I'm starting testing again on the "cpumd" multi-threaded CPU app. Please post observations here.

Matt

14/10/12 08:21:16 | GPUGRID | No tasks are available for Test application for CPU MD

14/10/12 08:22:31 | GPUGRID | No tasks are available for Test application for CPU MD

14/10/12 08:23:55 | GPUGRID | No tasks are available for Test application for CPU MD

14/10/12 08:28:16 | GPUGRID | No tasks are available for the applications you have selected.

Are CPUMD available now?

Yes, there are a few hundred there.

All set- received 8 tasks.
The CPUMD batch a few months back included a file that gave information about individual atoms ( I can't remember the name of file) - now I only see in progress file the energies (Bond Angle/ Proper Dih./Improper Dih./ Coulomb-14/LJ (SR)/ Coulomb (SR)/ Coul. recip./Potential/ Kinetic En./ Total Energy /Conserved En./ Temperature Pressure (bar)) for every thousand steps along with the input parameters.

Acceleration most likely to fit this hardware: AVX_256
Acceleration selected at GROMACS compile time: SSE2

Is AVX available? Or there no speed up with AVX?

Only SSE2 at the moment. Will probably make builds with higher levels of optimisation later but for now I'm concerned about correctness rather than performance.

Matt

Matt,

I was able to get a task on my Windows box which only runs CPU tasks. That task is currently under way.

On my Linux box, I run GPU tasks most of the time. When I tried to pull a CPU task, the event log says that the computer has reached a limit on tasks in progress, even when there are no CPU tasks downloaded. I'm guessing that it has reached a limit on GPU tasks in progress so it won't pull anything else down.

If you need more information, please let me know.

Edit:

I just changed my device profile to only pull CPU tasks and now it says that there are no CPU tasks available. Maybe it was out earlier and gave the misleading message.

Hi Matt,

rigs are ready to accept beta app and CPU tasks but nothing coming in yet.

Message:
10/12/2014 3:12:37 PM | GPUGRID | Sending scheduler request: To fetch work.
10/12/2014 3:12:37 PM | GPUGRID | Requesting new tasks for CPU
10/12/2014 3:12:39 PM | GPUGRID | Scheduler request completed: got 0 new tasks
10/12/2014 3:12:39 PM | GPUGRID | No tasks sent
10/12/2014 3:12:39 PM | GPUGRID | No tasks are available for ACEMD beta version
10/12/2014 3:12:39 PM | GPUGRID | No tasks are available for Long runs (8-12 hours on fastest card)
10/12/2014 3:12:39 PM | GPUGRID | No tasks are available for CPU only app
10/12/2014 3:12:39 PM | GPUGRID | No tasks are available for Test application for CPU MD
10/12/2014 3:12:57 PM | GPUGRID | work fetch suspended by user

However there are some tasks, according to server page. Could be a BOINC thing though.

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Greetings from TJ

exapower - is it using all CPU cores?

Matt

Hi Matt,

Win7 x64, BOINC 7.2.42. I have got one and it runs on 5 CPU's. I have set in BOINC to use maximum 70% of CPU's (have 8 threads). So this is correct as two are working on GPUGRID LR's.
So it works! 1.5% done in 3.20 minutes on i7-4774 3.50GHz.

However CPU usage to task manager is 100%. mdrun.846,exe is using 60 or 61% CPU acoording to task mamager.

If you need/want more information please let me know and I will provide it.

---

Greetings from TJ

exapower - is it using all CPU cores?

Matt

Yes- Working flawlessly- CPUMD running at consist 92-95% (I have an audio program running along with a total of 17 background process/19 windows processes) in task manager- with program HWiNFO64 [2] physical [2} logical are always utilizing 96-98%. The program SIV64X reads BOINC usage for each core(thread)- showing 98% for CPUMD.

4hours of processing- BOINC @ 56% of task progress.

Observation about steps: This is from stderr file- Reading file topol.tpr, VERSION 4.6.1 (single precision)
Using 1 MPI thread
Using 4 OpenMP threads
starting mdrun 'Protein in water'
5000000 steps, 10000.0 ps.

And in progress file where input parameters are: nsteps= 5000000

Yet the Progress file reads 740000 step done so far- with BOINC task progress at 79.260%. Are the total number of steps 1million instead of 5million?

Task: 1315-MJHARVEY_CPUDHFR-0-1-RND2531_0

This Test Application is anounced with a runtime round about 2,5 hrs.

Now it's running over 5 hrs. WU is ready by 80% .

http://www.gpugrid.net/result.php?resultid=13198539

http://www.gpugrid.net/result.php?resultid=13196328

17hr runtime so far- Boinc @ 97% (been at this percentage for last few hours without moving) Progress file shows steps currently @ 1.5million. If task is 5million total steps- total runtime time for one work unit will be 56~hr. Is there way to increase deadline? I have 8 tasks downloaded. Or should I just boot them when close to being expired?

First results are in - runtime 170-400Hr. ~20hr* each core. 8threads=160hr 16threads=320hr. Will CPUMD tasks be in performance tab? There certainly enough of them to compare.

Hi,

That's a shame, those run times are rather longer than I'd anticipated. Probably have to dial down the length, though they are already close to the usable minimum.

Yes, they'll appear in the performance tab in due course.

Matt

Long runtimes are not bothersome to me- BOINC not reliable estimating runtimes. If steps are bare minimum already- Is there a way to split tasks in half- where different users receive a half?

BTW- HFR is a great research choice- each chain has many Biological process- positive regulation of T cell mediated cytotoxicity-antigen processing and presentation of peptide antigen via MHC class I- regulation of defense response to virus by virus along with many others.

What is specifically rendered in work units? (how I miss the old file with atom/bonds description) Stderr has "starting mdrun 'Protein in water'"
A few websites to understand type of research being done here not all specific to this work unit.
http://www.ebi.ac.uk/pdbe-srv/view/entry/1a6z/summary

http://www.ebi.ac.uk/pdbe-srv/view/entry/1de4/summary

http://www.rcsb.org/pdb/gene/B2M

http://amigo.geneontology.org/amigo/term/GO:0019882

http://www.gpugrid.net/result.php?resultid=13196328

17hr runtime so far- Boinc @ 97% (been at this percentage for last few hours without moving) Progress file shows steps currently @ 1.5million. If task is 5million total steps- total runtime time for one work unit will be 56~hr. Is there way to increase deadline? I have 8 tasks downloaded. Or should I just boot them when close to being expired?

First results are in - runtime 170-400Hr. ~20hr* each core. 8threads=160hr 16threads=320hr. Will CPUMD tasks be in performance tab? There certainly enough of them to compare.

I confirm this

http://www.gpugrid.net/results.php?userid=58967&offset=0&show_names=0&state=0&appid=27

after 14-17 Hours stops at 98% without moving on ...

aborted all Wus

I fired up an extra rig yesterday evening, with no usable GPU's for here but an older i7.
What I now see on three rigs doing the CPU, (two use 5 threads, one 4 threads) is that the first 99% gets done in about 17 hours and the last 1% takes a way more. At the older i7 it is now 20 hours running (0.300% to go) and the others are 22 hours running and not yet finished. I will let them run off course, but wouldn't it be better for a GPU to handle this?

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Greetings from TJ

I fired up an extra rig yesterday evening, with no usable GPU's for here but an older i7.
What I now see on three rigs doing the CPU, (two use 5 threads, one 4 threads) is that the first 99% gets done in about 17 hours and the last 1% takes a way more. At the older i7 it is now 20 hours running (0.300% to go) and the others are 22 hours running and not yet finished. I will let them run off course, but wouldn't it be better for a GPU to handle this?

TJ- in the progress file- how many steps so far? I've been at 98% for last 7 hours running 4 threads with about 2.5million steps left out 5mil total.

I fired up an extra rig yesterday evening, with no usable GPU's for here but an older i7.
What I now see on three rigs doing the CPU, (two use 5 threads, one 4 threads) is that the first 99% gets done in about 17 hours and the last 1% takes a way more. At the older i7 it is now 20 hours running (0.300% to go) and the others are 22 hours running and not yet finished. I will let them run off course, but wouldn't it be better for a GPU to handle this?

TJ- in the progress file- how many steps so far? I've been at 98% for last 7 hours running 4 threads with about 2.5million steps left out 5mil total.

eXaPower, there is a lot of information in the progress file, but I don't see it. Or better I don't know where to look. Can you give me a hint?

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Greetings from TJ

Stroll down to very end of file- this where most current step is- Every ten minutes a checkpoint is created.

Every thousand steps should show
[list=] Step Time Lambda
1680000 3360.00000 0.00000

Energies (kJ/mol)
Bond Angle Proper Dih. Improper Dih. LJ-14
1.98361e+003 5.27723e+003 6.64863e+003 3.42704e+002 2.23267e+003
Coulomb-14 LJ (SR) Coulomb (SR) Coul. recip. Potential
2.89505e+004 3.73032e+004 -3.83508e+005 3.47532e+003 -2.97294e+005
Kinetic En. Total Energy Conserved En. Temperature Pressure (bar)
6.02571e+004 -2.37037e+005 -2.60930e+005 2.99386e+002 -3.39559e+002[/list]