[gmx-users] Problems during installation

[Rajat Desikan]

Justin,

Lovely advice. I'll definitely consider it :) Thank you.

Regards,
Rajat

On Mon, Jul 16, 2018 at 11:15 PM Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> 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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> >>>
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Assistant Professor
> Virginia Tech Department of Biochemistry
>
> 303 Engel Hall
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> Blacksburg, VA 24061
>
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-- 
Dr. Rajat Desikan (Post Doctoral Fellow)
Prof. Narendra M Dixit's Lab (no 1),
Dept. of Chemical Engineering,
Indian Institute of Science, Bangalore