Czit notes

Build ParaView with OSMesa

przez kszyh | 19 lipca 2018 - 18:12 |19 lipca 2018 Linux, Science

Detailed manual: https://www.paraview.org/Wiki/ParaView/ParaView_And_Mesa_3D LLVM (works only with 3.x, tested with 3.9.1):

cmake ../ -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/packages/llvm/3.9.1 -DLLVM_BUILD_LLVM_DYLIB=ON -DLLVM_ENABLE_RTTI=ON  -DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD:STRING=X86

1	cmake ../ -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX=/packages/llvm/3.9.1 -DLLVM_BUILD_LLVM_DYLIB=ON -DLLVM_ENABLE_RTTI=ON -DLLVM_INSTALL_UTILS=ON -DLLVM_TARGETS_TO_BUILD:STRING=X86

OSMesa (works only with 13.x, tested with 13.0.6):

./configure --prefix=/packages/mesa/13.0.6-gcc520 --enable-opengl --disable-gles1 --disable-gles2 --disable-va --disable-xvmc --disable-vdpau  --enable-shared-glapi --disable-texture-float  --enable-gallium-llvm --with-gallium-drivers=swrast,swr --disable-dri --with-dri-drivers=  --disable-egl --with-egl-platforms= --disable-gbm  --disable-glx --disable-osmesa --enable-gallium-osmesa --with-llvm-prefix=/packages/llvm/3.9.1/

./configure --prefix=/packages/mesa/13.0.6-gcc520 --enable-opengl --disable-gles1 --disable-gles2 --disable-va --disable-xvmc --disable-vdpau --enable-shared-glapi --disable-texture-float --enable-gallium-llvm --with-gallium-drivers=swrast,swr --disable-dri --with-dri-drivers= --disable-egl --with-egl-platforms= --disable-gbm --disable-glx --disable-osmesa --enable-gallium-osmesa --with-llvm-prefix=/packages/llvm/3.9.1/

ParaView (tested with 5.5.2)

cmake ../   -DPARAVIEW_BUILD_QT_GUI=OFF  -DVTK_USE_X=OFF -DOPENGL_INCLUDE_DIR=IGNORE  -DOPENGL_xmesa_INCLUDE_DIR=IGNORE -DOPENGL_gl_LIBRARY=IGNORE -DOSMESA_INCLUDE_DIR=/packages/mesa/13.0.6-gcc520/include/ -DOSMESA_LIBRARY=/packages/mesa/13.0.6-gcc520/lib/libOSMesa.so -DVTK_OPENGL_HAS_OSMESA=ON -DVTK_USE_OFFSCREEN=OFF -DCMAKE_INSTALL_PREFIX=/packages/paraview/5.5.2/ -DCMAKE_BUILD_TYPE=Release -DPARAVIEW_USE_MPI=ON

cmake ../ -DPARAVIEW_BUILD_QT_GUI=OFF -DVTK_USE_X=OFF -DOPENGL_INCLUDE_DIR=IGNORE -DOPENGL_xmesa_INCLUDE_DIR=IGNORE -DOPENGL_gl_LIBRARY=IGNORE -DOSMESA_INCLUDE_DIR=/packages/mesa/13.0.6-gcc520/include/ -DOSMESA_LIBRARY=/packages/mesa/13.0.6-gcc520/lib/libOSMesa.so -DVTK_OPENGL_HAS_OSMESA=ON -DVTK_USE_OFFSCREEN=OFF -DCMAKE_INSTALL_PREFIX=/packages/paraview/5.5.2/ -DCMAKE_BUILD_TYPE=Release -DPARAVIEW_USE_MPI=ON

Works fine with MPI from Intel Parallel Studio 2018. Built with GCC 5.2.0 Requires Python 2.7

Build OpenCV 3 using Intel Compiler 2018

przez kszyh | 18 lipca 2018 - 15:56 |18 lipca 2018 C++, Linux, Science

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cmake ../ -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_INSTALL_PREFIX=/packages/opencv/3.4.2-intel2018 -DWITH_TBB=ON -DWITH_V4L=OFF -DWITH_QT=OFF -DWITH_OPENGL=OFF -DWITH_OPENCL=OFF -DWITH_GTK=OFF -DBUILD_TIFF=ON  -DBUILD_JAVA=OFF -DWITH_GPHOTO2=OFF  -DCMAKE_BUILD_TYPE=Release -DWITH_OPENCL=OFF -DWITH_IPP=OFF -DENABLE_CXX11=ON -DBUILD_opencv_video=OFF -DBUILD_TESTS=OFF -DBUILD_opencv_ts=OFF

cmake ../ -DCMAKE_C_COMPILER=icc -DCMAKE_CXX_COMPILER=icpc -DCMAKE_Fortran_COMPILER=ifort -DCMAKE_INSTALL_PREFIX=/packages/opencv/3.4.2-intel2018 -DWITH_TBB=ON -DWITH_V4L=OFF -DWITH_QT=OFF -DWITH_OPENGL=OFF -DWITH_OPENCL=OFF -DWITH_GTK=OFF -DBUILD_TIFF=ON -DBUILD_JAVA=OFF -DWITH_GPHOTO2=OFF -DCMAKE_BUILD_TYPE=Release -DWITH_OPENCL=OFF -DWITH_IPP=OFF -DENABLE_CXX11=ON -DBUILD_opencv_video=OFF -DBUILD_TESTS=OFF -DBUILD_opencv_ts=OFF

ReStream rtmp to rtmp

przez kszyh | 20 czerwca 2018 - 15:52 |20 czerwca 2018 Linux

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Requirements: ffmpeg – works fine with static builds – https://www.johnvansickle.com/ffmpeg/ Simple-RTMP-Server – https://github.com/ossrs/srs Build and run srs

./configure
make
./objs/srs -c conf/srs.conf

./configure

make

./objs/srs -c conf/srs.conf

Stream ffmpeg to srs:

ffmpeg -re -i "rtmp://source.stream.com:1935/live/" -ar 44100 -vcodec libx264 -r 50 -b:v 2000k -f flv rtmp://127.0.0.1/app/live

1	ffmpeg -re -i "rtmp://source.stream.com:1935/live/" -ar 44100 -vcodec libx264 -r 50 -b:v 2000k -f flv rtmp://127.0.0.1/app/live

Adapt bitrate (-b:v) and framerate (-r) to your needs.

MongoDB – lookup example

przez kszyh | 11 kwietnia 2018 - 12:07 |11 kwietnia 2018 Java Script, MongoDB

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db.getCollection('log').aggregate([
{
 $lookup: {
     from: 'users',
     localField: 'meta.user',
     foreignField: '_id',
     as: 'user'
     }   
},
{
 $lookup: {
     from: 'patients',
     localField: 'meta.patient',
     foreignField: '_id',
     as: 'patient'
     }   
},
{
  $sort: {
      timestamp: -1
  }
}
])

db.getCollection('log').aggregate([

{

$lookup: {

from: 'users',

localField: 'meta.user',

foreignField: '_id',

as: 'user'

}

{

$lookup: {

from: 'patients',

localField: 'meta.patient',

foreignField: '_id',

as: 'patient'

}

{

$sort: {

timestamp: -1

}

])

Build ParaView on Prometheus

przez kszyh | 25 marca 2018 - 12:47 |26 marca 2018 Linux, Science

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Tutorial

module load plgrid/libs/boost/1.66.0 plgrid/tools/cmake/3.10.2
export CC=/net/software/local/software/GCC/6.4.0/bin/gcc

tar xf ParaView-v5.5.0-RC3.tar.gz
cd ParaView-v5.5.0-RC3
mkdir build
cd build/

cmake ../ -DCMAKE_INSTALL_PREFIX=/net/people/`whoami`/usr/ -DPARAVIEW_BUILD_QT_GUI=OFF -DPARAVIEW_USE_MPI=ON
make

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

export CC=/net/software/local/software/GCC/6.4.0/bin/gcc

tar xf ParaView-v5.5.0-RC3.tar.gz

cd ParaView-v5.5.0-RC3

mkdir build

cd build/

cmake ../ -DCMAKE_INSTALL_PREFIX=/net/people/`whoami`/usr/ -DPARAVIEW_BUILD_QT_GUI=OFF -DPARAVIEW_USE_MPI=ON

make

Format integers in ParaView legend

przez kszyh | 12 marca 2018 - 11:01 |12 marca 2018 Science

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%.0f

%.0f

deal.ii on Prometheus

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

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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

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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

Dealii with MPI+PETSc+p4est

przez kszyh | 30 listopada 2017 - 08:32 |30 listopada 2017 dealii, Linux

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cmake3 ../dealii-8.5.1 -DHDF5_DIR=/packages/hdf5/1.8.15p1 -DCMAKE_INSTALL_PREFIX=/packages/deal.ii/8.5.1-mpi -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_PETSC=ON -DP4EST_DIR=/packages/p4est/1.1/ -DDEAL_II_WITH_P4EST=ON

1	cmake3 ../dealii-8.5.1 -DHDF5_DIR=/packages/hdf5/1.8.15p1 -DCMAKE_INSTALL_PREFIX=/packages/deal.ii/8.5.1-mpi -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_PETSC=ON -DP4EST_DIR=/packages/p4est/1.1/ -DDEAL_II_WITH_P4EST=ON

Build dealii with PETSC

przez kszyh | 26 października 2017 - 17:56 |26 października 2017 Bez kategorii

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System has own OpenBLAS libraries in/usr but PETSc was build with another version of libraries.

cmake3 ../dealii-8.5.0 -DHDF5_DIR=/packages/hdf5/1.8.15p1 -DCMAKE_INSTALL_PREFIX=/packages/deal.ii/8.5.0-mpi -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_PETSC=ON -DBLAS_openblas_LIBRARY=/packages/OpenBLAS/0.2.20/lib/libopenblas.so -DLAPACK_openblas_LIBRARY=/packages/OpenBLAS/0.2.20/lib/libopenblas.so

1	cmake3 ../dealii-8.5.0 -DHDF5_DIR=/packages/hdf5/1.8.15p1 -DCMAKE_INSTALL_PREFIX=/packages/deal.ii/8.5.0-mpi -DDEAL_II_WITH_MPI=ON -DDEAL_II_WITH_PETSC=ON -DBLAS_openblas_LIBRARY=/packages/OpenBLAS/0.2.20/lib/libopenblas.so -DLAPACK_openblas_LIBRARY=/packages/OpenBLAS/0.2.20/lib/libopenblas.so

Build ParaView with OSMesa

Build OpenCV 3 using Intel Compiler 2018

ReStream rtmp to rtmp

MongoDB – lookup example

Build ParaView on Prometheus

Format integers in ParaView legend

deal.ii on Prometheus

Deal.ii build with Intel Parallel Studio on Linux

Dealii with MPI+PETSc+p4est

Build dealii with PETSC

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