nicolas
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gpu_server_setup
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clean up, adding "set -e"

This commit is contained in:
Nicolas 2022-05-05 10:41:19 +02:00
parent 0d573fce40
commit a46f685ff2
4 changed files with 144 additions and 98 deletions
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7
jupyterhub_config.py
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@ -1,3 +1,8 @@
c.JupyterHub.bind_url = 'http://:8000/deepserv'
# Configuration file for jupyterhub. # Configuration file for jupyterhub.
#------------------------------------------------------------------------------ #------------------------------------------------------------------------------
@ -141,7 +146,7 @@
# This is the address on which the proxy will bind. # This is the address on which the proxy will bind.
# Sets protocol, ip, base_url # Sets protocol, ip, base_url
# Default: 'http://:8000' # Default: 'http://:8000'
c.JupyterHub.bind_url = 'http://:8000/deepserv' #c.JupyterHub.bind_url = 'http://:8000'
## Whether to shutdown the proxy when the Hub shuts down. ## Whether to shutdown the proxy when the Hub shuts down.
# #

69
setup_apps.sh
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@ -1,4 +1,5 @@
#!/bin/bash #!/bin/bash
set -e
if [ "$EUID" -ne 0 ] if [ "$EUID" -ne 0 ]
then echo "Please run as root" then echo "Please run as root"
@ -15,32 +16,62 @@ if [ ! -s "~/.ssh/authorized_keys" ]; then
fi fi
echo "" echo ""
echo "Install and config python & jupyter..." echo "Install supermicro system tools..."
apt-get update && \ apt-get update
apt-get install -y ipmitool && modprobe ipmi_devintf && \ apt-get install -y ipmitool && modprobe ipmi_devintf
curl -fsSL https://deb.nodesource.com/setup_current.x | bash - \
apt-get install -y python3-pip nodejs npm git && \ echo "Install a recent notejs for jupyterhub from nodesource..."
apt-add-repository -y ppa:cantera-team/cantera && \ curl -fsSL https://deb.nodesource.com/setup_current.x | bash -
apt-get install -y cantera-python3 && \ apt-get install -y nodejs npm
python3 -m pip install jupyterhub && \
npm install -g configurable-http-proxy && \ echo "Install JupyterHub..."
python3 -m pip install jupyterlab notebook jupyterlab-git tensorflow-gpu && \ apt-get install -y language-pack-de python3-pip
python3 -m pip install h5py tqdm pandas ipywidgets pillow matplotlib && \ python3 -m pip install jupyterhub
python3 -m pip install scipy scikit-learn && \ npm install -g configurable-http-proxy
mkdir /etc/jupyterhub/ && \ python3 -m pip install jupyterlab notebook jupyterlab-git
cp jupyterhub_config.py /etc/jupyterhub/jupyterhub_config.py && \ jupyter labextension install @jupyterlab/server-proxy
cp jupyterhub.service /etc/systemd/system/jupyterhub.service && \
systemctl enable jupyterhub && \ echo "Setup JupyterHub..."
mkdir /etc/jupyterhub/
cp jupyterhub_config.py /etc/jupyterhub/jupyterhub_config.py
cp jupyterhub.service /etc/systemd/system/jupyterhub.service
systemctl enable jupyterhub
systemctl start jupyterhub systemctl start jupyterhub
echo "Install Tensorflow..."
python3 -m pip install tensorflow-gpu
echo "Install cantera..."
apt-add-repository -y ppa:cantera-team/cantera
apt-get install -y cantera-python3
echo "Install common Python libs..."
python3 -m pip install h5py tqdm pandas ipywidgets pillow matplotlib opencv-python
#python3 -m pip install scipy scikit-learn numba
#System monitoring
#echo "Install netdata..."
#wget -O /tmp/netdata-kickstart.sh https://my-netdata.io/kickstart.sh && sh /tmp/netdata-kickstart.sh
#echo "nvidia_smi: yes" >> /usr/lib/netdata/conf.d/python.d.conf
#service netdata restart
#on http://0.0.0.0:19999
echo "Install gpuview..."
python3 -m pip install gpuview
gpuview service --host 127.0.0.1 --port 9988
echo "Disable services that delays startup by wating for network connectivity..."
systemctl disable cloud-config
systemctl disable cloud-final.service
systemctl disable iscsid.service
systemctl disable open-iscsi.service
if [ $? -eq 0 ]; then echo "show gpu state..."
echo "check nvidia drivers..."
nvidia-smi nvidia-smi
echo "" echo ""
echo "Setup successfully finished" echo "Setup successfully finished"
fi

62
setup_bcache.sh
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@ -12,10 +12,15 @@ ssddev=/dev/sdb
#Block device to use with cache: #Block device to use with cache:
hdddev=/dev/sdc hdddev=/dev/sdc
#Cache sequential writes files, no cutoff #Name of the mounted device:
#There is an issue with parsing of prefixes, max 4 GB mountname=/mnt/bcache
#Cache setting for sequential writes
#There is an issue with parsing prefixes, max 4 GB, use 0 for no cutoff
sequential_cutoff=0 sequential_cutoff=0
set -e
if [ "$EUID" -ne 0 ]; then if [ "$EUID" -ne 0 ]; then
echo "Please run as root" echo "Please run as root"
exit exit
@ -32,39 +37,42 @@ while [ -b /dev/bcache0 ]; then
exit exit
fi fi
echo
echo "Clean disks and setup bcache... " echo "Clean disks and setup bcache... "
dd if=/dev/zero of=$ssddev bs=512 count=8 && \ dd if=/dev/zero of=$ssddev bs=512 count=8
dd if=/dev/zero of=$hdddev bs=512 count=8 && \ dd if=/dev/zero of=$hdddev bs=512 count=8
wipefs -a $ssddev && \ wipefs -a $ssddev
wipefs -a $hdddev && \ wipefs -a $hdddev
apt-get update && \ apt-get update
apt-get install -y bcache-tools && \ apt-get install -y bcache-tools
make-bcache -C $ssddev -B $hdddev --writeback make-bcache -C $ssddev -B $hdddev --writeback
echo
echo "Wait until device is ready... " echo "Wait until device is ready... "
while [ ! -b /dev/bcache0 ]; do sleep 1; done while [ ! -b /dev/bcache0 ]; do sleep 1; done
if [ $? -eq 0 ]; then echo
echo "Config, format and mount bcache device... " echo "Config bcache device... "
echo $sequential_cutoff > /sys/block/bcache0/bcache/sequential_cutoff && \ echo $sequential_cutoff > /sys/block/bcache0/bcache/sequential_cutoff
echo "ACTION==\"add\", SUBSYSTEM==\"block\", ENV{MAJOR}==\"252\", ATTR{bcache/sequential_cutoff}=\"$sequential_cutoff\"" \ echo "ACTION==\"add\", SUBSYSTEM==\"block\", ENV{MAJOR}==\"252\", ATTR{bcache/sequential_cutoff}=\"$sequential_cutoff\"" \
> /etc/udev/rules.d/99-bcache_sequential_cutoff.rules && \ > /etc/udev/rules.d/99-bcache_sequential_cutoff.rules
udevadm test /sys/block/bcache0 && \ udevadm test /sys/block/bcache0
mkfs.ext4 /dev/bcache0 && \
mkdir /mnt/bcache && \
mount /dev/bcache0 /mnt/bcache && \
echo "/dev/bcache0 /mnt/bcache ext4 rw 0 0" >> /etc/fstab
fi
if [ $? -eq 0 ]; then echo
echo "Format and mount bcache device..."
mkfs.ext4 /dev/bcache0
mkdir $mountname
mount /dev/bcache0 $mountname
echo "/dev/bcache0 $mountname ext4 rw 0 0" >> /etc/fstab
echo
echo "Config default home directory for new users on bcache partition... " echo "Config default home directory for new users on bcache partition... "
mkdir /mnt/bcache/home && \ echo "home path of exising users will not be moved automaticaly"
echo "#" >> /etc/default/useradd && \ mkdir $mountname/home
echo "# Modifications:" >> /etc/default/useradd && \ echo "#" >> /etc/default/useradd
echo "HOME=/mnt/bcache/home" >> /etc/default/useradd echo "# Modifications:" >> /etc/default/useradd
fi echo "HOME=$mountname/home" >> /etc/default/useradd
if [ $? -eq 0 ]; then echo
echo ""
echo "Setup successfully finished" echo "Setup successfully finished"
fi

70
setup_cuda.sh
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@ -15,6 +15,8 @@
#sudo apt-get autoremove #sudo apt-get autoremove
#------------------------------------ #------------------------------------
set -e
if [ "$EUID" -ne 0 ] if [ "$EUID" -ne 0 ]
then echo "Please run as root" then echo "Please run as root"
exit exit
@ -23,56 +25,56 @@ fi
distribution=$(. /etc/os-release;echo $ID$VERSION_ID | sed -e 's/\.//g') distribution=$(. /etc/os-release;echo $ID$VERSION_ID | sed -e 's/\.//g')
architecture="x86_64" architecture="x86_64"
echo "" #echo
echo "Disable cloud-init..." #echo "Disable cloud-init..."
#this is optional, not a requirement #this is optional, not a requirement
touch /etc/cloud/cloud-init.disabled #touch /etc/cloud/cloud-init.disabled
echo "" echo
echo "Install requirements..." echo "Install pre-requirements..."
apt-get update && \ apt-get update
apt-get install -y linux-headers-$(uname -r) software-properties-common apt-get install -y linux-headers-$(uname -r) software-properties-common
if [ $? -eq 0 ]; then
echo "" echo
echo "Setup the CUDA repository public GPG key..." echo "Setup the CUDA repository public GPG key..."
apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/7fa2af80.pub && \ apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/7fa2af80.pub
wget https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/cuda-$distribution.pin && \ wget https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/cuda-$distribution.pin
mv cuda-$distribution.pin /etc/apt/preferences.d/cuda-repository-pin-600 mv cuda-$distribution.pin /etc/apt/preferences.d/cuda-repository-pin-600
#add-apt-repository contrib #add-apt-repository contrib
fi
if [ $? -eq 0 ]; then
echo ""
echo
echo "Setup the CUDA network repository..." echo "Setup the CUDA network repository..."
add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/ /" add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/ /"
fi
if [ $? -eq 0 ]; then
echo ""
echo "install CUDA..." echo
echo "Install CUDA..."
#Installs CUDA Toolkit and Driver packages. #Installs CUDA Toolkit and Driver packages.
#Use the --no-install-recommends option should prevent install any dependencies on X packages #Use the --no-install-recommends option should prevent install any dependencies on X packages
#It still installes alot of dependencies, but fortunately it seams not to setup x-server #It still installes alot of dependencies, but fortunately it seams not to setup x-server
apt-get update && \ apt-get update
apt-get install -y --no-install-recommends cuda-11-2 apt-get install -y --no-install-recommends cuda-11-2
fi
if [ $? -eq 0 ]; then
echo ""
echo "install libcudnn8..."
#Latest available version from nvidia ubuntu1804 repo
#For the current Ubuntu version it was not available. But it seams to work anyway.
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/libcudnn8_8.1.1.33-1+cuda11.2_amd64.deb && \
apt-get install -y ./libcudnn8_8.1.1.33-1+cuda11.2_amd64.deb && \
rm ./libcudnn8_8.1.1.33-1+cuda11.2_amd64.deb && \
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/libcudnn8-dev_8.1.1.33-1+cuda11.2_amd64.deb && \
apt-get install -y ./libcudnn8-dev_8.1.1.33-1+cuda11.2_amd64.deb && \
rm ./libcudnn8-dev_8.1.1.33-1+cuda11.2_amd64.deb
fi
if [ $? -eq 0 ]; then
echo "" echo
echo "Install libcudnn..."
apt-get install -y libcudnn8_8.1.1.33-1+cuda11.2 libcudnn8-dev_8.1.1.33-1+cuda11.2
#get an other version:
#wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/libcudnn8_8.1.1.33-1+cuda11.2_amd64.deb
#apt-get install -y ./libcudnn8_8.1.1.33-1+cuda11.2_amd64.deb
#rm ./libcudnn8_8.1.1.33-1+cuda11.2_amd64.deb
#wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu1804/x86_64/libcudnn8-dev_8.1.1.33-1+cuda11.2_amd64.deb
#apt-get install -y ./libcudnn8-dev_8.1.1.33-1+cuda11.2_amd64.deb
#rm ./libcudnn8-dev_8.1.1.33-1+cuda11.2_amd64.deb
echo
echo "Setup successfully finished" echo "Setup successfully finished"
echo "Type \"sudo systemctl reboot\" to reboot system for loading GPU drivers)" echo "Type \"sudo systemctl reboot\" to reboot system for loading GPU drivers)"
fi