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 <jmsstarli...@gmail.com>wrote: > Dear Szilárd, thanks for help again! > > 2013/1/9 Szilárd Páll <szilard.p...@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@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 > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use the > www interface or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > > -- ORNL/UT Center for Molecular Biophysics cmb.ornl.gov 865-241-1537, ORNL PO BOX 2008 MS6309 -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists