[gmx-users] Build problem with 4.6beta1

[Justin Lemkul]

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
-- 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
-- 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

========================================