[gmx-users] Using GROMACS with (AMD) OpenCL

Sat Dec 3 16:02:23 CET 2016

Hi Milan and Szilárd,

Many thanks for your comments.  So I installed Ubuntu 16.04, installed the AMDGPU-PRO driver, installed the AMD APP SDK.  Then I attempted to install GROMACS 5.1.4 as follows:

cmake .. -DGMX_BUILD_OWN_FFTW=ON -DREGRESSIONTEST_DOWNLOAD=ON -DGMX_GPU=ON -DGMX_USE_OPENCL=ON

Then when I invoked make, things went fine for a bit, then halted with:

[  1%] Built target fftwBuild
make[2]: *** No rule to make target '/home/popeye/AMDAPPSDK-3.0/lib/x86_64/libOpenCL.so', needed by 'lib/libgromacs.so.1.4.0'.  Stop.
CMakeFiles/Makefile2:2026: recipe for target 'src/gromacs/CMakeFiles/libgromacs.dir/all' failed
make[1]: *** [src/gromacs/CMakeFiles/libgromacs.dir/all] Error 2
Makefile:160: recipe for target 'all' failed

I am not nearly good enough to make out what is going on, except to guess that something may not be correct with the AMDAPPSDK-3.0 installation.  The folder is there, and I checked the install log -- it didn't report any error there.

Thanks again for your continued help.

Gregory

________________________________
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se <gromacs.org_gmx-users-bounces at maillist.sys.kth.se> on behalf of Szilárd Páll <pall.szilard at gmail.com>
Sent: Friday, December 2, 2016 11:22:29 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Using GROMACS with (AMD) OpenCL

Hi,

While for the pre-Polaris hardware Milan is right, for Polaris you
*need* a AMDGPU-PRO (which only runs on newer distros/kernels).

The current AMDGPU-PRO from the OpenCL point of view is, AFAIK more or
less the same compiler/runtime as the last catalyst release (15.12).

One notable caveat is that with AMDGPU-PRO power management seems to
be overly aggressive (messed up?) -- at least for the load GROMACS
generates. Uou can loose quite some performance unless you force the
performance level to "high" (hint use radcard to set
power_dpm_force_performance_level=high); this has been obsered on both
Polaris and Fiji.

See here:
https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Fwiki.archlinux.org%2Findex.php%2FATI%23Dynamic_power_management&data=01%7C01%7Cgpoon%40gsu.edu%7Cee289917aa5a4b74dc5808d41acf7095%7C515ad73d8d5e4169895c9789dc742a70%7C0&sdata=H0FRzdUGcKtgWvVRkE7fawUX7PZtmrz%2FcwaJq7AaC%2Bo%3D&reserved=0

Cheers,
--
Szilárd

On Fri, Dec 2, 2016 at 4:13 PM,  <melichercik at leaf.nh.cas.cz> wrote:
> Hi Gregory,
> it is possible to use with both - Catalyst or AMDGPU, so you can choose. As there won't be (I think) any more updates for Catalyst, I'd prefer to use newer AMDGPU (PRO) choice. I don't have Polaris based card, only some 79xx/R9 280 (X) (uding Catalyst) and one Fury Nano (used Catalyst also, but now AMDGPU PRO). I made the Gromacs' compilation only with the Catalyst drivers, but with AMDGPU shouldn't be more complicated. Just install the system with AMDGPU (I don't know it "PRO part" is needed, probably yes) and try to compile (don't forget about the OpenCL switch). If there would be some missing libraries, than you have to install some -dev versions of packages. Probably Ubuntu has it's own way how to find the right package, but you can also use site at packages.debian.org (as Ubuntu is based on Debian).
> Anyway I'm trying to have most of things directly from the distribution, cause it would automatically upgrades and fixes bugs. Outside the distro I have only Gromacs (performancd issues - compilation to exact machine - and several version installed) and AMDGPU PRO (on that node with Fury Nano, cause Debian doesn't have it in its repositories.
> If any problem, plaase ask more with some details.
>
> Best,
>
> Milan
>
> On Fri, Dec 02, 2016 at 01:56:03PM +0000, Gregory Man Kai Poon wrote:
>> Hello all,
>>
>>
>> I would like to get some practical advice on setting up GROMACS with OpenCL using an AMD GPU (an RX 480 is what I happen to have).  The AMD APP SDK indicates that it supports the Catalyst Omega 15.7 driver -- is that compatible to the proprietary Catalyst driver for Linux?  Since this proprietary driver is only compatible with Ubuntu up to version 15.10, does that mean that best software configuration (say for GROMACS 5.1.4) is:
>>
>>
>> Ubuntu 15.10 + propriety Catalyst driver + AMD APP SDK
>>
>>
>> There is also a newer AMDGPU driver that works with Ubuntu 16.04 -- is that compatible with the AMD APP SDK and would allow GROMACS to be set up on a newer OS?  If I really should be going about some other way (given the GPU), please suggest also.
>>
>>
>> I have googled the subject a bit but was unable to find enough info to proceed.  Thanks in advance for your insight.
>>
>>
>> Best regards,
>>
>> Gregory
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