[gmx-users] Problems during installation

[Szilárd Páll]

On Mon, Jul 16, 2018 at 7:43 PM Rajat Desikan <rajatdesikan at gmail.com>
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.
>

For that you'd need the ~8 year old GROMACS 4.5 with OpenMM 2.x (IIRC)
support which is ancient and unsupported so really not a good idea.

Instead, use the latest release. Hardware-wise, ddeally you'd want to have
2-3 faster (wokstation) or 3-5 slower (server) cores per GPU for good
CPU-GPU balance.
--
Szilárd


> If you and others have alternate suggestions, we would be really eager to
> hear them. Thank you for your time.
>
> 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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