Gromacs GPU work units now available

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Jim1348

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Message 4955 - Posted: 7 Oct 2017, 23:34:53 UTC
Last modified: 7 Oct 2017, 23:44:41 UTC

The Good News: I am now getting GPU work units for my GTX 980 running under Ubuntu 16.04
The Bad News: They all error out immediately
(Same for a second machine with a GTX 1070 running under Ubuntu 17.04).

Stderr output

<core_client_version>7.8.3</core_client_version>
<![CDATA[
<message>
process exited with code 195 (0xc3, -61)</message>
<stderr_txt>
18:58:28 (13176): wrapper (7.5.26014): starting
18:58:28 (13176): wrapper: running gmx (mdrun -nt 1 -quiet -deffnm md)

Back Off! I just backed up md.log to ./#md.log.1#

-------------------------------------------------------
Program:     gmx mdrun, VERSION 5.1.4
Source file: src/gromacs/utility/path.cpp (line 238)
Function:    static bool gmx::Path::isEquivalent(const string&, const string&)

System I/O error:
Path::isEquivalent called with two invalid files
  Reason: No such file or directory
  (call to stat() returned error code 2)

For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
18:58:29 (13176): gmx exited; CPU time 0.000000
18:58:29 (13176): app exit status: 0x100
18:58:29 (13176): called boinc_finish(195)

</stderr_txt>
]]>
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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4964 - Posted: 14 Oct 2017, 20:27:52 UTC - in response to Message 4955.  

It looks like the app needs libc6 package installed in system.
Krzysztof 'krzyszp' Piszczek

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[BOINC@Poland]goofyx
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Message 4965 - Posted: 14 Oct 2017, 22:23:43 UTC - in response to Message 4964.  

Gromacs/GMC is still is still beta version
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Jim1348

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Message 4966 - Posted: 14 Oct 2017, 22:40:30 UTC - in response to Message 4965.  
Last modified: 14 Oct 2017, 22:41:04 UTC

Gromacs/GMC is still is still beta version

OK, I will wait for a fix (both 0.07 and 0.08 gromacs work units fail now).

I tried the following:
sudo apt-get update
sudo apt-get install libc6
https://www.howtoinstall.co/en/ubuntu/xenial/libc6

and also:
sudo apt-get update
sudo apt-get install libc6-i386
https://www.howtoinstall.co/en/ubuntu/xenial/libc6-i386

Both of them just give an "Unable to locate package" message on Ubuntu 16.04.3.
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Message 4967 - Posted: 14 Oct 2017, 23:50:48 UTC - in response to Message 4966.  

Can you try:
apt-get install libc6-amd64

Please?
Krzysztof 'krzyszp' Piszczek

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Jim1348

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Message 4968 - Posted: 15 Oct 2017, 1:44:15 UTC - in response to Message 4967.  

Can you try:
apt-get install libc6-amd64

Yes, that worked! I will await new work units to see if they run.
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Jim1348

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Message 4969 - Posted: 15 Oct 2017, 7:24:14 UTC - in response to Message 4968.  
Last modified: 15 Oct 2017, 7:29:13 UTC

My most recent work units have failed even with libc6-amd64 installed.
But I must have made a typo before, because I tried again:
sudo apt-get install libc6
sudo apt-get install libc6-i386

and they worked this time. So I will try again when I receive more work units, to see if they make any difference.

But I am also wondering about the CUDA version. Is it really 2.3? My drivers are 387.12, which are capable of CUDA 9.1. I wonder if they can work with such an old CUDA version?
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Message 4970 - Posted: 15 Oct 2017, 13:35:06 UTC - in response to Message 4969.  

It should, but now we have problem with path to CUDA libs... I'm working on it.
Krzysztof 'krzyszp' Piszczek

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europe64

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Message 4971 - Posted: 15 Oct 2017, 17:24:54 UTC

hi,
it works now on a xeon 2630 v3 with a gtx1050ti
running ubuntu 16.04

the deadline with 2 days is very short
my boincmanager tells me that it takes about 1d22h to complete 1 wu

you could try to install gromacs if it does not work
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Message 4972 - Posted: 15 Oct 2017, 18:32:16 UTC - in response to Message 4971.  

It should finish quicker on your card. Test execution on my GTX650 takes about 7-8 hours. (But on old Gromacs version, v14 is Gromacs 2016.3)
Krzysztof 'krzyszp' Piszczek

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Message 4973 - Posted: 15 Oct 2017, 18:54:16 UTC - in response to Message 4971.  

you could try to install gromacs if it does not work

Yes, it looks like that installing gromacs (apt install gromacs under Debian-like systems) helps... So, looks like app isn't still fully portable :(
Krzysztof 'krzyszp' Piszczek

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Message 4974 - Posted: 15 Oct 2017, 20:08:07 UTC - in response to Message 4972.  

my gpu utilization is only about 30 to 40 percent
how can i change this ?
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Message 4976 - Posted: 15 Oct 2017, 23:33:38 UTC - in response to Message 4974.  

my gpu utilization is only about 30 to 40 percent
how can i change this ?


Run several tasks at once with app_config file.

I moved a GPU over to a Linux computer. Just need some tasks now.
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Jim1348

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Message 4977 - Posted: 16 Oct 2017, 13:38:46 UTC

After installing gromacs using "apt install gromacs" on my Ubuntu 16.04 machine, I am now running a 0.14 work unit. But on a GTX 980 the estimated time is 2 days 10 hours, and the GPU utilization is only about 10%. As a result, it is running "high priority", and I don't think it will make the two day time limit.
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Message 4978 - Posted: 16 Oct 2017, 14:25:41 UTC - in response to Message 4977.  

I set 2 days limit because I haven't compared different cards (I just have not really strong GTX650 with CUDA) and can't predict execution time.
GPU utilisation strongly depends on CPU (CPU need to feed GPU with sufficient data).
Krzysztof 'krzyszp' Piszczek

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Jim1348

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Message 4979 - Posted: 16 Oct 2017, 14:51:43 UTC - in response to Message 4978.  

I set 2 days limit because I haven't compared different cards (I just have not really strong GTX650 with CUDA) and can't predict execution time.
GPU utilisation strongly depends on CPU (CPU need to feed GPU with sufficient data).

I have one core of my i7-3770 reserved for the GTX 980, and that normally is enough. I think that the Maxwell (and later) cards just don't work well with CUDA 2.3. Probably the Kepler cards will be better for this project.
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Message 4980 - Posted: 16 Oct 2017, 15:17:33 UTC - in response to Message 4979.  

I just finish compilation for Windows CUDA Gromacs. It work fine on my computer but wrapper will need some modifications.
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Message 4981 - Posted: 16 Oct 2017, 15:27:22 UTC
Last modified: 16 Oct 2017, 15:31:14 UTC

My windows 10pc just start cuda gromacs task
and as I can see it didn't do anything
gpu use is zero after 20min completed 0.6% on 1080 card
in process tree there is NO gromacs process
https://yadi.sk/i/GzObl2LD3NoNou
may be additional software must be installed like Linux mashines?
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Message 4982 - Posted: 16 Oct 2017, 15:35:06 UTC - in response to Message 4981.  

after boinc restart
16.10.2017 18:41:10 | DrugDiscovery@Home | Task gmx_GMX-T014_XXXX_TTTTT_tasks.gmx_1_100.in_2 exited with zero status but no 'finished' file
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Message 4983 - Posted: 16 Oct 2017, 15:45:13 UTC - in response to Message 4982.  

oh all my windows pc's with NVidia gpus stop amicable and launch dd gromacs. and it's fine. but gpu use 0
boinc think that task is running but is 100% buggy (slow speed and 0 use of GPU)
please give some advice
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Message boards : Number crunching : Gromacs GPU work units now available


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