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MAINT: installation scripts with hnn-core
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Blake Caldwell committed Mar 21, 2021
1 parent f876500 commit 80987dc
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95 changes: 66 additions & 29 deletions installer/ubuntu/hnn-ubuntu.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,7 @@
set -e

[[ "$LOGFILE" ]] || LOGFILE="ubuntu_install.log"
[[ "$USE_CONDA" ]] || USE_CONDA=0

function start_download {
echo "Downloading $2"
Expand Down Expand Up @@ -61,17 +62,17 @@ echo "Using python version $PYTHON_VERSION" | tee -a "$LOGFILE"
export DEBIAN_FRONTEND=noninteractive

echo "Updating package repository..." | tee -a "$LOGFILE"
sudo -E apt-get update &>> "$LOGFILE"
sudo -E apt-get update &> "$LOGFILE"

echo "Updating OS python packages..." | tee -a "$LOGFILE"
if [[ "${PYTHON_VERSION}" =~ "3.7" ]] && [[ "$DISTRIB" =~ "bionic" ]]; then
sudo -E apt-get install --no-install-recommends -y python3.7 python3-pip python3.7-tk python3.7-dev &>> "$LOGFILE" && \
sudo python3.7 -m pip install --upgrade pip setuptools &>> "$LOGFILE"
sudo -E apt-get install --no-install-recommends -y python3.7 python3-pip python3-tk python3.7-dev &> "$LOGFILE" && \
sudo python3.7 -m pip install --upgrade pip setuptools &> "$LOGFILE"
sudo ln -s /usr/lib/python3/dist-packages/apt_pkg.cpython-36m-x86_64-linux-gnu.so \
/usr/lib/python3/dist-packages/apt_pkg.so
else
sudo -E apt-get install --no-install-recommends -y python3 python3-pip python3-tk python3-setuptools &>> "$LOGFILE" && \
sudo pip3 install --upgrade pip &>> "$LOGFILE"
sudo -E apt-get install --no-install-recommends -y python3 python3-pip python3-tk python3-setuptools &> "$LOGFILE" && \
sudo pip3 install --upgrade pip &> "$LOGFILE"
fi

if which python3 &> /dev/null; then
Expand All @@ -87,22 +88,68 @@ elif which python &> /dev/null; then
fi
echo "Using python: $PYTHON with pip: $PIP" | tee -a "$LOGFILE"

if [[ "$USE_CONDA" -eq 0 ]]; then
echo "Downloading python packages for HNN with pip..." | tee -a "$LOGFILE"
$PIP download pyqt5 nlopt psutil hnn-core &> "$LOGFILE" &
PIP_PID=$!
fi

echo "Installing OS compilation toolchain..." | tee -a "$LOGFILE"
# get prerequisites from pip. requires gcc to build psutil
sudo -E apt-get install --no-install-recommends -y \
make gcc g++ python3-dev &>> "$LOGFILE"
make gcc g++ python3-dev &> "$LOGFILE"

if [[ "$USE_CONDA" -eq 0 ]]; then
echo "Waiting for python packages for HNN downloads to finish..."
NAME="downloading python packages for HNN "
wait_for_pid "${PIP_PID}" "$NAME"

# install hnn-core and prerequisites (e.g. NEURON)
echo "Installing python prequisites for HNN with pip..." | tee -a "$LOGFILE"
$PIP install --no-cache-dir pyqt5 nlopt psutil hnn-core &> "$LOGFILE"

# WSL may not have nrnivmodl in PATH
if ! which nrnivmodl &> /dev/null; then
export PATH="$PATH:$HOME/.local/bin"
echo 'export PATH="$PATH:$HOME/.local/bin"' >> ~/.bashrc
fi
else
URL="https://repo.anaconda.com/miniconda/Miniconda3-latest-Linux-x86_64.sh"
FILENAME="$HOME/miniconda.sh"
start_download "$FILENAME" "$URL"

echo "Installing miniconda..."
chmod +x "$HOME/miniconda.sh"
"$HOME/miniconda.sh" -b -p "${HOME}/Miniconda3"
export PATH=${HOME}/Miniconda3/bin:$PATH

$PIP install --no-cache-dir NEURON
# create conda environment
conda env create -f environment.yml

# WSL may not have nrnivmodl in PATH
if ! which nrnivmodl &> /dev/null; then
export PATH="$PATH:$HOME/.local/bin"
echo 'export PATH="$PATH:$HOME/.local/bin"' >> ~/.bashrc
# conda is faster to install nlopt
conda install -y -n hnn -c conda-forge nlopt

source activate hnn && echo "activated conda HNN environment"

echo "Installing MPI compilation toolchain..." | tee -a "$LOGFILE"
# get prerequisites to build mpi4py
sudo -E apt-get install --no-install-recommends -y \
libopenmpi-dev &> "$LOGFILE"

# install hnn-core and prerequisites (e.g. NEURON)
pip install mpi4py pyqt5 hnn-core
fi

echo "Installing python packages for HNN with pip..." | tee -a "$LOGFILE"
$PIP install --no-cache-dir --user matplotlib PyOpenGL \
pyqt5 pyqtgraph scipy numpy nlopt psutil &>> "$LOGFILE"
echo "Downloading runtime prerequisite packages..." | tee -a "$LOGFILE"
apt-get download \
openmpi-bin lsof libfontconfig1 libxext6 libx11-xcb1 libxcb-glx0 \
libxkbcommon-x11-0 libgl1-mesa-glx \
libc6-dev libtinfo-dev libncurses5-dev \
libx11-dev libreadline-dev \
libxcb-icccm4 libxcb-util1 libxcb-image0 libxcb-keysyms1 \
libxcb-render0 libxcb-shape0 libxcb-randr0 libxcb-render-util0 \
libxcb-xinerama0 &> "$LOGFILE" &
APT_DOWNLOAD=$!

# save dir installing hnn to
startdir=$(pwd)
Expand All @@ -115,11 +162,11 @@ if [[ $TRAVIS_TESTING -ne 1 ]]; then

cd hnn_source_code
if [ -d "$source_code_dir/.git" ]; then
git pull origin master &>> "$LOGFILE"
git pull origin master &> "$LOGFILE"
fi
else
echo "Downloading and extracting HNN..." | tee -a "$LOGFILE"
wget --no-hsts --no-check-certificate -O hnn.tar.gz https://github.com/jonescompneurolab/hnn/releases/latest/download/hnn.tar.gz | tee -a "$LOGFILE"
wget -O hnn.tar.gz https://github.com/jonescompneurolab/hnn/releases/latest/download/hnn.tar.gz | tee -a "$LOGFILE"
mkdir hnn_source_code
tar -x --strip-components 1 -f hnn.tar.gz -C hnn_source_code &>> "$LOGFILE" && \
cd hnn_source_code &>> "$LOGFILE"
Expand All @@ -132,10 +179,6 @@ else
fi
fi

echo "Building HNN..." | tee -a "$LOGFILE"
make -j4 &>> "$LOGFILE"
MAKE_PID=$!

# create the global session variables
echo '# these lines define global session variables for HNN' >> ~/.bashrc
echo "export PATH=\$PATH:\"$source_code_dir\"" >> ~/.bashrc
Expand All @@ -147,7 +190,7 @@ if [[ -d "$HOME/Desktop" ]]; then
cp -f hnn.desktop "$HOME/Desktop" && \
sed -i "s~/home/hnn_user\(.*\)$~\"$startdir\"\1~g" "$HOME/Desktop/hnn.desktop" && \
chmod +x "$HOME/Desktop/hnn.desktop"
} &>> "$LOGFILE"
} &> "$LOGFILE"
fi

echo "Installing prerequisites..." | tee -a "$LOGFILE"
Expand All @@ -160,17 +203,11 @@ sudo -E apt-get install --no-install-recommends -y \
libx11-dev libreadline-dev \
libxcb-icccm4 libxcb-util1 libxcb-image0 libxcb-keysyms1 \
libxcb-render0 libxcb-shape0 libxcb-randr0 libxcb-render-util0 \
libxcb-xinerama0 libxcb-xfixes0 &>> "$LOGFILE"
libxcb-xinerama0 libxcb-xfixes0 &> "$LOGFILE"

# Clean up a little
echo "Cleaning up..." | tee -a "$LOGFILE"
sudo -E apt-get clean &>> "$LOGFILE"

if [[ $TRAVIS_TESTING -ne 1 ]]; then
echo "Waiting for HNN module build to finish..."
NAME="building HNN modules"
wait_for_pid "${MAKE_PID}" "$NAME"
fi
sudo -E apt-get clean &> "$LOGFILE"

echo "HNN installation successful" | tee -a "$LOGFILE"
echo "Source code is at $source_code_dir" | tee -a "$LOGFILE"
Expand Down
51 changes: 23 additions & 28 deletions installer/windows/hnn-windows.ps1
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Original file line number Diff line number Diff line change
Expand Up @@ -6,7 +6,7 @@ install Miniconda:
- Miniconda3-latest-Windows-x86_64.exe
Additionally the following will be installed if they are not found:
- nrn-7.7.w64-mingwsetup.exe
- nrn-7.8.w64-mingwsetup.exe
Other requirements:
- Only 64-bit installs are supported due to NEURON compatibility
Expand Down Expand Up @@ -310,8 +310,8 @@ if ($script:installMiniconda) {

$program = "NEURON"
if (!(Test-Installed($program))) {
$file = "nrn-7.7.w64-mingwsetup.exe"
$url = "https://neuron.yale.edu/ftp/neuron/versions/v7.7/$file"
$file = "nrn-7.8.w64-mingwsetup.exe"
$url = "https://neuron.yale.edu/ftp/neuron/versions/v7.8/$file"
Download-Program $program $file $url
$dirpath = $script:NEURON_PATH
Write-Host "Installing $program to $dirpath..."
Expand Down Expand Up @@ -379,6 +379,13 @@ if ($proc1) {
Write-Host "Miniconda is finished"
}

if ($proc2) {
Write-Host "Waiting for NEURON install to finish..."
$proc2.WaitForExit() 2>$null
Update-User-Paths("$script:NEURON_PATH\bin")
Write-Host "NEURON is finished"
}

# setup python with virtualenv or 'conda
if ($null -ne $script:VIRTUALENV) {
Write-Host "Creating Python virtualenv at $HOME\venv\hnn..."
Expand All @@ -390,7 +397,9 @@ if ($null -ne $script:VIRTUALENV) {
$script:PYTHON = "$HOME\venv\hnn\Scripts\python.exe"
if (Test-Python-3($script:PYTHON)) {
# use pip3 for good measure
Start-Process "$HOME\venv\hnn\Scripts\pip3" "install PyOpenGL pyqtgraph matplotlib scipy PyQt5 psutil nlopt" -Wait
Start-Process "$HOME\venv\hnn\Scripts\pip3" "install matplotlib scipy PyQt5 psutil nlopt" -Wait
# get hnn-core, but skip NEURON dependency
Start-Process "$HOME\venv\hnn\Scripts\pip3" "install --no-deps mpi4py hnn-core" -Wait
}
else {
Write-Warning "Virtualenv failed to create a valid python3 environment"
Expand All @@ -415,14 +424,21 @@ elseif ($null -ne $script:CONDA_PATH) {

if (!$script:env_exists) {
Write-Host "Setting up anaconda hnn environment..."
conda create -y -n hnn python=3.7 PyOpenGL pyqtgraph matplotlib scipy conda psutil
conda env create -f environment.yml
conda install -y -n hnn -c conda-forge nlopt

# need to call the right pip to install in miniconda environment
# get hnn-core, but skip NEURON dependency
Set-Location $HOME
Miniconda3\envs\hnn\Scripts\pip install --no-deps mpi4py hnn-core

Set-Location $CONDA_ENV
mkdir .\etc\conda\activate.d 2>&1>$null
mkdir .\etc\conda\deactivate.d 2>&1>$null

#"set NRN_PYLIB=$script:PYTHON_DLL" | Set-Content "$CONDA_ENV\etc\conda\activate.d\env_vars.bat"
"set PYTHONHOME=$CONDA_ENV" | Add-Content "$CONDA_ENV\etc\conda\activate.d\env_vars.bat"
# "set NRN_PYLIB=$script:PYTHON_DLL" | Set-Content "$CONDA_ENV\etc\conda\activate.d\env_vars.bat"
"set PYTHONPATH=$script:NEURON_PATH\lib\python" | Add-Content "$CONDA_ENV\etc\conda\activate.d\env_vars.bat"
"export PYTHONPATH=/c/nrn/lib/python" | Add-Content "$CONDA_ENV\etc\conda\activate.d\env_vars.sh"
}
else {
Write-Host "Miniconda hnn environment already exists"
Expand All @@ -433,27 +449,6 @@ else {

}


if ($proc2) {
Write-Host "Waiting for NEURON install to finish..."
$proc2.WaitForExit() 2>$null
Update-User-Paths("$script:NEURON_PATH\bin")
Write-Host "NEURON is finished"
}

if (!(Test-Path "$HNN_PATH\nrnmech.dll" -PathType Leaf)) {
Write-Host "Creating nrnmech.dll"
Set-Location $HNN_PATH\mod
Start-Process "$script:NEURON_PATH\mingw\usr\bin\sh.exe" "$script:NEURON_ESC_PATH/lib/mknrndll.sh C:\nrn\"
$obj = New-Object -com Wscript.Shell
sleep -s 10
$obj.SendKeys("{ENTER}")
Copy-Item $HNN_PATH\mod\nrnmech.dll -Destination $HNN_PATH
}
else {
Write-Host "nrnmech.dll already exists $HNN_PATH\nrnmech.dll"
}

Write-Host ""
Write-Host "Finished installing HNN and prerequisites."
Write-Host "Activate the environment from cmd.exe (not Powershell):"
Expand Down

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