[gmx-users] gromacs on GPU

James Starlight jmsstarlight at gmail.com
Wed Jan 9 20:27:11 CET 2013

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
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
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
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,
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,


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