Dear James,
On 05/11/13 11:16, James Starlight wrote:
My suggestions:
1) During compilstion using -march=corei7-avx-i I have obtained error that
somethng now found ( sorry I didnt save log) so I compile gromacs without
this flag
2) I have twice as better performance using just 1 gpu by means of
mdrun -ntmpi 1 -ntomp 12 -gpu_id 0 -v -deffnm md_CaM_test
than using of both gpus
mdrun -ntmpi 2 -ntomp 12 -gpu_id 01 -v -deffnm md_CaM_test
in the last case I have obtained warning
WARNING: Oversubscribing the available 12 logical CPU cores with 24 threads.
This will cause considerable performance loss!
here you are requesting 2 thread mpi processes each with 12 openmp
threads, hence a total of 24 threads however even with hyper threading
enabled there are only 12 threads on your machine. Therefore, only
allocate 12. Try
mdrun -ntmpi 2 -ntomp 6 -gpu_id 01 -v -deffnm md_CaM_test
or even
mdrun -v -deffnm md_CaM_test
I believe it should autodetect the GPUs and run accordingly for details
of how to use gromacs with mpi/thread mpi openmp and GPUs see
http://www.gromacs.org/Documentation/Acceleration_and_parallelization
Which describes how to use these systems
Richard
How it could be fixed?
All gpu are recognized correctly
2 GPUs detected:
#0: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC: no, stat:
compatible
#1: NVIDIA GeForce GTX TITAN, compute cap.: 3.5, ECC: no, stat:
compatible
James
2013/11/4 Szilárd Páll <pall.szil...@gmail.com>
You can use the "-march=native" flag with gcc to optimize for the CPU
your are building on or e.g. -march=corei7-avx-i for Intel Ivy Bridge
CPUs.
--
Szilárd Páll
On Mon, Nov 4, 2013 at 12:37 PM, James Starlight <jmsstarli...@gmail.com>
wrote:
Szilárd, thanks for suggestion!
What kind of CPU optimisation should I take into account assumint that
I'm
using dual-GPU Nvidia TITAN workstation with 6 cores i7 (recognized as 12
nodes in Debian).
James
2013/11/4 Szilárd Páll <pall.szil...@gmail.com>
That should be enough. You may want to use the -march (or equivalent)
compiler flag for CPU optimization.
Cheers,
--
Szilárd Páll
On Sun, Nov 3, 2013 at 10:01 AM, James Starlight <
jmsstarli...@gmail.com>
wrote:
Dear Gromacs Users!
I'd like to compile lattest 4.6 Gromacs with native GPU supporting on
my
i7
cpu with dual GeForces Titans gpu mounted. With this config I'd like
to
perform simulations using cpu as well as both gpus simultaneously.
What flags besides
cmake .. -DGMX_GPU=ON -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.5
should I define to CMAKE for compiling optimized gromacs on such
workstation?
Thanks for help
James
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