LINUX@ARM app and wrapper

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koschi

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Message 4709 - Posted: 6 Feb 2017, 12:05:57 UTC

Hi there,

I noticed you are using Autodock Vina to do the actual crunching. Vina 1.1.2 (same version that you provide) is also included in the Ubuntu repository on my Odroid C2 ARM boards, hence easily available.
Doing some tests with a slot copied from my i7 3770, the Intel needs 3:38 minutes, the C2 9:27 minutes and with 4 threads only 3:10 minutes.
Given the cost of such a board, I'd say that is pretty competitive.

Any chance this could be used and the wrapper or its source be provided for Linux@ARM?


Thanks :-)
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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4717 - Posted: 6 Feb 2017, 20:43:24 UTC - in response to Message 4709.  

:)
I'm compiling smina right now on RaspberryPi (in fact, I'm doing it fith time as I need do it again and again to play with static compilation) :)

Very possible that 32bit ARM smina will be available tomorrow.
Krzysztof 'krzyszp' Piszczek

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Message 4724 - Posted: 7 Feb 2017, 9:58:33 UTC

Thanks Krzysztof!

Any idea whether these apps could benefit from a 64bit/ARMv8a build?

I haven't had any smina WUs yet, just Vina.
That makes comparisons onto the efficiency of the app rather difficult I fear.
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Profile Krzysztof Piszczek - wspieram Polski Projekt Boinc
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Message 4727 - Posted: 7 Feb 2017, 10:58:54 UTC - in response to Message 4724.  
Last modified: 7 Feb 2017, 11:04:10 UTC

I already have smina compiled on OdroidXU4 (but is 32bit), 32bit ARM (Raspbian) version is still compiling as I had to re-compile OpenBabel with different flags.
(The mine problem is that single compilation for smina on standard RaspberryPie takes up to 6 hours and if something went wrong - it always happens at the end of this process).

I'm playing now with OdroidC2 (aarch64).
Krzysztof 'krzyszp' Piszczek

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Message 4728 - Posted: 7 Feb 2017, 12:21:16 UTC

Compiling on the C2, thats what I wanted to hear ;-)

Those compile orgies require quite a bit of patience, take your time.
Reminds me of compiling KDE on an Ultra Sparc II 400MHz running Gentoo, that took almost 1.5 days if I remember well...
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Message 4729 - Posted: 7 Feb 2017, 12:49:41 UTC - in response to Message 4728.  
Last modified: 7 Feb 2017, 21:01:08 UTC

Compilation on RaspberryPie (32bit) and Odroid C2 (64bit) finished succesfully :)
We will add both this evening/night to server.

Edit:
I have tested both versions on my OdroidXU4 and Odroid C2 with new (not released yet) smina WU, those WU's will be longer then in previous batches.

So times are:

Odroid XU4 (32bit, 2GHz)
single WU, using single core: 18m32s
single WU, using eight cores: 4m27s

Odroid C2 (64bit, 1.5GHz)
single WU, using single core: 32m40s
single WU, using four cores: 8m57s

Odroid C2 (32bit application)
single WU = 36m9.232s
single WUx4 = 10m0.568s

Xeon E3-1245
single WU, using single thread: 5m30s
single WU, using eight threads: 1m38s
Krzysztof 'krzyszp' Piszczek

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Message 4730 - Posted: 7 Feb 2017, 18:48:13 UTC

Great, that looks promising!

I have attached a RPi3 and a C2 for now, waiting for the release :-)
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[BOINC@Poland]goofyx
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Message 4731 - Posted: 7 Feb 2017, 21:46:05 UTC - in response to Message 4730.  

Great, that looks promising!

I have attached a RPi3 and a C2 for now, waiting for the release :-)

Release are ready for smina-mol2 app with about 300k WU
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[BOINC@Poland]goofyx
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Message 4732 - Posted: 7 Feb 2017, 21:48:35 UTC - in response to Message 4729.  


Edit:
I have tested both versions on my OdroidXU4 and Odroid C2 with new (not released yet) smina WU, those WU's will be longer then in previous batches.

So times are:

Odroid XU4 (32bit, 2GHz)
single WU, using single core: 18m32s
single WU, using eight cores: 4m27s


Times from my Odroid-XU4 (I have 3xXU4 at this moment):
- WU on 1,4GHz core - about 30m
- WU on 2GHz core - about 20m
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koschi

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Message 4733 - Posted: 7 Feb 2017, 22:19:19 UTC
Last modified: 7 Feb 2017, 22:42:27 UTC

Good stuff, my C2 and RPi3 are crunching.
So far 4 WUs completed in 800 seconds / 13:33min on the Pi, guess I was lucky with those, no chance the Pi's A53 beats the A15 in the XU4 otherwise...
I would expect though the A15 to perform at least 2x as fast as the A7 cores in the XU4.

http://www.cnx-software.com/2015/04/09/relative-performance-of-arm-cortex-a-32-bit-and-64-bit-cores/


edit:

btw, the aarch64 wrapper is 32bit, right?

Does the wrapper do any other magic beyond unpacking the Zip and running smina with the right parameters? I was thinking of replacing it with a shell script that does the same and could eg. run smina with --cpu 4 or like that...
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Message 4734 - Posted: 8 Feb 2017, 0:17:24 UTC - in response to Message 4733.  
Last modified: 8 Feb 2017, 0:18:59 UTC

Yes, wrapper is 32bit as is no point to write special one as it just start 64bit app, but yes, it start few shell commands in sequence.
Krzysztof 'krzyszp' Piszczek

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Message 4738 - Posted: 8 Feb 2017, 21:18:40 UTC

My C2 receives WUs for both apps (32/64bit), BOINC estimates for 32bit is 00:38:07 and for 64bit 00:31:20.
When I benchmarked a short WU with both apps, the difference was only a 10% advantage for the 64bit application though.
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Message 4740 - Posted: 9 Feb 2017, 14:03:07 UTC - in response to Message 4738.  

Unfortunately, current WU's get a various execution time, so comparing two WU's is not really correct.
Krzysztof 'krzyszp' Piszczek

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Message 4748 - Posted: 10 Feb 2017, 22:15:44 UTC

Well my local benchmarks were done on the same short WU smina-mol2_A1-smina-mol2-10_config-4a55_sdfActives_PI3Kactives-chunk-0002657.sdf_02657_3995.in, there I did see the 10% lead for 64bit...

The C2 has settled on the faster 64bit app, seems the server side scheduler (?) has recognized there is no use sending out WUs for the slower app to this host.
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Questions and Answers : Wish list : LINUX@ARM app and wrapper


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