What's the simplest case you can make work? Mark
On Fri, Jul 19, 2013 at 8:38 AM, Éric Germaneau <german...@sjtu.edu.cn> wrote: > I actually submitted using two MPI process per node but log files do not > get updated, it's like the calculation gets stuck. > > Here is how I proceed: > > mpirun -np $NM -machinefile nodegpu mdrun_mpi -nb gpu -v -deffnm > test184000atoms_verlet.tpr >& mdrun_mpi.log > > with the content of /nodegpu/: > > gpu04 > gpu04 > gpu11 > gpu11 > > and with > > NM=`cat nodegpu | wc -l` > > /bjobs/ gives > > 3983 hpceric RUN gpu mu05 16*gpu11 gromacs Jul 19 > 12:12 > 16*gpu04 > > /mdrun_mpi.log/ contains the description of the options and > /test184000atoms_verlet.tpr.log/ stops after "PLEASE READ AND CITE THE > FOLLOWING REFERENCE". > > The top of /test184000atoms_verlet.tpr.log/ is: > > Log file opened on Fri Jul 19 13:47:36 2013 > Host: gpu11 pid: 124677 nodeid: 0 nnodes: 4 > Gromacs version: VERSION 4.6.3 > Precision: single > Memory model: 64 bit > MPI library: MPI > OpenMP support: enabled > GPU support: enabled > invsqrt routine: gmx_software_invsqrt(x) > CPU acceleration: AVX_256 > FFT library: fftw-3.3.3-sse2-avx > Large file support: enabled > RDTSCP usage: enabled > Built on: Mon Jul 15 13:44:42 CST 2013 > Built by: name@node [CMAKE] > Build OS/arch: Linux 2.6.32-279.el6.x86_64 x86_64 > Build CPU vendor: GenuineIntel > Build CPU brand: Intel(R) Xeon(R) CPU E5-2670 0 @ 2.60GHz > Build CPU family: 6 Model: 45 Stepping: 7 > Build CPU features: aes apic avx clfsh cmov cx8 cx16 htt lahf_lm mmx > msr nonstop_tsc pcid pclmuldq pdcm pdpe1gb popcnt pse rdtscp sse2 > sse3 sse4.1 sse4.2 ssse3 tdt x2apic > C compiler: /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicc > GNU gcc (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) > C compiler flags: -mavx -Wextra -Wno-missing-field-initializers > -Wno-sign-compare -Wall -Wno-unused -Wunused-value > -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG > C++ compiler: > /lustre/utility/intel/impi/4.1.1.036/intel64/bin/mpicxx GNU g++ > (GCC) 4.4.6 20120305 (Red Hat 4.4.6-4) > C++ compiler flags: -mavx -Wextra -Wno-missing-field-initializers > -Wno-sign-compare -Wall -Wno-unused -Wunused-value > -fomit-frame-pointer -funroll-all-loops -O3 -DNDEBUG > CUDA compiler: /lustre/utility/cuda-5.0/bin/nvcc 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 compiler > > flags:-gencode;arch=compute_20,code=sm_20;-gencode;arch=compute_20,code=sm_21;-gencode;arch=compute_30,code=sm_30;-gencode;arch=compute_30,code=compute_30;-use_fast_math;-Xcompiler;-fPIC > ; > > -mavx;-Wextra;-Wno-missing-field-initializers;-Wno-sign-compare;-Wall;-Wno-unused;-Wunused-value;-fomit-frame-pointer;-funroll-all-loops;-O3;-DNDEBUG > CUDA driver: 5.0 > CUDA runtime: 5.0 > > Does any have any idea about what's going wrong here? > Thanks, > > Éric. > > > On 07/19/2013 09:35 AM, Éric Germaneau wrote: >> >> Dear all, >> >> I'm note a gromacs user, I've installed gromacs 4.6.3 on our cluster and >> making some test. >> Each node of our machine has 16 cores and 2 GPU. >> I'm trying to figure how to submit efficient multiple nodes LSF jobs using >> the maximum of resources. >> After reading the documentation >> <http://www.gromacs.org/Documentation/Acceleration_and_parallelization#Locking_threads_to_physical_cores> >> on "Acceleration and parallelization" I got confused and inquire some help. >> I'm just wondering whether someone with some experiences on this matter. >> I thank you in advance, >> >> Éric. >> > > -- > /Be the change you wish to see in the world > / --- Mahatma Gandhi --- > > Éric Germaneau <http://hpc.sjtu.edu.cn/index.htm> > > Shanghai Jiao Tong University > Network & Information Center > room 205 > Minhang Campus > 800 Dongchuan Road > Shanghai 200240 > China > > View Éric Germaneau's profile on LinkedIn > <http://cn.linkedin.com/pub/%C3%A9ric-germaneau/30/931/986> > > /Please, if possible, don't send me MS Word or PowerPoint attachments > Why? See: http://www.gnu.org/philosophy/no-word-attachments.html/ > > -- > 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 -- 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