which is still not recommended on Berkeley's site) ?

The message in the Boinc Manager I get is :
"GPUGRID Output file 406-KASHIF_HIVPR_n1_unbound_so_ba1-62-100-RND1104_0_0 for task 406-KASHIF_HIVPR_n1_unbound_so_ba1-62-100-RND1104_0 absent"
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Message 19426 - Posted: 11 Nov 2010, 13:16:07 UTC

6.12 task were running good on my GT240 now I have three in a row that have died.

<core_client_version>6.10.56</core_client_version>
<![CDATA[
<message>
process exited with code 127 (0x7f, -129)
</message>
<stderr_txt>

</stderr_txt>
]]>

This is the same error that my GTX 470s are getting now, and they were getting the same error on the beta work units.

Both systems are Ubuntu 10.4 with driver 260.19.12

The project has been reset on both systems, any suggestions?
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Message 19427 - Posted: 11 Nov 2010, 13:20:02 UTC - in response to Message 19426.  

6.13 cuda31 for Linux is now out.

gdf
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Message 19428 - Posted: 11 Nov 2010, 17:58:28 UTC - in response to Message 19427.  
Last modified: 11 Nov 2010, 17:58:49 UTC

Running CUDA 3.1 on GT240s does not presently offer high resource utilization or credit. On a quad GT240 system I have been running tasks on the CUDA 3.1 app for several days. The run times vary between 70,000sec and 107,000sec. Only the KASHIF_HIVPR tasks have a reasonably short runtime and finish between 70000sec and 75,000sec (within 24h). However, even these tasks are about 38% slower than the 6.05 app; KASHIF_HIVPR took between 51,000sec and 54,000sec.
Most other tasks take over 24h and miss the 24h return time bonus. Hence the systems daily average credit dropped from 60K to 34K.

Examples of KASHIF_HIVPR tasks (all W7 x64 1.59GHz or Vista x64 1.60GHz):

(6.05 app) Time per step = 51ms V
(6.05 app) Time per step = 47ms V
(6.05 app) Time per step = 52ms V
(6.05 app) Time per step = 54ms 7
(6.05 app) Time per step = 53ms 7
(6.12 app) Time per step = 58ms 7
(6.12 app) Time per step = 59ms 7
(6.12 app) Time per step = 55ms 7
(6.11 app) Time per step = 78ms V
(6.11 app) Time per step = 72ms V
(6.11 app) Time per step = 75ms V
(6.11 app) Time per step = 72ms V

Examples of IBUCH_*_pYEEI tasks:

(6.05 app) Time per step = 48ms V
(6.05 app) Time per step = 52ms V
(6.05 app) Time per step = 49ms V
(6.05 app) Time per step = 53ms 7
(6.12 app) Time per step = 58ms 7
(6.12 app) Time per step = 58ms 7
(6.12 app) Time per step = 58ms 7
(6.11 app) Time per step = 70ms V
(6.11 app) Time per step = 73ms V
(6.11 app) Time per step = 70ms V
(6.11 app) Time per step = 92ms 7

Note the card in the Windows 7 system (7) is usually about 5% slower than the Vista (V)systems cards; due to the card spec, slight speed difference and different system hardware (CPU).

For GT240’s on Windows, 6.12 is on average (over different tasks) about 8% slower than 6.05, and 6.11 is around 43% slower than 6.05.
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