Linux MDrun Cuda app

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Profile Tim Turner
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Message 1214 - Posted: 8 Sep 2009, 20:32:47 UTC
Last modified: 8 Sep 2009, 20:43:41 UTC

Just to keep the two cuda apps separate from each other in the forums.

currently(as of this post): the app is missing a file in the CUDA directory and errors out.

I'm not a Linux owner/user so we need more feedback from our Linux volunteers.
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Message 1225 - Posted: 9 Sep 2009, 15:13:18 UTC - in response to Message 1214.  

Shall I crunch some CUDA-WUs ???

UP,DOWN,CPU WU ERRORS wrote:
my 64-bit Linux-Host (ubuntu) crashed many workunits

<stderr_txt>
mdrun_cuda_0.120_i686-pc-linux-gnu__cuda: error while loading shared libraries: libOpenMM.so: cannot open shared object file: No such file or directory
</stderr_txt>

And I can not find libOpenMM.so in any repository!
Where can I get it or is it a project-file which was not delivered ???

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Message 1226 - Posted: 9 Sep 2009, 15:16:35 UTC - in response to Message 1225.  
Last modified: 9 Sep 2009, 15:17:54 UTC

i think they were canceled.
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Message 1230 - Posted: 9 Sep 2009, 17:17:27 UTC - in response to Message 1226.  

I'll generate a smaller batch now
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Message 1264 - Posted: 11 Sep 2009, 11:57:23 UTC

As you mentioned in "Nvidia Minimum Driver Requirement" Driver Version 190.x is needed. Highest avail version for linux 64-bit is 185.18.36 !

Following that, there is no dd@home-cuda-app for linux 64-bit ?
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Message 1266 - Posted: 11 Sep 2009, 15:56:50 UTC - in response to Message 1264.  

As you mentioned in "Nvidia Minimum Driver Requirement" Driver Version 190.x is needed. Highest avail version for linux 64-bit is 185.18.36 !

Following that, there is no dd@home-cuda-app for linux 64-bit ?


woops, i'll adjust my post to reflect that.
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Message 1286 - Posted: 13 Sep 2009, 14:27:42 UTC
Last modified: 13 Sep 2009, 14:58:14 UTC

crashed one cuda-Workunit (this one):
stderr out wrote:
<core_client_version>6.6.37</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)
</message>
<stderr_txt>
wrapper: starting
16:21:40 (28326): wrapper: running mdrun_openmm.exe (-v -deffnm md --device 0)
app exit status: 0x7f00
16:21:41 (28326): called boinc_finish

</stderr_txt>
]]>

I can not see why ....

GPU: NVIDIA GeForce 8400 GS
Host: this one
Cuda-Version: 185.18.36

EDIT:
done a ldd to the app:
$ sudo ldd mdrun_openmm_0.121_i686-pc-linux-gnu__cuda
        linux-gate.so.1 =>  (0xf7f53000)
        libOpenMM.so => not found
        libxml2.so.2 => /usr/lib32/libxml2.so.2 (0xf7e04000)
        libnsl.so.1 => /lib32/libnsl.so.1 (0xf7deb000)
        libboinc_api.so.6 => not found
        libboinc.so.6 => not found
        libSM.so.6 => /usr/lib32/libSM.so.6 (0xf7de2000)
        libICE.so.6 => /usr/lib32/libICE.so.6 (0xf7dc9000)
        libX11.so.6 => /usr/lib32/libX11.so.6 (0xf7cda000)
        libstdc++.so.6 => /usr/lib32/libstdc++.so.6 (0xf7beb000)
        libm.so.6 => /lib32/libm.so.6 (0xf7bc5000)
        libgcc_s.so.1 => /usr/lib32/libgcc_s.so.1 (0xf7bb6000)
        libpthread.so.0 => /lib32/libpthread.so.0 (0xf7b9d000)
        libc.so.6 => /lib32/libc.so.6 (0xf7a39000)
        libdl.so.2 => /lib32/libdl.so.2 (0xf7a35000)
        libz.so.1 => /usr/lib32/libz.so.1 (0xf7a1f000)
        libuuid.so.1 => /lib32/libuuid.so.1 (0xf7a1a000)
        libxcb.so.1 => /usr/lib32/libxcb.so.1 (0xf7a00000)
        /lib/ld-linux.so.2 (0xf7f54000)
        libXau.so.6 => /usr/lib32/libXau.so.6 (0xf79fb000)
        libXdmcp.so.6 => /usr/lib32/libXdmcp.so.6 (0xf79f6000)


as you can see - something is not found
I will check this, but "libOpenMM.so => not found" was a known error ...

EDIT2:
I can not locate these files:
libboinc_api.so.6 => not found
libboinc.so.6 => not found
and I do not know, where to get it ...
The same problem to libOpenMM.so :(
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Message 1287 - Posted: 13 Sep 2009, 20:16:06 UTC - in response to Message 1286.  

Glad to see that the project is still running fine !
(I was in holidays) and as soon I get my ADSL acces I'm gonna try the CUDA app on my gentoo 64b !
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Message 1288 - Posted: 13 Sep 2009, 23:03:50 UTC - in response to Message 1287.  

Well have not managed to get any of the cuda apps to run properly. Kind of annoying.
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Message 1297 - Posted: 14 Sep 2009, 22:14:39 UTC - in response to Message 1288.  

Well have not managed to get any of the cuda apps to run properly. Kind of annoying.


OK.. i can't resist any more it's itching in my fingers...

I think this whole "project" is way above your heads. You can't even get the server to run properly and now you're messing around with cuda ?

I'd suggest you start all over again with a clean install of the server software.

1. Have a look at a good book that teaches you how to code php to get rid of this "homepage" thingy ..(honestly, who did that ? iframes ? scroll bars in the UoTd ?).

2. Next thing to read would be something about coding in c/c++ . Your fist "Hello World" will sure make you happy.

3. Now that you got some basic understanding on how things work, you can start on your first project app for CPU.

4. Get familiar with using a debugger, that sometimes can help figuring out where your own app crashes.

5. Start porting your cpu app to different OSes.

6. If all works as it should... guess what's next ;) Right! read and comprehend how to code using cuda.

7. Repeat step 6 for CAL

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Message 1298 - Posted: 14 Sep 2009, 22:20:30 UTC - in response to Message 1297.  
Last modified: 14 Sep 2009, 22:26:18 UTC

Well have not managed to get any of the cuda apps to run properly. Kind of annoying.


OK.. i can't resist any more it's itching in my fingers...

I think this whole "project" is way above your heads. You can't even get the server to run properly and now you're messing around with cuda ?

I'd suggest you start all over again with a clean install of the server software.

1. Have a look at a good book that teaches you how to code php to get rid of this "homepage" thingy ..(honestly, who did that ? iframes ? scroll bars in the UoTd ?).

2. Next thing to read would be something about coding in c/c++ . Your fist "Hello World" will sure make you happy.

3. Now that you got some basic understanding on how things work, you can start on your first project app for CPU.

4. Get familiar with using a debugger, that sometimes can help figuring out where your own app crashes.

5. Start porting your cpu app to different OSes.

6. If all works as it should... guess what's next ;) Right! read and comprehend how to code using cuda.

7. Repeat step 6 for CAL



jack has well for :

1. had to learn from scratch on building, maintaining, porting, learning cuda.

2. don't expect an alpha project with 1 person dedicated to doing all the work to work at your speed preferences.

3. this project is still on level 1 of a 10 story building. lets work our stuff(problems) out before we get to level 10 and crash the building and realize we have made a mistake like you would have us do.

4. cuda is hard enough to get to work with openmm much less cal. so forgive jack if cal is on the bottom of his list.. Ageless has tried to build with cal and from what i gather the source coding isn't complete or something to that affect.

5. now; if you'll excuse me, I'll go work on the translations for the site.
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Message 1299 - Posted: 15 Sep 2009, 12:34:13 UTC - in response to Message 1298.  
Last modified: 15 Sep 2009, 12:34:25 UTC

Its great to have people who criticize but its even greater to have people who contribute. To tell you the truth, I have spent two years trying to build collaborations with people only to find the people who talk the most tend to be the most lazy and unhelpful. So please I am well aware of these issues but have you ever heard of the saying "Perfection is the enemy of the good?"
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Message 1323 - Posted: 16 Sep 2009, 5:14:37 UTC

A little OT.
I am not sure that Crunch3r critisies, as I know he helped some projects to increase and optimize applications. He knows what to do and how to do.
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Message 1326 - Posted: 16 Sep 2009, 16:52:53 UTC - in response to Message 1321.  

Were they working perfectly on your machine before you put the app on the actual server?


yes the cuda work stand alone on my computer. We tried it it failed. We will rebuild. There is no more point in posting to this thread unless you can contribute insights into the cause of the problem.

mdrun, will work for cpu if you supply good parameters. given the indeterminant nature of such simulations, you have to have accept a degree of chaos. These are stochastic simulations that will break. Sometimes when they use the same parameters you used successfully on previous runs.
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Message 1327 - Posted: 16 Sep 2009, 17:03:17 UTC - in response to Message 1326.  

The other reason for testing cuda apps is to learn enough to ask the right types of questions this October when I will meet some of the people involved with GPUGrid. Generally I learn more from making mistakes then just reading documentation. Well we have done all we can in testing cuda on this DD@H. Unless I can find a way to fix our problems by rebuilding the app, we won't be seeing any more for a while.
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Message 1621 - Posted: 26 Oct 2009, 13:48:15 UTC

This MIGHT be a source for the openmm files you couldn't find:


Stanford goes fully molecular with OpenMM

http://www.tgdaily.com/content/view/41352/140/


I don't run Linux, so I can't check.
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Message 1639 - Posted: 28 Oct 2009, 17:43:37 UTC - in response to Message 1621.  

Our meeting at Barcelona went well and I had some good discussions with the GPU Grid developers. They have an amazing project! Regarding the OpenMM project, it still needs work. I need to discuss with their developers ways it can improve and better communicate issues I still have. Despite my efforts all summer, I still cannot get the cuda platform to detect the gpu. I also get that their support on this is voluntary and I cannot expect immediate improvements. If there are some good developers with cuda looking to provide some assistance, I could use the help.
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Message 1645 - Posted: 28 Oct 2009, 21:58:49 UTC - in response to Message 1327.  

The other reason for testing cuda apps is to learn enough to ask the right types of questions this October when I will meet some of the people involved with GPUGrid. Generally I learn more from making mistakes then just reading documentation. Well we have done all we can in testing cuda on this DD@H. Unless I can find a way to fix our problems by rebuilding the app, we won't be seeing any more for a while.

Well, when it comes to Linux Cuda apps, I'd be more than willing to help test. So far, I can only crunch Collatz with my GPU.
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Message 1646 - Posted: 29 Oct 2009, 11:09:24 UTC - in response to Message 1645.  

What we need is someone with some programming experience to take a look at what is going on here. I can provide some build instructions.
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Message 1649 - Posted: 29 Oct 2009, 14:12:59 UTC - in response to Message 1646.  

Well, I have no useful programming experience outside of college. I know who does, but don't know how willing he would be. I think he would have spoken up by now if he was.
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