[gmx-users] Build problem with 4.6beta1

[Szilárd Páll]

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 :)
>
> 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
>

Note that on AMD you might have to use less threads per process than the
default and therefore more than one process per GPU: set -gpu_id=00 for two
processes in a node to both use the first GPU. Additionally, you might want
to use a newer gcc and CUDA, both will provide performance improvements.


>
> 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
> -- Found CUDA: /cm/shared/apps/cuda40/**toolkit/4.0.17 (found suitable
> version "4.0", minimum required is "3.2")
> ...
>

That is just an informative message. We try to detect GPUs on the build
machine to suggest users compiling with GPU acceleration enabled.


>
> 2. It says FFTW isn't detected, but it actually is:
>
> ...
> -- 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
>

That's bad and I don't exactly know why does it happen, it looks like the
nvcc host compiler gets double-set. Could you put your CMakeCache.txt of
this configuration into pastbin and link it (attachments are blocked, I
think)?

One option to get it work is to remove the "-ccbin=/path/to/your/gcc" form
the CUDA_NVCC_FLAGS cache variable and re-configure.

--
Szilárd


>
> 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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