[gmx-users] Problems during installation

[Justin Lemkul]

On 7/16/18 1:42 PM, Rajat Desikan wrote:
> Hi Mark,
>
> Thank you for the quick answer. My group is experimenting with a GPU-heavy
> processor-light configuration similar to the Amber machines available from
> Exxact (https://www.exxactcorp.com/AMBER-Certified-MD-Systems). In our
> understanding, for this configuration to be successful performance-wise,
> gromacs would've to do all the calculating on GPUs, and not just
> electrostatics. That's why we're looking at openmm enabled versions.
>
> If you and others have alternate suggestions, we would be really eager to
> hear them. Thank you for your time.

IIRC, the OpenMM code in GROMACS only ever did implicit solvent 
calculations. With GROMACS 2018, all the nonbonded calculations are done 
on GPU with PME offload, which sounds exactly like what you want. You 
should be using a current version, not an ancient one :)

-Justin

> Regards,
> Rajat
>
> On Mon, 16 Jul 2018, 10:25 pm Mark Abraham, <mark.j.abraham at gmail.com>
> wrote:
>
>> Hi,
>>
>> This code was not ever functional in the 4.6 branch, so if you want it to
>> work, try 4.5.7. But really there is no reason to want to build it any more
>> - use the CUDA and OpenCL ports available in more recent GROMACS.
>>
>> Mark
>>
>> On Mon, Jul 16, 2018 at 6:47 PM Rajat Desikan <rajatdesikan at gmail.com>
>> wrote:
>>
>>> Dear all,
>>> I'm trying to install openmm enabled version of gromacs 4.6.7 on a 6-core
>>> i7 machine with two GTX 1080 Ti GPUs. I am repeatedly facing a rather
>>> strange error while running make:
>>>
>>> /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c: In function
>> ‘cmain’:
>>> /home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: warning:
>>> missing braces around initializer [-Wmissing-braces]
>>>     gmx_hw_opt_t hw_opt={0,0,0,0,TRUE,FALSE,0,NULL};
>>>                         ^
>>> */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:221:23: note: (near
>>> initialization for ‘hw_opt’)*
>>> */home/sujit/gromacs-4.6.7/src/contrib/mdrun_openmm.c:247:41: error:
>>> ‘gmx_hw_opt_t {aka struct <anonymous>}’ has no member named ‘gpu_id’; did
>>> you mean ‘gpu_opt’?*
>>> *     { "-gpu_id",  FALSE, etSTR, {&hw_opt.gpu_id},*
>>>                                           ^
>>> src/kernel/CMakeFiles/mdrun.dir/build.make:302: recipe for target
>>> 'src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o' failed
>>> make[2]: ***
>> [src/kernel/CMakeFiles/mdrun.dir/__/contrib/mdrun_openmm.c.o]
>>> Error 1
>>> CMakeFiles/Makefile2:1902: recipe for target
>>> 'src/kernel/CMakeFiles/mdrun.dir/all' failed
>>> make[1]: *** [src/kernel/CMakeFiles/mdrun.dir/all] Error 2
>>> Makefile:162: recipe for target 'all' failed
>>> make: *** [all] Error 2
>>>
>>> I have installed cuda 9.1, openmm, fftw, open-mpi and all other necessary
>>> software, so I'm at a loss. Please help me out. Google did not have much
>>> leads.
>>>
>>> Thank you.
>>>
>>> Regards,
>>> Rajat
>>>
>>> --
>>> Dr. Rajat Desikan (Post Doctoral Fellow)
>>> Prof. Narendra M Dixit's Lab (no 1),
>>> Dept. of Chemical Engineering,
>>> Indian Institute of Science, Bangalore
>>> --
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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