Commit 3bdbe349 authored by Francesco Tomba's avatar Francesco Tomba
Browse files

Merge branch 'h1_optimization' into 'main' 

H1 optimization

See merge request !1
parents 9b4a2351 1e241ec6

Makefile

+3 −1
Original line number Diff line number Diff line 
CC=mpicc

CFLAGS=-O3 -g -fopenmp

#CC=mpiicx

#CFLAGS=-O3 -march=native -flto -funroll-loops -fopenmp

CFLAGS=-O3 -fopenmp 

LDFLAGS=-lm 



all: main

README.md

+2 −1
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@@ -15,7 +15,8 @@ The suggestion is to run it with one mpi task per socket. 


# Todo



 - [ ] H1: implementation of lock free centers elimination

 - [ ] argument parsing: find an elegant way to pass parameters and file (maybe a config file?)

 - [~] H1: implementation of lock free centers elimination (*work in progress*)

 - [ ] context: open all windows in a single shot, close them all togheter

 - [ ] io: curation of IO using mpi IO or other solutions 

 - [ ] kdtree: optimization an profiling

run_leo

+16 −5
Original line number Diff line number Diff line 
#!/bin/bash



#SBATCH --nodes=6

#SBATCH --nodes=2

#SBATCH --ntasks-per-node=2

#SBATCH --cpus-per-task=56

#SBATCH --time=04:00:00

#SBATCH --job-name=dadp_test

#SBATCH --partition=dcgp_usr_prod 

#SBATCH --account=IscrC_dadp

#SBATCH --account=EUHPC_D18_045

#SBATCH --output=out_leo

#SBATCH --error=err_leo

#SBATCH --mem=480G
@@ -14,8 +14,11 @@ 




cd $SLURM_SUBMIT_DIR

module restore my_gcc

#module restore my_intel



#module load gcc

#module load openmpi

module load intel-oneapi-mpi



make clean

make

ulimit -s unlimited
@@ -31,10 +34,18 @@ mkdir bb 
OUT_ASSIGNMENT=/leonardo_scratch/large/userexternal/ftomba00/assignment

OUT_DATA=/leonardo_scratch/large/userexternal/ftomba00/data



IN_DATA=/leonardo_work/IscrC_dadp

IN_DATA=/leonardo_work/EUHPC_D18_045



#10^6 points 

time mpirun -n ${SLURM_NTASKS} --map-by ppr:1:socket:PE=${SLURM_CPUS_PER_TASK}  ./main -t f32 -i ${IN_DATA}/norm_data/std_LR_091_0001 -d 5 -a ${OUT_ASSIGNMENT} -o ${OUT_DATA}

#time mpirun -n ${SLURM_NTASKS} --map-by core  ./main -t f32 -i ${IN_DATA}/norm_data/std_LR_091_0001 -d 5 -a ${OUT_ASSIGNMENT} -o ${OUT_DATA}



#34 * 10^6 points

#time mpirun -n ${SLURM_NTASKS} --map-by ppr:1:socket:PE=${SLURM_CPUS_PER_TASK}  ./main -t f32 -i ${IN_DATA}/norm_data/std_g1212639_091_0001 -d 5 -a ${OUT_ASSIGNMENT} -o ${OUT_DATA}



#88 * 10^6 points 

#time mpirun -n ${SLURM_NTASKS} --map-by ppr:1:socket:PE=${SLURM_CPUS_PER_TASK}  ./main -t f32 -i ${IN_DATA}/norm_data/std_g5503149_091_0000 -d 5 -a ${OUT_ASSIGNMENT} -o ${OUT_DATA}





#200 * 10^6 points

#time mpirun -n ${SLURM_NTASKS} --map-by ppr:1:socket:PE=${SLURM_CPUS_PER_TASK}  ./main -t f32 -i ${IN_DATA}/norm_data/std_g2980844_091_0000 -d 5 -a ${OUT_ASSIGNMENT} -o ${OUT_DATA}

src/adp/adp.c

+409 −101

File changed.

Preview size limit exceeded, changes collapsed.

src/adp/adp.h

+15 −0
Original line number Diff line number Diff line
@@ -45,6 +45,21 @@ typedef struct merge_t 
    float_t density;

} merge_t;



typedef struct center_removal_t

{

    int     rank;

    idx_t   source_id;

    idx_t   target_id;

    float_t source_density;

} center_removal_t;



typedef struct center_removal_queue_t

{

    center_removal_t* data;

    idx_t count;

    idx_t size;

} center_removal_queue_t;







void compute_density_kstarnn_rma(global_context_t* ctx, const float_t d, int verbose);