[gmx-users] gromacs on GPU

[Roland Schulz]

Hi,

is this an implicit water calculation? If so it shouldn't use PME.

Roland


On Wed, Jan 9, 2013 at 2:27 PM, James Starlight <jmsstarlight at gmail.com>wrote:

> Dear Szilárd, thanks for help again!
>
> 2013/1/9 Szilárd Páll <szilard.pall at cbr.su.se>:
>
> >
> > There could be, but I/we can't well without more information on what and
> > how you compiled and ran. The minimum we need is a log file.
> >
> I've compilated gromacs 4.6-3 beta via simple
>
>
> cmake CMakeLists.txt -DGMX_GPU=ON
> -DCUDA_TOOLKIT_ROOT_DIR=/usr/local/cuda-5.0
> make
> sudo make install
>
> I have not added any special params to the grompp or mdrun.
>
> After that I've run tested simulation of the calmodulin in explicit
> water ( 60k atoms ) 100ps and obtain next output
>
> Host: starlight  pid: 21028  nodeid: 0  nnodes:  1
> Gromacs version:    VERSION 4.6-beta3
> Precision:          single
> MPI library:        thread_mpi
> OpenMP support:     enabled
> GPU support:        enabled
> invsqrt routine:    gmx_software_invsqrt(x)
> CPU acceleration:   AVX_256
> FFT library:        fftw-3.3.2-sse2-avx
> Large file support: enabled
> RDTSCP usage:       enabled
> Built on:           Wed Jan  9 20:44:51 MSK 2013
> Built by:           own at starlight [CMAKE]
> Build OS/arch:      Linux 3.2.0-2-amd64 x86_64
> Build CPU vendor:   GenuineIntel
> Build CPU brand:    Intel(R) Core(TM) i5-3570 CPU @ 3.40GHz
> Build CPU family:   6   Model: 58   Stepping: 9
> Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt lahf_lm
> mmx msr nonstop_tsc pcid pclmuldq pdcm popcnt pse rdrnd rdtscp sse2
> sse3 sse4.1 sse4.2 ssse3 tdt x2apic
> C compiler:         /usr/bin/gcc GNU gcc (Debian 4.6.3-11) 4.6.3
> C compiler flags:   -mavx  -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
> -DNDEBUG
> C++ compiler:       /usr/bin/c++ GNU c++ (Debian 4.6.3-11) 4.6.3
> C++ compiler flags: -mavx  -Wextra -Wno-missing-field-initializers
> -Wno-sign-compare -Wall -Wno-unused -Wunused-value
> -fomit-frame-pointer -funroll-all-loops -fexcess-precision=fast  -O3
> -DNDEBUG
> CUDA compiler:      nvcc: NVIDIA (R) Cuda compiler driver;Copyright
> (c) 2005-2012 NVIDIA Corporation;Built on
> Fri_Sep_21_17:28:58_PDT_2012;Cuda compilation tools, release 5.0,
> V0.2.1221
> CUDA driver:        5.0
> CUDA runtime:       5.0
>
> ****************
>
>                Core t (s)   Wall t (s)        (%)
>        Time:     2770.700     1051.927      263.4
>                  (ns/day)    (hour/ns)
> Performance:        8.214        2.922
>
> full log can be found here http://www.sendspace.com/file/inum84
>
>
> Finally when I check CPU usage I notice that only 1 CPU was full
> loaded ( 100%) and 2-4 cores were loaded on only 60% but  gave me
> strange results that GPU is not used (I've only monitored temperature
> of video card and noticed increase of the temperature up to 65 degrees
> )
>
> +------------------------------------------------------+
> | NVIDIA-SMI 4.304.54   Driver Version: 304.54         |
>
> |-------------------------------+----------------------+----------------------+
> | GPU  Name                     | Bus-Id        Disp.  | Volatile Uncorr.
> ECC |
> | Fan  Temp  Perf  Pwr:Usage/Cap| Memory-Usage         | GPU-Util  Compute
> M. |
>
> |===============================+======================+======================|
> |   0  GeForce GTX 670          | 0000:02:00.0     N/A |
>  N/A |
> | 38%   63C  N/A     N/A /  N/A |   9%  174MB / 2047MB |     N/A
>  Default |
>
> +-------------------------------+----------------------+----------------------+
>
>
> +-----------------------------------------------------------------------------+
> | Compute processes:                                               GPU
> Memory |
> |  GPU       PID  Process name                                     Usage
>    |
>
> |=============================================================================|
> |    0            Not Supported
>     |
>
> +-----------------------------------------------------------------------------+
>
>
> Thanks for help again,
>
> James
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