From c6417048397db00cfeca4b767c03808cdb04b3d4 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Sebasti=C3=A1n=20Santisi?= Date: Tue, 2 May 2023 20:45:54 +0000 Subject: [PATCH] Install only via venv --- Makefile | 10 +--- requirements.txt | 113 ++++++++++++++++++++++++++++++++++++++---- script_install.sh | 24 +++------ script_install_py2.sh | 71 -------------------------- 4 files changed, 110 insertions(+), 108 deletions(-) mode change 100755 => 100644 script_install.sh delete mode 100755 script_install_py2.sh diff --git a/Makefile b/Makefile index ab34035..b238ad4 100644 --- a/Makefile +++ b/Makefile @@ -1,19 +1,13 @@ install: - . ./script_install.sh + ./script_install.sh run: ./run_simulation.sh -fftma: - cd fftma_module/gen && python3 setup.py install --user - -binaries: - ./script_fortran.sh - test: binaries cd tests/integration && python3 -m unittest test.py perf: binaries cd tests/performance && python3 generation.py - cd tests/performance && python3 connectivity.py \ No newline at end of file + cd tests/performance && python3 connectivity.py diff --git a/requirements.txt b/requirements.txt index ca21216..653bc3d 100644 --- a/requirements.txt +++ b/requirements.txt @@ -1,11 +1,102 @@ -numpy -scipy -matplotlib -ipython -jupyter -pandas -sympy -nose -mpi4py -Benchmarker==4.0.1 -memory_profiler \ No newline at end of file +anyio==3.6.2 +argon2-cffi==21.3.0 +argon2-cffi-bindings==21.2.0 +arrow==1.2.3 +asttokens==2.2.1 +attrs==23.1.0 +backcall==0.2.0 +beautifulsoup4==4.12.2 +bleach==6.0.0 +cffi==1.15.1 +comm==0.1.3 +contourpy==1.0.7 +cycler==0.11.0 +debugpy==1.6.7 +decorator==5.1.1 +defusedxml==0.7.1 +executing==1.2.0 +fastjsonschema==2.16.3 +fonttools==4.39.3 +fqdn==1.5.1 +idna==3.4 +ipykernel==6.22.0 +ipython==8.13.1 +ipython-genutils==0.2.0 +ipywidgets==8.0.6 +isoduration==20.11.0 +jedi==0.18.2 +Jinja2==3.1.2 +jsonpointer==2.3 +jsonschema==4.17.3 +jupyter==1.0.0 +jupyter-console==6.6.3 +jupyter-events==0.6.3 +jupyter_client==8.2.0 +jupyter_core==5.3.0 +jupyter_server==2.5.0 +jupyter_server_terminals==0.4.4 +jupyterlab-pygments==0.2.2 +jupyterlab-widgets==3.0.7 +kiwisolver==1.4.4 +MarkupSafe==2.1.2 +matplotlib==3.7.1 +matplotlib-inline==0.1.6 +memory-profiler==0.61.0 +mistune==2.0.5 +mpi4py==3.1.4 +mpmath==1.3.0 +nbclassic==0.5.6 +nbclient==0.7.4 +nbconvert==7.3.1 +nbformat==5.8.0 +nest-asyncio==1.5.6 +nose==1.3.7 +notebook==6.5.4 +notebook_shim==0.2.3 +numpy==1.24.3 +packaging==23.1 +pandas==2.0.1 +pandocfilters==1.5.0 +parso==0.8.3 +petsc==3.19.0 +petsc4py==3.19.0 +pexpect==4.8.0 +pickleshare==0.7.5 +Pillow==9.5.0 +platformdirs==3.5.0 +prometheus-client==0.16.0 +prompt-toolkit==3.0.38 +psutil==5.9.5 +ptyprocess==0.7.0 +pure-eval==0.2.2 +pycparser==2.21 +Pygments==2.15.1 +pyparsing==3.0.9 +pyrsistent==0.19.3 +python-dateutil==2.8.2 +python-json-logger==2.0.7 +pytz==2023.3 +PyYAML==6.0 +pyzmq==25.0.2 +qtconsole==5.4.2 +QtPy==2.3.1 +rfc3339-validator==0.1.4 +rfc3986-validator==0.1.1 +scipy==1.10.1 +Send2Trash==1.8.2 +six==1.16.0 +sniffio==1.3.0 +soupsieve==2.4.1 +stack-data==0.6.2 +sympy==1.11.1 +terminado==0.17.1 +tinycss2==1.2.1 +tornado==6.3.1 +traitlets==5.9.0 +tzdata==2023.3 +uri-template==1.2.0 +wcwidth==0.2.6 +webcolors==1.13 +webencodings==0.5.1 +websocket-client==1.5.1 +widgetsnbextension==4.0.7 diff --git a/script_install.sh b/script_install.sh old mode 100755 new mode 100644 index bd4a541..2c40551 --- a/script_install.sh +++ b/script_install.sh @@ -1,21 +1,9 @@ -#!/bin/bash +python3 -m venv venv +source venv/bin/activate -export WORKSPACE=$(pwd) -rm -r ~/.cache/pip - -# gfortran - -sudo apt install build-essential -sudo apt install gfortran -gsettings set org.gnome.nautilus.preferences default-folder-viewer 'list-view' - -pip3 install --user numpy scipy matplotlib ipython jupyter pandas sympy nose mpi4py - -# install open mpi latest version - -sudo apt install openmpi-bin +export PETSC_CONFIGURE_OPTIONS="--download-fblaslapack --download-chaco --download-hdf5" +pip3 install -r requirements.txt -# setup petsc4py +./script_fortran.sh -export PETSC_CONFIGURE_OPTIONS="--download-fblaslapack --download-chaco --download-hdf5" -pip3 install petsc petsc4py \ No newline at end of file +cd fftma_module/gen && python3 setup.py install diff --git a/script_install_py2.sh b/script_install_py2.sh deleted file mode 100755 index 179d18c..0000000 --- a/script_install_py2.sh +++ /dev/null @@ -1,71 +0,0 @@ -#!/bin/bash - -export WORKSPACE=$(pwd) - -# gfortran - -sudo apt install build-essential -sudo apt install gfortran -gsettings set org.gnome.nautilus.preferences default-folder-viewer 'list-view' - -# install open mpi 2.1.1 - -curl https://download.open-mpi.org/release/open-mpi/v2.1/openmpi-2.1.1.tar.bz2 --output openmpi-2.1.1.tar.bz2 -tar -jxf openmpi-2.1.1.tar.bz2 -cd openmpi-2.1.1 - -./configure --prefix=$HOME/opt/openmpi -make all -make install - -echo "export PATH=\$PATH:\$HOME/opt/openmpi/bin" >> $HOME/.bashrc - -echo "export LD_LIBRARY_PATH=\$LD_LIBRARY_PATH:\$HOME/opt/openmpi/lib" >> $HOME/.bashrc - -source ~/.$1rc - -cd .. - -# 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 - -source ~/.$1rc - -# create python 2.7 environment - -conda init $1 - -source ~/.$1rc - -conda create -n py2_7 python=2.7 -conda activate py2_7 - -pip install --user numpy scipy matplotlib ipython jupyter pandas sympy nose - -# setup petsc - -git clone https://gitlab.com/petsc/petsc - -cd petsc - -git checkout maint-3.8 -./configure --with-cc=mpicc --with-cxx=mpicxx --with-fc=mpif90 --download-fblaslapack --with-debugging=0 COPTFLAGS='-O3 -march=native -mtune=native' CXXOPTFLAGS='-O3 -march=native -mtune=native' FOPTFLAGS='-O3 -march=native -mtune=native' - -make PETSC_DIR=$WORKSPACE/petsc PETSC_ARCH=arch-linux2-c-opt all - -make PETSC_DIR=$WORKSPACE/petsc PETSC_ARCH=arch-linux-c-opt check - -cd .. - -# setup petsc4py - -git clone https://Icolecchio@bitbucket.org/petsc/petsc4py.git -cd petsc4py -git checkout maint-3.8 -export PETSC_DIR=$WORKSPACE/petsc -python setup.py build -python setup.py install --user -python setup.py test \ No newline at end of file