[gmx-users] Build problem with 4.6beta1

[Justin Lemkul]

On 11/29/12 9:34 PM, Roland Schulz wrote:
> 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?
>

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

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