Gromacs GPU work units now available

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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4984 - Posted: 16 Oct 2017, 16:01:25 UTC - in response to Message 4983.  
Last modified: 16 Oct 2017, 16:02:55 UTC

Do you have "gmx.exe" process in task manager?

Anyway, I'm constantly changing wrapper today, so please give me app version when you report how it is going on your machine.

Edit:
It can also not use GPU for few seconds from start as it prepare data for GPU. On my windows machine with GTX 1060 6GB it use about 60% of GPU.
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Message 4985 - Posted: 16 Oct 2017, 16:51:11 UTC - in response to Message 4984.  

Can somebody confirm that doing "apt-get install gromacs" solves errors on Debian based systems, please?
Krzysztof 'krzyszp' Piszczek

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Message 4986 - Posted: 16 Oct 2017, 17:30:31 UTC

Get this error after 4-6 Seconds of run time on a Windows 7 Pro Box ...

PBOYZTOY04

3725 DrugDiscovery@Home 10/16/2017 1:26:12 PM [error] Can't rename output file slots/25/md.log to projects/boinc.drugdiscoveryathome.com/gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_6_100.in_1_r1913621387_3: Error 32
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Message 4987 - Posted: 16 Oct 2017, 17:36:47 UTC - in response to Message 4986.  

Get this error after 4-6 Seconds of run time on a Windows 7 Pro Box ...

PBOYZTOY04

3725 DrugDiscovery@Home 10/16/2017 1:26:12 PM [error] Can't rename output file slots/25/md.log to projects/boinc.drugdiscoveryathome.com/gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_6_100.in_1_r1913621387_3: Error 32

After uploading manager have cleared slot folder?
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Message 4988 - Posted: 16 Oct 2017, 17:41:34 UTC

Just started getting these work unit.

Windows Nvidia gromaks 0.17 cuda23 getting computation error within seconds.

Tasks shows perrmission denied? https://boinc.drugdiscoveryathome.com/result.php?resultid=12168439

Local message log:


10/16/2017 1:32:53 PM | DrugDiscovery@Home | Requesting new tasks for CPU and NVIDIA GPU
10/16/2017 1:32:54 PM | DrugDiscovery@Home | Scheduler request completed: got 1 new tasks
10/16/2017 1:32:56 PM | DrugDiscovery@Home | Started download of gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in
10/16/2017 1:33:01 PM | DrugDiscovery@Home | Finished download of gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in
10/16/2017 1:33:10 PM | DrugDiscovery@Home | [error] Can't rename output file slots/7/md.edr to projects/boinc.drugdiscoveryathome.com/gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_1: Error 32
10/16/2017 1:33:16 PM | DrugDiscovery@Home | [error] Can't rename output file slots/7/md.log to projects/boinc.drugdiscoveryathome.com/gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_3: Error 32
10/16/2017 1:33:21 PM | DrugDiscovery@Home | [error] Can't rename output file slots/7/md.xtc to projects/boinc.drugdiscoveryathome.com/gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_4: Error 32
10/16/2017 1:33:26 PM | DrugDiscovery@Home | Computation for task gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0 finished
10/16/2017 1:33:26 PM | DrugDiscovery@Home | Output file gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_1 for task gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0 absent
10/16/2017 1:33:26 PM | DrugDiscovery@Home | Output file gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_2 for task gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0 absent
10/16/2017 1:33:26 PM | DrugDiscovery@Home | Output file gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_3 for task gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0 absent
10/16/2017 1:33:26 PM | DrugDiscovery@Home | Output file gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_4 for task gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0 absent
10/16/2017 1:33:26 PM | DrugDiscovery@Home | Output file gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_5 for task gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0 absent
10/16/2017 1:33:27 PM | DrugDiscovery@Home | Started upload of gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_0
10/16/2017 1:33:31 PM | DrugDiscovery@Home | Finished upload of gmx_GMX-T017_XXXX_TTTTT_tasks.gmx_8_100.in_0_r1397127827_0
10/16/2017 1:34:17 PM | DrugDiscovery@Home | Sending scheduler request: To report completed tasks.
10/16/2017 1:34:17 PM | DrugDiscovery@Home | Reporting 1 completed tasks
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Message 4989 - Posted: 16 Oct 2017, 17:41:42 UTC - in response to Message 4984.  
Last modified: 16 Oct 2017, 17:49:28 UTC

Ok 2 of 3 my mashines run tasks with gpu but it very low load 5-15% on 1070 and above cards
third seems not receive task after I make project restart (update receive tasks again on 3rd pc gromacs ver 0.17 no gmx process no gpu use no cpu use)
1st and 2nd PCs have 0.14 ver with gmx that take slight gpu use and 1 cpu core)
please pay attention that cuda work different on windows 7 and windows 10 PC (know it from mining threads)
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Message 4990 - Posted: 16 Oct 2017, 18:00:44 UTC - in response to Message 4989.  

I can create some tasks where 2 (or more if you wish) threads will be used to feed GPU.
Also, right now I'm compile application with AVX256 (instead of SSE4.1) support - this should also help.
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Message 4991 - Posted: 16 Oct 2017, 18:08:39 UTC - in response to Message 4985.  

Can somebody confirm that doing "apt-get install gromacs" solves errors on Debian based systems, please?

The installation worked for me with a GTX-980 on a Ubuntu 16.04 machine, as I noted below. But the total time, originally about 2 days 10 hours, increased to about 2 days 11 hours after about three hours of computing time. That was too much for me, so I bailed out and cancelled the work unit. I think it would have completed successfully though.
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Message 4992 - Posted: 16 Oct 2017, 18:10:48 UTC - in response to Message 4991.  

It will take few hours only to finish, but application doesn't report progress to manager and this is why it shows so long time.
Also, application do it's own checkpoints so no work will be lost if manager switch tasks to different projects before it finish.
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Message 4993 - Posted: 16 Oct 2017, 18:11:06 UTC - in response to Message 4990.  

I can create some tasks where 2 (or more if you wish) threads will be used to feed GPU.
Also, right now I'm compile application with AVX256 (instead of SSE4.1) support - this should also help.

I think better way is universal solution that will work on any common PC. Or it must be autodetect type of supported instructions and use best of them.
Also please chek work in system where is 2 or more GPUs
I just found that first my card is near zero load then 2nd at 40-60 range
when boinc say that running 2 tasks each on different gpu
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Message 4994 - Posted: 16 Oct 2017, 18:17:08 UTC - in response to Message 4993.  

still 0.17 ver didn't run GMX and have 0 load (on my amd fx8120 pc maybe it cause?)
0.14 ver autorestart over and over after i restart boinc and I kill this tasks manualy on 2nd PC
now on current PC I running 2 ver 0.14 tasks but only 1 gpu is loaded
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Message 4995 - Posted: 16 Oct 2017, 18:25:41 UTC - in response to Message 4994.  

I think both tasks try to use same GPU on your host. I will investigate this but the problem is that I can't test it myself as I have just one NVidia card in my windows host (second card is AMD).
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Message 4996 - Posted: 16 Oct 2017, 18:27:21 UTC - in response to Message 4994.  

2nd machine just receive 0.18 ver. after few min no gmx process and 0 load (0.14 ver on this PC at least run gmx with little load)
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Message 4997 - Posted: 16 Oct 2017, 18:43:20 UTC - in response to Message 4996.  

still no gmx and no load on 0.18 need to abort this tasks
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Message 4998 - Posted: 16 Oct 2017, 18:54:32 UTC - in response to Message 4997.  

0.19 ver crash on startup
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Message 4999 - Posted: 16 Oct 2017, 18:55:58 UTC - in response to Message 4992.  

It will take few hours only to finish, but application doesn't report progress to manager and this is why it shows so long time.

OK, I will try again.
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Message 5000 - Posted: 16 Oct 2017, 18:56:55 UTC

0.19 Windows 10 , NVIDIA


10/16/2017 2:55:09 PM | DrugDiscovery@Home | Finished download of gmx_GMX-T018_XXXX_TTTTT_tasks.gmx_19_100.in
10/16/2017 2:55:17 PM | DrugDiscovery@Home | [error] Can't rename output file slots/7/md.edr to projects/boinc.drugdiscoveryathome.com/gmx_GMX-T018_XXXX_TTTTT_tasks.gmx_19_100.in_1_r1354982808_1: Error 32
10/16/2017 2:55:22 PM | DrugDiscovery@Home | [error] Can't rename output file slots/7/md.log to projects/boinc.drugdiscoveryathome.com/gmx_GMX-T018_XXXX_TTTTT_tasks.gmx_19_100.in_1_r1354982808_3: Error 32
10/16/2017 2:55:28 PM | DrugDiscovery@Home | [error] Can't rename output file slots/7/md.xtc to projects/boinc.drugdiscoveryathome.com/gmx_GMX-T018_XXXX_TTTTT_tasks.gmx_19_100.in_1_r1354982808_4: Error 32
10/16/2017 2:55:33 PM | DrugDiscovery@Home | Computation for task gmx_GMX-T018_XXXX_TTTTT_tasks.gmx_19_100.in_1 finished

11:44:35 (13828): wrapper: running gmx.exe (mdrun -nt 1 -deffnm md)
Exit code: error: zipfile probably corrupt (segmentation violation)
:-) GROMACS - gmx mdrun, VERSION 5.1.4 (-:
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Message 5002 - Posted: 16 Oct 2017, 19:10:11 UTC - in response to Message 5000.  

Delete all files from slot directory if Manager didn't clear it.
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Message 5003 - Posted: 16 Oct 2017, 19:17:04 UTC - in response to Message 5002.  
Last modified: 16 Oct 2017, 19:29:08 UTC

Actually I found that there was old gmx.exe process that had not died.

Killed that process and things appear to be running.now

50% GPU
100% CPU core - appears to be spending its time in GPU Copy

BOINC says 18 hours remaining
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Message 5004 - Posted: 16 Oct 2017, 19:23:59 UTC - in response to Message 5002.  

I use "relaunch project" button in boinc- didn't help
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