[gmx-users] Compiling GMX for GPU

Tue Jun 30 23:45:54 CEST 2015

Hey Mark,

Let me first try
http://www.r-tutor.com/gpu-computing/cuda-installation/cuda7.0-ubuntu
Somehow in a few tutorials people assumed that apt-get update/upgrade after
installing that deb package would automatically install CUDA, which does
not at all seem to be the case. Let's see if a manual install gives me
something to write home about.

Thanks,

Alex

On Tue, Jun 30, 2015 at 3:41 PM, Mark Abraham <mark.j.abraham at gmail.com>
wrote:

> Hi,
>
> Find out from dpkg docs how to query where it put stuff. /opt/cuda/xyz is
> my bet
>
> Mark
>
> On Tue, Jun 30, 2015 at 11:27 PM Alex <nedomacho at gmail.com> wrote:
>
> > I do get that I need the SDK, but the Nvidia's deb package was installed
> > with dpkg and now none of the default locations have the CUDA libs.
> Also, I
> > feel like I don't know what I am doing. :)
> >
> > Alex
> >
> > On Tue, Jun 30, 2015 at 3:17 PM, Mark Abraham <mark.j.abraham at gmail.com>
> > wrote:
> >
> > > Hi,
> > >
> > > apt provides functionality to let you know where stuff got put :-) You
> do
> > > need the SDK, not just the driver.
> > >
> > > Mark
> > >
> > > On Tue, Jun 30, 2015 at 11:15 PM Alex <nedomacho at gmail.com> wrote:
> > >
> > > > That's the problem... I can't see CUDA anywhere in the system. :)
> > > >
> > > > Alex
> > > >
> > > > On Tue, Jun 30, 2015 at 2:54 PM, Mark Abraham <
> > mark.j.abraham at gmail.com>
> > > > wrote:
> > > >
> > > > > Hi,
> > > > >
> > > > > Is there something unclear about the message? You need to let CMake
> > > know
> > > > > where CUDA is, and apparently your package is installed in a place
> > > where
> > > > > standard mechanisms can't find it. So when you find out where it
> is,
> > > you
> > > > > can use cmake -Dthatvariable=/some/path. Good luck!
> > > > >
> > > > > Mark
> > > > >
> > > > > On Tue, Jun 30, 2015 at 10:49 PM Alex <nedomacho at gmail.com> wrote:
> > > > >
> > > > > > Hi all,
> > > > > >
> > > > > > I am setting up my local box to get GPU acceleration. This is
> Mint
> > > 17.1
> > > > > > (latest Ubuntu kernel).
> > > > > >
> > > > > > Here is what I am doing:
> > > > > >
> > > > > > sudo dpkg -i cuda-repo-ubuntu1404-7-0-local_7.0-28_amd64.deb
> > > > > > apt-get update
> > > > > > apt-get upgrade
> > > > > >
> > > > > > Then, compiling GMX 5.0.5 with -DGMX_GPU=on. Here is what I get:
> > > > > >
> > > > > > ...
> > > > > >
> > > > > > -- Looking for NVIDIA GPUs present in the system
> > > > > >
> > > > > > -- Number of NVIDIA GPUs detected: 1
> > > > > >
> > > > > > CUDA_TOOLKIT_ROOT_DIR not found or specified
> > > > > >
> > > > > > -- Could NOT find CUDA (missing:  CUDA_TOOLKIT_ROOT_DIR
> > > > > > CUDA_NVCC_EXECUTABLE CUDA_INCLUDE_DIRS CUDA_CUDART_LIBRARY)
> > (Required
> > > > is
> > > > > at
> > > > > > least version "4.0") CMake Error at cmake/gmxManageGPU.cmake:145
> > > > > (message):
> > > > > >
> > > > > >   mdrun supports native GPU acceleration on NVIDIA hardware with
> > > > compute
> > > > > >
> > > > > >   capability >= 2.0 (Fermi or later).  This requires the NVIDIA
> > CUDA
> > > > > > toolkit,
> > > > > >
> > > > > >   which was not found.  Its location can be hinted by setting the
> > > > > >
> > > > > >   CUDA_TOOLKIT_ROOT_DIR CMake option (does not work as an
> > environment
> > > > > >
> > > > > >   variable).  The typical location would be
> > > /usr/local/cuda[-version].
> > > > > > Note
> > > > > >
> > > > > >   that CPU or GPU acceleration can be selected at runtime.
> > > > > >
> > > > > > ...
> > > > > >
> > > > > > It seems like the entire library is missing! Note: I was able to
> > > > compile
> > > > > > without CUDA before on the same system, everything worked fine.
> Any
> > > > > > suggestions?
> > > > > >
> > > > > > Thanks,
> > > > > >
> > > > > > Alex
> > > > > > --
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