On 7/25/14, 4:17 PM, Seyyed Mohtadin Hashemi wrote:
On Fri, Jul 25, 2014 at 3:00 PM, Seyyed Mohtadin Hashemi <haa...@gmail.com>
wrote:
Hi everyone,
I'm having a very weird problem with GROMACS 4.6.6:
I am currently testing out GPU capabilities and was trying to compile
GROMACS with CUDA (v6.0). I can not make this work if I compile GROMACS
with SIMD, no matter what kernel I choose - I have tried everything from
SSE2 to AVX_256.
The log-in node, where I compile, has AMD Interlagos CPUs (worker nodes
use Xeon E5-2630 and are equipped with Tesla K20), but I do not think this
is the problem - I have compiled GROMACS, using the log-in node, without
CUDA but with AVX_256 SIMD and everything works. As soon as CUDA is added
to the mix, I get "Illegal Instruction" every time I try to run on the
worker nodes.
Compiling on worker nodes gives the same result. However, as soon as I set
SIMD=None everything works and I am able to run simulation using GPUs, this
is regardless of if I use log-in node or worker node to compile.
The cmake string used to configure is:
ccmake .. -DCMAKE_INSTALL_PREFIX=/work/gromacs4gpu -DGMX_DOUBLE=OFF
-DGMX_DEFAULT_SUFFIX=OFF -DGMX_BINARY_SUFFIX=_4gpu -DGMX_LIBS_SUFFIX=_4gpu
-DGMX_GPU=ON -DBUILD_SHARED_LIBS=OFF -DGMX_PREFER_STATIC_LIBS=ON
-GMX_MPI=OFF -DGMX_CPU_ACCELERATION=AVX_256
CUDA v6.0 and FFTW v3.3.4 (single precision) libs are set globally and
correctly identified by GROMACS. To remove OpenMPI as a problem I am
compiling without it (compiling with OpenMPI produced the same behavior as
without), once I have found the error I will compile with OpenMPI v1.6.5.
I get these warnings during the configuration, nothing important:
A BLAS library was not found by CMake in the paths available to it.
Falling back on the GROMACS internal version of the BLAS library instead.
This is fine for normal usage.
A LAPACK library was not found by CMake in the paths available to it.
Falling back on the GROMACS internal version of the LAPACK library instead.
This is fine for normal usage.
I am currently trying to compile and test GROMACS 5.0 to see if it also
exhibits the same behavior.
I hope that someone can point me in the direction of a possible solution,
if not then I will file a bug report.
Regards,
Mohtadin
Forgot to attached the md.log. Please find attached md.log for both v4.6.6
and v5.0
The list does not accept attachments. Please post the files somewhere for
download.
-Justin
--
==================================================
Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow
Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201
jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul
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