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Richard Haselgrove Send message Joined: 4 Jul 99 Posts: 14676 Credit: 200,643,578 RAC: 874 |
So you need to install Intel SDK."I may be some time" |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
But remember the final 'compilation for BOINC' is done by IBM, not Scripps. I even didn't attached to this project :) So absolutely no idea how, who and what :) But yes, seems it's "that" sources. #include "autostop.hpp" #include "performdocking.h" #include "stringify.h" #include "correct_grad_axisangle.h" Familiar name :) SETI apps news We're not gonna fight them. We're gonna transcend them. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
So you need to install Intel SDK."I may be some time" Time ... it's the limiting factor indeed. Could you zip offline runnable bench and put it somewhere to download? SETI apps news We're not gonna fight them. We're gonna transcend them. |
Richard Haselgrove Send message Joined: 4 Jul 99 Posts: 14676 Credit: 200,643,578 RAC: 874 |
Could you zip offline runnable bench and put it somewhere to download?It's on GoogleDrive already. I'll PM you a link. I also need to find and copy my notes to the original beneficiary - give me a few minutes. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
It seems VTune has OpenCL support now. It's very reverend tool since I would say Pentium era or even earlier... Huh? Intel C++ compiler included? In free download? Remember that scandal with Intel optimizing compiler usage for free SETI project?... Well... But we need only vTune currently from this pack. EDIT: so many years passed and still can't provide adequate installer. Mighty intel... If one selects only vTune (and interface allows it!) installation fails complaining about compiler... Attempt two... SETI apps news We're not gonna fight them. We're gonna transcend them. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
C:\__Test>wcgrid_beta29_autodockgpu_7.28_windows_x86_64__opencl_intel_gpu_102 -jobs OPNG_0000025_00056.job -input OPNG_0000025_00056.zip -seed 160279976 -wcgruns 1700 -wcgdpf 34 Running 1 jobs in pipeline mode Warning: value of -devnum argument ignored. Value must be an integer between 1 and 65536. AutoDock-GPU version: 51800118f2c7e78ac6794e087a956e50737c5d85-dirty Kernel source file: ./device/calcenergy.cl Kernel compilation flags: -I ./device -I ./common -DN128WI -cl-mad-enable OpenCL device: Intel(R) HD Graphics 500 (Thread 0 is setting up Job #1) Running Job #1: Fields from: receptor.maps.fld Ligands from: ZINC000309335454-ACR2.13_RX1--fr2266benz_001--CYS114.pdbqt Using heuristics: (capped) number of evaluations set to 2818671 Local-search chosen method is: ADADELTA (ad) Executing docking runs, stopping automatically after either reaching 0.15 kcal/mol standard deviation of the best molecules of the last 4 * 5 generations, 27000 generations, or 2818671 evaluations: Generations | Evaluations | Threshold | Average energy of best 10% | Samples | Best energy ------------+--------------+------------------+------------------------------+---------+------------------- 0 | 100 | 2.90 kcal/mol | 0.30 +/- 1.04 kcal/mol | 4 | -0.82 kcal/mol 5 | 34051 | 2.90 kcal/mol | -1.73 +/- 1.33 kcal/mol | 978 | -5.86 kcal/mol 10 | 63164 | -1.71 kcal/mol | -4.94 +/- 0.41 kcal/mol | 70 | -5.87 kcal/mol 15 | 90893 | -4.88 kcal/mol | -5.76 +/- 0.18 kcal/mol | 23 | -6.28 kcal/mol 20 | 118377 | -5.68 kcal/mol | -6.01 +/- 0.23 kcal/mol | 19 | -6.78 kcal/mol it runs offline at least. If I cut jobs list to just single entry? SETI apps news We're not gonna fight them. We're gonna transcend them. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
-cl-mad-enable and iGPU.... danger :)))) SETI apps news We're not gonna fight them. We're gonna transcend them. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
And it just finished first job. Seems my HD500 is powerful enough to pass w/o watchdog triggering SETI apps news We're not gonna fight them. We're gonna transcend them. |
Richard Haselgrove Send message Joined: 4 Jul 99 Posts: 14676 Credit: 200,643,578 RAC: 874 |
-cl-mad-enable and iGPU.... danger :))))I've told him that. At the moment, they're requiring validation against same device class only - so it says it's OK, but might not mean it. He's been warned about that too - all those faulty drivers polluting the database here by cross-validating. |
Richard Haselgrove Send message Joined: 4 Jul 99 Posts: 14676 Credit: 200,643,578 RAC: 874 |
If I cut jobs list to just single entry?Haven't tried to find exactly how to do that. Feel free - it would certainly be quicker. But CPU load between sub-jobs needs optimising too. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
If I cut jobs list to just single entry?Haven't tried to find exactly how to do that. Feel free - it would certainly be quicker. It works as expected. Just optimizes first atom config and exits. But.... different energies! Quite different! Finished evaluation after reaching -6.68 +/- 0.13 kcal/mol combined. 45 samples, best energy -6.94 kcal/mol. I'll try to run test few times and will edit this post with values Richard's run: Finished evaluation after reaching -8.37 +/- 0.06 kcal/mol combined. 51 samples, best energy -8.49 kcal/mol. My second run: Finished evaluation after reaching -6.92 +/- 0.07 kcal/mol combined. 48 samples, best energy -7.09 kcal/mol. One more run: Finished evaluation after reaching -6.91 +/- 0.15 kcal/mol combined. 23 samples, best energy -7.07 kcal/mol. So, they DEFINITELY didn't reach real minimum in those runs. Interesting task - to validate between 2 results when each new run even on the very same host/device/initial setup gives different data :)))) EDIT: genetic algorithms tend to give different results between runs cause random "mutations"included, but usually final value approx the same, just length and trajectory to it will differ from run to run. Here is quite different situation, final optimized energy value differs between runs and quite strongly. [Hence, assuming they know what they doing, result value is not the final energy minimum and some additional stage to find true minimum will be done on servers] But from "number crunching" point of view it's not quite clear how to correctly validate such results? Especially if -cl-mad-enable can add subtle errors in calculations. Such errors can be much smaller than deviation between runs .... SETI apps news We're not gonna fight them. We're gonna transcend them. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
all those faulty drivers polluting the database here by cross-validating. And non-reproducible results add to that complexity. SETI apps news We're not gonna fight them. We're gonna transcend them. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
OK, got some initial profile data separate spikes.... SETI apps news We're not gonna fight them. We're gonna transcend them. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
some unbelievable low numbers :// Sampling overhead too big?... SETI apps news We're not gonna fight them. We're gonna transcend them. |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
Seems I found adequate metrics and config: That gradient_minAD takes 4s per launch. Why TDR tolerates - no idea, maybe some time ago I disabled it... launch space(global size) is huge, 640000 per kernel call. Maybe worth do decrease it to avoid crashes. That's all for today, Richard, at least smth to start with. There are 19 launches catched in log going one by one. Maybe dev can launch twice more but smaller... (19 is arbitrary number, just length of data collection while 4s per launch and 640000 items per launch characterize kernel itself. SETI apps news We're not gonna fight them. We're gonna transcend them. |
Richard Haselgrove Send message Joined: 4 Jul 99 Posts: 14676 Credit: 200,643,578 RAC: 874 |
Thanks for that. I'm about to go down and see if my little Celeron can provide any matching figures for that. Not sure yet if I'll be able to pass anything on today - partly depends if Uplinger comes back with anything after his weekend. Otherwise, tomorrow. |
Sirius B Send message Joined: 26 Dec 00 Posts: 24909 Credit: 3,081,182 RAC: 7 |
What I find fascinating is the variations in numbers that crunching throws our way. For example The teams stats for Sun 11/04/2021 49 12 59 7 843,522 679 For Mon 12/04/2021 49 7 3 50 1,043,506 681 A few more of those 2 wu's please. :-) Yet for 300 results less 01/04/2021 57 19 32 20 312,045 375 |
Richard Haselgrove Send message Joined: 4 Jul 99 Posts: 14676 Credit: 200,643,578 RAC: 874 |
Finally got mine to work - I think the first run stalled, but I didn't see any messages about driver restarts. It's now free to carry on as long as it wants. Pretty much confirms your result. So, what's the best way to convey this to WCG/Scripps? I can't see any way of capturing the report except by screen-grabbing. (This data came from a full run of the first job in the data file. Many parts of the report say "No data to show. The collected data is not sufficient." I'll run it again on the full-length task, and see if that changes anything. Test machine details are here as host 8888441) |
Raistmer Send message Joined: 16 Jun 01 Posts: 6325 Credit: 106,370,077 RAC: 121 |
I think this picture is enough to point to main problem - there is kernel that runs too long on low-level hardware. And there are good chances that issue can be solved very easy - just to split single call to few. Global size of 640000 easely allows that. There are 640k /128 workgroups so will fill almost any GPU, even biggest ones. So, kernel could be split even unconditionally (not only for low-level ones). SETI apps news We're not gonna fight them. We're gonna transcend them. |
Richard Haselgrove Send message Joined: 4 Jul 99 Posts: 14676 Credit: 200,643,578 RAC: 874 |
This data came from a full run of the first job in the data file. Many parts of the report say "No data to show. The collected data is not sufficient."So, the full run (34 jobs) also failed - not enough disk space for analysis. I've freed some up, and I'm trying again with 15 jobs - hoping that's the Goldilocks setting. Otherwise, we're going to need a bigger disk... |
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