Dear all, Could you please tell me, if this is normal during running a simulation. I am running mdrun with -v flag and i receive this, . . vol 0.23! imb F 2264% pme/F 0.57 step 1496300, will finish Mon Jan 21 00:13:42 2019 vol 0.23 imb F 3249% pme/F 0.75 step 1496400, will finish Mon Jan 21 00:13:49 2019 vol 0.23 imb F 0% pme/F 1.95 step 1496500, will finish Mon Jan 21 00:13:47 2019 vol 0.23 imb F 526% pme/F 1.33 step 1496600, will finish Mon Jan 21 00:13:50 2019 vol 0.21! imb F 130% pme/F 1.65 step 1496700, will finish Mon Jan 21 00:13:49 2019 . . The command i used for the mdrun is as follows: mpirun -np 64 gmx_mpi mdrun -v -deffnm md_0_10 -cpi md_0_10.cpt -append -ntomp 1 -npme 32
gmx_mpi versio is as follows: GROMACS: gmx_mpi, version 2018 Executable: /usr/local/gromacs2018/bin/gmx_mpi Data prefix: /usr/local/gromacs2018 Working dir: /home/bio1 Command line: gmx_mpi --version GROMACS version: 2018 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 64) GPU support: CUDA SIMD instructions: AVX_256 FFT library: fftw-3.3.5-fma-sse2-avx-avx2-avx2_128-avx512 RDTSCP usage: enabled TNG support: enabled Hwloc support: hwloc-1.11.0 Tracing support: disabled Built on: 2018-12-29 04:38:41 Built by: root@node04 [CMAKE] Build OS/arch: Linux 4.4.0-21-generic x86_64 Build CPU vendor: Intel Build CPU brand: Intel(R) Xeon(R) CPU E5-4610 v2 @ 2.30GHz Build CPU family: 6 Model: 62 Stepping: 4 Build CPU features: aes apic avx clfsh cmov cx8 cx16 f16c htt intel lahf mmx msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdrnd rdtscp sse2 sse3 sse4.1 sse4.2 ssse3 tdt x2apic C compiler: /usr/bin/cc GNU 5.4.0 C compiler flags: -mavx -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast C++ compiler: /usr/bin/c++ GNU 5.4.0 C++ compiler flags: -mavx -std=c++11 -O3 -DNDEBUG -funroll-all-loops -fexcess-precision=fast CUDA compiler: /usr/local/cuda/bin/nvcc nvcc: NVIDIA (R) Cuda compiler driver;Copyright (c) 2005-2016 NVIDIA Corporation;Built on Tue_Jan_10_13:22:03_CST_2017;Cuda compilation tools, release 8.0, V8.0.61 CUDA compiler flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_35,code=sm_35;-gencode;arch=compute_37,code=sm_37;-gencode;arch=compute_50,code=sm_50;-gencode;arch=compute_52,code=sm_52;-gencode;arch=compute_60,code=sm_60;-gencode;arch=compute_61,code=sm_61;-gencode;arch=compute_60,code=compute_60;-gencode;arch=compute_61,code=compute_61;-use_fast_math;-Wno-deprecated-gpu-targets;-D_FORCE_INLINES;; ;-mavx;-std=c++11;-O3;-DNDEBUG;-funroll-all-loops;-fexcess-precision=fast; CUDA driver: 8.0 CUDA runtime: 8.0 Thank you in advance. On Sat, Dec 29, 2018 at 2:33 PM Prasanth G, Research Scholar < prasanthgha...@sssihl.edu.in> wrote: > Dear all, > I was able to overcome the issue, by introducing the command "mpirun -np > x" before the command. > Here is the exact command- > > mpirun -np 32 gmx_mpi mdrun -v -deffnm md_0_10 -cpi md_0_10.cpt -append > -ntomp 4 > > Thank you. > > > On Fri, Dec 28, 2018 at 12:12 PM Prasanth G, Research Scholar < > prasanthgha...@sssihl.edu.in> wrote: > >> Dear all, >> >> Though the GROMACS was configured with MPI support during installation. >> >> installation cmake.txt >> <https://drive.google.com/a/sssihl.edu.in/file/d/1Io1QhMJg7x88LhRj6_iTsXdUxZkAmIbV/view?usp=drive_web> >> >> I am able to use only one MPI process on the node for the simulation. >> This happens when i try to use ntmpi >> >> ntmpi 4 ntomp 8.txt >> <https://drive.google.com/a/sssihl.edu.in/file/d/152ea2HmpEL4_gSSn2_A_L0MoIwoTt8iy/view?usp=drive_web> >> >> I am attaching the md log file and md.mdp of a previous simulation here. >> >> md.mdp >> <https://drive.google.com/a/sssihl.edu.in/file/d/1h6Lsb0MzJ8b3U4jPIMUn3T9DcnIxNvDi/view?usp=drive_web> >> >> md_0_10.log >> <https://drive.google.com/a/sssihl.edu.in/file/d/141LtTSoishQG3Q6mqbHibHCbpXgxA5OS/view?usp=drive_web> >> >> I am also attaching the nvsmi log >> >> nvsmi log.txt >> <https://drive.google.com/a/sssihl.edu.in/file/d/1Agh_0BsPKw5x5_sTsVShCfAZaOnm7Bud/view?usp=drive_web> >> >> I had tried to decrease the number of threads for running current >> simulation and here are the results >> >> ntomp 8 >> <https://drive.google.com/a/sssihl.edu.in/file/d/1KdlqxWs7peqwftvW1bhsYVAYNZLF6s-H/view?usp=drive_web> >> >> ntomp 16 >> <https://drive.google.com/a/sssihl.edu.in/file/d/1Md3rwKdl8h1WYVMpbON0avQN7ZF46Vl7/view?usp=drive_web> >> >> ntomp 32 >> <https://drive.google.com/a/sssihl.edu.in/file/d/1v5vIu2BbU7zs9HnZw9xMXM29hLkJa2LL/view?usp=drive_web> >> >> Can you please suggest a solution, as I am currently getting efficiency >> of about 2.5ns/day. >> Thanks in advance. >> >> -- >> Regards, >> Prasanth. >> > > > -- > Regards, > Prasanth. > -- Regards, Prasanth. -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.