From a46f685ff2e7a607a422c9c32e60a04049bee017 Mon Sep 17 00:00:00 2001
From: Nicolas <Nicolas@nonan.net>
Date: Thu, 5 May 2022 10:41:19 +0200
Subject: [PATCH] clean up, adding "set -e"

---
 jupyterhub_config.py |  7 +++-
 setup_apps.sh        | 75 +++++++++++++++++++++++++-----------
 setup_bcache.sh      | 68 +++++++++++++++++---------------
 setup_cuda.sh        | 92 ++++++++++++++++++++++----------------------
 4 files changed, 144 insertions(+), 98 deletions(-)

diff --git a/jupyterhub_config.py b/jupyterhub_config.py
index 38ffd64..9f6dea5 100644
--- a/jupyterhub_config.py
+++ b/jupyterhub_config.py
@@ -1,3 +1,8 @@
+c.JupyterHub.bind_url = 'http://:8000/deepserv'
+
+
+
+
 # Configuration file for jupyterhub.
 
 #------------------------------------------------------------------------------
@@ -141,7 +146,7 @@
 #          This is the address on which the proxy will bind.
 #          Sets protocol, ip, base_url
 #  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.
 #  
diff --git a/setup_apps.sh b/setup_apps.sh
index ae8e8d6..df01d4c 100644
--- a/setup_apps.sh
+++ b/setup_apps.sh
@@ -1,4 +1,5 @@
 #!/bin/bash
+set -e
 
 if [ "$EUID" -ne 0 ]
   then echo "Please run as root"
@@ -15,32 +16,62 @@ if [ ! -s "~/.ssh/authorized_keys" ]; then
 fi
 
 echo ""
-echo "Install and config python & jupyter..."
-apt-get update && \
-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 && \
-apt-add-repository -y ppa:cantera-team/cantera && \
-apt-get install -y cantera-python3 && \
-python3 -m pip install jupyterhub && \
-npm install -g configurable-http-proxy && \
-python3 -m pip install jupyterlab notebook jupyterlab-git tensorflow-gpu && \
-python3 -m pip install h5py tqdm pandas ipywidgets pillow matplotlib && \
-python3 -m pip install scipy scikit-learn && \
-mkdir /etc/jupyterhub/ && \
-cp jupyterhub_config.py /etc/jupyterhub/jupyterhub_config.py && \
-cp jupyterhub.service /etc/systemd/system/jupyterhub.service && \
-systemctl enable jupyterhub && \
+echo "Install supermicro system tools..."
+apt-get update
+apt-get install -y ipmitool && modprobe ipmi_devintf
+
+echo "Install a recent notejs for jupyterhub from nodesource..."
+curl -fsSL https://deb.nodesource.com/setup_current.x | bash -
+apt-get install -y nodejs npm
+
+echo "Install JupyterHub..."
+apt-get install -y language-pack-de python3-pip
+python3 -m pip install jupyterhub
+npm install -g configurable-http-proxy
+python3 -m pip install jupyterlab notebook jupyterlab-git
+jupyter labextension install @jupyterlab/server-proxy
+
+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
 
+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 "check nvidia drivers..."
-  nvidia-smi
+echo "show gpu state..."
+nvidia-smi
+
+echo ""
+echo "Setup successfully finished"
 
-  echo ""
-  echo "Setup successfully finished"
-fi
 
 
diff --git a/setup_bcache.sh b/setup_bcache.sh
index 74de33e..2810e7d 100644
--- a/setup_bcache.sh
+++ b/setup_bcache.sh
@@ -12,10 +12,15 @@ ssddev=/dev/sdb
 #Block device to use with cache:
 hdddev=/dev/sdc
 
-#Cache sequential writes files, no cutoff
-#There is an issue with parsing of prefixes, max 4 GB
+#Name of the mounted device:
+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
 
+set -e
+
 if [ "$EUID" -ne 0 ]; then
   echo "Please run as root"
   exit
@@ -32,39 +37,42 @@ while [ -b /dev/bcache0 ]; then
   exit
 fi
 
+echo
 echo "Clean disks and setup bcache... "
-dd if=/dev/zero of=$ssddev bs=512 count=8 && \
-dd if=/dev/zero of=$hdddev bs=512 count=8 && \
-wipefs -a $ssddev && \
-wipefs -a $hdddev && \
-apt-get update && \
-apt-get install -y bcache-tools && \
+dd if=/dev/zero of=$ssddev bs=512 count=8
+dd if=/dev/zero of=$hdddev bs=512 count=8
+wipefs -a $ssddev
+wipefs -a $hdddev
+apt-get update
+apt-get install -y bcache-tools
 make-bcache -C $ssddev -B $hdddev --writeback
 
+echo
 echo "Wait until device is ready... "
 while [ ! -b /dev/bcache0 ]; do sleep 1; done
 
-if [ $? -eq 0 ]; then
-  echo "Config, format and mount bcache device... "
-  echo $sequential_cutoff > /sys/block/bcache0/bcache/sequential_cutoff && \
-  echo "ACTION==\"add\", SUBSYSTEM==\"block\", ENV{MAJOR}==\"252\", ATTR{bcache/sequential_cutoff}=\"$sequential_cutoff\"" \
-  > /etc/udev/rules.d/99-bcache_sequential_cutoff.rules && \
-  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
+echo
+echo "Config bcache device... "
+echo $sequential_cutoff > /sys/block/bcache0/bcache/sequential_cutoff
+echo "ACTION==\"add\", SUBSYSTEM==\"block\", ENV{MAJOR}==\"252\", ATTR{bcache/sequential_cutoff}=\"$sequential_cutoff\"" \
+  > /etc/udev/rules.d/99-bcache_sequential_cutoff.rules
+udevadm test /sys/block/bcache0
 
-if [ $? -eq 0 ]; then
-  echo "Config default home directory for new users on bcache partition... "
-  mkdir /mnt/bcache/home && \
-  echo "#" >> /etc/default/useradd && \
-  echo "# Modifications:" >> /etc/default/useradd && \
-  echo "HOME=/mnt/bcache/home" >> /etc/default/useradd
-fi
+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 "home path of exising users will not be moved automaticaly"
+mkdir $mountname/home
+echo "#" >> /etc/default/useradd
+echo "# Modifications:" >> /etc/default/useradd
+echo "HOME=$mountname/home" >> /etc/default/useradd
+
+echo
+echo "Setup successfully finished"
 
-if [ $? -eq 0 ]; then
-  echo ""
-  echo "Setup successfully finished"
-fi
diff --git a/setup_cuda.sh b/setup_cuda.sh
index 2b28332..72383cf 100644
--- a/setup_cuda.sh
+++ b/setup_cuda.sh
@@ -15,6 +15,8 @@
 #sudo apt-get autoremove
 #------------------------------------
 
+set -e
+
 if [ "$EUID" -ne 0 ]
   then echo "Please run as root"
   exit
@@ -23,56 +25,56 @@ fi
 distribution=$(. /etc/os-release;echo $ID$VERSION_ID | sed -e 's/\.//g')
 architecture="x86_64"
 
-echo ""
-echo "Disable cloud-init..."
+#echo
+#echo "Disable cloud-init..."
 #this is optional, not a requirement
-touch /etc/cloud/cloud-init.disabled
+#touch /etc/cloud/cloud-init.disabled
 
-echo ""
-echo "Install requirements..."
-apt-get update && \
+echo
+echo "Install pre-requirements..."
+apt-get update
 apt-get install -y linux-headers-$(uname -r) software-properties-common
 
-if [ $? -eq 0 ]; then
-  echo ""
-  echo "Setup the CUDA repository public GPG key..."
-  apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/7fa2af80.pub && \
-  wget https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/cuda-$distribution.pin && \
-  mv cuda-$distribution.pin /etc/apt/preferences.d/cuda-repository-pin-600
-  #add-apt-repository contrib
-fi
 
-if [ $? -eq 0 ]; then
-  echo ""
-  echo "Setup the CUDA network repository..."
-  add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/ /"
-fi
+echo
+echo "Setup the CUDA repository public GPG key..."
+apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/7fa2af80.pub
+wget https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/cuda-$distribution.pin
+mv cuda-$distribution.pin /etc/apt/preferences.d/cuda-repository-pin-600
+#add-apt-repository contrib
 
-if [ $? -eq 0 ]; then
-  echo ""
-  echo "install CUDA..."
-  #Installs CUDA Toolkit and Driver 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
-  apt-get update && \
-  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 [ $? -eq 0 ]; then
-  echo ""
-  echo "Setup successfully finished"
-  echo "Type \"sudo systemctl reboot\" to reboot system for loading GPU drivers)"
-fi
+echo
+echo "Setup the CUDA network repository..."
+add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/$distribution/$architecture/ /"
+
+
+
+echo
+echo "Install CUDA..."
+#Installs CUDA Toolkit and Driver 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
+apt-get update
+apt-get install -y --no-install-recommends cuda-11-2
+
+
+
+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 "Type \"sudo systemctl reboot\" to reboot system for loading GPU drivers)"
+