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=Intro=
+
=About this page=
This page is a collection of (hopefully) useful information and trivia
+
This page is a collection of various and often unrelated bits of information available elsewhere but kept
which may be required to build a Web service based on Django/Apache/PostgreSQL
+
here for quick reference and occasionally useful in building a functional system in the Linux environment.
and to manage a small pool of machines for testing purposes.
+
For ease of access, a lot of the information previously contained here has been factored out into separate
 +
articles accessible via the navigation sidebar on the left.
  
=Python Versions=
+
=Remote Access and Execution=
At the time of writing the system version of Python is often 2.7, whereas newer applications
+
==Overview==
benefit from using Python 3.*. One way to deal with that is to include "env" in hashbang pointing
+
It is convenient to control a few machines from a single host. Typically ssh is used for this purpose,
to the exact version you want to use. Apache/WSGI deployments may require additional footwork
+
but if security is not a concern (e.g. then the network is strictly local) telnet can be also used as a quick solution.
to ensure the correct version of Python runtime is used in mod_wsgi etc.
+
It will also server to "bootstrap" ssh connectivity i.e. debug ssh configuration remotely to make it operational.
  
'''Debian "Alternatives"''' - Debian has a way to specify the default version of an app. For example, if more than one version of Python
+
Among advantages of ssh is X11 forwarding, which functionality telnet does not have.
is present on the system, the command "update-alternatives" can be used to activate any of the available choices.
 
  
'''Caution''' - it's not a good idea to switch from the version of Python which came with your distro, since there
+
==ssh==
documented and undocumented dependencies in various places, on that particular version. Random things may break
 
such as software update, applications like Dropbox etc. ''Caveat Emptor''.
 
  
Remove an alternative version:
+
<h4>Installation and keys</h4>
<pre>sudo update-alternatives --remove python /usr/bin/python3</pre>
+
You'll need to run the '''sshd''' service on every machine you want to connect to. On Linux, this is most frequently '''openssh-server''' and it can be trivially installed. Make sure there is a ssh entry in /etc/services, with the desired port number.
 +
 
 +
To be used productively, private and public keys will need to be generated or imported as necessary. For the private/public key pair to work, public keys should be added to the file ".ssh/authorized_keys". A matching private key must be loaded to an identity managing service (e.g. ssh-agent in case of Linux) on the machine ''from'' which you are going to connect. If it's not cached, you will likely be prompted to enter the passphrase for the key.
 +
 
 +
Typically (this depends on the flavor of your sshd) you will get a message specifying which public key is used during the login that you are attempting. This is useful to know if you have many keys and forget which was used for what connection.
 +
 
 +
Restarting the service:
 +
<pre>sudo systemctl restart ssh</pre>
 +
 
 +
Adding a key to the agent:
 +
<pre>
 +
eval "$(ssh-agent -s)"
 +
ssh-add key_file
 +
</pre>
  
Example above allows to fall back on the previous version, such as Python 2.7.
+
You can also check which keys are loaded
 +
<pre>ssh-add -l</pre>
  
It is recommended that instead of replacing the default, relevant scripts contain explicit reference to version 3+ if possible.
+
In case of problems while connecting, it may be helpful to check the log on the ssh server machine: /var/log/auth.log.
  
=Django & PostgreSQL=
 
* Moved to a separate [[Django]] page.
 
* Moved to a separate [[PostgreSQL]] page.
 
  
=Apache=
+
Gateways such as one operating at BNL and other Labs typically require that your public key would be uploaded and cached on their side in advance. The exact way this can be done is site-dependent. Some sites require to verify the upload by providing the public key's fingerprint. Example of how to get it:
==Installation==
 
On Ubuntu:
 
 
<pre>
 
<pre>
sudo apt-get install apache2 # Apache
+
ssh-keygen -E md5 -lf my_public_key_file
sudo apt-get install libapache2-mod-wsgi-py3 # mod_wsgi for Python3
 
 
</pre>
 
</pre>
  
==Start-Stop-Restart==
+
If you lost your public key (while still having your private one) you can re-create it:
===Ubuntu===
 
To start/stop/restart Apache 2 web server, enter one of the commands in each category:
 
 
<pre>
 
<pre>
### START
+
ssh-keygen -yf my_private_key_file
/etc/init.d/apache2 start
 
sudo /etc/init.d/apache2 start
 
sudo service apache2 start
 
### STOP
 
/etc/init.d/apache2 stop
 
sudo /etc/init.d/apache2 stop
 
sudo service apache2 stop
 
### RESTART
 
/etc/init.d/apache2 restart
 
sudo /etc/init.d/apache2 restart
 
sudo service apache2 restart
 
 
</pre>
 
</pre>
  
System status:
+
Once it's done, a connection becomes possible, for example:
 
<pre>
 
<pre>
systemctl status apache2.service
+
ssh username@atlasgw.usatlas.bnl.gov
 
</pre>
 
</pre>
  
 +
The '-X' option is needed to enable X11 forwarding in a connection established in this manner.
  
===CentOS/RH===
+
<h4>Tunnels</h4>
On RedHat Linux, the name of the daemon is httpd.
+
Using proxies at BNL:
Also, "service" command may be aliased to systemctl.
+
<pre>ssh -L 8080:130.199.23.54:3128 yourAccount@your.gateway.bnl.gov</pre>
 +
 
 +
The port 8080 is chosen as an example - it must be a number larger than a certain lower limit to satisfy a security policy. On your local machine, you would need to specify a proxy which looks like this:
 
<pre>
 
<pre>
systemctl status -l httpd.service # or:
+
localhost:8080
sudo systemctl start httpd.service
 
 
</pre>
 
</pre>
  
==Apache Configuration==
+
Another example when going from one Linux box to another:
===General Items===
+
<pre>
KeepAlive sets the tradeoff between memory and CPU usage by Apache.
+
ssh -L 8000:localhost:8000 myRemoteHost
 +
</pre>
  
Serving static files:
+
The above gives you access to the remote port 8000 on the local machine via localhost:8000. For example, this works for accessing a machine
https://docs.djangoproject.com/en/1.10/howto/deployment/wsgi/modwsgi/#serving-files
+
on the internal CERN netword via http:
 +
<pre>
 +
ssh -L 8008:neutdqm.cern.ch:8008 user@lxplus015.cern.ch
 +
</pre>
 +
 
 +
If there is a need to access a HTTPS site, port number 443 needs to be forwarded. Forwarding to low-numbered ports (e.g. forwarding 443 remote to 443 local)
 +
will require sudo or root on most systems.
  
Official Layout of the Config Files:
+
If there is a certificate issue it needs to be resolved either in the browser, or, if wget is used, by applying the --no-check-certificate option.
https://wiki.apache.org/httpd/DistrosDefaultLayout
 
This, however, is not written in stone. Some details
 
are given below.
 
  
===Ubuntu===
 
See /etc/apache2/apache2.conf
 
  
Snippet from 000-default.conf on Ubuntu:
+
<h4>Password Automation</h4>
 +
There are a few cases when key-based auth is not suitable and one has to use passwords with ssh. To automate logging in one may choose to install and use the "sshpass" utility, provided the credentials you supply are not stored in the open. To force the password authentication method instead of the public key this option can be used:
 
<pre>
 
<pre>
        ServerName promptproc
+
-o PubkeyAuthentication=no
        ServerAlias promptproc
+
</pre>
 +
 
 +
<h4>Windows clients</h4>
 +
Once in a while you may need to use a Windows client to connect to various services via ssh. In Windows 10 there is a variation of steps to get the ssh client(s) operational depending on the software release. The more recent updates (as of Spring 2019) have OpenSSH installed under Windows\System32\OpenSSH, with the usual complement of tools.
 +
 
 +
==telnet==
 +
While using ssh is in general preferable for many reasons and foremost due to security concerns, sometimes there is a chicken and an egg problem where
 +
you need to establish access fast in order to debug ssh on a remote machine. In these cases, and if security
 +
is not a concern (rare, but could happen on an entirely internal network), one may opt to use telnet.
 +
 
 +
On Ubuntu one can install the software necessary to run the telnet service in the following manner:
 +
<pre>
 +
sudo apt-get install xinetd telnetd
 +
</pre>
 +
 
 +
Make sure there is an entry in /etc/services which looks like
 +
<pre>
 +
telnet        23/tcp
 +
</pre>
  
 +
Also, create a file /etc/xinetd.d/telnet with contents similar to this:
 +
<pre>
 +
service telnet {   
 +
        disable        = no
 +
        flags          = REUSE
 +
        socket_type    = stream
 +
        wait            = no
 +
        user            = root
 +
        server          = /usr/sbin/in.telnetd
 +
        log_on_failure  += USERID HOST
 +
        log_on_success  += PID HOST EXIT
 +
        log_type        = FILE /var/log/xinetd.log
 +
}
 +
</pre>
  
        WSGIScriptAlias / /home/maxim/projects/p3s/promptproc/promptproc/wsgi.py
+
...and start the service as follows:
 +
<pre>
 +
sudo /etc/init.d/xinetd start
 +
</pre>
  
        Alias /static/ /var/www/static/
+
==pdsh==
        <Directory /var/www/static>
+
This is an advanced parallel shell designed for cluster management. It often uses ssh as the underlying protocol although there are other options as well. Configuration is defined by files residing in /etc/pdsh. For example, the file "machines" needs to contain the list of computers to be targeted by pdsh. Optionally, this is also the place for a file that can be sourced for convenience of setup, cf
        Require all granted
+
<pre>
        </Directory>
+
# setup pdsh for cluster users
 +
export PDSH_RCMD_TYPE='ssh'
 +
export WCOLL='/etc/pdsh/machines'
 +
</pre>
  
        <Directory /home/maxim/projects/p3s/promptproc/promptproc>
+
This of course can be done from the command line anyway, cf
        <Files wsgi.py>
+
<pre>
        Require all granted
+
export PDSH_RCMD_TYPE=ssh
        </Files>
+
</pre>
        </Directory>
 
  
 +
Using ssh as the underlying protocol for pdsh implies that you have set up private and public keys just like you normally would for ordinary ssh login.
 +
Once this is done, you should be able to do something like this as a basic test of your setup:
 +
<pre>
 +
pdsh -w targetHost "ls"
 
</pre>
 
</pre>
The "static directory must contain static content such as themes for the tables2 package.
 
Keep in mind that while this is served automatically by the Django development server,
 
it's not the case under Apache.
 
  
 +
If the targetHost is omitted, the command will be run against all machines listed in the "machines" file as explained above. Should a command fail on a particular machine, this will be indicated (with an error code) in the output of the command, with the name of the machine listed. Redirection of stderr with something like "2>/dev/null" included with the command you run won't work with pdsh.
  
The file wsgi.conf needs to contain a reference to Python runtime like:
+
Example of installation on CentOS:
 
<pre>
 
<pre>
WSGIPythonPath /home/maxim/.local/lib/python3.5/site-packages
+
yum install pdsh
 
</pre>
 
</pre>
  
=== CentOS ===
+
==curl==
See /etc/httpd/. Examples:
 
  
 +
To post a form:
 
<pre>
 
<pre>
[mxp@neutdqm p3s]$ ls /etc/httpd/
+
curl -X POST -F 'username=minime' -F 'password=something' http://blah.com
conf  conf.d  conf.modules.d  logs  modules  run
+
curl -X POST -F 'username=minime' -H "Content-Type: application/x-www-form-urlencoded" http://blah.com
[mxp@neutdqm p3s]$ ls /etc/httpd/conf.d/
 
autoindex.conf  django.conf  php.conf  README  userdir.conf welcome.conf
 
[mxp@neutdqm p3s]$ ls /etc/httpd/conf/
 
httpd.conf  magic
 
 
</pre>
 
</pre>
  
===Permissions===
+
=Miscellania=
In addition to granting permissions in the Apache configuration file (an example is given below), correct permissions need to be set for the directory tree containing wsgi.py and other crucial files. If for example the tree is contained in your home directory and it's not readable to others, it won't work. One example (perhaps not the best) of how to make it work is to set 755 to your home dir.
+
 
 +
==Linux Version and Distribution==
  
On top of that, SELinux will impose it's own restriction. See:
 
 
<pre>
 
<pre>
getenforce
+
cat /etc/os-release
 +
lsb_release -a
 +
hostnamectl
 +
# Linux kernel version:
 +
uname -r
 
</pre>
 
</pre>
  
If it shows "Enforcing", try
+
This seems to work reliably:
 
<pre>
 
<pre>
sudo setenforce 0
+
cat /proc/version
 
</pre>
 
</pre>
  
===mod_wsgi===
+
Also,
* When using mod_wsgi one has to make sure the version matches the Python version, this needs to be specified when mod_wsgi is installed (see "Installation" above)
+
<pre>
* https://www.sitepoint.com/deploying-a-django-app-with-mod_wsgi-on-ubuntu-14-04/
+
cat /etc/*release
* Methods of setting up the environment for wsgi described in the current Django documentation may or may not work on a particular installation of Apache due to a few bugs and general complexity of *.conf and related files
+
# or
 +
cat /etc/issue*
 +
# or
 +
cat /proc/version
 +
</pre>
  
 +
==Linux User Management==
 +
 +
https://www.digitalocean.com/community/tutorials/how-to-create-a-sudo-user-on-centos-quickstart
  
===Ports===
 
SELinux may prevent you from configuring Apache with a non-standard port.
 
Useful commands:
 
 
<pre>
 
<pre>
semanage port -l # list ports
+
adduser username
semanage port -a -t http_port_t -p tcp 81 # add a rule
+
passwd username
 
</pre>
 
</pre>
  
==Deploying DB for Django==
+
Use the usermod command to add the user to the wheel group.
===sqlite permissions===
 
Assuming you are using sqlite, the file permissions on the DB file do matter if when you deploy under Apache.
 
So you either need to set wide permissions (may not be a good idea depending on the security situation) or
 
change the owner to "www-data" (on Ubuntu) or "apache" (on CentOS). Other OS may require similar tweaks.
 
  
===PostgreSQL===
 
An example of the "settings.py" clause:
 
 
<pre>
 
<pre>
DATABASES = {
+
usermod -aG wheel username
    'default': {
 
        'ENGINE': 'django.db.backends.postgresql',
 
        'NAME': 'foo',
 
        'USER': 'bar',
 
        'PASSWORD': '***',
 
        'HOST': '',
 
        'PORT': '',
 
    }
 
}
 
 
</pre>
 
</pre>
  
=Misc Tools=
+
By default, on CentOS, members of the ''wheel'' group have sudo privileges.
==ssh, telnet and other access methods==
+
 
It is convenient to control a few machines from a single host. Typically ssh is used for this purpose,
+
==Network==
but if security is not a concern (e.g. then the network is strictly local) telnet can be also used as a quick solution.
+
"nslookup" is a useful network information utility with diverse functionality. One simple function is to translate qualified host names to IP addresses and back.
It will also server to "bootstrap" ssh connectivity i.e. debug ssh configuration remotely to make it operational.
+
 
 +
"sha" headers one may need while installing xrootd can be obtained by running (on Ubuntu):
 +
<pre>
 +
sudo apt-get install libssl-dev
 +
</pre>
 +
...or as follows on CentOS
 +
<pre>
 +
sudo yum install openssl openssl-devel
 +
</pre>
  
Among advantages of ssh is X11 forwarding, which functionality telnet does not have.
+
libssl may be necessary also for installation of pip3 etc.
  
===ssh===
+
A few other dependencies of xrootd can be met by installing glib2.0.
You'll need to run the '''sshd''' service on every machine you want to connect to. On Linux, this is most frequently '''openssh-server''' and it can be trivially installed. Make sure there is a ssh entry in /etc/services, with the desired port number.
 
  
To be used productively, private and public keys will need to be generated or imported as necessary. For the private/public key pair to work, public keys should be added to the file ".ssh/authorized_keys". A matching private key must be loaded to an identity managing service (e.g. ssh-agent in case of Linux) on the machine ''from'' which you are going to connect. If it's not cached, you will likely be prompted to enter the passphrase for the key.
+
In case the network connection becomes stale, on Ubuntu:
 +
<pre>
 +
sudo service network-manager restart
 +
</pre>
  
Typically (this depends on the flavor of your sshd) you will get a message specifying which public key is used during the login that you are attempting. This is useful to know if you have many keys and forget which was used for what connection.
+
An extremely useful command (at least on Ubuntu) - lists IPs, DNSs etc:
 +
<pre>
 +
nmcli device show
 +
</pre>
  
Restarting the service:
+
To see what process is listening on a given port:
 
<pre>
 
<pre>
sudo systemctl restart ssh
+
lsof -i :8000
 
</pre>
 
</pre>
  
Adding a key to the agent:
+
==Shell==
 +
 
 +
White space when using "sed":
 
<pre>
 
<pre>
eval "$(ssh-agent -s)"
+
$ sed -e "s/\s\{3,\}/  /g" inputFile
ssh-add key_file
+
will substitute every sequence of at least 3 whitespaces with two spaces.
 
</pre>
 
</pre>
  
You can also check which keys are loaded
+
Produce a convenient timestamp for various uses:
 
<pre>
 
<pre>
ssh-add -l
+
date -d "today" +"%Y%m%d%H%M"
 
</pre>
 
</pre>
  
Gateways such as one operating at BNL and other Labs typically require that your public key would be uploaded and cached on their side in advance. The exact way this can be done is site-dependent. Some sites require to verify the upload by providing the public key's fingerprint. Example of how to get it:
+
To get timestamps in history:
 
<pre>
 
<pre>
ssh-keygen -E md5 -lf my_public_key_file
+
HISTTIMEFORMAT="%d/%m/%y %T "
 
</pre>
 
</pre>
  
If you lost your public key (while still having your private one) you can re-create it:
+
"find"
 
<pre>
 
<pre>
ssh-keygen -yf my_private_key_file
+
find . -maxdepth 1 -mmin +400
 
</pre>
 
</pre>
  
Once it's done, a connection becomes possible, for example:
+
'mmin' means it accepts minutes, 'mtime' days.
 +
 
 +
Find and recurcively delete directories modified more than 5 hours ago:
 
<pre>
 
<pre>
ssh username@atlasgw.usatlas.bnl.gov
+
find . -maxdepth 1 -mindepth 1 -mmin +300 -exec rm -fr {} \;
 
</pre>
 
</pre>
  
The '-X' option is needed to enable X11 forwarding in a connection established in this manner.
+
If you don't specify 'mindepth', the current directory will show up in the results and will be deleted in the case presented above.
 +
 
 +
Find files modified in a particular date:
 +
<pre>
 +
find . -type f -newermt 2018-04-11 ! -newermt 2018-04-12 -exec ls -l {} \;
 +
</pre>
  
Tunneling at BNL:
+
Alternatively, this will find files between the two dates & times
 
<pre>
 
<pre>
ssh -L 8080:130.199.23.54:3128 yourAccount@your.gateway.bnl.gov
+
touch -t 0810010000 /tmp/t1
 +
touch -t 0810011000 /tmp/t2
 +
 
 +
find / -newer /tmp/t1 -and -not -newer /tmp/t2
 
</pre>
 
</pre>
  
The port 8080 is chosen as an example - it must be a number larger than a certain lower limit to satisfy a security policy. On your local machine, you would need to specify a proxy which looks like this:
+
"cksum" - calculates CRC and byte count.
 +
 
 +
Remove line breaks from a file:
 +
<pre>echo $(cat $1)</pre>
 +
 
 +
Redirect stdout to one file and stderr to another file: <pre>command > out 2>error</pre>
 +
 
 +
Redirect stderr to stdout (&1), and then redirect stdout to a file:<pre>command >out 2>&1</pre>
 +
 
 +
Redirect both to a file:<pre>command &> out</pre>
 +
 
 +
 
 +
Find the name of the file, minus the complete path:
 
<pre>
 
<pre>
localhost:8080
+
f=$(basename /home/maxim/JOB.html)
 +
echo $f
 
</pre>
 
</pre>
  
Another example when going from one Linux box to another:
+
==SUDO==
 +
To change the password prompt timeout for sudo, you will need to run the command ''sudo visudo'' (which is the way to safely edit the ''sudoers'' file) and modify the following line by adding the timeout clause set to the desired number of minutes:
 
<pre>
 
<pre>
ssh -L 8000:localhost:8000 myRemoteHost
+
Defaults        env_reset, timestamp_timeout=XX
 
</pre>
 
</pre>
  
The above gives you access to the remote port 8000 on the local machine via localhost:8000. Another example which works for accessing the neutdqm machine via http:
+
==Crontab==
 +
*    minute (from 0 to 59)
 +
*    hour (from 0 to 23)
 +
*    day of month (from 1 to 31)
 +
*    month (from 1 to 12)
 +
*    day of week (from 0 to 6) (0=Sunday)
 +
 
 +
 
 
<pre>
 
<pre>
ssh -L 8008:neutdqm.cern.ch:8008 user@lxplus015.cern.ch
+
crontab -r # clear out your crontab
 +
crontab -l # list your crontab
 
</pre>
 
</pre>
  
If there is a need to access a HTTPS site, port number 443 needs to be forwarded, and if there is a certificate issue it needs to be resolved either in the browser, or, if wget is used, by applying the --no-check-certificate option.
+
==Checksum==
 +
<pre>
 +
xrdadler32
 +
</pre>
 +
==CVMFS==
  
===telnet===
+
https://cernvm.cern.ch/portal/filesystem/downloads
While using ssh is in general preferable for many reasons and foremost due to security concerns, sometimes there is a chicken and an egg problem where
 
you need to establish access fast in order to debug ssh on a remote machine. In these cases, and if security
 
is not a concern (rare, but could happen on an entirely internal network), one may opt to use telnet.
 
  
On Ubuntu one can install the software necessary to run the telnet service in the following manner:
 
 
<pre>
 
<pre>
sudo apt-get install xinetd telnetd
+
sudo apt-get install cvmfs cvmfs-config-default
 +
https://cernvm.cern.ch/portal/filesystem/quickstart
 
</pre>
 
</pre>
  
Make sure there is an entry in /etc/services which looks like
+
==Encrypt a directory==
 
<pre>
 
<pre>
telnet        23/tcp
+
tar cz myDir/ | mcrypt -k myPassword > myDir.z.nc
 
</pre>
 
</pre>
  
Also, create a file /etc/xinetd.d/telnet with contents similar to this:
+
=Version Control (git)=
 +
[[ Git ]]
 +
 
 +
==Starting out==
 +
Notify git of your identity and ID:
 
<pre>
 
<pre>
service telnet {   
+
git config --global user.email "yourname@yoursite.yourdomain"
        disable        = no
+
git config --global user.name yourID
        flags          = REUSE
 
        socket_type    = stream
 
        wait            = no
 
        user           = root
 
        server          = /usr/sbin/in.telnetd
 
        log_on_failure  += USERID HOST
 
        log_on_success  += PID HOST EXIT
 
        log_type        = FILE /var/log/xinetd.log
 
}
 
 
</pre>
 
</pre>
  
...and start the service as follows:
+
Pick a better editor for commit messages:
 
<pre>
 
<pre>
sudo /etc/init.d/xinetd start
+
git config --global core.editor "nano"
 
</pre>
 
</pre>
  
===pdsh===
+
To avoid entering git userID and password:
This is an advanced parallel shell designed for cluster management. It often uses ssh as the underlying protocol although there are other options as well. Configuration is defined by files residing in /etc/pdsh. For example, the file "machines" needs to contain the list of computers to be targeted by pdsh. Optionally, this is also the place for a file that can be sourced for convenience of setup, cf
+
<pre>git config --global credential.helper 'cache --timeout 7200'</pre>
 +
 
 +
To address the usual "^M" problem when switching between Linux and Windows environments
 
<pre>
 
<pre>
# setup pdsh for cluster users
+
$ git config --global core.autocrlf true
export PDSH_RCMD_TYPE='ssh'
+
# Remove everything from the index
export WCOLL='/etc/pdsh/machines'
+
$ git rm --cached -r .
 +
 
 +
# Re-add all the deleted files to the index
 +
# You should get lots of messages like: "warning: CRLF will be replaced by LF in <file>."
 +
$ git diff --cached --name-only -z | xargs -0 git add
 +
 
 +
# Commit
 +
$ git commit -m "Fix CRLF"
 
</pre>
 
</pre>
  
This of course can be done from the command line anyway, cf
+
(Also see https://stackoverflow.com/questions/1889559/git-diff-to-ignore-m)
 +
 
 +
==Restoring Files==
 +
First, see this link:
 +
 
 +
https://stackoverflow.com/questions/953481/find-and-restore-a-deleted-file-in-a-git-repository
 +
 
 +
A recipe that may work well:
 
<pre>
 
<pre>
export PDSH_RCMD_TYPE=ssh
+
git log --diff-filter=D --summary # finds deleted files
 +
git checkout $commit~1 filename # where "$commit" stands for the actual commit name (a long string)
 
</pre>
 
</pre>
 +
In the above, it's best to operate from the top level directory of the project and use path relative to that.
 +
Also, you may want to "git add" the restored files and commit them to make it permanent.
  
Using ssh as the underlying protocol for pdsh implies that you have set up private and public keys just like you normally would for ordinary ssh login.
+
If you want to get a specific previous revision of a file, just capture the stdout of the following command:
Once this is done, you should be able to do something like this as a basic test of your setup:
 
 
<pre>
 
<pre>
pdsh -w targetHost "ls"
+
git show $REV:$FILE
 
</pre>
 
</pre>
 +
...and rename the output as you see fit.
  
If the targetHost is omitted, the command will be run against all machines listed in the "machines" file as explained above. Should a command fail on a particular machine, this will be indicated (with an error code) in the output of the command, with the name of the machine listed. Redirection of stderr with something like "2>/dev/null" included with the command you run won't work with pdsh.
+
==Undoing a commit==
 +
See:
 +
 
 +
https://sethrobertson.github.io/GitFixUm/fixup.html
  
Example of installation on CentOS:
+
If you want to reverse your latest commit to the HEAD:
 
<pre>
 
<pre>
yum install pdsh
+
git reset --hard HEAD
 
</pre>
 
</pre>
  
===Misc===
+
To remove two or one last commits:
"nslookup" is a useful network information utility with diverse functionality. One simple function is to translate qualified host names to IP addresses and back.
+
<pre>
 +
git reset --hard HEAD~2
 +
git reset --hard HEAD~1
 +
</pre>
  
 +
==gitHub quirks ==
 +
Sometimes a cloned repo will end up in a state where you can't push local content. Things you might want to try this:
 +
<pre>
 +
git remote set-url origin https://myNameOnGithub@github.com/DUNE/dqmconfig.git
 +
</pre>
  
==Version Control==
+
And in case it was not annoying enough, if you see something like "can't open display"
Notify git of your identity:
+
this may help:
<pre>git config --global user.email "yourname@yoursite.yourdomain"</pre>
+
<pre>
 +
unset SSH_ASKPASS
 +
</pre>
  
To avoid entering git userID and password:
+
==Empty Commit==
<pre>git config --global credential.helper 'cache --timeout 7200'</pre>
+
When you need to trigger an action on GitHub or in other similar situation the following
 +
"empty commit" can be used (and then pushed):
 +
<pre>
 +
git commit -m 'rebuild pages' --allow-empty
 +
</pre>
  
==LaTeX==
+
=LaTeX=
 
One can choose to install all of tex packages or just a few:
 
One can choose to install all of tex packages or just a few:
 
<pre>
 
<pre>
Line 330: Line 435:
 
config files still around ("dpkg --purge" or "apt-get remove --purge"
 
config files still around ("dpkg --purge" or "apt-get remove --purge"
 
gets rid of the "rc" but they are just harmless cruft).
 
gets rid of the "rc" but they are just harmless cruft).
 +
 +
=Setting the environment for HTCondor=
 +
 +
It is often desirable to dynamically modify the content of the condor submit file (typically
 +
having the JDL extension). While it does not appear possible to access the shell environment
 +
variables within the submit file directly, a similar effect can be obtained by setting
 +
the internal HTCondor parameters on the command line, cf:
 +
<pre>
 +
condor_submit A=100 foo.jdl
 +
</pre>
 +
Then, one can access the value of "A" within the JDL file as $(A).
 +
 +
To find a number of idle jobs:
 +
<pre>
 +
/usr/bin/condor_q 2>&1| tail -1 | cut -d' ' -f 7
 +
</pre>

Latest revision as of 23:31, 30 November 2020

About this page

This page is a collection of various and often unrelated bits of information available elsewhere but kept here for quick reference and occasionally useful in building a functional system in the Linux environment. For ease of access, a lot of the information previously contained here has been factored out into separate articles accessible via the navigation sidebar on the left.

Remote Access and Execution

Overview

It is convenient to control a few machines from a single host. Typically ssh is used for this purpose, but if security is not a concern (e.g. then the network is strictly local) telnet can be also used as a quick solution. It will also server to "bootstrap" ssh connectivity i.e. debug ssh configuration remotely to make it operational.

Among advantages of ssh is X11 forwarding, which functionality telnet does not have.

ssh

Installation and keys

You'll need to run the sshd service on every machine you want to connect to. On Linux, this is most frequently openssh-server and it can be trivially installed. Make sure there is a ssh entry in /etc/services, with the desired port number.

To be used productively, private and public keys will need to be generated or imported as necessary. For the private/public key pair to work, public keys should be added to the file ".ssh/authorized_keys". A matching private key must be loaded to an identity managing service (e.g. ssh-agent in case of Linux) on the machine from which you are going to connect. If it's not cached, you will likely be prompted to enter the passphrase for the key.

Typically (this depends on the flavor of your sshd) you will get a message specifying which public key is used during the login that you are attempting. This is useful to know if you have many keys and forget which was used for what connection.

Restarting the service:

sudo systemctl restart ssh

Adding a key to the agent:

eval "$(ssh-agent -s)"
ssh-add key_file

You can also check which keys are loaded

ssh-add -l

In case of problems while connecting, it may be helpful to check the log on the ssh server machine: /var/log/auth.log.


Gateways such as one operating at BNL and other Labs typically require that your public key would be uploaded and cached on their side in advance. The exact way this can be done is site-dependent. Some sites require to verify the upload by providing the public key's fingerprint. Example of how to get it:

ssh-keygen -E md5 -lf my_public_key_file

If you lost your public key (while still having your private one) you can re-create it:

ssh-keygen -yf my_private_key_file

Once it's done, a connection becomes possible, for example:

ssh username@atlasgw.usatlas.bnl.gov

The '-X' option is needed to enable X11 forwarding in a connection established in this manner.

Tunnels

Using proxies at BNL:

ssh -L 8080:130.199.23.54:3128 yourAccount@your.gateway.bnl.gov

The port 8080 is chosen as an example - it must be a number larger than a certain lower limit to satisfy a security policy. On your local machine, you would need to specify a proxy which looks like this:

localhost:8080

Another example when going from one Linux box to another:

ssh -L 8000:localhost:8000 myRemoteHost

The above gives you access to the remote port 8000 on the local machine via localhost:8000. For example, this works for accessing a machine on the internal CERN netword via http:

ssh -L 8008:neutdqm.cern.ch:8008 user@lxplus015.cern.ch

If there is a need to access a HTTPS site, port number 443 needs to be forwarded. Forwarding to low-numbered ports (e.g. forwarding 443 remote to 443 local) will require sudo or root on most systems.

If there is a certificate issue it needs to be resolved either in the browser, or, if wget is used, by applying the --no-check-certificate option.


Password Automation

There are a few cases when key-based auth is not suitable and one has to use passwords with ssh. To automate logging in one may choose to install and use the "sshpass" utility, provided the credentials you supply are not stored in the open. To force the password authentication method instead of the public key this option can be used:

-o PubkeyAuthentication=no

Windows clients

Once in a while you may need to use a Windows client to connect to various services via ssh. In Windows 10 there is a variation of steps to get the ssh client(s) operational depending on the software release. The more recent updates (as of Spring 2019) have OpenSSH installed under Windows\System32\OpenSSH, with the usual complement of tools.

telnet

While using ssh is in general preferable for many reasons and foremost due to security concerns, sometimes there is a chicken and an egg problem where you need to establish access fast in order to debug ssh on a remote machine. In these cases, and if security is not a concern (rare, but could happen on an entirely internal network), one may opt to use telnet.

On Ubuntu one can install the software necessary to run the telnet service in the following manner:

sudo apt-get install xinetd telnetd

Make sure there is an entry in /etc/services which looks like

telnet        23/tcp

Also, create a file /etc/xinetd.d/telnet with contents similar to this:

service telnet {    
        disable         = no
        flags           = REUSE
        socket_type     = stream
        wait            = no
        user            = root
        server          = /usr/sbin/in.telnetd
        log_on_failure  += USERID HOST
        log_on_success  += PID HOST EXIT
        log_type        = FILE /var/log/xinetd.log
}

...and start the service as follows:

sudo /etc/init.d/xinetd start

pdsh

This is an advanced parallel shell designed for cluster management. It often uses ssh as the underlying protocol although there are other options as well. Configuration is defined by files residing in /etc/pdsh. For example, the file "machines" needs to contain the list of computers to be targeted by pdsh. Optionally, this is also the place for a file that can be sourced for convenience of setup, cf

# setup pdsh for cluster users
export PDSH_RCMD_TYPE='ssh'
export WCOLL='/etc/pdsh/machines'

This of course can be done from the command line anyway, cf

export PDSH_RCMD_TYPE=ssh

Using ssh as the underlying protocol for pdsh implies that you have set up private and public keys just like you normally would for ordinary ssh login. Once this is done, you should be able to do something like this as a basic test of your setup:

pdsh -w targetHost "ls"

If the targetHost is omitted, the command will be run against all machines listed in the "machines" file as explained above. Should a command fail on a particular machine, this will be indicated (with an error code) in the output of the command, with the name of the machine listed. Redirection of stderr with something like "2>/dev/null" included with the command you run won't work with pdsh.

Example of installation on CentOS:

yum install pdsh

curl

To post a form:

curl -X POST -F 'username=minime' -F 'password=something' http://blah.com
curl -X POST -F 'username=minime'  -H "Content-Type: application/x-www-form-urlencoded" http://blah.com

Miscellania

Linux Version and Distribution

cat /etc/os-release
lsb_release -a
hostnamectl
# Linux kernel version:
uname -r

This seems to work reliably:

cat /proc/version

Also,

cat /etc/*release
# or
cat /etc/issue*
# or
cat /proc/version

Linux User Management

https://www.digitalocean.com/community/tutorials/how-to-create-a-sudo-user-on-centos-quickstart

adduser username
passwd username

Use the usermod command to add the user to the wheel group.

usermod -aG wheel username

By default, on CentOS, members of the wheel group have sudo privileges.

Network

"nslookup" is a useful network information utility with diverse functionality. One simple function is to translate qualified host names to IP addresses and back.

"sha" headers one may need while installing xrootd can be obtained by running (on Ubuntu):

sudo apt-get install libssl-dev

...or as follows on CentOS

sudo yum install openssl openssl-devel

libssl may be necessary also for installation of pip3 etc.

A few other dependencies of xrootd can be met by installing glib2.0.

In case the network connection becomes stale, on Ubuntu:

sudo service network-manager restart

An extremely useful command (at least on Ubuntu) - lists IPs, DNSs etc:

nmcli device show

To see what process is listening on a given port:

lsof -i :8000

Shell

White space when using "sed":

$ sed -e "s/\s\{3,\}/  /g" inputFile
will substitute every sequence of at least 3 whitespaces with two spaces.

Produce a convenient timestamp for various uses:

date -d "today" +"%Y%m%d%H%M"

To get timestamps in history:

HISTTIMEFORMAT="%d/%m/%y %T "

"find"

find . -maxdepth 1 -mmin +400

'mmin' means it accepts minutes, 'mtime' days.

Find and recurcively delete directories modified more than 5 hours ago:

find . -maxdepth 1 -mindepth 1 -mmin +300 -exec rm -fr {} \;

If you don't specify 'mindepth', the current directory will show up in the results and will be deleted in the case presented above.

Find files modified in a particular date:

find . -type f -newermt 2018-04-11 ! -newermt 2018-04-12 -exec ls -l {} \;

Alternatively, this will find files between the two dates & times

touch -t 0810010000 /tmp/t1
touch -t 0810011000 /tmp/t2

find / -newer /tmp/t1 -and -not -newer /tmp/t2

"cksum" - calculates CRC and byte count.

Remove line breaks from a file:

echo $(cat $1)

Redirect stdout to one file and stderr to another file:

command > out 2>error

Redirect stderr to stdout (&1), and then redirect stdout to a file:

command >out 2>&1

Redirect both to a file:

command &> out


Find the name of the file, minus the complete path:

f=$(basename /home/maxim/JOB.html)
echo $f

SUDO

To change the password prompt timeout for sudo, you will need to run the command sudo visudo (which is the way to safely edit the sudoers file) and modify the following line by adding the timeout clause set to the desired number of minutes:

Defaults        env_reset, timestamp_timeout=XX

Crontab

  • minute (from 0 to 59)
  • hour (from 0 to 23)
  • day of month (from 1 to 31)
  • month (from 1 to 12)
  • day of week (from 0 to 6) (0=Sunday)


crontab -r # clear out your crontab
crontab -l # list your crontab

Checksum

xrdadler32

CVMFS

https://cernvm.cern.ch/portal/filesystem/downloads

sudo apt-get install cvmfs cvmfs-config-default
https://cernvm.cern.ch/portal/filesystem/quickstart

Encrypt a directory

tar cz myDir/ | mcrypt -k myPassword > myDir.z.nc

Version Control (git)

Git

Starting out

Notify git of your identity and ID:

git config --global user.email "yourname@yoursite.yourdomain"
git config --global user.name yourID

Pick a better editor for commit messages:

git config --global core.editor "nano"

To avoid entering git userID and password:

git config --global credential.helper 'cache --timeout 7200'

To address the usual "^M" problem when switching between Linux and Windows environments

$ git config --global core.autocrlf true
# Remove everything from the index
$ git rm --cached -r .

# Re-add all the deleted files to the index
# You should get lots of messages like: "warning: CRLF will be replaced by LF in <file>."
$ git diff --cached --name-only -z | xargs -0 git add

# Commit
$ git commit -m "Fix CRLF"

(Also see https://stackoverflow.com/questions/1889559/git-diff-to-ignore-m)

Restoring Files

First, see this link:

https://stackoverflow.com/questions/953481/find-and-restore-a-deleted-file-in-a-git-repository

A recipe that may work well:

git log --diff-filter=D --summary # finds deleted files
git checkout $commit~1 filename # where "$commit" stands for the actual commit name (a long string)

In the above, it's best to operate from the top level directory of the project and use path relative to that. Also, you may want to "git add" the restored files and commit them to make it permanent.

If you want to get a specific previous revision of a file, just capture the stdout of the following command:

git show $REV:$FILE

...and rename the output as you see fit.

Undoing a commit

See:

https://sethrobertson.github.io/GitFixUm/fixup.html

If you want to reverse your latest commit to the HEAD:

git reset --hard HEAD

To remove two or one last commits:

git reset --hard HEAD~2
git reset --hard HEAD~1

gitHub quirks

Sometimes a cloned repo will end up in a state where you can't push local content. Things you might want to try this:

git remote set-url origin https://myNameOnGithub@github.com/DUNE/dqmconfig.git

And in case it was not annoying enough, if you see something like "can't open display" this may help:

unset SSH_ASKPASS

Empty Commit

When you need to trigger an action on GitHub or in other similar situation the following "empty commit" can be used (and then pushed):

git commit -m 'rebuild pages' --allow-empty

LaTeX

One can choose to install all of tex packages or just a few:

apt install texlive texlive-humanities texlive-science

To see what is installed

dpkg -l

The little two-leter code at the front of each line says the status of the package. "ii" means installed and "rc" means removed but with config files still around ("dpkg --purge" or "apt-get remove --purge" gets rid of the "rc" but they are just harmless cruft).

Setting the environment for HTCondor

It is often desirable to dynamically modify the content of the condor submit file (typically having the JDL extension). While it does not appear possible to access the shell environment variables within the submit file directly, a similar effect can be obtained by setting the internal HTCondor parameters on the command line, cf:

condor_submit A=100 foo.jdl

Then, one can access the value of "A" within the JDL file as $(A).

To find a number of idle jobs:

/usr/bin/condor_q 2>&1| tail -1 | cut -d' ' -f 7