[gmx-users] Build problem with 4.6beta1

[Roland Schulz]

On Thu, Nov 29, 2012 at 9:20 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
> Hooray for being the first to report a problem with the beta :)
>
> 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:
>
> ...-- Looking for NVIDIA GPUs present in the system
> -- Could not detect NVIDIA GPUs
>
This is not a warning just a note. Is this confusing?


> -- 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:
>
> ...
> -- checking for module 'fftw3f'
> --   package 'fftw3f' not found
>
It checks several ways. The first (pgkconfig) din't work. Again just a note.


> -- 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.
>

Could be this cmake bug: http://www.gccxml.org/Bug/view.php?id=13674
Could you try whether any other cmake version (e.g. 2.8.9) works?

Roland


>
> -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
>
> ========================================
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