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gmx_mpi - 2024-08-05 19:31:18 - MAQAO 2.20.7

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Global Metrics

Total Time (s)15.59
Profiled Time (s)13.41
Time in analyzed loops (%)38.3
Time in analyzed innermost loops (%)31.1
Time in user code (%)47.4
Compilation Options Score (%)100
Array Access Efficiency (%)53.0
Potential Speedups
Perfect Flow Complexity1.03
Perfect OpenMP + MPI + Pthread1.17
Perfect OpenMP + MPI + Pthread + Perfect Load Distribution1.53
No Scalar IntegerPotential Speedup1.03
Nb Loops to get 80%13
FP VectorisedPotential Speedup1.02
Nb Loops to get 80%10
Fully VectorisedPotential Speedup1.10
Nb Loops to get 80%30
FP Arithmetic OnlyPotential Speedup1.09
Nb Loops to get 80%26

CQA Potential Speedups Summary

Loop Based Profile

Innermost Loop Based Profile

Application Categorization

Compilation Options

Source ObjectIssue
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
pairs.cpp
vec.h
update.cpp
md_support.cpp
pme.cpp
mdatoms.cpp
lincs.cpp
calc_verletbuf.h
pme_redistribute.cpp
md.cpp
fft.cpp
constr.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
domdec.cpp
sim_util.cpp
grid.cpp
settle.cpp
arrayref.h
domdec_constraints.cpp
pairlist.cpp
pme_only.cpp
atomdata.cpp
[vdso]
-g is missing for some functions (possibly ones added by the compiler), it is needed to have more accurate reports. Other recommended flags are: -O2/-O3, -march=(target)

Loop Path Count Profile

Cumulated Speedup If No Scalar Integer

Cumulated Speedup If FP Vectorized

Cumulated Speedup If Fully Vectorized

Cumulated Speedup If FP Arithmetic Only

Experiment Summary

Application../../install_gcc/bin/gmx_mpi
Timestamp2024-08-05 19:31:18 Universal Timestamp1722879078
Number of processes observed192 Number of threads observed192
Experiment TypeMPI; OpenMP;
Machineins01.benchmarkcenter.megware.com
Model NameAMD EPYC 9654 96-Core Processor
Architecturex86_64 Micro ArchitectureZEN_V4
Cache Size1024 KB Number of Cores96
OS VersionLinux 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 analysisx86_64 Micro Architecture used during static analysisZEN_V4
Frequency Driveracpi-cpufreq Frequency Governorperformance
Huge Pagesalways Hyperthreadingon
Number of sockets2 Number of cores per socket96
Compilation Options+ [vdso]: N/A
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
CommentsGROMACS 2024.2 compiled with gcc 13.2 running on two 96 cores AMD Zen 4 processors, using 192 MPI ranks (no OMP). Pinning is controlled by GROMACS.

Configuration Summary

Dataset
Run Command<executable> mdrun -s ion_channel.tpr -nsteps 10000 -pin on -deffnm gcc
MPI Commandmpirun -genv I_MPI_FABRICS=shm -n <number_processes>
Number Processes192
Number Nodes1
Number Processes per Nodes192
FilterNot Used
Profile StartNot Used
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