csml-wiki.northwestern.edu - User contributions [en]

General Usage of Quest

2015-03-25T18:38:10Z

Teirm:

<ul>
<li>Login
<pre>
ssh [netid]@quest.it.northwestern.edu
</pre>
where <tt>[netid]</tt> is your NETID. The first time you login, it will ask you to enter file in which to save the key and then to enter passphrase twice. Just press "enter" for these three questions and you should be able to login successfully.

Our group folder is located in /projects/b1011/luijten-group
</li>
<li>Example of job.mbs file
<pre>
# ### AUTOMATICALLY GENERATED BATCH FILE
#MOAB -q [queue_name]
#MOAB -A b1011
#MOAB -l walltime=[dd:hh:mm:ss]

# ###name of job
#MOAB -N [name_of_job]

# ### mail for begin/end/abort
#MOAB -m ea
#MOAB -M [email_address]

# ### number of nodes and processors per node
#MOAB -l nodes=2:ppn=6

# ### indicates that job should not rerun if it fails
#MOAB -r n

# ### stdout and stderr merged as stderr
#MOAB -j eo

# ### write stderr to file
#MOAB -e log.err

# ### the shell that interprets the job script
#MOAB -S /bin/bash

module load [module]
cd /projects/b1011/luijten-group/[job_location]
time mpirun -np 12 [directory_name]/[lammps_version] -in input.dat

if [ $? -eq 0 ] ; then
touch COMPLETED
fi
</pre>
<tt>[queue_name]</tt>
There are two options for queue name: collab or collab-preempt. Both of them have startup priority of 5000. Collab has maximum cores of 262 and maximum walltime of 7 days. There is no resource restrictions for collab-preempt, but note that queues ending in ‘-preempt’ contain jobs that can be interrupted and re-queued by jobs from a higher priority queue.

<tt>[dd:hh:mm:ss]</tt>
This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.

<tt>[name_of_job]</tt>
This is the name of your job that will be showed in the queue.

<tt>[email_address]</tt>
This is the email address you used to receive the system notice when job begins, aborted or ended.

<tt>[module]</tt>
Load a module. For mpirun this would be the module mpi. For full list of available modules run <i>module available</i> from the command line.

<tt>[job_location]</tt>
This is the address of the folder where your input file is located.

<tt>[directory_name]</tt>
This is the address of the lammps executable.

<tt>[lammps_version]</tt>
This is the build of lammps you want to run. Must be in [directory_name].

</li>
<li>Submit jobs
<pre>
msub job.mbs
</pre>
</li>
<li>Cancel jobs
<pre>
canceljob [job_number]
canceljob `seq [first_job_number] [last_job_number]`
</pre>
<li>Check job status
<pre>
showq
</pre>
show all jobs
<pre>
showq -r
</pre>
show running jobs
<pre>
showq -i
</pre>
show idle jobs
<pre>
showq -w user=[netid]
</pre>
where [netid] is your NETID. This command will show only jobs belonging to user specified.
<pre>
qstat
</pre>
show your own jobs
<pre>
checkjob [job_ID]
</pre>
This command displays detailed information about a submitted job’s status and diagnostic information that can be useful for troubleshooting submission issues. It can also be used to obtain useful information about completed jobs such as the allocated nodes, resources used, and exit codes. NUIT recommends using the flag ‘-vvv’ or ‘-v –v –v’ to gather additional diagnostic information.
</ul>

General Usage of Quest

2015-03-25T17:24:22Z

Teirm:

<ul>
<li>Login
<pre>
ssh [netid]@quest.it.northwestern.edu
</pre>
where <tt>[netid]</tt> is your NETID. The first time you login, it will ask you to enter file in which to save the key and then to enter passphrase twice. Just press "enter" for these three questions and you should be able to login successfully.

Our group folder is located in /projects/b1011/luijten-group
</li>
<li>Example of job.mbs file
<pre>
# ### AUTOMATICALLY GENERATED BATCH FILE
#MOAB -q [queue_name]
#MOAB -A b1011
#MOAB -l walltime=[dd:hh:mm:ss]

# ###name of job
#MOAB -N [name_of_job]

# ### mail for begin/end/abort
#MOAB -m ea
#MOAB -M [email_address]

# ### number of nodes and processors per node
#MOAB -l nodes=2:ppn=6

# ### indicates that job should not rerun if it fails
#MOAB -r n

# ### stdout and stderr merged as stderr
#MOAB -j eo

# ### write stderr to file
#MOAB -e log.err

# ### the shell that interprets the job script
#MOAB -S /bin/bash

module load [module]
cd /projects/b1011/luijten-group/[job_location]
time mpirun -np 12 [directory_name]/[lammps_version] -in input.dat

if [ $? -eq 0 ] ; then
touch COMPLETED
fi
</pre>
<tt>[queue_name]</tt>
There are two options for queue name: collab or collab-preempt. Both of them have startup priority of 5000. Collab has maximum cores of 262 and maximum walltime of 7 days. There is no resource restrictions for collab-preempt, but note that queues ending in ‘-preempt’ contain jobs that can be interrupted and re-queued by jobs from a higher priority queue.

<tt>[dd:hh:mm:ss]</tt>
This is the maximum allowed running time for your job. dd: days; hh: hours; mm: minutes; ss: seconds.

<tt>[name_of_job]</tt>
This is the name of your job that will be showed in the queue.

<tt>[email_address]</tt>
This is the email address you used to receive the system notice when job begins, aborted or ended.

<tt>[module]</tt>
Load a module. For mpirun this would be the module mpi. For full list of available modules run <i>module available</i> from the command line.

<tt>[job_location]</tt>
This is the address of the folder where your input file is located.

<tt>[directory_name]</tt>
This is the address of lammps executable.

<tt>[lammps_version]</tt>
This is the build of lammps you want to run. Must be in [directory_name]

</li>
<li>Submit jobs
<pre>
msub job.mbs
</pre>
</li>
<li>Cancel jobs
<pre>
canceljob [job_number]
canceljob `seq [first_job_number] [last_job_number]`
</pre>
<li>Check job status
<pre>
showq
</pre>
show all jobs
<pre>
showq -r
</pre>
show running jobs
<pre>
showq -i
</pre>
show idle jobs
<pre>
showq -w user=[netid]
</pre>
where [netid] is your NETID. This command will show only jobs belonging to user specified.
<pre>
qstat
</pre>
show your own jobs
<pre>
checkjob [job_ID]
</pre>
This command displays detailed information about a submitted job’s status and diagnostic information that can be useful for troubleshooting submission issues. It can also be used to obtain useful information about completed jobs such as the allocated nodes, resources used, and exit codes. NUIT recommends using the flag ‘-vvv’ or ‘-v –v –v’ to gather additional diagnostic information.
</ul>

Dropbox

2015-02-05T20:20:50Z

Teirm:

===Creating a Dropbox Folder on Your Machine===
It is easy to link your home folder with your Dropbox. By default, the Dropbox will be accessible as <tt>~/Dropbox</tt>. Before doing so, there are two important considerations:

* If you have a large Dropbox, you may wish to make sure that the Dropbox contents are not actually stored in your $HOME folder (where they would count against your quota). The easiest way to do this is to create a folder in your scratch partition (e.g., ~/Scratch/Dropbox) and then create a symbolic link to this folder, via
<pre>
ln -s /scratch/Dropbox ~/Dropbox
</pre>
The only drawback is that your scratch partition is typically only available on a few machines (e.g., not on ariadne itself).

* Clearly, if you store your Dropbox on scratch it will be ignored in the daily backup. However, even if you keep it actually in your home folder, the backup script will skip the Dropbox.

===Installing Dropbox===
* To install the dropbox daemon on your machine, run the following command from your terminal:
<pre>
$ cd ~ && wget -O - "https://www.dropbox.com/download?plat=lnx.x86_64" | tar xzf -
</pre>
* Next, run the Dropbox daemon from the newly created .dropbox-dist folder, using the following command:
<pre>
~/.dropbox-dist/dropboxd
</pre>

===Additional Notes===

* The Dropbox daemon (which synchronizes your ~/Dropbox folder with the actual Dropbox) starts automatically when you log in to the graphical desktop. However, if your machine is restarted (so that the daemon is killed) and you log in remotely (before logging in to the graphical desktop), the Dropbox daemon will have to be started manually. This is done via
<pre>
dropbox start
</pre>
'''It is important to do this ''only'' on your home machine.''' If you do it on multiple machines (or even by accident, by putting the <tt>dropbox start</tt> command in your <tt>~/.bashrc</tt> script --- ''clearly, do NOT do this!''), you will end up with conflicts, since multiple independent daemons will all start to synchronize the same folder.

* If you have NOT put your Dropbox on scratch and wish to change this, proceed as follows:
** On your home machine, stop the Dropbox daemon via <tt>dropbox stop</tt>
** Create the Dropbox folder on scratch
** Move the contents from ~/Dropbox to this new scratch folder
** Remove the (now empty) folder ~/Dropbox
** Create a symbolic link ~/Dropbox to the Dropbox folder on scratch (as described near the top of this page)
** Restart the Dropbox daemon via <tt>dropbox start</tt>

==Dropbox gets stuck "Connecting"==
Remove ~/.dropbox and ~/.dropbox-dist and reinstall. This results from stopping dropbox during the synch process or trying to selectively synch without first pausing.

Dropbox

2015-02-05T20:20:23Z

Teirm:

===Creating a Dropbox Folder on Your Machine===
It is easy to link your home folder with your Dropbox. By default, the Dropbox will be accessible as <tt>~/Dropbox</tt>. Before doing so, there are two important considerations:

* If you have a large Dropbox, you may wish to make sure that the Dropbox contents are not actually stored in your $HOME folder (where they would count against your quota). The easiest way to do this is to create a folder in your scratch partition (e.g., ~/Scratch/Dropbox) and then create a symbolic link to this folder, via
<pre>
ln -s /scratch/Dropbox ~/Dropbox
</pre>
The only drawback is that your scratch partition is typically only available on a few machines (e.g., not on ariadne itself).

* Clearly, if you store your Dropbox on scratch it will be ignored in the daily backup. However, even if you keep it actually in your home folder, the backup script will skip the Dropbox.

===Installing Dropbox===
* To install the dropbox daemon on your machine, run the following command from your terminal:
<pre>
$ cd ~ && wget -O - "https://www.dropbox.com/download?plat=lnx.x86_64" | tar xzf -
</pre>
* Next, run the Dropbox daemon from the newly created .dropbox-dist folder, using the following command:
<pre>
~/.dropbox-dist/dropboxd
</pre>

===Additional Notes===

* The Dropbox daemon (which synchronizes your ~/Dropbox folder with the actual Dropbox) starts automatically when you log in to the graphical desktop. However, if your machine is restarted (so that the daemon is killed) and you log in remotely (before logging in to the graphical desktop), the Dropbox daemon will have to be started manually. This is done via
<pre>
dropbox start
</pre>
'''It is important to do this ''only'' on your home machine.''' If you do it on multiple machines (or even by accident, by putting the <tt>dropbox start</tt> command in your <tt>~/.bashrc</tt> script --- ''clearly, do NOT do this!''), you will end up with conflicts, since multiple independent daemons will all start to synchronize the same folder.

* If you have NOT put your Dropbox on scratch and wish to change this, proceed as follows:
** On your home machine, stop the Dropbox daemon via <tt>dropbox stop</tt>
** Create the Dropbox folder on scratch
** Move the contents from ~/Dropbox to this new scratch folder
** Remove the (now empty) folder ~/Dropbox
** Create a symbolic link ~/Dropbox to the Dropbox folder on scratch (as described near the top of this page)
** Restart the Dropbox daemon via <tt>dropbox start</tt>

* Dropbox gets stuck "Connecting"
Remove ~/.dropbox and ~/.dropbox-dist and reinstall. This results from stopping dropbox during the synch process or trying to selectively synch without first pausing.

Dropbox

2015-02-05T20:20:01Z

Teirm:

===Creating a Dropbox Folder on Your Machine===
It is easy to link your home folder with your Dropbox. By default, the Dropbox will be accessible as <tt>~/Dropbox</tt>. Before doing so, there are two important considerations:

* If you have a large Dropbox, you may wish to make sure that the Dropbox contents are not actually stored in your $HOME folder (where they would count against your quota). The easiest way to do this is to create a folder in your scratch partition (e.g., ~/Scratch/Dropbox) and then create a symbolic link to this folder, via
<pre>
ln -s /scratch/Dropbox ~/Dropbox
</pre>
The only drawback is that your scratch partition is typically only available on a few machines (e.g., not on ariadne itself).

* Clearly, if you store your Dropbox on scratch it will be ignored in the daily backup. However, even if you keep it actually in your home folder, the backup script will skip the Dropbox.

===Installing Dropbox===
* To install the dropbox daemon on your machine, run the following command from your terminal:
<pre>
$ cd ~ && wget -O - "https://www.dropbox.com/download?plat=lnx.x86_64" | tar xzf -
</pre>
* Next, run the Dropbox daemon from the newly created .dropbox-dist folder, using the following command:
<pre>
~/.dropbox-dist/dropboxd
</pre>

===Additional Notes===

* The Dropbox daemon (which synchronizes your ~/Dropbox folder with the actual Dropbox) starts automatically when you log in to the graphical desktop. However, if your machine is restarted (so that the daemon is killed) and you log in remotely (before logging in to the graphical desktop), the Dropbox daemon will have to be started manually. This is done via
<pre>
dropbox start
</pre>
'''It is important to do this ''only'' on your home machine.''' If you do it on multiple machines (or even by accident, by putting the <tt>dropbox start</tt> command in your <tt>~/.bashrc</tt> script --- ''clearly, do NOT do this!''), you will end up with conflicts, since multiple independent daemons will all start to synchronize the same folder.

* If you have NOT put your Dropbox on scratch and wish to change this, proceed as follows:
** On your home machine, stop the Dropbox daemon via <tt>dropbox stop</tt>
** Create the Dropbox folder on scratch
** Move the contents from ~/Dropbox to this new scratch folder
** Remove the (now empty) folder ~/Dropbox
** Create a symbolic link ~/Dropbox to the Dropbox folder on scratch (as described near the top of this page)
** Restart the Dropbox daemon via <tt>dropbox start</tt>

* Dropbox gets stuck "Connecting"
Remove ~/.dropbox and ~/.dropbox-dist and reinstall. This results from stopping dropbox during the synch process or trying to selectively synch without first pausing.

Password-less login via ssh

2014-12-30T04:06:58Z

Teirm:

[http://www.linuxproblem.org/art_9.html Password-less login via ssh]