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Total Time (s) 18.23 Profiled Time (s) 16.60 Time in analyzed loops (%) 48.9 Time in analyzed innermost loops (%) 41.1 Time in user code (%) 52.0 Compilation Options Score (%) 100 Array Access Efficiency (%) 52.1 Potential Speedups Perfect Flow Complexity 1.02 Perfect OpenMP + MPI + Pthread 1.23 Perfect OpenMP + MPI + Pthread + Perfect Load Distribution 2.14 No Scalar Integer Potential Speedup 1.03 Nb Loops to get 80% 14 FP Vectorised Potential Speedup 1.02 Nb Loops to get 80% 8 Fully Vectorised Potential Speedup 1.10 Nb Loops to get 80% 33 FP Arithmetic Only Potential Speedup 1.10 Nb Loops to get 80% 32
1.00
1.02
1.04
1.06
1.08
1.10
1.12
If No Scalar Integer If FP vectorized If fully vectorized If FP only
Source Object Issue ▼ libgromacs_mpi.so.9.0.0– ○ fft5d.cpp○ threaded_force_buffer.cpp○ pme_pp.cpp○ pme_gather.cpp○ listed_forces.cpp○ simd_prune_kernel.cpp○ partition.cpp○ settle.cpp○ pairlist.cpp○ update.cpp○ md_support.cpp○ kernel_common.cpp○ mdatoms.cpp○ lincs.cpp○ pbc.cpp○ calc_verletbuf.h○ pme_redistribute.cpp○ domdec_specatomcomm.cpp○ pme_grid.cpp○ localtopology.cpp○ pme_solve.cpp○ pme_spread.cpp○ calc_verletbuf.cpp○ simd_kernel.h○ fft_mkl.cpp○ bonded.cpp○ sim_util.cpp○ grid.cpp○ vec.h○ domdec_constraints.cpp○ pairs.cpp○ domdec.cpp○ atomdata.cpp
Application ../../install_gcc/bin/gmx_mpi Timestamp 2024-08-05 19:41:40
Universal Timestamp 1722879700 Number of processes observed 48
Number of threads observed 192 Experiment Type MPI; OpenMP; Machine ins01.benchmarkcenter.megware.com Model Name AMD EPYC 9654 96-Core Processor Architecture x86_64
Micro Architecture ZEN_V4 Cache Size 1024 KB
Number of Cores 96 OS Version Linux 5.14.0-427.18.1.el9_4.x86_64 #1 SMP PREEMPT_DYNAMIC Tue May 28 06:27:02 EDT 2024 Architecture used during static analysis x86_64
Micro Architecture used during static analysis ZEN_V4 Frequency Driver acpi-cpufreq
Frequency Governor performance Huge Pages always
Hyperthreading on Number of sockets 2
Number of cores per socket 96 Compilation Options libgromacs_mpi.so.9.0.0 : GNU C++17 13.2.0 -march=skylake-avx512 -g -O3 -std=c++17 -fno-omit-frame-pointer -fPIC -fexcess-precision=fast -funroll-all-loops -fopenmp Comments GROMACS 2024.2 compiled with gcc 13.2 running on two 96 cores AMD Zen 4 processors, using 48 MPI ranks and 4 OMP threads per MPI rank. Pinning is controlled by GROMACS.
Dataset Run Command <executable> mdrun -s ion_channel.tpr -nsteps 10000 -pin on -deffnm gcc MPI Command mpirun -genv I_MPI_FABRICS=shm -n <number_processes> Number Processes 48 Number Nodes 1 Number Processes per Nodes 48 Filter Not Used Profile Start Not Used
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