On 11/29/12 10:25 PM, Szilárd Páll wrote:
On Fri, Nov 30, 2012 at 3:20 AM, Justin Lemkul <jalem...@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.
Thanks for the tips. I may be able to get the sysadmins to install a newer gcc,
but I've already been told that CUDA can't be upgraded past 4.0, for a variety
of technical reasons that I quite honestly don't understand.
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.
OK, I just wanted to make sure this wouldn't be an issue.
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.
I can try to play around with it a little more later today, though it seems like
simply using a pre-2.8.10 version of CMake does the trick.
-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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