du -sh * | sort -h

mkdir -p /data2/users/${USER}
mv ~/.conda /data2/users/${USER}/      # If you already have ~/.conda
mkdir -p /data2/users/${USER}/.conda   # If you do not have ~/.conda
ln -s /data2/users/${USER}/.conda ~/

md5 ~/Downloads/lubuntu-18.04-alternate-i386.iso

!ssh swan cat /proc/cpuinfo

!ssh swan lsb_release -a

!ssh swan nvidia-smi -q

!ssh swan "uname -m && cat /etc/*release"

!ssh swan "uname -m && cat /etc/*release"

sudo apt-get install openssh-server

sudo apt-get update
sudo apt-get install hg etckeeper
sudo etckeeper init

sudo apt update
sudo apt install aptitude

sudo aptitude update
sudo aptitude upgrade
sudo aptitude install -y                                                        \
     fail2ban   # Limits failed logins - 10min wait after 3 fails              \
     wget                                                                      \
     subversion git                                                            \
     #mercurial                                                  \
     duply  # Backup                                                           \
     python3 python3-pip                                                       \
     etckeeper   # Version control /etc                                        \
     bzr                                                                       \
     environment-modules                                                       \
     myrepos                                                                   \
     libfftw3-dev swig                                                         \
     gfortran libopenmpi-dev openmpi-common openmpi-bin   # MCTDH-X            \
     gsl-bin                                                                   \
     pandoc                                                                    \
     emacs                                                                     \
     gnuplot                                                                   \
     smbclient   # To connect to remote drives using smb.  I use for backup    \
     apache2 npm                                                               \
     ffmpeg mencoder      # To make movies and animations                      \
     xvfb        # Virtual frame buffer for X11.  Required for headless Mayavi \
     ocl-icd-opencl-dev   # For OpenCL                                         \
     apt-rdepends         # For visualizing software dependencies              \
     iperf3               # Profiling nenwork behaviour                        \
     libcrypto++6         # Needed by the bbcp tool                            \
     tigervnc-standalone-server tigervnc-common                                \
     uidmap dbus-user-session # Needed for docker rootless                     \
     awscli

# The following are for OneDrive Free Client github.com/skilion/onedrive
sudo aptitude install -y libcurl4-openssl-dev libsqlite3-dev
sudo snap install --classic dmd && sudo snap install --classic dub

# Evolve extension for system mercurial.  As of June 2020 Ubuntu does not support
# Mercurial with python 3, so we install this manually.
#sudo -H /usr/bin/pip3 install --upgrade mercurial hg-evolve hg-git

#DOES NOT WORK YET...
sudo aptitude install -y python2 python2-dev
curl https://bootstrap.pypa.io/get-pip.py --output get-pip.py
sudo /usr/bin/python2 get-pip.py
rm get-pip.py
sudo -H /usr/local/bin/pip2 install --upgrade mercurial==5.2 hg-evolve hg-git dulwich==0.19.16

sudo adduser admin
sudo mkdir /data
sudo chown admin /data

su admin
mkdir -p /data/src/
wget http://repo.continuum.io/miniconda/Miniconda-latest-Linux-x86_64.sh /data/src/
bash Miniconda-latest-Linux-x86_64.sh -p /data/apps/conda -b -f
export PATH="/data/apps/conda/bin:$PATH"

su admin
export PATH="/data/apps/conda/bin:$PATH"
conda install mercurial
conda update -y --all
pip install hg-git python-hglib
hg clone https://bitbucket.org/marmoute/mutable-history -u stable /data/src/hg/mutable-history
pip install /data/src/hg/mutable-history

su admin
export PATH="/data/apps/conda/bin:$PATH"
conda env create mforbes/work

module load cuda  # See below - install cuda and the module files first
for _e in work; 
  do . activate $_e
  pip install pycuda \
              scikit-cuda
done

$ groups
mforbes adm cdrom sudo dip plugdev lpadmin sambashare students

sudo mkdir /data/shared
sudo mkdir /data2/shared
sudo chown :students -R /data/shared
sudo chmod a-rwx,g+rwsX -R /data/shared
sudo chown :students -R /data2/shared
sudo chmod a-rwx,g+rwsX -R /data2/shared

sudo mkdir /data/users
sudo mkdir /data2/users
sudo chown :students -R /data/users
sudo chmod a-rwx,g+rwx -R /data/users
sudo chown :students -R /data2/users
sudo chmod a-rwx,g+rwx -R /data2/users

mkdir -p ~/work/mmfbb
mkdir ~/current

hg clone ssh://hg@bitbucket.org/mforbes/configurations ~/work/mmfbb/configurations
export PATH="$(cd ~/work/mmfbb/configurations/scripts && pwd):$PATH"
cd ~/work/mmfbb/configurations/common && mmf_initial_setup -v
cd ~/work/mmfbb/configurations/machines/generic && mmf_initial_setup -v
cd ~/work/mmfbb/configurations/machines/linux/common && mmf_initial_setup -v
cd ~/work/mmfbb/configurations/personal/mmf && mmf_initial_setup -v

ln -s /data/apps/conda ~/.anaconda

# Think about this: it should be done at a system level.
#hg clone ssh://[email protected]/mforbes/mmfhg ~/work/mmfbb/mmfhg
#cd ~/work/mmfbb/mmfhg && make install

do-release-upgrade

$ sudo do-release-upgrade 
Checking for a new Ubuntu release
Your Ubuntu release is not supported anymore.
For upgrade information, please visit:
http://www.ubuntu.com/releaseendoflife
...
An upgrade from 'cosmic' to 'eoan' is not supported with this tool.

$ screen -S Backup
$ sudo rsync -vaxhWE --no-compress --progress --delete --ignore-errors / /mnt/data2/swan_backup/13May2020

$ lsb_release -a
...
Description:	Ubuntu 18.10
Release:	18.10
Codename:	cosmic

deb http://archive.ubuntu.com/ubuntu focal main restricted universe
deb http://archive.ubuntu.com/ubuntu focal-security main restricted universe
deb http://archive.ubuntu.com/ubuntu focal-backports main restricted universe
deb http://archive.ubuntu.com/ubuntu focal-updates main restricted universe

$ cd /boot
$ uname -a
Linux swan 4.18.0-25-generic #26-Ubuntu SMP Mon Jun 24 09:32:08 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux
$ ls -la
...
$ rm ...  # Remove anything that is not 4.18.0-25*

$ conda deactivate   # Don't use my custom python kernels.
$ sudo apt-get update
...
$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
The following packages have been kept back:
  linux-generic linux-headers-generic linux-image-generic
0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
$ sudo apt-get dist-upgrade

[ui]
#ignore.mmfhg = ${MMFHG}/hgignore
[extensions]
#evolve=
#hggit =

$ service atd stop
...
polkit-agent-helper-1: needs to be setuid root
Error: Incorrect permissions on /usr/lib/policykit-1/polkit-agent-helper-1 (needs to be setuid root)
$ sudo chmod 5755 /usr/lib/policykit-1/polkit-agent-helper-1 
$ service atd stop
$ systemctl daemon-reexec

$ sudo vgck --updatemetadata lubuntu-vg

$ sudo rm -i /boot/*22*

$ sudo apt autoremove

$ sudo shutdown -r now

$ sudo rm /var/lib/ubuntu-release-upgrader/release-upgrade-available 

$ sudo do-release-upgrade 
Checking for a new Ubuntu release
Your Ubuntu release is not supported anymore.
For upgrade information, please visit:
http://www.ubuntu.com/releaseendoflife

$ lsb_release -a
...
Description:	Ubuntu 18.10
Release:	18.10
Codename:	cosmic

deb http://old-releases.ubuntu.com/ubuntu/ cosmic main restricted universe multiverse
deb http://old-releases.ubuntu.com/ubuntu/ cosmic-updates main restricted universe multiverse
deb http://old-releases.ubuntu.com/ubuntu/ cosmic-security main restricted universe multiverse

$ sudo apt-get update
...
$ sudo apt-get upgrade
Reading package lists... Done
Building dependency tree       
Reading state information... Done
Calculating upgrade... Done
The following packages have been kept back:
  linux-generic linux-headers-generic linux-image-generic
0 upgraded, 0 newly installed, 0 to remove and 3 not upgraded.
$ sudo apt-get upgrade linux-generic linux-headers-generic linux-image-generic
...
$ sudo apt autoremove

sudo apt update && sudo apt dist-upgrade
sudo vi /etc/update-manager/release-upgrades  # Change Prompt=lts to Prompt=normal
sudo apt install update-manager-core
do-release-upgrade

conda install cupy

sudo apt-get install nvidia-visual-profiler nvidia-cuda-toolkit

sudo add-apt-repository ppa:graphics-drivers/ppa

$ lsb_release -a
No LSB modules are available.
Distributor ID:	Ubuntu
Description:	Ubuntu 18.10
Release:	18.10
Codename:	cosmic
$ uname -a
Linux swan 4.18.0-22-generic #23-Ubuntu SMP Tue Jun 4 20:22:46 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

# As of 12 May 2022
# Optional: remove old versions
sudo apt-get purge "^cuda" "^nvidia" "^libnvidia" "^libcuda"
sudo apt-get autoremove

# Optional: Update packages
sudo apt-get update
sudo apt-get upgrade

# Current instructions for 20.04 LTS
wget https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/cuda-ubuntu2004.pin
sudo mv cuda-ubuntu2004.pin /etc/apt/preferences.d/cuda-repository-pin-600
sudo apt-key adv --fetch-keys https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/3bf863cc.pub

# The following adds line sto /etc/apt/sources.list
sudo add-apt-repository "deb https://developer.download.nvidia.com/compute/cuda/repos/ubuntu2004/x86_64/ /"
sudo apt-get update
sudo apt-get -y install cuda

# Restart as suggested
#sudo shutdown -r now

Older still

Note: CUDA does not work with this by default since it requires ``gcc-4.9``.  See the instructions here:

* http://askubuntu.com/questions/693145/installing-cuda-7-5-toolkit-on-ubuntu-15-10

Here is what I did:

```bash
sudo mkdir -p /opt/compiler_cuda
cd /opt/compiler_cuda
sudo ln -s /usr/bin/gcc-4.9 gcc
sudo ln -s /usr/bin/g++-4.9 g++
sudo ln -s /opt/compiler_cuda/gcc cc

sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-5 60 --slave /usr/bin/g++ g++ /usr/bin/g++-5
sudo update-alternatives --install /usr/bin/gcc gcc /usr/bin/gcc-4.9 50 --slave /usr/bin/g++ g++ /usr/bin/g++-4.9
sudo sh cuda_7.5.18_linux.run --silent --toolkit --override
sudo sh cuda_7.5.18_linux.run --silent --samples --override

wget http://developer.download.nvidia.com/compute/cuda/repos/ubuntu1410/x86_64/cuda-repo-ubuntu1410_7.0-28_amd64.deb
sudo dpkg -i cuda-repo-ubuntu1410_7.0-28_amd64.deb
sudo apt-get update
sudo apt-get install cuda

su admin
module load cuda  # See below - install cuda and the module files first
for _e in work2 work3; do
  . activate $_e
  pip install --upgrade ipdb pycuda scikit-cuda
done

$ dpkg -s cuda
Package: cuda
Status: install ok installed
Priority: optional
Section: multiverse/devel
Installed-Size: 25
Maintainer: cudatools <cudatools@nvidia.com>
Architecture: amd64
Version: 10.1.168-1
Depends: cuda-10-1 (>= 10.1.168)
Description: CUDA meta-package
 Meta-package containing all the available packages required for native CUDA
 development. Contains the toolkit, samples, driver and documentation.

sudo service --status-all

systemctl list-unit-files | grep enabled

sudo usermod --shell /bin/bash mforbes

/etc/profile
/etc/bash.bashrc

$ touch ~/.trace

$ ssh swan
Welcome to Ubuntu 18.10 (GNU/Linux 4.18.0-22-generic x86_64)
...
Welcome to Swan.

* To debug your startup configuration:
  $ touch ~/.trace    # rm ~/.trace when done
* To run jupyter use the j function:
  $ j MyNotebook.ipynb 
* For detailed instructions run
  $ j --help            # Show port and instructions
* Remember to activate the appropriate conda environment such as
  $ conda activate cugpe2

Last login: Sat Mar 21 14:59:58 2020 from 98.146.197.72
Tracing all sourced files...
/etc/profile
'/etc/bash.bashrc'
  /etc/profile.d/modules.sh
    '/etc/profile.d/modules.sh'
      '/usr/share/modules/init/bash'
        /usr/share/modules/init/bash_completion
          '/usr/share/modules/init/bash_completion'

NBPORT=18888: For more information run 'j --help'

  '/data/apps/conda/etc/profile.d/conda.sh'
  '/usr/share/bash-completion/bash_completion'
    ...
'/etc/profile.d/01-locale-fix.sh'
...
'/home/mforbes/.bash_login'
  ...

!mkdir -p _generated/linux_config/etc

%%file _generated/linux_config/etc/helper_functions
# Bash Helper Functions; -*-Shell-script-*-
# dest = /etc/helper_functions  # Keep this as the 2nd line for mmf_init_setup

# This file defines useful helper functions for adding elemnts to
# path-like variables without duplication.

shopt -s extglob

function source_if_exists() {            # Source file iff it exists.
    test -f "$1" && . $*
}

if [ -a ~/.trace ]; then
    # If there is a file ~/.trace, then we overload the source and . functions to
    # print the files that are sourced.
    declare -f source > /dev/null || {
        TRACE_INDENT=""
        echo "Tracing all sourced files..."
        echo "${BASH_ARGV[0]}"

        function source() {
            echo "$TRACE_INDENT$1"
            TRACE_INDENT="${TRACE_INDENT}  "
            source_if_exists $*
            TRACE_INDENT="${TRACE_INDENT:2}"
        }

        # Slightly different definition here - use . if you want an error reported
        # if the file does not exist.
        function .() {
            echo "$TRACE_INDENT'$*'"
            TRACE_INDENT="${TRACE_INDENT}  "
            builtin . $*
            TRACE_INDENT="${TRACE_INDENT:2}"
        }
    }
else
    alias source=source_if_exists
fi

function _prepend_path () {           # Prepends path $2 to $1
    local DIRTY_PATH=$2:${!1}         # Simple path for checking colons
    local TMP_PATH=:${!1%:}:          # Add leading and trailing colons
    TMP_PATH=:$2${TMP_PATH//:$2:/:}   # Do not duplicate
    TMP_PATH=${TMP_PATH//+(:)/:}      # Remove duplicate colons
    if [ -n "${DIRTY_PATH/#:*/}" ]; then
        TMP_PATH=${TMP_PATH#:}        # Remove leading colon
    fi
    if [ -n "${DIRTY_PATH/%*:/}" ]; then
        TMP_PATH=${TMP_PATH%:}        # Remove trailing colon
    fi
    export $1="$TMP_PATH"
}

function _append_path () {            # Appends path $2 to $1
    local DIRTY_PATH=${!1}:$2         # Simple path for checking colons
    local TMP_PATH=:${!1%:}:          # Add leading and trailing colons
    TMP_PATH=${TMP_PATH//:$2:/:}$2:   # Do not duplicate
    TMP_PATH=${TMP_PATH//+(:)/:}      # Remove duplicate colons
    if [ -n "${DIRTY_PATH/#:*/}" ]; then
        TMP_PATH=${TMP_PATH#:}        # Remove leading colon
    fi
    if [ -n "${DIRTY_PATH/%*:/}" ]; then
        TMP_PATH=${TMP_PATH%:}        # Remove trailing colon
    fi
    export $1="$TMP_PATH"
}

function clean_path () {        # Cleans up the specified path
    local DIRTY_PATH=${!1}      # Simple path for checking colons
    local IFS=:                 # Use : as word separator for paths
    local reversed_path
    local clean_path
    for dir in ${!1};           # Reverse the path so that resultant
    do                          # path list is in correct order
        reversed_path=$dir:$reversed_path
    done

    for dir in ${reversed_path}; # Clean the path
    do
        _prepend_path clean_path $dir
    done
    clean_path=:$clean_path:
    clean_path=${clean_path//+(:)/:} # Remove duplicate colons
    if [ -n "${DIRTY_PATH/#:*/}" ]; then
        clean_path=${clean_path#:}  # Remove leading colon
    fi
    if [ -n "${DIRTY_PATH/%*:/}" ]; then
        clean_path=${clean_path%:}  # Remove trailing colon
    fi
    export $1="$clean_path"
}

function _contains () {
    local pattern=":$1:"
    local target=$2

    case $pattern in
        *:$target:* ) return 1;;
        *           ) return 0;;
    esac
}

function _clean_path () {        # Cleans up the specified path
    echo "Cleaning..."
    export $1=`echo ${!1} | tr ":" "\n" | uniq | tr "\n" ":"`
}

function _clean_path () {        # Cleans up the specified path
    echo "Cleaning..."
    local DIRTY_PATH=${!1}
    local IFS=:                 # Use : as word separator for paths
    local clean_path
    for dir in ${!1};           # Reverse the path so that resultant
    do                          # path list is in correct order
        reversed_path=$dir:$reversed_path
    done
    for dir in ${reversed_path};
    do
        _contains "${clean_path}" "${dir}" && \
            clean_path="${clean_path}:${dir}"
    done
    export $1="$clean_path"
}

function clean_path () {
    local new_path=`/usr/bin/python3 -E -c \
'path="'"${!1}"'"
while "::" in path:
    path = path.replace("::",":")

clean=[]
for dir in path.split(":"):
    if dir not in clean:
        clean.append(dir)
clean = ":".join(clean)
if path.startswith(":"):
    clean = ":" + clean
if path.endswith(":"):
    clean = clean + ":"
print(clean)'`
    export $1="${new_path}"
}

function prepend_path () {            # Prepends path $2 to $1 and cleans
    export $1="$2:${!1}"
}

function append_path () {            # Appends path $2 to $1 and cleans
    export $1="${!1}:$2"
}

function prepend_and_clean_path () { # Prepends path $2 to $1 and cleans
    export $1="$2:${!1}"
    clean_path $1
}

function append_and_clean_path () {  # Appends path $2 to $1 and cleans
    export $1="${!1}:$2"
    clean_path $1
}

%%file _generated/linux_config/etc/profile
# /etc/profile: 
#dest = /etc/profile
# system-wide .profile file for the Bourne shell (sh(1)) and Bourne compatible shells 
# (bash(1), ksh(1), ash(1), ...).

if [ "$BASH" ] && [ "$BASH" != "/bin/sh" ]; then
  . /etc/helper_functions
fi

if [ "$PS1" ]; then
  if [ "$BASH" ] && [ "$BASH" != "/bin/sh" ]; then
    # The file bash.bashrc already sets the default PS1.
    # PS1='\h:\w\$ '
    if [ -f /etc/bash.bashrc ]; then
      . /etc/bash.bashrc
    fi
  else
    if [ "`id -u`" -eq 0 ]; then
      PS1='# '
    else
      PS1='$ '
    fi
  fi
fi

# The default umask is now handled by pam_umask.
# See pam_umask(8) and /etc/login.defs.

if [ -d /etc/profile.d ]; then
  for i in /etc/profile.d/*.sh; do
    if [ -r $i ]; then
      . $i
    fi
  done
  unset i
fi

%%file _generated/linux_config/etc/bash.bashrc
# System-wide .bashrc file for interactive bash(1) shells.
#dest = /etc/bash.bashrc

# The following is needed so that the source alias (which is aliased
# to source_if_exists) works in non-login shells.  See:
# http://stackoverflow.com/a/1615973/1088938
shopt -s expand_aliases

. /etc/helper_functions

# Setup Modules
# The files in /etc/profile.d/modules.sh do not get source for non-login
# shells, but the module command is often needed by these, so we include
# it explicitly here.
source /etc/profile.d/modules.sh

# Add my mercurial goodies for everyone.
export MMFHG=${MMFHG-"/data/apps/repositories/mmfhg"}

# Set the NBPORT variable for the user from /etc/nbports
export NBPORT=$(sed -n -e "s/${USER}: //p" /etc/nbports)
if [ -z "$NBPORT" ]; then
   # https://unix.stackexchange.com/a/132524/37813
   export NBPORT=$(python - <<END
import socket
s = socket.socket()
s.bind(("", 0))
print(s.getsockname()[1])
s.close()
END
)
   >&2 echo "Warning: ${USER} not in /etc/nbports.  Using random port ${NBPORT}"
fi

>&2 echo "NBPORT=${NBPORT}: For more information run 'j --help'"

j_help_message="\
Usage: j Notebook.ipynb

This will run the notebook with --port ${NBPORT}.
To view this on your laptop, use ssh to forward this port.
I.e. add this to your '~/.ssh/config' file on your laptop:

Host swannb
  HostName swan.physics.wsu.edu
  User ${USER}
  ForwardAgent yes
  LocalForward 10001 localhost:10001
  LocalForward 10002 localhost:10002
  LocalForward 10003 localhost:10003
  LocalForward ${NBPORT} localhost:${NBPORT}
  # The following is for snakeviz
  LocalForward 8080 localhost:8080

If you subsequently connect with 'ssh swannb', then you can 
view the notebook on your laptop at 

http://localhost:${NBPORT}/tree

(but use the link specified by Jupyter as it contains a required
security token.)

Conda Environments
==================
Please create your own conda environments for your work
from an environment.yml file for reproducible computing.
These environments will be stored in ~/.conda/envs/ and
will appear as special Kernels when Jupyter notebooks are
run.  Here is a sample environment.mpl3.yml file that
creates an environment with matplotlib and Python 3:

cat > environment.mpl3.yml <<EOF
name: mpl3
channels:
  - defaults
dependencies:
  - python=3
  - matplotlib
EOF

This can be installed with:

    conda env create --file environment.mpl3.yml

Now you can activate it (and should see it as a valid Kernel):

    conda activate mpl3

This is stored in the following directory:

    ~/.conda/envs/mpl3

Simply delete this to remove the environment:

    rm -rf ~/.conda/envs/mpl3

For more examples see

https://bitbucket.org/mforbes/configurations/src/trunk/anaconda/
"

# Function to open jupyter notebooks, reading local config files
# if they exist.
function j {
    if [ "$1" = "-h" -o "$1" = "--help" ]; then
        echo "${j_help_message}"
        return
    elif [ -f './jupyter_notebook_config.py' ]; then
        CONFIG_FLAG="--config=./jupyter_notebook_config.py"
    elif [ -f "$(hg root)/jupyter_notebook_config.py" ]; then
        CONFIG_FLAG="--config=$(hg root)/jupyter_notebook_config.py"
    else
       CONFIG_FLAG=""
    fi
    echo "conda activate jupyter"
    conda activate jupyter
    echo "jupyter notebook ${CONFIG_FLAG} --port ${NBPORT} $*"
    jupyter notebook "${CONFIG_FLAG}" --port ${NBPORT} "$*"
    conda deactivate
}

# To enable the settings / commands in this file for login shells as well,
# this file has to be sourced in /etc/profile.

# If not running interactively, don't do anything
[ -z "$PS1" ] && return

# check the window size after each command and, if necessary,
# update the values of LINES and COLUMNS.
shopt -s checkwinsize

# set variable identifying the chroot you work in (used in the prompt below)
if [ -z "${debian_chroot:-}" ] && [ -r /etc/debian_chroot ]; then
    debian_chroot=$(cat /etc/debian_chroot)
fi

# set a fancy prompt (non-color, overwrite the one in /etc/profile)
PS1='${debian_chroot:+($debian_chroot)}\u@\h:\w\$ '

# Commented out, don't overwrite xterm -T "title" -n "icontitle" by default.
# If this is an xterm set the title to user@host:dir
#case "$TERM" in
#xterm*|rxvt*)
#    PROMPT_COMMAND='echo -ne "\033]0;${USER}@${HOSTNAME}: ${PWD}\007"'
#    ;;
#*)
#    ;;
#esac

# enable bash completion in interactive shells
if ! shopt -oq posix; then
  if [ -f /usr/share/bash-completion/bash_completion ]; then
    . /usr/share/bash-completion/bash_completion
  elif [ -f /etc/bash_completion ]; then
    . /etc/bash_completion
  fi
fi

# sudo hint
if [ ! -e "$HOME/.sudo_as_admin_successful" ] && [ ! -e "$HOME/.hushlogin" ] ; then
    case " $(groups) " in *\ admin\ *|*\ sudo\ *)
    if [ -x /usr/bin/sudo ]; then
        cat <<EOF
To run a command as administrator (user "root"), use "sudo <command>".
See "man sudo_root" for details.

EOF
    fi
    esac
fi

# if the command-not-found package is installed, use it
if [ -x /usr/lib/command-not-found -o -x /usr/share/command-not-found/command-not-found ]; then
        function command_not_found_handle {
                # check because c-n-f could've been removed in the meantime
                if [ -x /usr/lib/command-not-found ]; then
                   /usr/lib/command-not-found -- "$1"
                   return $?
                elif [ -x /usr/share/command-not-found/command-not-found ]; then
                   /usr/share/command-not-found/command-not-found -- "$1"
                   return $?
                else
                   printf "%s: command not found\n" "$1" >&2
                   return 127
                fi
        }
fi

# Commandline History
export INPUTRC="${INPUTRC:-/etc/inputrc}"

!mkdir -p _generated/linux_config/usr/share/modules/modulefiles

%%file _generated/linux_config/usr/share/modules/modulefiles/conda
#%Module1.0
#dest = /usr/share/modules/modulefiles/conda
proc ModulesHelp { } {
    puts stderr "\tAdds Conda directory to the PATH (includes hg)."
}

module-whatis "Adds Conda to the PATH (includes hg)."

# Add to back too so that it is always available.  We use this to provide
# Mercurial for example which we install in the default environment
prepend-path PATH /data/apps/conda/bin
append-path PATH /data/apps/conda/bin/.
prepend-path DYLD_LIBRARY_PATH /data/apps/conda/lib

%%file _generated/linux_config/usr/share/modules/modulefiles/conda
#%Module1.0
#dest = /usr/share/modules/modulefiles/cuda
proc ModulesHelp { } {
    puts stderr "\tAdds CUDA directory to the PATH, CPATH etc."
}

module-whatis "Adds CUDA to your environment variable"

# Add to back too so that it is always available.  We use this to provide
# Mercurial for example which we install in the default environment
prepend-path    PATH            /usr/local/cuda/bin
prepend-path    LD_LIBRARY_PATH /usr/local/cuda/lib64
prepend-path    CPATH           /usr/local/cuda/include

sudo su admin
mkdir -p /data/apps/repositories/
hg clone https://mforbes@bitbucket.org/mforbes/mmfhg
cd mmfhg
make install
sudo ln -s /data/apps/repositories/mmfhg/hgrc /etc/mercurial/hgrc.d/mmfhg.rc

!mkdir -p _generated/linux_config/etc

%%file _generated/linux_config/etc/pip.conf
# Global PIP configuration
#dest = /etc/pip.conf
[global]
find-links = https://bitbucket.org/mforbes/mypi/

eval "$(register-python-argcomplete conda)"

conda deactivate   # Make sure you are in the base environment
conda install python=3 mercurial git-annex \
              nbstripout                   \
              conda-devenv conda-tree      \
              conda-verify conda-build anaconda-client
pip install --upgrade hg-evolve hg-git # Not yet available on conda for python=3?

# environment.cugpe2.yml
name: cugpe2

su admin
export PATH="/data/apps/conda/bin:$PATH"
conda create -y -n cugpe2 python=2
conda install -y -n cugpe2 numba \
                           jupyter \
                           scipy \
                           cudatoolkit \
                           numexpr \
                           matplotlib \
                           bokeh \
                           sympy \
                           theano \
                           docutils

. activate cugpe2
pip install ipdb \
            line_profiler \
            memory_profiler \
            snakeviz \
            uncertainties \
            pyfftw

module load cuda  # See below - install cuda and the module files first
pip install pycuda \
            scikit-cuda \
            nbopen

# Conda does not load the correct pexpect on Mac OS X, so do this
# https://github.com/ipython/ipython/issues/9065
# https://github.com/conda/conda/issues/2010
pip install -U pexpect

sudo apt-get install apache2

sudo apt-get update
sudo apt-get install tasksel
sudo tasksel install lamp-server

sudo mkdir /var/www/html/forbes
sudo chown mforbes /var/www/html/forbes
ln -s /var/www/html/forbes ~/www-forbes

sudo service apache2 restart

/etc/apache2/
|-- apache2.conf
|       `--  ports.conf
|-- mods-enabled
|       |-- *.load
|       `-- *.conf
|-- conf-enabled
|       `-- *.conf
`-- sites-enabled
        |-- 000-default.conf
        |-- 000-default-le-ssl.conf
        `*.conf

sudo apt update
sudo apt install software-properties-common
sudo add-apt-repository universe
#sudo add-apt-repository ppa:certbot/certbot
sudo apt update
sudo apt install certbot python3-certbot-apache
sudo certbot --apache
#sudo apt-add-repository -r ppa:certbot/certbot

E: The repository 'http://ppa.launchpad.net/certbot/certbot/ubuntu focal Release' does not have a Release file.

#/etc/letsencrypt/cli.ini
...
post-hook = chmod 0640 /etc/letsencrypt/archive/*/privkey*.pem && chmod g+rx /etc/letsencrypt/live /etc/letsencrypt/archive && chown -R root:ssl-cert /etc/letsencrypt/live /etc/letsencrypt/archive

sudo usermod -a -G ssl-cert mumble-server

sudo a2enmod headers

<!--/etc/apached2/mods-enabled/headers.conf-->
<Directory "/var/www/html/Public">
  Header set Access-Control-Allow-Origin "*"
</Directory>

sudo apachectl -t
sudo service apache2 reload

%%HTML
<iframe src="https://viewer.pyvista.org/?fileURL=https://swan.physics.wsu.edu/Public/papers/Mossman_2021/fig1.vtkjs"></iframe>

sudo apt-get install npm
su admin
sudo apt-get install build-essential git python-pip python-virtualenv libffi-dev python-dev
hg clone https://kallithea-scm.org/repos/kallithea
cd kallithea
conda create -n kallithea python=2
conda activate kallithea
pip install --upgrade .
mkdir -p "${CONDA_PREFIX}/etc/conda/activate.d"
echo "export LC_ALL='C.UTF-8'" >> "${CONDA_PREFIX}/etc/conda/activate.d/env_vars.sh"

su admin
conda activate kallithea
mkdir /data/kallithea
cd /data/kallithea
kallithea-cli config-create my.ini
kallithea-cli db-create -c my.ini  #Created with root path `/data/kallithea`, user `mforbes` etc.
kallithea-cli front-end-build
gearbox serve -c my.ini

ssh swan
sudo apt-get update
sudo apt-get upgrade
sudo apt-get install uidmap
sudo apt-get purge docker docker.io  # Remove old root-version of docker.
sudo apt-get autoremove --purge

sudo useradd -m docker
sudo usermod -aG sudo docker         # Enable sudo for docker.
sudo su docker
chsh -s /bin/bash
bash
curl -fsSL https://get.docker.com/rootless | sh

sudo loginctl enable-linger docker
systemctl --user start docker

...
# Docker install (rootless)
export PATH=/home/docker/bin:$PATH
export DOCKER_HOST=unix:///run/user/1017/docker.sock

sudo service docker stop
sudo systemctl disable docker
sudo apt-get remove docker 
#sudo rm /var/run/docker.sock /lib/systemd/system/docker.service

$ systemctl --user start docker
$ docker run hello-world
docker: Cannot connect to the Docker daemon at unix:///tmp/docker-1017/docker.sock. Is the docker daemon running?.
See 'docker run --help'.

ssh docker@swan                         # Login to swan as docker
echo 'export GITLAB_HOME="${HOME}/srv/heptapod' >> ~/.bashrc
sudo mkdir -p /data2/docker             # Make the data directory for docker
sudo chown docker /data2/docker         # Change owner...
sudo chmod a-wrx,u+rwxs /data2/docker   # ...and give appropriate permissions
mkdir -p /data2/docker/heptapod         # Now create the heptapod directory.
sudo ln -s /data2/docker/heptapod /srv/ # Link it to /srv/heptapod...
ln -s /data2/docker ~docker/srv         # ...and to the docker home directory.

docker pull octobus/heptapod
docker create                                            \
       --name heptapod-local                             \
       --restart always                                  \
       --hostname localhost                              \
       --publish 127.0.0.1:11080:80                       \
       --publish 127.0.0.1:11443:443                      \
       --publish 127.0.0.1:11022:22                       \
       --volume ${GITLAB_HOME}/config:/etc/gitlab        \
       --volume ${GITLAB_HOME}/logs:/var/log/gitlab      \
       --volume ${GITLAB_HOME}/data:/var/opt/gitlab      \
       octobus/heptapod

docker create                                            \
       --name heptapod-public                            \
       --restart always                                  \
       --hostname swan.physics.wsu.edu                   \
       --publish 11080:80                                 \
       --publish 11443:443                                \
       --publish 11022:22                                 \
       --volume ${GITLAB_HOME}/config:/etc/gitlab        \
       --volume ${GITLAB_HOME}/logs:/var/log/gitlab      \
       --volume ${GITLAB_HOME}/data:/var/opt/gitlab      \
       octobus/heptapod

docker start heptapod-local       # Use this in general.
#docker start heptapod-public      # Use this when needed.

cd ~/srv/heptapod
# For some reason, the following file is given rw permission only
# for the user in the docker image, so we can't back it up...
sudo chgrp docker config/heptapod.hgrc
sudo chmod g+rw config/heptapod.hgrc
hg init
cat > .hgignore <<EOF
syntax: glob

data/
logs/
EOF
hg add
hg com -m "Initial commit"

docker exec -it heptapod-public gitlab-ctl tail

docker exec -t heptapod-public gitlab-backup create

screen -S RCloneBackup
rclone sync -Pl repo_backups gwsu_backups:

#/etc/apache2/sites-enabled/000-default.conf 
<Virtualhost *:80>
    ...
    Redirect /heptapod http://swan.physics.wsu.edu:11080/
    Redirect /discourse http://swan.physics.wsu.edu:10080/    
</VirtualHost>

#/etc/apache2/sites-enabled/000-default-le-ssl.conf 
<Virtualhost *:443>
    ...
    Redirect /heptapod https://swan.physics.wsu.edu:11443/
    Redirect /discourse https://swan.physics.wsu.edu:10443/    
</VirtualHost>

sudo service apache2 restart

vi ~docker/srv/heptapod/config/gitlab.rb

#/etc/gitlab/gitlab.rb
gitlab_rails['omniauth_enabled'] = true
...
gitlab_rails['omniauth_providers'] = [
  {
    "name" => "bitbucket",
    "app_id" => "Rc...",
    "app_secret" => "hA...",
    "url" => "https://bitbucket.org/",
  }
]

ssh docker@swan
docker start heptapod-public

docker exec -it heptapod-public gitlab-ctl reconfigure

ssh docker@swan
mkdir repositories
cd repositories
git clone https://github.com/discourse/discourse_docker.git
cd discourse_docker

  DISCOURSE_DEVELOPER_EMAILS: '[email protected]'
  DISCOURSE_SMTP_ADDRESS: in-v3.mailjet.com
  DISCOURSE_SMTP_USER_NAME: ******
  DISCOURSE_SMTP_PASSWORD: *********

## The Docker container is stateless; all data is stored in /shared
volumes:
  - volume:
      host: /home/docker/srv/discourse/shared/standalone
      guest: /shared
  - volume:
      host: /home/docker/srv/discourse/shared/standalone/log/var-log
      guest: /var/log

...
  ## If you want to set the 'From' email address for your first registration, uncomment and change:
  ## After getting the first signup email, re-comment the line. It only needs to run once.
  - exec: rails r "SiteSetting.notification_email='[email protected]'"

rm -rf ~/srv/discourse
mkdir ~/srv/discourse

./launcher rebuild app

#/etc/apache2/sites-enabled/000-default.conf 
<Virtualhost *:443>
    ...
    Redirect /heptapod https://swan.physics.wsu.edu:11443/
    Redirect /discourse https://swan.physics.wsu.edu:10443/    
</VirtualHost>

sudo service apache2 restart

#!/bin/bash
# initialize_cocalc.sh
docker create                                            \
       --name cocalc-local                               \
       --restart always                                  \
       --hostname localhost                              \
       --publish 127.0.0.1:9443:443                      \
       --volume ~/srv/cocalc:/projects                   \
       sagemathinc/cocalc

docker create                                            \
       --name cocalc-public                              \
       --restart always                                  \
       --hostname localhost                              \
       --publish 9443:443                                \
       --volume ~/srv/cocalc:/projects                   \
       sagemathinc/cocalc

ssh swandocker

su admin
sudo apt-get update
sudo aptitude install awscli

!ssh swan df -h

!ssh swan 'du -sh ~/* | sort -h | tail'

$ sudo fdisk -l
Disk /dev/sda: 238.5 GiB, 256060514304 bytes, 500118192 sectors
...
Device     Boot  Start       End   Sectors   Size Id Type
/dev/sda1  *      2048    499711    497664   243M 83 Linux
/dev/sda2       501758 500117503 499615746 238.2G  5 Extended
/dev/sda5       501760 500117503 499615744 238.2G 8e Linux LVM
...

Disk /dev/sdb: 5.5 TiB, 6001175126016 bytes, 11721045168 sectors
...

$ sudo parted /dev/sdb
GNU Parted 3.2
Using /dev/sdb
Welcome to GNU Parted! Type 'help' to view a list of commands.
(parted) mklabel gpt
Warning: The existing disk label on /dev/sdb will be destroyed and all data on this disk will be lost. Do you want to continue?
Yes/No? Yes
(parted) unit GB
(parted) mkpart boot ext4 0 1             # Boot partition at start
(parted) set 1 boot on                    # Set the boot flag
(parted) mkpart hdclone ext4 1 257        # Backup for /dev/sda
(parted) mkpart data ext4 257 -0          # Remaining partition
(parted) print                            # Check             
Model: ATA WDC WD60EFRX-68L (scsi)
Disk /dev/sdb: 6001GB
Sector size (logical/physical): 512B/4096B
Partition Table: gpt
Disk Flags: pmbr_boot

Number  Start   End     Size    File system  Name     Flags
 1      0.00GB  1.00GB  1.00GB  ext4         boot     boot, esp
 2      1.00GB  257GB   256GB   ext4         hdclone
 3      257GB   6001GB  5744GB  ext4         data
(parted) quit
Information: You may need to update /etc/fstab.

$ sudo fdisk -l
...
Disk /dev/sdb: 5.5 TiB, 6001175126016 bytes, 11721045168 sectors
...
Device         Start         End     Sectors   Size Type
/dev/sdb1       2048     1953791     1951744   953M EFI System
/dev/sdb2    1953792   501952511   499998720 238.4G Linux filesystem
/dev/sdb3  501952512 11721043967 11219091456   5.2T Linux filesystem

$ sudo mkfs.ext4 /dev/sdb1
mke2fs 1.44.4 (18-Aug-2018)
Creating filesystem with 243968 4k blocks and 61056 inodes
Filesystem UUID: 23e3fcf9-2e01-4869-8bc4-3069e122d5d3
Superblock backups stored on blocks: 
	32768, 98304, 163840, 229376

Allocating group tables: done                            
Writing inode tables: done                            
Creating journal (4096 blocks): done
Writing superblocks and filesystem accounting information: done

$ sudo mkfs.ext4 /dev/sdb2
mke2fs 1.44.4 (18-Aug-2018)
Creating filesystem with 62499840 4k blocks and 15630336 inodes
Filesystem UUID: 7e5eefff-68d7-40e0-a4c6-9cbdd65a6263
Superblock backups stored on blocks: 
	32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208, 
	4096000, 7962624, 11239424, 20480000, 23887872

Allocating group tables: done                            
Writing inode tables: done                            
Creating journal (262144 blocks): done
Writing superblocks and filesystem accounting information: done     

$ sudo mkfs.ext4 /dev/sdb3
mke2fs 1.44.4 (18-Aug-2018)
Creating filesystem with 1402386432 4k blocks and 175300608 inodes
Filesystem UUID: 0971a9ee-aeab-4e76-b45a-fc63103ca489
Superblock backups stored on blocks: 
	32768, 98304, 163840, 229376, 294912, 819200, 884736, 1605632, 2654208, 
	4096000, 7962624, 11239424, 20480000, 23887872, 71663616, 78675968, 
	102400000, 214990848, 512000000, 550731776, 644972544

Allocating group tables: done                            
Writing inode tables: done                            
Creating journal (262144 blocks): done
Writing superblocks and filesystem accounting information:

sudo mkdir /mnt/data2
sudo mkdir /mnt/hdclone

sudo mount /dev/sdb2 /mnt/hdclone
sudo mount /dev/sdb3 /mnt/data2

$ sudo blkid
...
/dev/sdb1: UUID="23e3fcf9-2e01-4869-8bc4-3069e122d5d3" TYPE="ext4" PARTLABEL="boot" PARTUUID=...
/dev/sdb2: UUID="7e5eefff-68d7-40e0-a4c6-9cbdd65a6263" TYPE="ext4" PARTLABEL="hdclone" PARTUUID=...
/dev/sdb3: UUID="0971a9ee-aeab-4e76-b45a-fc63103ca489" TYPE="ext4" PARTLABEL="data" PARTUUID=...

$ sudo vi /etc/fstab
# <file system>                            <mount point> <type> <options>         <dump> <pass>
...
# New internal 6TB drive on /dev/sdb/
#UUID="23e3fcf9-2e01-4869-8bc4-3069e122d5d3" /boot        ext4 defaults 0 2
UUID="7e5eefff-68d7-40e0-a4c6-9cbdd65a6263" /mnt/hdclone ext4 defaults 0 2
UUID="0971a9ee-aeab-4e76-b45a-fc63103ca489" /mnt/data2   ext4 defaults 0 2

$ lsblk
NAME                   MAJ:MIN RM   SIZE RO TYPE MOUNTPOINT
sda                      8:0    0 238.5G  0 disk 
|-sda1                   8:1    0   243M  0 part /boot
|-sda2                   8:2    0     1K  0 part 
`-sda5                   8:5    0 238.2G  0 part 
  |-lubuntu--vg-root   253:0    0 222.3G  0 lvm  /
  `-lubuntu--vg-swap_1 253:1    0    16G  0 lvm  [SWAP]
sdb                      8:16   0 931.5G  0 disk 
`-sdb1                   8:17   0 931.5G  0 part /mnt/Khalids_usb_drive
sr0                     11:0    1  1024M  0 rom  

$ sudo fdisk -l
Disk /dev/sda: 238.5 GiB, 256060514304 bytes, 500118192 sectors
...
Device     Boot  Start       End   Sectors   Size Id Type
/dev/sda1  *      2048    499711    497664   243M 83 Linux
/dev/sda2       501758 500117503 499615746 238.2G  5 Extended
/dev/sda5       501760 500117503 499615744 238.2G 8e Linux LVM
...
Disk /dev/sdb: 931.5 GiB, 1000204885504 bytes, 1953525167 sectors
...
Device     Boot Start        End    Sectors   Size Id Type
/dev/sdb1        2048 1953521663 1953519616 931.5G  7 HPFS/NTFS/exFAT
...
Disk /dev/mapper/lubuntu--vg-root: 222.3 GiB, 238681063424 bytes, 466173952 sectors
...
Disk /dev/mapper/lubuntu--vg-swap_1: 16 GiB, 17116954624 bytes, 33431552 sectors
...

sudo aptitude install -y libcurl4-openssl-dev libsqlite3-dev
sudo snap install --classic dmd && sudo snap install --classic dub
su admin
. /etc/profiled         # Path to /snap/bin set here: needed for dmd
cd ~/repositories
git clone https://github.com/skilion/onedrive.git
cd onedrive
make
sudo make install

install -D onedrive /usr/local/bin/onedrive
install -D -m 644 onedrive.service /usr/lib/systemd/user/onedrive.service

mkdir -p ~/.config/onedrive
cp ~admin/repositories/onedrive/config ~/.config/onedrive/config
mkdir ~/data2/OneDriveSync
ln -s ~/data2/OneDriveSync/ OneDrive
echo > ~/.config/onedrive/sync_list <<EOF
OneDriveSync/
EOF

$ onedrive --resync
Authorize this app visiting:

https://login.microsoftonline.com/common/oauth2/v2.0/authorize?client_id=22c49a0d-d21c-4792-aed1-8f163c982546&scope=files.readwrite%20files.readwrite.all%20offline_access&response_type=code&redirect_uri=https://login.microsoftonline.com/common/oauth2/nativeclient

Enter the response uri:   

sudo fdisk -l

sudo rsync -vaxhWE --no-compress --progress --delete --ignore-errors / /mnt/data2/swan_backup/14Mar2020

sudo apt-add-repository -y ppa:teejee2008/ppa
sudo apt-get update
sudo apt-get install timeshift

sudo mkdir -p /mnt/Khalids_usb_drive
sudo mount -t ntfs /dev/sdb1 /mnt/Khalids_usb_drive
sudo mkdir -p /data/external_data
sudo mount -t ext4 /dev/sdc5 /data/external_data/

su admin
cd ~
mkdir .duplicity
cd .duplicity
touch ignore
touch credentials

# Duplicity Credentials file; -*-Shell-script-*-
# dest = ~/.duplicity/credentials  # Keep this as the 2nd line for mmf_init_setup

client_config_backend: settings  
client_config:  
   client_id: xxx.apps.googleusercontent.com
   client_secret: yyyy
save_credentials: True  
save_credentials_backend: file  
save_credentials_file: gdrive.cache  
get_refresh_token: True

# Environment for Duplicity
# dest = ~/.duplicity/environment.yml
name: app_duplicity
channels:
  - defaults
  - conda-forge
dependencies:
  - python
  - setuptools_scm
  - pydrive
  - pip
  - pip:
    - duplicity

sudo apt-get install librsync-dev
unset CFLAGS
conda env update -f environment.yml --prune

#!/bin/bash
# dest = ~/usr/local/bin/duplicity_backup_home  # Keep this as the 2nd line for mmf_init_setup
export GOOGLE_DRIVE_SETTINGS=~/.duplicity/credentials
duplicity --exclude-filelist ~/.duplicity/ignore ~/ gdocs://m.forbes@wsu.edu/backups/swan_mforbes_current

conda run -n app_duplicity duplicity_backup_home

rclone config

screen -R RClone   # Optional, but prevents hangup when you logout
rclone sync -Pl --exclude ~/_trash ~ gwsu:swan/mforbes_current

screen -R RClone   # Optional, but prevents hangup when you logout
rclone sync -Pl gwsu:swan/mforbes_current /tmp/restored_home_directory

# sync_to_google_team_drive.bash
hg clone . /tmp/paper_soc_soliton
rclone sync -Pl --exclude ".hg/**" /tmp/paper_soc_soliton \
         gwsu_EngelsForbesCollaboration:paper_soc_soliton

# sync_from_google_team_drive.bash
hg clone . /tmp/paper_soc_soliton
rclone sync -Pl --exclude ".hg/**"                 \
  gwsu_EngelsForbesCollaboration:paper_soc_soliton \
                            /tmp/paper_soc_soliton

curl https://rclone.org/install.sh | sudo bash

$ rclone config
...
name> mswsu_Phys521
...
Storage> onedrive
...  # Blank client_id and client_secret. No advanced config.
Remote config...
y/n> n
For this to work, you will need rclone available on a machine that has a web browser available.
Execute the following on your machine:
	rclone authorize "onedrive"
Then paste the result below:          # Not sure when this will expire with MFA
result> {"access_token":"eyJ0eXAiO...","expiry":"2021-04-21T11:47:35.052577-07:00"}
Choose a number from below, or type in an existing value
 1 / OneDrive Personal or Business
   \ "onedrive"
 2 / Root Sharepoint site
   \ "sharepoint"
 3 / Type in driveID
   \ "driveid"
 4 / Type in SiteID
   \ "siteid"
 5 / Search a Sharepoint site
   \ "search"
Your choice> 5   # This was the key.  Then search for something in you teams
What to search for> Physics.521
Found 2 sites, please select the one you want to use:
0: Physics.521 (https://emailwsu.sharepoint.com/teams/PHYSICS.521)...
...
Chose drive to use:> 0
Found 4 drives, please select the one you want to use:
0: Class Files (documentLibrary)...
1: Class Materials (documentLibrary)...
2: Documents (documentLibrary)...
...
Chose drive to use:> 2
Found drive 'root' of type 'documentLibrary', URL: https://emailwsu.sharepoint.com/teams/PHYSICS.521/Shared%20Documents
Is that okay?
y) Yes
n) No
y/n> y

(server) $ nc -l 12345
(client) $ nc -c swan.physics.wsu.edu 12345

socat TCP4-LISTEN:12345,fork EXEC:cat

ncat -l 2000 -k -c 'xargs -n1 echo'

fail2ban-client status  # See if anyone is banned, and get the jailname
fail2ban-client set <jailname> unbanip <ipaddress>  # Unban them

(kamiak)$ ssh atacker@swan.physics.wsu.edu
attacker@swan.physics.wsu.edu's password: 
Permission denied, please try again.
[email protected]'s password: 
Permission denied, please try again.
...  # Repeat until ban is triggered
(kamiak)$ ssh attacker@swan.physics.wsu.edu   # Now connections are refused
ssh: connect to host swan.physics.wsu.edu port 22: Connection refused

(swan)$ sudo iptables -n -L
...
Chain f2b-sshd (1 references)
target     prot opt source               destination         
REJECT     all  --  198.17.13.7          0.0.0.0/0            reject-with icmp-port-unreachable
...

(kamiak)$ ip a 
... inet 198.17.13.7...

(swan)$ sudo fail2ban-client status
Status
|- Number of jail:	1
`- Jail list:	sshd

(swan)$ sudo fail2ban-client set sshd unbanip 198.17.13.7
1
(swan)$ sudo iptables -n -L
...
Chain f2b-sshd (1 references)
target     prot opt source               destination         
RETURN     all  --  0.0.0.0/0            0.0.0.0/0           

$ ssh swan
$ su admin
$ lsb_release -a
...
Description:	Ubuntu 20.04.1 LTS
Release:	20.04
...
$ mkdir -p ~/zips/visit
$ cd ~/zips/visit
# Make sure you download an appropriate version here.  I did 2.13.3 and 3.1.2
$ wget https://github.com/visit-dav/visit/releases/download/v3.1.2/visit3_1_2.linux-x86_64-ubuntu20.tar.gz
$ wget https://github.com/visit-dav/visit/releases/download/v3.1.2/visit-install3_1_2
$ bash visit-install3_1_2 3.1.2 linux-x86_64-ubuntu20 /data/apps/visit

$ wget https://github.com/visit-dav/visit/releases/download/v2.13.3/visit2_13_3.linux-x86_64-ubuntu18.tar.gz
$ wget https://github.com/visit-dav/visit/releases/download/v2.13.3/visit-install2_13_3
$ bash visit-install2_13_3 2.13.3 linux-x86_64-ubuntu18 /data/apps/visit

sudo cat > /usr/share/modules/modulefiles/visit <<EOF
#%Module4.4.1
proc ModulesHelp { } {
    puts stderr "\tVisIt visualization tool."
}

module-whatis "VisIt visualization tool."

# Add to back too so that it is always available.  We use this to provide
# Mercurial for example which we install in the default environment
prepend-path    PATH            /data/apps/visit/bin
EOF

# Missing dependencies
sudo aptitude install cmake libpcre16-3
module load visit

# Get W-SLDA repo
git clone ssh://git@git2.if.pw.edu.pl/gabrielw/cold-atoms.git ~/repositories/WSLDA_cold-atoms
cat ~/repositories/WSLDA_cold-atoms/lib-wdata/visit-plugin/README.txt
cd ~/repositories/WSLDA_cold-atoms/lib-wdata/

# Build in a clean directory
mkdir _build; cd _build
rm -rf *

g++ -O3 -c ../wdata.c -fPIC
ar crf libwdata.a wdata.o

xml2cmake -v 3.1 -public -clobber ../visit-plugin/wdata.xml
mv CMakeLists.txt ../visit-plugin/
cmake -DCMAKE_BUILD_TYPE:STRING=Debug ../visit-plugin/

make

ssh swandocker
sudo add-apt-repository ppa:mumble/release
sudo apt-get update
sudo aptitude install mumble-server
sudo dpkg-reconfigure mumble-server

; /etc/mumble-server.ini
...
database=/var/lib/mumble-server/mumble-server.sqlite
...
ice="tcp -h 127.0.0.1 -p 6502"
icesecretwrite=
logfile=/var/log/mumble-server/mumble-server.log
pidfile=/var/run/mumble-server/mumble-server.pid
welcometext=" Welcome to the Forbes Group Murmur server. Enjoy your stay! "
port=64738
serverpassword=<ask me>
bandwidth=72000
users=100
messageburst=5
messagelimit=1
allowping=true
sslCert=/etc/letsencrypt/live/swan.physics.wsu.edu/fullchain.pem
sslKey=/etc/letsencrypt/live/swan.physics.wsu.edu/privkey.pem
uname=mumble-server
[Ice]
Ice.Warn.UnknownProperties=1
Ice.MessageSizeMax=65536

sudo aptitude install tigervnc-standalone-server tigervnc-common

vncpasswd

# VNC Server config file; -*-Shell-script-*-
# dest = ~/.vnc/config   # Keep this as the 2nd line for mmf_init_setup
session=lxqt
geometry=1920x1080
localhost          # Only listen locally - use an ssh tunnel to connect.
alwaysshared

# ~/.ssh/config
...
Host swanvnc
  Compression yes
  LocalForward 5901 localhost:5901
...

ssh swanvnc    # Forwards port 5901
tigervncserver -xstartup firefox

(Mac OS X)$ open vnc://localhost:5901

tigervncserver -kill :*

from IPython.display import HTML
def show(res):
    return HTML('<pre style="font-size: 6pt;line-height: normal;">{}</pre>'.format("\n".join(res)))

swan.physics.wsu.edu
IP: 134.121.40.108
Gateway: 134.121.47.254
Subnet Mask: 255.255.248.0
DNS Servers: 134.121.139.10  and 134.121.80.36
WINS Servers: 134.121.143.28 and 134.121.143.29

# /etc/fstab: static file system information.
# 
# Use 'blkid' to print the universally unique identifier for a
# device; this may be used with UUID= as a more robust way to name devices
# that works even if disks are added and removed. See fstab(5).
#
# <file system> <mount point> <type> <options> <dump> <pass>
/dev/mapper/lubuntu--vg-root / ext4 errors=remount-ro 0 1
UUID=10f14fbd-9d53-43f2-be32-c9ab8c6aab99 /boot ext2 defaults 0 2
/dev/mapper/lubuntu--vg-swap_1 none swap sw 0 0

# New internal 6TB drive on
UUID=123e3fcf9-2e01-4869-8bc4-3069e122d5d  /boot                   ext4   defaults          0      2
UUID=7e5eefff-68d7-40e0-a4c6-9cbdd65a6263  /mnt/hdclone            ext4   defaults          0      2
UUID=0971a9ee-aeab-4e76-b45a-fc63103ca489  /mnt/data2              ext4   defaults          0      2

# Khalid's drive
UUID=A6905C57905C3053                      /mnt/Khalids_usb_drive  auto nosuid,nodev,nofail 0      2

# MMF Seagate
UUID=6163f638-a6ca-495b-abc7-232026b7d32e  /mnt/MMF_External       ext4 nosuid,nodev,nofail 0      2

$ sudo fdisk -l 
Disk /dev/sda: 931.5 GiB, 1000204885504 bytes, 1953525167 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 33553920 bytes
Disklabel type: dos
Disk identifier: 0x542acb8f

Device     Boot Start        End    Sectors   Size Id Type
/dev/sda1        2048 1953521663 1953519616 931.5G  7 HPFS/NTFS/exFAT

Disk /dev/sdb: 238.5 GiB, 256060514304 bytes, 500118192 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes
Disklabel type: dos
Disk identifier: 0x8f7f2947

Device     Boot  Start       End   Sectors   Size Id Type
/dev/sdb1  *      2048    499711    497664   243M 83 Linux
/dev/sdb2       501758 500117503 499615746 238.2G  5 Extended
/dev/sdb5       501760 500117503 499615744 238.2G 8e Linux LVM

Disk /dev/sdc: 5.5 TiB, 6001175126016 bytes, 11721045168 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: gpt
Disk identifier: E22CB7F1-B1F8-403F-9C09-6CF02E1392E1

Device         Start         End     Sectors   Size Type
/dev/sdc1       2048     1953791     1951744   953M EFI System
/dev/sdc2    1953792   501952511   499998720 238.4G Linux filesystem
/dev/sdc3  501952512 11721043967 11219091456   5.2T Linux filesystem

Disk /dev/mapper/lubuntu--vg-root: 222.3 GiB, 238681063424 bytes, 466173952 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes

Disk /dev/sdd: 3.7 TiB, 4000752599040 bytes, 7813969920 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 4096 bytes
I/O size (minimum/optimal): 4096 bytes / 4096 bytes
Disklabel type: gpt
Disk identifier: 636CB648-76E8-4FFD-BA07-D5873D03596D

Device          Start        End    Sectors   Size Type
/dev/sdd1          40     409639     409600   200M EFI System
/dev/sdd2      409640 1133222135 1132812496 540.2G Apple HFS/HFS+
/dev/sdd3  1133484280 2266296775 1132812496 540.2G Apple HFS/HFS+
/dev/sdd4  2266558920 3399882359 1133323440 540.4G Apple HFS/HFS+
/dev/sdd5  3399882752 7813969886 4414087135   2.1T Linux filesystem

Disk /dev/mapper/lubuntu--vg-swap_1: 16 GiB, 17116954624 bytes, 33431552 sectors
Units: sectors of 1 * 512 = 512 bytes
Sector size (logical/physical): 512 bytes / 512 bytes
I/O size (minimum/optimal): 512 bytes / 512 bytes

$ lsblk -f
NAME                   FSTYPE      LABEL                     UUID                                   MOUNTPOINT
sda                                                                                                 
`-sda1                 ntfs        Seagate Backup Plus Drive A6905C57905C3053                       
sdb                                                                                                 
|-sdb1                 ext2                                  10f14fbd-9d53-43f2-be32-c9ab8c6aab99   /boot
|-sdb2                                                                                              
`-sdb5                 LVM2_member                           HQtaOr-nUK1-cshj-lty2-ZDc8-MAum-MwMBBo 
  |-lubuntu--vg-root   ext4                                  afe81057-f92c-47a6-b724-26e0ad1b2880   /
  `-lubuntu--vg-swap_1 swap                                  c1da1cdc-718c-47e3-92ed-3f34e6fca27b   [SWAP]
sdc                                                                                                 
|-sdc1                 ext4                                  23e3fcf9-2e01-4869-8bc4-3069e122d5d3   
|-sdc2                 ext4                                  7e5eefff-68d7-40e0-a4c6-9cbdd65a6263   /mnt/hdclone
`-sdc3                 ext4                                  0971a9ee-aeab-4e76-b45a-fc63103ca489   /mnt/data2
sdd                                                                                                 
|-sdd1                 vfat        EFI                       67E3-17ED                              
|-sdd2                 hfsplus     KSB NFS Medtner           b64f66fc-0a37-3bd9-96df-a15b01b3860e   
|-sdd3                 hfsplus     MMF NFS Medtner           ea008a86-12be-3278-a913-5182ad395ea9   
|-sdd4                 hfsplus     Data NFS Medtner          f3013eb6-af22-37ef-bb78-92f8e7d4ff8e   
`-sdd5                 ext4                                  6163f638-a6ca-495b-abc7-232026b7d32e   
sr0                                                                                                 

$ blkid
/dev/sda1: LABEL="Seagate Backup Plus Drive" UUID="A6905C57905C3053" TYPE="ntfs" PTTYPE="atari" PARTUUID="542acb8f-01"
/dev/sdb1: UUID="10f14fbd-9d53-43f2-be32-c9ab8c6aab99" TYPE="ext2" PARTUUID="8f7f2947-01"
/dev/sdb5: UUID="HQtaOr-nUK1-cshj-lty2-ZDc8-MAum-MwMBBo" TYPE="LVM2_member" PARTUUID="8f7f2947-05"
/dev/sdc1: UUID="23e3fcf9-2e01-4869-8bc4-3069e122d5d3" TYPE="ext4" PARTLABEL="boot" PARTUUID="24d9965c-595d-413f-9d28-1e8238441970"
/dev/sdc2: UUID="7e5eefff-68d7-40e0-a4c6-9cbdd65a6263" TYPE="ext4" PARTLABEL="hdclone" PARTUUID="ecd06215-d0df-4407-9b59-144e81a9ee2c"
/dev/sdc3: UUID="0971a9ee-aeab-4e76-b45a-fc63103ca489" TYPE="ext4" PARTLABEL="data" PARTUUID="4545ada2-dc89-47d8-b1f8-6ac72b15f02f"
/dev/mapper/lubuntu--vg-root: UUID="afe81057-f92c-47a6-b724-26e0ad1b2880" TYPE="ext4"
/dev/sdd1: LABEL="EFI" UUID="67E3-17ED" TYPE="vfat" PARTLABEL="EFI System Partition" PARTUUID="4ca9a0a1-8b8f-4f13-819d-d28528a7e5e0"
/dev/sdd2: UUID="b64f66fc-0a37-3bd9-96df-a15b01b3860e" LABEL="KSB NFS Medtner" TYPE="hfsplus" PARTLABEL="Untitled" PARTUUID="2ad2eaa6-5064-4d18-8451-6797b426d2b7"
/dev/sdd3: UUID="ea008a86-12be-3278-a913-5182ad395ea9" LABEL="MMF NFS Medtner" TYPE="hfsplus" PARTLABEL="MMF NFS Medtner" PARTUUID="105629a2-a227-4aff-a726-85db2a167db1"
/dev/sdd4: UUID="f3013eb6-af22-37ef-bb78-92f8e7d4ff8e" LABEL="Data NFS Medtner" TYPE="hfsplus" PARTLABEL="Data NFS Medtner" PARTUUID="99311db6-7ca1-495b-88ff-5680325de291"
/dev/sdd5: UUID="6163f638-a6ca-495b-abc7-232026b7d32e" TYPE="ext4" PARTUUID="9a718cb6-d326-5a45-b4ca-e5748c45414d"

from IPython.display import HTML
def show(res):
    return HTML('<pre style="font-size: 6pt;line-height: normal;">{}</pre>'.format("\n".join(res)))
res = !ssh swan dpkg -l | grep ii
show(res)

# /etc/default/grub
...
#GRUB_CMDLINE_LINUX_DEFAULT="quiet splash"
GRUB_CMDLINE_LINUX_DEFAULT=""

Table of Contents

Swan Policies

Disk

Install

Hardware Details

OS

Configuration

Software

Apt Repositories

References

Modules

Users and Groups

Personal Configuration

Update Kernel

Difficulties

Old

Old

CUDA

Optional: remove old versions

Optional: Update packages

Restart as suggested

Daemons

Config Files

Bash

Modules

Mercurial

Python, PIP etc.

Conda Environments

Web Server

Apache Configuration

Let's Encrypt and Certbot

References

Version Control Hosting

Kallithea (incomplete)

Heptapod

Docker

Docker Cheatsheet

Heptapod

Debugging

Heptapod Backup (incomplete)

HTTP Redirect

Bitbucket Import

References

Issues

Discourse

HTTP Redirect

CoCalc

Issues

Nextcloud (incomplete)

AWS Command Line

Disk Usage

Partition Scheme

Installing a New Drive

References

Remote Drives (NFS etc.)

Backup

OneDrive Free Client (incomplete)

Duply/Duplicity

TL;DR

Timeshift (incomplete)

References

Mounting External Drives

Duplicity (incomplete)

References

RClone

Cheatsheet

Users

Performance (Google Application Client Id)

Admin

Microsoft Teams

References

Network

Fail2Ban

Unlocking

References

Misc. Software

VisIt

Resources

Plugins

Mumble/Murmer