deal.ii – Czit notes

deal.ii on Prometheus

przez kszyh | 11 marca 2018 - 17:59 |11 marca 2018 Linux

p4est

wget http://p4est.github.io/release/p4est-1.1.tar.gz
tar xf http://p4est.github.io/release/p4est-1.1.tar.gz
cd p4est-1.1

username=`whoami`
export CC=mpiicc
export CXX=mpiicpc
export FC=mpiifort
export F77=mpiifort
export LIBS="-lmkl_intel_lp64 -lmkl_core -lmkl_sequential"
module load plgrid/libs/boost/1.66.0

./configure --prefix=/net/people/$username/usr/ --enable-mpi
make
make install

wget http://p4est.github.io/release/p4est-1.1.tar.gz

tar xf http://p4est.github.io/release/p4est-1.1.tar.gz

cd p4est-1.1

username=`whoami`

export CC=mpiicc

export CXX=mpiicpc

export FC=mpiifort

export F77=mpiifort

export LIBS="-lmkl_intel_lp64 -lmkl_core -lmkl_sequential"

module load plgrid/libs/boost/1.66.0

./configure --prefix=/net/people/$username/usr/ --enable-mpi

make

make install

petsc

wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.8.3.tar.gz
tar xf petsc-lite-3.8.3.tar.gz
cd petsc-3.8.3

username=`whoami`
module load plgrid/libs/boost/1.66.0
export PETSC_DIR=`pwd`
export PETSC_ARCH=x86_64

./configure \
--with-shared=1 \
--with-x=0 \
--with-mpi=1 \
--download-hypre=1 \
--with-debugging=0 \
--prefix=/net/people/$username/usr \
--with-blas-lapack-dir=/net/software/local/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64_lin \
COPTFLAGS='-O3 -march=native -mtune=native' \
CXXOPTFLAGS='-O3 -march=native -mtune=native' \
FOPTFLAGS='-O3 -march=native -mtune=native'

make
make install

wget http://ftp.mcs.anl.gov/pub/petsc/release-snapshots/petsc-lite-3.8.3.tar.gz

tar xf petsc-lite-3.8.3.tar.gz

cd petsc-3.8.3

username=`whoami`

module load plgrid/libs/boost/1.66.0

export PETSC_DIR=`pwd`

export PETSC_ARCH=x86_64

./configure \

--with-shared=1 \

--with-x=0 \

--with-mpi=1 \

--download-hypre=1 \

--with-debugging=0 \

--prefix=/net/people/$username/usr \

--with-blas-lapack-dir=/net/software/local/intel/compilers_and_libraries_2018.0.128/linux/mkl/lib/intel64_lin \

COPTFLAGS='-O3 -march=native -mtune=native' \

CXXOPTFLAGS='-O3 -march=native -mtune=native' \

FOPTFLAGS='-O3 -march=native -mtune=native'

make

make install

metis

wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz
tar xf metis-5.1.0.tar.gz
cd metis-5.1.0

module load tools/cmake/3.10.2
module load plgrid/libs/boost/1.66.0

username=`whoami`
make config shared=1 prefix=/net/people/$username/usr/ cc=/net/software/local/software/GCC/6.4.0/bin/gcc
make
make install

wget http://glaros.dtc.umn.edu/gkhome/fetch/sw/metis/metis-5.1.0.tar.gz

tar xf metis-5.1.0.tar.gz

cd metis-5.1.0

module load tools/cmake/3.10.2

module load plgrid/libs/boost/1.66.0

username=`whoami`

make config shared=1 prefix=/net/people/$username/usr/ cc=/net/software/local/software/GCC/6.4.0/bin/gcc

make

make install

deal.ii

wget https://github.com/dealii/dealii/releases/download/v8.5.1/dealii-8.5.1.tar.gz
tar xf dealii-8.5.1.tar.gz
mkdir dealii-8.5.1-build

module load tools/cmake/3.10.2
module load plgrid/libs/boost/1.66.0

username=`whoami`
export PATH=/net/people/$username/usr/bin:$PATH
export LD_LIBRARY_PATH=/net/people/$username/usr/lib:$LD_LIBRARY_PATH

cmake \
../dealii-8.5.1 \
-DCMAKE_INSTALL_PREFIX=/net/people/$username/usr/ \
-DDEAL_II_WITH_MPI=ON \
-DDEAL_II_WITH_PETSC=ON \
-DCMAKE_BUILD_TYPE=Release \
-DDEAL_II_COMPONENT_EXAMPLES=OFF
make
make install

wget https://github.com/dealii/dealii/releases/download/v8.5.1/dealii-8.5.1.tar.gz

tar xf dealii-8.5.1.tar.gz

mkdir dealii-8.5.1-build

module load tools/cmake/3.10.2

module load plgrid/libs/boost/1.66.0

username=`whoami`

export PATH=/net/people/$username/usr/bin:$PATH

export LD_LIBRARY_PATH=/net/people/$username/usr/lib:$LD_LIBRARY_PATH

cmake \

../dealii-8.5.1 \

-DCMAKE_INSTALL_PREFIX=/net/people/$username/usr/ \

-DDEAL_II_WITH_MPI=ON \

-DDEAL_II_WITH_PETSC=ON \

-DCMAKE_BUILD_TYPE=Release \

-DDEAL_II_COMPONENT_EXAMPLES=OFF

make

make install

Deal.ii build with Intel Parallel Studio on Linux

przez kszyh | 21 lutego 2018 - 13:54 |4 października 2018 Linux

Dodaj komentarz

source /packages/intel/2019/bin/compilervars.sh intel64
source /packages/intel/2019/mkl/bin/mklvars.sh intel64
source /packages/intel/2019/tbb/bin/tbbvars.sh intel64
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/packages/boost/1.63.0/lib
export BOOST_ROOT=/packages/boost/1.63.0/
cmake ../dealii-9.0.0  -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_BUILD_TYPE=Release -DDEAL_II_CXX_VERSION_FLAG="-std=c++14" -DDEAL_II_COMPONENT_EXAMPLES=OFF -DCMAKE_INSTALL_PREFIX=/packages/dealii/9.0 -DLAPACK_LIBRARIES:STRING="-lmkl_rt -lpthread -lm -ldl" -DTBB_DIR=/packages/intel/2019/tbb -DTBB_LIBRARY=/packages/intel/2019/tbb/lib/intel64/gcc4.7/libtbb.so -DNANOFLANN_DIR=/packages/nanoflann/1.3.0

source /packages/intel/2019/bin/compilervars.sh intel64

source /packages/intel/2019/mkl/bin/mklvars.sh intel64

source /packages/intel/2019/tbb/bin/tbbvars.sh intel64

export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/packages/boost/1.63.0/lib

export BOOST_ROOT=/packages/boost/1.63.0/

cmake ../dealii-9.0.0 -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_BUILD_TYPE=Release -DDEAL_II_CXX_VERSION_FLAG="-std=c++14" -DDEAL_II_COMPONENT_EXAMPLES=OFF -DCMAKE_INSTALL_PREFIX=/packages/dealii/9.0 -DLAPACK_LIBRARIES:STRING="-lmkl_rt -lpthread -lm -ldl" -DTBB_DIR=/packages/intel/2019/tbb -DTBB_LIBRARY=/packages/intel/2019/tbb/lib/intel64/gcc4.7/libtbb.so -DNANOFLANN_DIR=/packages/nanoflann/1.3.0

Building deal.ii with HDF5 and OpenBlas

przez kszyh | 10 kwietnia 2017 - 11:14 |10 kwietnia 2017 Linux

Dodaj komentarz

Build HDF5 (only 1.8.15p1 is supported by deal.ii):

./configure --prefix=/packages/hdf5/1.8.15p1 --enable-shared --disable-static
make
sudo make install

./configure --prefix=/packages/hdf5/1.8.15p1 --enable-shared --disable-static

make

sudo make install

Build deal.ii

cmake ../deal.ii/ -DHDF5_DIR=/packages/hdf5/1.8.15p1 -DCMAKE_INSTALL_PREFIX=/packages/deal.ii/9.0pre -DBLAS_openblas_LIBRARY=/usr/lib64/libopenblaso.so -DLAPACK_openblas_LIBRARY=/usr/lib64/libopenblaso.so
make -8

1 2	cmake ../deal.ii/ -DHDF5_DIR=/packages/hdf5/1.8.15p1 -DCMAKE_INSTALL_PREFIX=/packages/deal.ii/9.0pre -DBLAS_openblas_LIBRARY=/usr/lib64/libopenblaso.so -DLAPACK_openblas_LIBRARY=/usr/lib64/libopenblaso.so make -8

Konwersja formatu macierzowego deal.ii na zgodny z Matlab

przez kszyh | 10 sierpnia 2015 - 10:47 |10 sierpnia 2015 C++, Linux, Python

Dodaj komentarz

Format wyjściowy biblioteki deal.ii

(0,0) 6.73636e-09
(0,1) 2.76187e-09
(0,2) -3.27721e-09
(0,3) -3.6236e-11
(0,4) 1.13877e-08
(0,5) -5.36419e-10

(0,0) 6.73636e-09

(0,1) 2.76187e-09

(0,2) -3.27721e-09

(0,3) -3.6236e-11

(0,4) 1.13877e-08

(0,5) -5.36419e-10

Matlab wymaga numeracji od 1 i linii ze spacjami zaraz przecinków:

1 1  6.73636e-09
1 2  2.76187e-09
1 3  -3.27721e-09
1 4  -3.6236e-11
1 5  1.13877e-08
1 6  -5.36419e-10

1 1 6.73636e-09

1 2 2.76187e-09

1 3 -3.27721e-09

1 4 -3.6236e-11

1 5 1.13877e-08

1 6 -5.36419e-10

Skrypt dokonujący konwersji:

#!/usr/bin/python
import sys
import re

with open(sys.argv[1]+".new", 'a+') as w:
    with open(sys.argv[1]) as file:
        for line in file:
            m = re.match(r'\((.*?),(.*?)\)(.*?)$', line)
            w.write('{0} {1} {2}\n'.format(int(m.group(1))+1, int(m.group(2))+1, m.group(3)))

#!/usr/bin/python

import sys

import re

with open(sys.argv[1]+".new", 'a+') as w:

with open(sys.argv[1]) as file:

for line in file:

m = re.match(r'$(.*?),(.*?)$(.*?)$', line)

w.write('{0} {1} {2}\n'.format(int(m.group(1))+1, int(m.group(2))+1, m.group(3)))

Uruchomienie:

./matrix_convert.py A.dat

1	./matrix_convert.py A.dat

Konwersja formatu macierzy deal.ii na MarketMatrix

przez kszyh | 30 grudnia 2013 - 09:31 |21 lutego 2014 Lifehacking, Linux, Skrypty

Dodaj komentarz

MATRIX_FILE="Matrix.dat"
RHS_FILE="rhs.dat"
SOLUTION_FILE="solution.dat"
perl -pi -w -e  's/\((.*?),(.*?)\).(.*)/($1+1)." ".($2+1)." ".$3/e' $MATRIX_FILE
lines=`grep -c ^ $MATRIX_FILE`
rows=`tail -n 1 $MATRIX_FILE | cut -f1 -d' '`
sed -i "1s/^/"$rows" "$rows" "$lines"\n/" $MATRIX_FILE
sed -i '1s/^/%%MatrixMarket matrix coordinate real general\n/' $MATRIX_FILE

sed -i "1s/^/"$rows"\n/" $SOLUTION_FILE
sed -i "1s/^/"$rows"\n/" $RHS_FILE

MATRIX_FILE="Matrix.dat"

RHS_FILE="rhs.dat"

SOLUTION_FILE="solution.dat"

perl -pi -w -e 's/$(.*?),(.*?)$.(.*)/($1+1)." ".($2+1)." ".$3/e' $MATRIX_FILE

lines=`grep -c ^ $MATRIX_FILE`

rows=`tail -n 1 $MATRIX_FILE | cut -f1 -d' '`

sed -i "1s/^/"$rows" "$rows" "$lines"\n/" $MATRIX_FILE

sed -i '1s/^/%%MatrixMarket matrix coordinate real general\n/' $MATRIX_FILE

sed -i "1s/^/"$rows"\n/" $SOLUTION_FILE

sed -i "1s/^/"$rows"\n/" $RHS_FILE

Archiwa tagu: deal.ii

deal.ii on Prometheus

Deal.ii build with Intel Parallel Studio on Linux

Building deal.ii with HDF5 and OpenBlas

Konwersja formatu macierzowego deal.ii na zgodny z Matlab

Konwersja formatu macierzy deal.ii na MarketMatrix

Ostatnie wpisy

Najnowsze komentarze

Kategorie

Meta