On 11/29/12 9:34 PM, Roland Schulz wrote:
On Thu, Nov 29, 2012 at 9:20 PM, Justin Lemkul <[email protected]> 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?
No, it's clear enough, and correct. I just wasn't sure how Gromacs would handle
building on a node where there is no GPU, but for which I am requesting a GPU
build. I guess it's not related (see below).
-- 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.
This one is weirder, but I guess harmless. It's just strange to have the build
system say "I can't find FFTW," and then say "just kidding, it's fine!" ;)
-- 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?
Yep, CMake bug. Our previous version was 2.8.3, and that one works fine. I'll
install 2.8.9 for future builds. Thanks, 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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