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

Gregory Man Kai Poon gpoon at gsu.edu
Sat Dec 3 19:58:03 CET 2016 

Hi Szilárd,


Thanks for your tips.  It turned out that between installing AMDGPU-PRO, then AMD APP SDK, the link to libopencl.so became broken.  Following your suggestions (if I interpreted them correctly), I linked against the copy installed by AMDGPU-PRO.  That resolved the error and I was able to complete the installation.  I also took the opportunity (as per your suggestion) to migrate to the 2016 release.  I had wanted to stay with 5.1.x because we had many simulations generated with 5.1.2 and 5.1.4 which we want to extend, and I was wary of potential issues with being 100% forward compatible.  I am testing one of these simulations now.  So far the program has not complained yet (expected I think) and is using the GPU.  If you know of any potential issues with extending simulations created by previous versions of GROMACS, I would be most interested in knowing them.


Thanks again,

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: Saturday, December 3, 2016 10:34:46 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] Using GROMACS with (AMD) OpenCL

Hi Gregory,

First of all, I'd strongly recommend you to start with the 2016
release, 2016.1 has been out for some time. This will be more robust
and has a lot of performance improvement too especially on AMD (see
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2F2016%2FReleaseNotes%2F&data=01%7C01%7Cgpoon%40gsu.edu%7C1c6c949cc26b455fee8f08d41b91eece%7C515ad73d8d5e4169895c9789dc742a70%7C0&sdata=4w9grG36HpkQGK%2F44RJhN3f9EQrhhcNBGxnXVxjL8WY%3D&reserved=0).

Regarding the link error, to be honest I can't tell what's wrong.
However, note that you do not necessarily need to link against the
SDK, I have clarified this in the last version of the docs:
https://na01.safelinks.protection.outlook.com/?url=http%3A%2F%2Fmanual.gromacs.org%2Fdocumentation%2F2016%2Finstall-guide%2Findex.html%23opencl-gpu-acceleration&data=01%7C01%7Cgpoon%40gsu.edu%7C1c6c949cc26b455fee8f08d41b91eece%7C515ad73d8d5e4169895c9789dc742a70%7C0&sdata=VKwlCmqzHORZ8PvEEjcYzR0pXx9WtH45S7LpiVUNBY4%3D&reserved=0

While linking against the APPSDK libOpenCL _should_ work,  I'd
recommend that you try to link against the stock libOpenCL.so. If that
does not work feel free to share the cmake invocation and cache file
and we may be able to figure out something.

Cheers,
--
Szilárd


On Sat, Dec 3, 2016 at 4:02 PM, Gregory Man Kai Poon <gpoon at gsu.edu> wrote:
> 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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