[gmx-users] Build problem with 4.6beta1

[Mark Abraham]

On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> Hooray for being the first to report a problem with the beta :)
>

:) Thanks!


>
> We have a cluster at our university that provides us with access to some
> CPU-only nodes and some CPU-GPU nodes.  I'm having problems with getting
> 4.6beta1 to build, and I suspect the issue is related to GPU detection.
>
> Here are some specifics:
>
> FFTW 3.3.3
> CMake 2.8.10
> gcc 4.3.4
> CUDA 4.0
> 64-bit Linux on AMD hardware
> GPU nodes have Tesla C2050 cards
>
> Commands:
>
> cmake ../gromacs-4.6-beta1 -DCMAKE_INSTALL_PREFIX=/home/**
> jalemkul/software/gromacs-**46beta1 -DGMX_X11=OFF -DGMX_GPU=ON
> -DCMAKE_C_COMPILER=gcc -DCMAKE_CXX_COMPILER=g++ -DCMAKE_PREFIX_PATH=/home/
> **jalemkul/software/fftw-3.3.3/
>
> The first step runs alright, but two things to note:
>
> 1. It doesn't detect any GPU, which is correct because I'm on a head node
> and not a compute node:
>

Yes, but we try to be vigilant about looking for them - however there's not
really an API to do that for unless you already have CUDA set up :-S. Need
to work on our install guide here too - the detection applies to the node
you're compiling on, but you can change that and compile however you like
within the limits of the compiler.


>
> ...-- Looking for NVIDIA GPUs present in the system
> -- Could not detect NVIDIA GPUs
> -- Found CUDA: /cm/shared/apps/cuda40/**toolkit/4.0.17 (found suitable
> version "4.0", minimum required is "3.2")
> ...
>
> 2. It says FFTW isn't detected, but it actually is:
>

Right. We try to use pkgconfig to help detect FFTW, but the former might
not exist and the latter might exist independently of the database of the
former. So we then do some independent checking (which succeeded in your
case). I've made a fix that I expect will keep pkgconfig quiet about its
failure, and thus not distract people :-).

Mark


> ...
> -- checking for module 'fftw3f'
> --   package 'fftw3f' not found
> -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/**
> software/fftw-3.3.3/lib/**libfftw3f.so
> -- Looking for fftwf_plan_r2r_1d in /home/jalemkul/ATHENA/**
> software/fftw-3.3.3/lib/**libfftw3f.so - found
> -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/**
> software/fftw-3.3.3/lib/**libfftw3f.so
> -- Looking for fftwf_have_simd_avx in /home/jalemkul/ATHENA/**
> software/fftw-3.3.3/lib/**libfftw3f.so - not found
> -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/**
> software/fftw-3.3.3/lib/**libfftw3f.so
> -- Looking for fftwf_have_simd_sse2 in /home/jalemkul/ATHENA/**
> software/fftw-3.3.3/lib/**libfftw3f.so - found
> ...
>
> Upon running "make," I get an immediate failure:
>
> [  0%] Building NVCC (Device) object src/gmxlib/gpu_utils/**
> CMakeFiles/gpu_utils.dir//./**gpu_utils_generated_gpu_utils.**cu.o
> nvcc fatal   : redefinition of argument 'compiler-bindir'
> CMake Error at gpu_utils_generated_gpu_utils.**cu.o.cmake:206 (message):
>   Error generating
>
> /home/jalemkul/gmxbuild/src/**gmxlib/gpu_utils/CMakeFiles/**
> gpu_utils.dir//./gpu_utils_**generated_gpu_utils.cu.o
>
>
> make[2]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/./**
> gpu_utils_generated_gpu_utils.**cu.o] Error 1
> make[1]: *** [src/gmxlib/gpu_utils/**CMakeFiles/gpu_utils.dir/all] Error 2
> make: *** [all] Error 2
>
> Any ideas?  I'm guessing it's related to the GPU detection failing,
> because I can build on a workstation in our lab that has a C2075 card.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
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