Posts by Krzysztof Piszczek - wspieram Polski Projekt Boinc

1) Questions and Answers : Unix/Linux : Linux Gromacs compilation (Message 5136)
Posted 24 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
Use your compiled gmx executable file instead the one from project.
2) Message boards : Number crunching : Gromacs GPU work units now available (Message 5132)
Posted 26 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
Wonder whats different with this version to make it a new app name.

v1 execute one task, v2 is 6 tasks (5 very short, prepare data for sixth) (look at job.xml).
3) Questions and Answers : Unix/Linux : Linux Gromacs compilation (Message 5116)
Posted 27 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
It looks like part of the issue that you are using some sort of wrapper program that the system does not have.

True, I think he have to compile BOINC wrapper also...
4) Message boards : News : CUDA app testing (Message 5114)
Posted 27 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
You just get failed batch, it's should fix in few minutes, when you update project (I'm working now on progress bar and checkpoint reporting).
5) Message boards : News : CUDA app testing (Message 5111)
Posted 27 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
Not inside Gromacs folder... Inside "Gromacs2016.4/build" folder...
6) Message boards : News : CUDA app testing (Message 5109)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
1. Unpack Gromacs2016.4
2. Inside unpacket directory create "build" folder.
3. Go inside folder created above.
4. Execute "cmake .. -DGMX_BUILD_OWN_FFTW=ON -DGMX_GPU=on -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_BUILD_SHARED_EXE=OFF".
6. Execute "make" command.
7) Message boards : News : CUDA app testing (Message 5107)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
Are you exactly do what is in my instruction?
This error says that probably you miss step where you need to go inside freshly created build directory (before do cmake command).
8) Message boards : News : CUDA app testing (Message 5105)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
In version 0.26 of gmx (for Windows) checkpoint and fraction done values are exported to wrapper.
Checkpoints are created from first version just wrapper doesn't know about it.

Checkpoints are done every 15 minutes. Also progress is reported every 15 minutes.
9) Message boards : News : CUDA app testing (Message 5102)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
Progress is lost if the task becomes paused

No, isn't, just at the moment checkpoints are not reported to Manager.

I will update application for proper progress bar and checkpoints reporting later today.
10) Questions and Answers : Unix/Linux : Linux Gromacs compilation (Message 5098)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
You have to use app_info (or app_config, can't remember) to use it as "anonymous" platform... I never do this, but probably some users can help.
11) Message boards : Number crunching : Gromacs GPU work units now available (Message 5097)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
I just switched off some debug output as it makes stderr.txt full of crap ;)

But, probably tomorrow I will make update for wrapper with some more functionality.
12) Message boards : Number crunching : Gromacs GPU work units now available (Message 5094)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
<cpu_usage>0.2</cpu_usage>

You have set that single work unit can use only 20% of CPU thread. This value should by "1".
13) Message boards : Number crunching : Gromacs GPU work units now available (Message 5092)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
As you have different configuration then I have you must just try which settings are best fit your machine.

Currently (for testing) I use 3 thread for WU and 2 WU at the same time (by editing app_config.xml file).
14) Message boards : Number crunching : Gromacs GPU work units now available (Message 5090)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
Yes, but I will set it bit later (maybe after a week) as I have now some more important tasks.
15) Message boards : Number crunching : Gromacs GPU work units now available (Message 5088)
Posted 28 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
By editing -nt 1 parameter in job file (in project folder) you can change CPU threads for WU. In my Windows PC with Xeon v2 and GTX1060 6GB using -nt 3 GPU usage jumps to 80%.
It should also dramatically decrease WU computing time.
16) Questions and Answers : Unix/Linux : Linux Gromacs compilation (Message 5087)
Posted 29 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
If somebody want to run two or more tasks on single card then need to add app_config.xml file to project directory:
<app_config>
	<app>
		<name>gmx</name>
		<max_concurrent>2</max_concurrent>
		<gpu_versions>
			<gpu_usage>0.5</gpu_usage>
			<cpu_usage>1</cpu_usage>
		</gpu_versions>
	</app>
</app_config>

"<gpu_usage>0.5</gpu_usage>" means "compute two tasks on single GPU".
For four tasks this value will be 0.25.
17) Message boards : Number crunching : Gromacs GPU work units now available (Message 5085)
Posted 29 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
Check in stderr.txt file if GPU is properly recognised (there should by a string like "Number of GPUs detected: 1" and "Running on 1 node with total 4 cores, 8 logical cores, 1 compatible GPU").

Checkpoints are not reported to wrapper but Gromacs application do it itself.
18) Message boards : News : CUDA app testing (Message 5082)
Posted 29 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
No, you have CUDA 6.5 where 8.0 is minimum, you need to update your CUDA driver.


Why is the plan class cuda23 if cuda80 is needed? Just call it cuda65 or cuda80 to match the requirement.

So just AVX? You said AVX256 and AVX and AVX2 added some 256 bit commands so it wasn't really specific enough.


Cuda 2.3 is "Compute capabilty" where Cuda 8.0 is driver version used in Gromacs compilation. Just CUDA capabilities are not same as CUDA runtime version...

For this app CUDA 2.3 version is need with CUDA 8.0 version driver.
19) Message boards : News : CUDA app testing (Message 5080)
Posted 29 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
Can you try to start gmx.exe in command line (outside of BOINC slot folder) and let me know if it starts without error (other that command line parameters are not given)?

OK, I went to the "C:\ProgramData\BOINC\projects\boinc.drugdiscoveryathome.com" folder and tried to run "gmx_23_x86_64_windows.exe", but got this error message:
"The program can't start because MSVCP110.dll is missing from your computer".

It mean, that you don't have some Microsoft libraries installed on system...
20) Message boards : News : CUDA app testing (Message 5076)
Posted 29 days ago by Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
Post:
"exit code 195" usually means that application can't load one of required libraries or haven't permission to use it.
Unfortunately, I have no idea what library it is as Windows doesn't report it...

Can you try to start gmx.exe in command line (outside of BOINC slot folder) and let me know if it starts without error (other that command line parameters are not given)?


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