Dear gromacs user, Now is more than one week that I am engaging with the fatal error due to domain decomposition, and I have not been succeeded yet, and it is more painful when I have to test different number of cpu's to see which one works in a cluster with a long queuing time, means being two or three days in the queue just to see again the fatal error in two minutes.
These are the dimensions of the cell " 3.53633, 4.17674, 4.99285", and below is the log file of my test submitted on 2 nodes with total 128 cores, I even reduced to 32 CPU's and even changed from "gmx_mpi mdrun" to "gmx mdrun", but the problem is still surviving. Please do not refer me to this link ( http://www.gromacs.org/Documentation/Errors#There_is_no_domain_decomposition_for_n_nodes_that_is_compatible_with_the_given_box_and_a_minimum_cell_size_of_x_nm ) as I know what is the problem but I can not solve it: Thanks, Regards, Alex Log file opened on Fri Jul 22 00:55:56 2016 Host: node074 pid: 12281 rank ID: 0 number of ranks: 64 GROMACS: gmx mdrun, VERSION 5.1.2 Executable: /home/fb_chem/chemsoft/lx24-amd64/gromacs-5.1.2-mpi/bin/gmx_mpi Data prefix: /home/fb_chem/chemsoft/lx24-amd64/gromacs-5.1.2-mpi Command line: gmx_mpi mdrun -ntomp 1 -deffnm min1.6 -s min1.6 GROMACS version: VERSION 5.1.2 Precision: single Memory model: 64 bit MPI library: MPI OpenMP support: enabled (GMX_OPENMP_MAX_THREADS = 32) GPU support: disabled OpenCL support: disabled invsqrt routine: gmx_software_invsqrt(x) SIMD instructions: AVX_128_FMA FFT library: fftw-3.2.1 RDTSCP usage: enabled C++11 compilation: disabled TNG support: enabled Tracing support: disabled Built on: Thu Jun 23 14:17:43 CEST 2016 Built by: reuter@marc2-h2 [CMAKE] Build OS/arch: Linux 2.6.32-642.el6.x86_64 x86_64 Build CPU vendor: AuthenticAMD Build CPU brand: AMD Opteron(TM) Processor 6276 Build CPU family: 21 Model: 1 Stepping: 2 Build CPU features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop C compiler: /usr/lib64/ccache/cc GNU 4.4.7 C compiler flags: -mavx -mfma4 -mxop -Wundef -Wextra -Wno-missing-field-initializers -Wno-sign-compare -Wpointer-arith -Wall -Wno-unused -Wunused-value -Wunused-parameter -O3 -DNDEBUG -funroll-all-loops -Wno-array-bounds C++ compiler: /usr/lib64/ccache/c++ GNU 4.4.7 C++ compiler flags: -mavx -mfma4 -mxop -Wundef -Wextra -Wno-missing-field-initializers -Wpointer-arith -Wall -Wno-unused-function -O3 -DNDEBUG -funroll-all-loops -Wno-array-bounds Boost version: 1.55.0 (internal) Running on 2 nodes with total 128 cores, 128 logical cores Cores per node: 64 Logical cores per node: 64 Hardware detected on host node074 (the node of MPI rank 0): CPU info: Vendor: AuthenticAMD Brand: AMD Opteron(TM) Processor 6276 Family: 21 model: 1 stepping: 2 CPU features: aes apic avx clfsh cmov cx8 cx16 fma4 htt lahf_lm misalignsse mmx msr nonstop_tsc pclmuldq pdpe1gb popcnt pse rdtscp sse2 sse3 sse4a sse4.1 sse4.2 ssse3 xop SIMD instructions most likely to fit this hardware: AVX_128_FMA SIMD instructions selected at GROMACS compile time: AVX_128_FMA Initializing Domain Decomposition on 64 ranks Dynamic load balancing: off Will sort the charge groups at every domain (re)decomposition Initial maximum inter charge-group distances: two-body bonded interactions: 3.196 nm, LJC Pairs NB, atoms 24 28 multi-body bonded interactions: 0.397 nm, Ryckaert-Bell., atoms 5 13 Minimum cell size due to bonded interactions: 3.516 nm Maximum distance for 5 constraints, at 120 deg. angles, all-trans: 0.218 nm Estimated maximum distance required for P-LINCS: 0.218 nm Guess for relative PME load: 0.19 Will use 48 particle-particle and 16 PME only ranks This is a guess, check the performance at the end of the log file Using 16 separate PME ranks, as guessed by mdrun Optimizing the DD grid for 48 cells with a minimum initial size of 3.516 nm The maximum allowed number of cells is: X 1 Y 1 Z 1 ------------------------------------------------------- Program gmx mdrun, VERSION 5.1.2 Source code file: /home/alex/gromacs-5.1.2/src/gromacs/domdec/domdec.cpp, line: 6987 Fatal error: There is no domain decomposition for 48 ranks that is compatible with the given box and a minimum cell size of 3.51565 nm Change the number of ranks or mdrun option -rdd Look in the log file for details on the domain decomposition For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors ------------------------------------------------------- -- 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.