Re: [gmx-users] Gromacs 2018.5 with CUDA

2019-01-30 Thread Владимир Богданов
|+-+ After unsuccesful gromacs run, I ran namdBest, Vlad  30.01.2019, 10:59, "Mark Abraham" :Hi,Does nvidia-smi report that your GPUs are available to use?MarkOn Wed, 30 Jan 2019 at 07:37 Владимир Богданов <bogdanov-vladi...@ya

[gmx-users] Gromacs 2018.5 with CUDA

2019-01-29 Thread Владимир Богданов
Hey everyone! I need help, please. When I try to run MD with GPU I get the next error: Command line:gmx_mpi mdrun -deffnm md -nb autoBack Off! I just backed up md.log to ./#md.log.4#NOTE: Detection of GPUs failed. The API reported:GROMACS cannot run tasks on a GPU.Reading file md.tpr, VERSION

[gmx-users] protein with ions

2018-06-26 Thread Владимир Богданов
Hey everyone! Could you help me please? When I make md.tpr file I get this note: gmx_mpi grompp -f md.mdp -c npt.gro -r npt.gro -n index.ndx -t npt.cpt -p topol.top -o md.tpr Replacing old mdp entry 'nstxtcout' by 'nstxout-compressed'Replacing old mdp entry 'xtc_grps' by

Re: [gmx-users] how to improve computing?

2018-06-21 Thread Владимир Богданов
can always select manually to use all threads by specifying e.g.-ntomp 16 to use 16 threads per rank/GPU.Cheers,--SzilárdOn Thu, Jun 14, 2018 at 4:38 AM, Владимир Богданов<bogdanov-vladi...@yandex.ru> wrote: Hey everyone! Could help me somebody, please. I have PC with 8 cores, 16 logical cores and 

Re: [gmx-users] Compilation issue, MacOS 10.13.5 - Gromacs 2018 - CUDA 9.2

2018-06-18 Thread Владимир Богданов
 HI, I tried to install gromacs with cuda support on MacBook Pro 2015 (macOS 10.13.4) + eGPU (nvidia titan xp) many times and always have got errors. I didn’t try to install Ubuntu on my MacBook and then install gromacs with cuda, but I guess it could work. Excuse me for my English.  Vlad.  

[gmx-users] how to improve computing?

2018-06-13 Thread Владимир Богданов
Hey everyone! Could help me somebody, please. I have PC with 8 cores, 16 logical cores and 1 compatible GPU, but gromacs calculates just with 1GPU, 1MPI thread and 8 OpenMP threads. Would it possible for me to use all of 16 logical cores? i7-7820XNvidia Titan Xpgromacs 2018 CUDA=onUbuntu 16.04 -- 

[gmx-users] Install Gromacs Cuda MacBook pro with eGPU OS X 10.13.4

2018-05-30 Thread Владимир Богданов
  Hey! Maybe somewhere could help me. I have some problems when I try to compile gromacs on OS X with eGPU: Copyright (c) 2005-2017 NVIDIA CorporationBuilt on Tue_Dec_19_21:36:29_CST_2017Cuda compilation tools, release 9.1, V9.1.128 when I use clang/clang++ compilers: clang -vclang version 6.0.0