typo

.gitignore

@@ -0,0 +1,6 @@
+petsc/
+petsc4py/
+openmpi-2.1.1/
+openmpi-2.1.1.tar.bz2
+tests/integration/tmp_output/
+output/

Makefile

@@ -0,0 +1,15 @@
+SHELL:= zsh
+
+env: 
+	source ./env.sh
+
+install: 
+	source ./script_install.sh $(SHELL)
+
+run: env 
+	./run_simulation.sh
+
+binaries: ./script_fortran.sh
+
+test: env binaries
+	cd tests/integration && python test.py

bash/AnidadoTupac_solver_runner.sh

@@ -0,0 +1,28 @@
+#!/usr/bin/env bash
+#SBATCH -J test_fftma
+#SBATCH -N 4
+#SBATCH --ntasks-per-node 32
+#SBATCH --output %j_output.out
+#SBATCH -p free-rider
+#SBATCH -t 2-23:00:00
+#source activate_env.sh
+ulimit -v  115343360 
+
+
+
+
+k=0
+
+for i in {1..4}  # num de jobs totales divido num de cores (redondear para arriba)
+do
+
+	for j in {1..1}  #Numero de "carpetas" en donde resuelve simultanemente
+		do
+		mpirun -np 4 python ./tools/solver/Ndar.py $k 1 & # job, refinamiento
+		k=$(($k+1))
+		done
+		wait
+	
+done
+
+wait

bash/Local_solver_runner.sh

@@ -0,0 +1,8 @@
+#!/usr/bin/env bash
+
+
+for i in {0..49}
+do
+	mpirun python ./tools/solver/Ndar.py $i 2
+done
+

bash/SolverTupac.sh

@@ -0,0 +1,25 @@
+#!/usr/bin/env bash
+#SBATCH -J test_fftma
+#SBATCH -N 1
+#SBATCH --ntasks-per-node 32
+#SBATCH --output %j_output.out
+#SBATCH -p free-rider
+#SBATCH -t 2-23:00:00
+source activate_env.sh
+ulimit -v  115343360 
+
+
+for i in {1..4}  
+	do
+	mpirun -np 32 python ./tools/solver/Ndar.py ./paper2_SinRef/$i/ 1 # job, refinamiento
+	k=$(($k+1))
+		
+	done
+
+for i in {1..4}  
+	do
+	mpirun -np 32 python ./tools/solver/Ndar.py ./paper2_ref4/$i/ 4 # job, refinamiento
+	k=$(($k+1))
+		
+	done
+

bash/Tupac_generta_media.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+#SBATCH -J test_fftma
+#SBATCH -N 4
+#SBATCH --ntasks-per-node 32
+#SBATCH --output %j_output.out
+#SBATCH -p free-rider
+#SBATCH -t 2-23:00:00
+source activate_env.sh
+ulimit -v  115343360 
+
+
+mpirun python -np 32 mpirunner.py

bash/activate_env.sh

@@ -0,0 +1,4 @@
+export PATH=$HOME/python/Python-2.7.13/:$PATH
+export PYTHONPATH=$HOME/python/Python-2.7.13
+export PATH=$HOME/.local/bin:$PATH
+export PETSC_DIR=$HOME/soft/petsc 

bash/run.sh

@@ -0,0 +1,12 @@
+#!/usr/bin/env bash
+#SBATCH -J connec3d_parte2
+#SBATCH -N 2
+#SBATCH --ntasks-per-node 32
+#SBATCH --output %j_output.out
+#SBATCH -p free-rider
+#SBATCH -t 2-23:00:00
+source activate_env.sh
+ulimit -v  115343360 
+
+
+mpirun python -np 64 mpirunner.py

bash/seq_solver.sh

@@ -0,0 +1,13 @@
+#!/usr/bin/env bash
+
+#SBATCH -J connec3d_parte2
+#SBATCH -N 2
+#SBATCH --ntasks-per-node 32
+#SBATCH --output %j_output.out
+#SBATCH -p free-rider
+#SBATCH -t 2-23:00:00
+
+for i in {0..4}  
+	do
+	mpirun -np 32 python ./tools/solver/Ndar.py ./data/$i/ 1 # job, refinamiento
+	done

config.ini

@@ -0,0 +1,44 @@
+[General]
+simDir=output
+startJob=0
+[Iterables]
+p=[10,39,15]
+seeds=[5462,2]
+lc=[4]
+connectivity=[1,2,3]
+variances=[1]
+
+[Generation]
+Nx = 16
+Ny = 16
+Nz = 16
+variogram_type=1
+binary = yes
+kh = 100
+kl = 0.01
+compute_lc = yes
+lcBin=yes
+genera=yes
+
+
+[Connectivity]
+keep_aspect= yes
+block_size = 4
+indicators_MinBlockSize =4 
+Max_sample_size = 12
+compGconec= 1
+conec=yes
+
+
+[Solver]
+num_of_cores = 1
+ref = 2
+solve = yes
+rtol = 1e-4
+
+[K-Postprocess]
+MinBlockSize =1
+Max_sample_size = 4
+kperm=yes
+postprocess=yes
+SaveVfield=yes

env.sh

@@ -0,0 +1,5 @@
+#!/bin/bash
+
+source ~/miniconda3/etc/profile.d/conda.sh
+conda activate py2_7
+python --version

mpirunner.py

@@ -0,0 +1,63 @@
+import numpy as np
+from mpi4py import MPI
+#from tools.realization import realization
+from tools.generation.config import DotheLoop, get_config
+import os
+import sys
+from tools.Prealization import realization
+
+CONFIG_FILE_PATH = 'config.ini' if 'CONFIG_FILE_PATH' not in os.environ else os.environ['CONFIG_FILE_PATH']
+
+def main():
+	comm = MPI.COMM_WORLD
+	rank = comm.Get_rank()
+	pn = comm.Get_size()
+
+	if pn==1:
+		sequential()
+		return
+	if rank==0:
+		manager()
+	else:
+		worker()
+	return
+
+
+
+def sequential():
+	comm = MPI.COMM_WORLD
+	conffile = CONFIG_FILE_PATH
+	parser,iterables = get_config(conffile)
+	njobs = DotheLoop(-1,parser,iterables)
+	start_job=0
+	for job in range(start_job,njobs):
+		realization(job)
+	return
+
+def manager():
+	comm = MPI.COMM_WORLD
+	conffile = CONFIG_FILE_PATH
+	parser,iterables = get_config(conffile)
+	njobs = DotheLoop(-1,parser,iterables)
+	start_job=0
+	for job in range(start_job,njobs):
+		dest=comm.recv(source=MPI.ANY_SOURCE)
+		comm.send(job,dest=dest)
+	for i in range(comm.Get_size()-1):
+		dest=comm.recv(source=MPI.ANY_SOURCE)
+		comm.send(-1,dest=dest)
+
+	return
+
+def worker():
+	comm = MPI.COMM_WORLD
+	rank = comm.Get_rank()
+	job=1
+	while job!=-1:
+		comm.send(rank,dest=0)
+		job =  comm.recv(source=0)
+		realization(job)
+	return
+
+
+main()

run_simulation.sh

@@ -0,0 +1,3 @@
+#!/bin/bash
+
+mpirun python mpirunner.py

script_fortran.sh

@@ -0,0 +1,8 @@
+#!/bin/bash
+
+rm ./tools/connec/connec2d
+rm ./tools/connec/connec2d
+
+cd ./tools/connec/connec-src && make clean && make all
+mv ./conec2d ..
+mv ./conec3d ..

script_install.sh

@@ -18,19 +18,21 @@ cd openmpi-2.1.1
 make all
 make install
 
-echo "export PATH=\$PATH:\$HOME/opt/openmpi/bin" >> $HOME/.bashrc
+echo "export PATH=\$PATH:\$HOME/opt/openmpi/bin" >> $HOME/.$1rc
 
-echo "export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:\$HOME/opt/openmpi/lib" >> $HOME/.bashrc
+echo "export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:\$HOME/opt/openmpi/lib" >> $HOME/.$1rc
 
 source ~/.$1rc
 
 cd ..
 
+rm openmpi-2.1.1.tar.bz2
+
 # install miniconda
 
 curl https://repo.anaconda.com/miniconda/Miniconda3-py39_4.10.3-Linux-x86_64.sh --output Miniconda3-py39_4.10.3-Linux-x86_64.sh
 
-bash Miniconda3-py39_4.10.3-Linux-x86_64.sh -b
+$1 Miniconda3-py39_4.10.3-Linux-x86_64.sh -b
 
 source ~/.$1rc
 
@@ -40,10 +42,17 @@ conda init $1
 
 source ~/.$1rc
 
+rm Miniconda3-py39_4.10.3-Linux-x86_64.sh
+
 conda create -n py2_7 python=2.7
+
+source ~/miniconda3/etc/profile.d/conda.sh
+
 conda activate py2_7
 
-pip install --user numpy scipy matplotlib ipython jupyter pandas sympy nose
+python --version
+
+pip install --user numpy scipy matplotlib ipython jupyter pandas sympy nose mpi4py
 
 # setup petsc
 
@@ -68,4 +77,5 @@ git checkout maint-3.8
 export PETSC_DIR=$WORKSPACE/petsc
 python setup.py build
 python setup.py install --user
-python setup.py test
+python setup.py test
+cd ..

test_loop/0/ConnSummary.txt

@@ -0,0 +1,5 @@
+# nbl,ttotal,tcmaps/ttotal,PostConTime/ttotal
+4.000000000000000000e+00
+4.437680244445800781e-01
+8.036789380314167675e-01
+4.117019413334135902e-02

test_loop/0/GenParams.txt

@@ -0,0 +1,13 @@
+# Runtime,Nx,Ny,Nz,con,lc,p,kh,kl,seed,variance,vario
+4.421949386596679688e-03
+1.600000000000000000e+01
+1.600000000000000000e+01
+1.600000000000000000e+01
+1.000000000000000000e+00
+4.000000000000000000e+00
+1.000000000000000056e-01
+1.000000000000000000e+02
+1.000000000000000021e-02
+5.462000000000000000e+03
+0.000000000000000000e+00
+1.000000000000000000e+00

test_loop/0/PosKeffSummary.txt

@@ -0,0 +1,5 @@
+# K_diss, K_average,ttotal,tDiss/ttotal
+2.044456438450047153e-02
+2.093990598307741979e-02
+1.699991226196289062e-01
+8.312436538256562021e-03

test_loop/0/RunTimes.out

@@ -0,0 +1,5 @@
+ref: 2
+Matrix creation: 0.322577953339
+Solver: 0.312026023865
+Keff: 0.02097657095221267
+N_cores: 1

test_loop/0/SolverRes.txt

@@ -0,0 +1,5 @@
+# Keff, ref, Runtime, N_cores
+2.097657095221266976e-02
+2.000000000000000000e+00
+6.346039772033691406e-01
+1.000000000000000000e+00

test_loop/0/connec.out

@@ -0,0 +1,4 @@
+
+ 6-CONNECTIVITY ANALYSIS
+
+ PROPORTION OF PHASE 1 IS:    0.00000000    

test_loop/0/lc.txt

@@ -0,0 +1,4 @@
+# lcG, lcNst, lcBin
+4.617108983572631331e+00
+4.617108983572631331e+00
+5.221092552049793944e+00

test_loop/0/tkperm_sub.txt

@@ -0,0 +1,3 @@
+4.433069229125976562e-01
+1.709461212158203125e-04
+1.268386840820312500e-04

test_loop/1/ConnSummary.txt

@@ -0,0 +1,5 @@
+# nbl,ttotal,tcmaps/ttotal,PostConTime/ttotal
+4.000000000000000000e+00
+4.130840301513671875e-01
+8.103774673900496772e-01
+3.892242871984301356e-02

test_loop/1/GenParams.txt

@@ -0,0 +1,13 @@
+# Runtime,Nx,Ny,Nz,con,lc,p,kh,kl,seed,variance,vario
+6.468057632446289062e-03
+1.600000000000000000e+01
+1.600000000000000000e+01
+1.600000000000000000e+01
+1.000000000000000000e+00
+4.000000000000000000e+00
+1.000000000000000056e-01
+1.000000000000000000e+02
+1.000000000000000021e-02
+5.463000000000000000e+03
+0.000000000000000000e+00
+1.000000000000000000e+00

test_loop/1/PosKeffSummary.txt

@@ -0,0 +1,5 @@
+# K_diss, K_average,ttotal,tDiss/ttotal
+2.226209553813355765e-02
+2.286500870826872062e-02
+4.626035690307617188e-03
+3.054682265629026228e-01

test_loop/1/RunTimes.out

@@ -0,0 +1,5 @@
+ref: 2
+Matrix creation: 0.324597120285
+Solver: 0.276505947113
+Keff: 0.022595141113124082
+N_cores: 1

test_loop/1/SolverRes.txt

@@ -0,0 +1,5 @@
+# Keff, ref, Runtime, N_cores
+2.259514111312408216e-02
+2.000000000000000000e+00
+6.011030673980712891e-01
+1.000000000000000000e+00

test_loop/1/connec.out

@@ -0,0 +1,7 @@
+
+ 6-CONNECTIVITY ANALYSIS
+
+ PROPORTION OF PHASE 1 IS:   0.125000000    
+ NCC :            1
+ NCC :            2
+ NCC :            3

test_loop/1/lc.txt

@@ -0,0 +1,4 @@
+# lcG, lcNst, lcBin
+8.214006169837110960e+00
+8.214006169837110960e+00
+2.860537317826781223e+00

test_loop/1/tkperm_sub.txt

@@ -0,0 +1,2 @@
+3.183081150054931641e-01
+1.590251922607421875e-04

test_loop/10/ConnSummary.txt

@@ -0,0 +1,5 @@
+# nbl,ttotal,tcmaps/ttotal,PostConTime/ttotal
+4.000000000000000000e+00
+5.578839778900146484e-01
+8.596443918313970700e-01
+2.408955804327898159e-02

test_loop/10/GenParams.txt

@@ -0,0 +1,13 @@
+# Runtime,Nx,Ny,Nz,con,lc,p,kh,kl,seed,variance,vario
+1.008915901184082031e-02
+1.600000000000000000e+01
+1.600000000000000000e+01
+1.600000000000000000e+01
+1.000000000000000000e+00
+4.000000000000000000e+00
+2.035714285714285698e-01
+1.000000000000000000e+02
+1.000000000000000021e-02
+5.462000000000000000e+03
+0.000000000000000000e+00
+1.000000000000000000e+00

test_loop/10/PosKeffSummary.txt

@@ -0,0 +1,5 @@
+# K_diss, K_average,ttotal,tDiss/ttotal
+4.053728556426364898e-02
+4.123944443032588614e-02
+1.776230335235595703e-01
+6.186535660834491246e-03

test_loop/10/RunTimes.out

@@ -0,0 +1,5 @@
+ref: 2
+Matrix creation: 0.356295824051
+Solver: 0.41558098793
+Keff: 0.041274959938125966
+N_cores: 1