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

Synology diskstation

2019-06-25T17:52:39Z

Tc387: /* Using Synology for OS X Time Machine backups */

Pergamon is a Synology diskstation that can be accessed in a number of ways. It offers each group member 1 TB of storage space (this may be expanded in the future).

== Usage scenarios ==

=== Logging in via ssh ===

You have the same username as on the main cluster. Log in from your workstation via 'ssh pergamon'. This is not a full Linux implementation; the main purpose of the shell is to navigate around the file system. Your home folder is '/volume1/homes/USERNAME'.

=== Web access ===

https://pergamon.ms.northwestern.edu:5001

=== Copying data to diskstation via scp ===

You can use scp as you would use it for copying files to any other machine:
<pre>
scp LOCAL_FILES pergamon:
</pre>

=== Copying data to diskstation via rsync ===

You must specify your home folder, i.e., from your workstation do
<pre>
rsync -avz LOCAL_FILES pergamon:/volume1/homes/USERNAME
</pre>

=== Mounting your Synology folder on OS X ===

On your Mac, start Finder, select 'Go' and then 'Connect to Server'. In server address, enter:
<pre>
afp://pergamon.ms.northwestern.edu
</pre>
From the folders offered, select 'home'. This folder is now available in Finder under 'Shared: pergamon' and from the command line on your Mac via '/Volumes/home'.

As an alternative, you can also mount your folder via the WebDAV protocol. This works in the same way, except that you enter the following for the server address:
<pre>
https://pergamon.ms.northwestern.edu:5006
</pre>

=== Using Synology for OS X Time Machine backups ===

Once the pergamon drive is mounted you can use it as a backup drive with Time Machine on a Mac OS. Simply chose the appropriate pergamon drive (e.g. home) in Time Machine and the backup should begin. Depending on the size of your disk the first backup might take up to two days. After the first backup the Time Machine will perform regular hourly backups whenever connected to the internet with pergamon drive mounted. Time Machine will create a folder "xx.sparsebundle", where "xx" is your computer name, within which all backup files are kept. Note the standard quota per user is 1TB (as of June 2019) so you might want to delete old backups manually to avoid overfilling the drive. When restoring files the Time Machine will take more time to load as compared to having an USB backup drive which is due to bandwidth limitations of the network connection.

=== Accessing your Synology folder on your Linux workstation via WebDAV ===

On Ubuntu, open Nautilus (see e.g. https://www.synology.com/en-global/knowledgebase/tutorials/610#t2_3) and choose '''Connect to server'''. Then enter as ''Server Address'':
<pre>
davs://pergamon.ms.northwestern.edu:5006
</pre>

On openSuSE, open Dolphin (from launcher go to "Computer" and then "Network"). Then choose '''Add Network Folder'''. In the dialog box, enter:
* '''Name:''' Pergamon
* '''User:''' your username
* '''Server:''' pergamon.ms.northwestern.edu
* '''Port:''' 5006
* '''Folder:''' /
* Check '''Use encryption'''. It is possible that the port is then reset to 443. If this happens, change it back to 5006.

Then proceed via '''Save & Connect'''. You will receive a warning about the SSL certificate. Accept this.

=== Mounting your Synology folder on your Linux workstation via WebDAV ===

Prerequisite: the davfs driver must have been installed and configured, see below under 'Enabling davfs'. Then, as regular user, do
<pre>
mount /mnt/pergamon
</pre>

To unmount, do
<pre>
umount /mnt/pergamon
</pre>

This works well, but one problem I observed is that the creation time of folders copied TO the Synology folder is not preserved when using 'cp -p' or 'cp -a'. In principle this should be possible (they are preserved when using rsync), so this appears to be a bug.

=== Mounting your Synology folder on your Linux workstation via NFS ===

This is technically possible, but currently not enabled.

== Administration ==

=== Creating a new user ===

* On the Control Panel, select ''User'', ''Create''.

** Choose the same username as in NIS.

** '''Join groups''': Only ''users''.

** '''Assign shared folder permissions''': ''read/write'' to '''homes''', ''no access'' to all other folders.

** '''User quota settings''': 1000 GB.

** '''Assign application permissions''':

** '''User speed limit setting''': no limit.

* After this, log in as root, and change /etc/passwd, such that for the new users '''/sbin/nologin''' is replaced with '''/bin/sh'''

* Also, while logged in as root, do '''chmod og-rx /volume1/homes/newuser''' (where '''newuser''' is the new username)

=== Enabling davfs on Linux ===

These instructions are for openSuSE 13.1.

* Install davfs2 (see https://software.opensuse.org/package/davfs2)
* Add this line to '''/etc/fstab''':
<pre>
https://pergamon:5006 /mnt/pergamon davfs rw,noauto,user,file_mode=600,dir_mode=700 0 0
</pre>
* Create mount point:
<pre>
mkdir /mnt/pergamon
</pre>

Synology diskstation

2019-06-25T17:27:21Z

Tc387: /* Using Synology for OS X Time Machine backups */

Pergamon is a Synology diskstation that can be accessed in a number of ways. It offers each group member 1 TB of storage space (this may be expanded in the future).

== Usage scenarios ==

=== Logging in via ssh ===

You have the same username as on the main cluster. Log in from your workstation via 'ssh pergamon'. This is not a full Linux implementation; the main purpose of the shell is to navigate around the file system. Your home folder is '/volume1/homes/USERNAME'.

=== Web access ===

https://pergamon.ms.northwestern.edu:5001

=== Copying data to diskstation via scp ===

You can use scp as you would use it for copying files to any other machine:
<pre>
scp LOCAL_FILES pergamon:
</pre>

=== Copying data to diskstation via rsync ===

You must specify your home folder, i.e., from your workstation do
<pre>
rsync -avz LOCAL_FILES pergamon:/volume1/homes/USERNAME
</pre>

=== Mounting your Synology folder on OS X ===

On your Mac, start Finder, select 'Go' and then 'Connect to Server'. In server address, enter:
<pre>
afp://pergamon.ms.northwestern.edu
</pre>
From the folders offered, select 'home'. This folder is now available in Finder under 'Shared: pergamon' and from the command line on your Mac via '/Volumes/home'.

As an alternative, you can also mount your folder via the WebDAV protocol. This works in the same way, except that you enter the following for the server address:
<pre>
https://pergamon.ms.northwestern.edu:5006
</pre>

=== Using Synology for OS X Time Machine backups ===

Once the pergamon drive is mounted you can use it as a back up drive with Time Machine on a Mac OS. Simply chose the appropriate pergamon drive (e.g. home) in Time Machine and the backup should begin. Depending on the size of your disk the first backup might take up to two days. After the first backup the Time Machine will perform regular hourly backups whenever connected to the internet with pergamon drive mounted. Time Machine will create a folder "xx.sparsebundle", where "xx" is your computer name, within which all backup files are kept. Note the standard quota per user is 1TB (as of June 2019) so you might want to delete old backups manually to avoid overfilling the drive. When restoring files the Time Machine will take more time to load as compared to having an USB backup drive which is due to bandwidth limitations of the network connection.

=== Accessing your Synology folder on your Linux workstation via WebDAV ===

On Ubuntu, open Nautilus (see e.g. https://www.synology.com/en-global/knowledgebase/tutorials/610#t2_3) and choose '''Connect to server'''. Then enter as ''Server Address'':
<pre>
davs://pergamon.ms.northwestern.edu:5006
</pre>

On openSuSE, open Dolphin (from launcher go to "Computer" and then "Network"). Then choose '''Add Network Folder'''. In the dialog box, enter:
* '''Name:''' Pergamon
* '''User:''' your username
* '''Server:''' pergamon.ms.northwestern.edu
* '''Port:''' 5006
* '''Folder:''' /
* Check '''Use encryption'''. It is possible that the port is then reset to 443. If this happens, change it back to 5006.

Then proceed via '''Save & Connect'''. You will receive a warning about the SSL certificate. Accept this.

=== Mounting your Synology folder on your Linux workstation via WebDAV ===

Prerequisite: the davfs driver must have been installed and configured, see below under 'Enabling davfs'. Then, as regular user, do
<pre>
mount /mnt/pergamon
</pre>

To unmount, do
<pre>
umount /mnt/pergamon
</pre>

This works well, but one problem I observed is that the creation time of folders copied TO the Synology folder is not preserved when using 'cp -p' or 'cp -a'. In principle this should be possible (they are preserved when using rsync), so this appears to be a bug.

=== Mounting your Synology folder on your Linux workstation via NFS ===

This is technically possible, but currently not enabled.

== Administration ==

=== Creating a new user ===

* On the Control Panel, select ''User'', ''Create''.

** Choose the same username as in NIS.

** '''Join groups''': Only ''users''.

** '''Assign shared folder permissions''': ''read/write'' to '''homes''', ''no access'' to all other folders.

** '''User quota settings''': 1000 GB.

** '''Assign application permissions''':

** '''User speed limit setting''': no limit.

* After this, log in as root, and change /etc/passwd, such that for the new users '''/sbin/nologin''' is replaced with '''/bin/sh'''

* Also, while logged in as root, do '''chmod og-rx /volume1/homes/newuser''' (where '''newuser''' is the new username)

=== Enabling davfs on Linux ===

These instructions are for openSuSE 13.1.

* Install davfs2 (see https://software.opensuse.org/package/davfs2)
* Add this line to '''/etc/fstab''':
<pre>
https://pergamon:5006 /mnt/pergamon davfs rw,noauto,user,file_mode=600,dir_mode=700 0 0
</pre>
* Create mount point:
<pre>
mkdir /mnt/pergamon
</pre>

Synology diskstation

2019-06-25T17:26:58Z

Tc387: /* Using Synology for OS X Time Machine backups */

Pergamon is a Synology diskstation that can be accessed in a number of ways. It offers each group member 1 TB of storage space (this may be expanded in the future).

== Usage scenarios ==

=== Logging in via ssh ===

You have the same username as on the main cluster. Log in from your workstation via 'ssh pergamon'. This is not a full Linux implementation; the main purpose of the shell is to navigate around the file system. Your home folder is '/volume1/homes/USERNAME'.

=== Web access ===

https://pergamon.ms.northwestern.edu:5001

=== Copying data to diskstation via scp ===

You can use scp as you would use it for copying files to any other machine:
<pre>
scp LOCAL_FILES pergamon:
</pre>

=== Copying data to diskstation via rsync ===

You must specify your home folder, i.e., from your workstation do
<pre>
rsync -avz LOCAL_FILES pergamon:/volume1/homes/USERNAME
</pre>

=== Mounting your Synology folder on OS X ===

On your Mac, start Finder, select 'Go' and then 'Connect to Server'. In server address, enter:
<pre>
afp://pergamon.ms.northwestern.edu
</pre>
From the folders offered, select 'home'. This folder is now available in Finder under 'Shared: pergamon' and from the command line on your Mac via '/Volumes/home'.

As an alternative, you can also mount your folder via the WebDAV protocol. This works in the same way, except that you enter the following for the server address:
<pre>
https://pergamon.ms.northwestern.edu:5006
</pre>

=== Using Synology for OS X Time Machine backups ===

Once the pergamon drive is mounted you can use it as a back up drive with Time Machine on a Mac OS. Simply chose the appropriate pergamon drive (e.g. home) in Time Machine and the backup should begin. Depending on the size of your disk the first backup might take up to two days. After the first backup the Time Machine will perform regular hourly backups whenever connected to the internet with pergamon drive mounted. These bakups Time Machine will create a folder "xx.sparsebundle", where "xx" is your computer name, within which all backup files are kept. Note the standard quota per user is 1TB (as of June 2019) so you might want to delete old backups manually to avoid overfilling the drive. When restoring files the Time Machine will take more time to load as compared to having an USB backup drive which is due to bandwidth limitations of the network connection.

=== Accessing your Synology folder on your Linux workstation via WebDAV ===

On Ubuntu, open Nautilus (see e.g. https://www.synology.com/en-global/knowledgebase/tutorials/610#t2_3) and choose '''Connect to server'''. Then enter as ''Server Address'':
<pre>
davs://pergamon.ms.northwestern.edu:5006
</pre>

On openSuSE, open Dolphin (from launcher go to "Computer" and then "Network"). Then choose '''Add Network Folder'''. In the dialog box, enter:
* '''Name:''' Pergamon
* '''User:''' your username
* '''Server:''' pergamon.ms.northwestern.edu
* '''Port:''' 5006
* '''Folder:''' /
* Check '''Use encryption'''. It is possible that the port is then reset to 443. If this happens, change it back to 5006.

Then proceed via '''Save & Connect'''. You will receive a warning about the SSL certificate. Accept this.

=== Mounting your Synology folder on your Linux workstation via WebDAV ===

Prerequisite: the davfs driver must have been installed and configured, see below under 'Enabling davfs'. Then, as regular user, do
<pre>
mount /mnt/pergamon
</pre>

To unmount, do
<pre>
umount /mnt/pergamon
</pre>

This works well, but one problem I observed is that the creation time of folders copied TO the Synology folder is not preserved when using 'cp -p' or 'cp -a'. In principle this should be possible (they are preserved when using rsync), so this appears to be a bug.

=== Mounting your Synology folder on your Linux workstation via NFS ===

This is technically possible, but currently not enabled.

== Administration ==

=== Creating a new user ===

* On the Control Panel, select ''User'', ''Create''.

** Choose the same username as in NIS.

** '''Join groups''': Only ''users''.

** '''Assign shared folder permissions''': ''read/write'' to '''homes''', ''no access'' to all other folders.

** '''User quota settings''': 1000 GB.

** '''Assign application permissions''':

** '''User speed limit setting''': no limit.

* After this, log in as root, and change /etc/passwd, such that for the new users '''/sbin/nologin''' is replaced with '''/bin/sh'''

* Also, while logged in as root, do '''chmod og-rx /volume1/homes/newuser''' (where '''newuser''' is the new username)

=== Enabling davfs on Linux ===

These instructions are for openSuSE 13.1.

* Install davfs2 (see https://software.opensuse.org/package/davfs2)
* Add this line to '''/etc/fstab''':
<pre>
https://pergamon:5006 /mnt/pergamon davfs rw,noauto,user,file_mode=600,dir_mode=700 0 0
</pre>
* Create mount point:
<pre>
mkdir /mnt/pergamon
</pre>

Synology diskstation

2019-06-25T17:26:04Z

Tc387: /* Using Synology for OSX Time Machine backups */

Pergamon is a Synology diskstation that can be accessed in a number of ways. It offers each group member 1 TB of storage space (this may be expanded in the future).

== Usage scenarios ==

=== Logging in via ssh ===

You have the same username as on the main cluster. Log in from your workstation via 'ssh pergamon'. This is not a full Linux implementation; the main purpose of the shell is to navigate around the file system. Your home folder is '/volume1/homes/USERNAME'.

=== Web access ===

https://pergamon.ms.northwestern.edu:5001

=== Copying data to diskstation via scp ===

You can use scp as you would use it for copying files to any other machine:
<pre>
scp LOCAL_FILES pergamon:
</pre>

=== Copying data to diskstation via rsync ===

You must specify your home folder, i.e., from your workstation do
<pre>
rsync -avz LOCAL_FILES pergamon:/volume1/homes/USERNAME
</pre>

=== Mounting your Synology folder on OS X ===

On your Mac, start Finder, select 'Go' and then 'Connect to Server'. In server address, enter:
<pre>
afp://pergamon.ms.northwestern.edu
</pre>
From the folders offered, select 'home'. This folder is now available in Finder under 'Shared: pergamon' and from the command line on your Mac via '/Volumes/home'.

As an alternative, you can also mount your folder via the WebDAV protocol. This works in the same way, except that you enter the following for the server address:
<pre>
https://pergamon.ms.northwestern.edu:5006
</pre>

=== Using Synology for OS X Time Machine backups ===

Once the pergamon drive is mounted you can use it as a back up drive with Time Machine on a Mac OS. Simply chose the appropriate pergamon drive (e.g. home) in Time Machine and the backup should begin. Depending on the size of your disk the first backup might take up to two days. After the first backup the Time Machine will perform regular hourly backups whenever connected to the internet and pergamon is mounted. These bakups Time Machine will create a folder "xx.sparsebundle", where "xx" is your computer name, within which all backup files are kept. Note the standard quota per user is 1TB (as of June 2019) so you might want to delete old backups manually to avoid overfilling the drive. When restoring files the Time Machine will take more time to load as compared to having an USB backup drive which is due to bandwidth limitations of the network connection.

=== Accessing your Synology folder on your Linux workstation via WebDAV ===

On Ubuntu, open Nautilus (see e.g. https://www.synology.com/en-global/knowledgebase/tutorials/610#t2_3) and choose '''Connect to server'''. Then enter as ''Server Address'':
<pre>
davs://pergamon.ms.northwestern.edu:5006
</pre>

On openSuSE, open Dolphin (from launcher go to "Computer" and then "Network"). Then choose '''Add Network Folder'''. In the dialog box, enter:
* '''Name:''' Pergamon
* '''User:''' your username
* '''Server:''' pergamon.ms.northwestern.edu
* '''Port:''' 5006
* '''Folder:''' /
* Check '''Use encryption'''. It is possible that the port is then reset to 443. If this happens, change it back to 5006.

Then proceed via '''Save & Connect'''. You will receive a warning about the SSL certificate. Accept this.

=== Mounting your Synology folder on your Linux workstation via WebDAV ===

Prerequisite: the davfs driver must have been installed and configured, see below under 'Enabling davfs'. Then, as regular user, do
<pre>
mount /mnt/pergamon
</pre>

To unmount, do
<pre>
umount /mnt/pergamon
</pre>

This works well, but one problem I observed is that the creation time of folders copied TO the Synology folder is not preserved when using 'cp -p' or 'cp -a'. In principle this should be possible (they are preserved when using rsync), so this appears to be a bug.

=== Mounting your Synology folder on your Linux workstation via NFS ===

This is technically possible, but currently not enabled.

== Administration ==

=== Creating a new user ===

* On the Control Panel, select ''User'', ''Create''.

** Choose the same username as in NIS.

** '''Join groups''': Only ''users''.

** '''Assign shared folder permissions''': ''read/write'' to '''homes''', ''no access'' to all other folders.

** '''User quota settings''': 1000 GB.

** '''Assign application permissions''':

** '''User speed limit setting''': no limit.

* After this, log in as root, and change /etc/passwd, such that for the new users '''/sbin/nologin''' is replaced with '''/bin/sh'''

* Also, while logged in as root, do '''chmod og-rx /volume1/homes/newuser''' (where '''newuser''' is the new username)

=== Enabling davfs on Linux ===

These instructions are for openSuSE 13.1.

* Install davfs2 (see https://software.opensuse.org/package/davfs2)
* Add this line to '''/etc/fstab''':
<pre>
https://pergamon:5006 /mnt/pergamon davfs rw,noauto,user,file_mode=600,dir_mode=700 0 0
</pre>
* Create mount point:
<pre>
mkdir /mnt/pergamon
</pre>

Synology diskstation

2019-06-25T17:25:50Z

Tc387: /* Usage scenarios */

Pergamon is a Synology diskstation that can be accessed in a number of ways. It offers each group member 1 TB of storage space (this may be expanded in the future).

== Usage scenarios ==

=== Logging in via ssh ===

You have the same username as on the main cluster. Log in from your workstation via 'ssh pergamon'. This is not a full Linux implementation; the main purpose of the shell is to navigate around the file system. Your home folder is '/volume1/homes/USERNAME'.

=== Web access ===

https://pergamon.ms.northwestern.edu:5001

=== Copying data to diskstation via scp ===

You can use scp as you would use it for copying files to any other machine:
<pre>
scp LOCAL_FILES pergamon:
</pre>

=== Copying data to diskstation via rsync ===

You must specify your home folder, i.e., from your workstation do
<pre>
rsync -avz LOCAL_FILES pergamon:/volume1/homes/USERNAME
</pre>

=== Mounting your Synology folder on OS X ===

On your Mac, start Finder, select 'Go' and then 'Connect to Server'. In server address, enter:
<pre>
afp://pergamon.ms.northwestern.edu
</pre>
From the folders offered, select 'home'. This folder is now available in Finder under 'Shared: pergamon' and from the command line on your Mac via '/Volumes/home'.

As an alternative, you can also mount your folder via the WebDAV protocol. This works in the same way, except that you enter the following for the server address:
<pre>
https://pergamon.ms.northwestern.edu:5006
</pre>

=== Using Synology for OSX Time Machine backups ===

Once the pergamon drive is mounted you can use it as a back up drive with Time Machine on a Mac OS. Simply chose the appropriate pergamon drive (e.g. home) in Time Machine and the backup should begin. Depending on the size of your disk the first backup might take up to two days. After the first backup the Time Machine will perform regular hourly backups whenever connected to the internet and pergamon is mounted. These bakups Time Machine will create a folder "xx.sparsebundle", where "xx" is your computer name, within which all backup files are kept. Note the standard quota per user is 1TB (as of June 2019) so you might want to delete old backups manually to avoid overfilling the drive. When restoring files the Time Machine will take more time to load as compared to having an USB backup drive which is due to bandwidth limitations of the network connection.

=== Accessing your Synology folder on your Linux workstation via WebDAV ===

On Ubuntu, open Nautilus (see e.g. https://www.synology.com/en-global/knowledgebase/tutorials/610#t2_3) and choose '''Connect to server'''. Then enter as ''Server Address'':
<pre>
davs://pergamon.ms.northwestern.edu:5006
</pre>

On openSuSE, open Dolphin (from launcher go to "Computer" and then "Network"). Then choose '''Add Network Folder'''. In the dialog box, enter:
* '''Name:''' Pergamon
* '''User:''' your username
* '''Server:''' pergamon.ms.northwestern.edu
* '''Port:''' 5006
* '''Folder:''' /
* Check '''Use encryption'''. It is possible that the port is then reset to 443. If this happens, change it back to 5006.

Then proceed via '''Save & Connect'''. You will receive a warning about the SSL certificate. Accept this.

=== Mounting your Synology folder on your Linux workstation via WebDAV ===

Prerequisite: the davfs driver must have been installed and configured, see below under 'Enabling davfs'. Then, as regular user, do
<pre>
mount /mnt/pergamon
</pre>

To unmount, do
<pre>
umount /mnt/pergamon
</pre>

This works well, but one problem I observed is that the creation time of folders copied TO the Synology folder is not preserved when using 'cp -p' or 'cp -a'. In principle this should be possible (they are preserved when using rsync), so this appears to be a bug.

=== Mounting your Synology folder on your Linux workstation via NFS ===

This is technically possible, but currently not enabled.

== Administration ==

=== Creating a new user ===

* On the Control Panel, select ''User'', ''Create''.

** Choose the same username as in NIS.

** '''Join groups''': Only ''users''.

** '''Assign shared folder permissions''': ''read/write'' to '''homes''', ''no access'' to all other folders.

** '''User quota settings''': 1000 GB.

** '''Assign application permissions''':

** '''User speed limit setting''': no limit.

* After this, log in as root, and change /etc/passwd, such that for the new users '''/sbin/nologin''' is replaced with '''/bin/sh'''

* Also, while logged in as root, do '''chmod og-rx /volume1/homes/newuser''' (where '''newuser''' is the new username)

=== Enabling davfs on Linux ===

These instructions are for openSuSE 13.1.

* Install davfs2 (see https://software.opensuse.org/package/davfs2)
* Add this line to '''/etc/fstab''':
<pre>
https://pergamon:5006 /mnt/pergamon davfs rw,noauto,user,file_mode=600,dir_mode=700 0 0
</pre>
* Create mount point:
<pre>
mkdir /mnt/pergamon
</pre>

Synology diskstation

2019-06-25T17:24:10Z

Tc387: /* Mounting your Synology folder on OS X */

Pergamon is a Synology diskstation that can be accessed in a number of ways. It offers each group member 1 TB of storage space (this may be expanded in the future).

== Usage scenarios ==

=== Logging in via ssh ===

You have the same username as on the main cluster. Log in from your workstation via 'ssh pergamon'. This is not a full Linux implementation; the main purpose of the shell is to navigate around the file system. Your home folder is '/volume1/homes/USERNAME'.

=== Web access ===

https://pergamon.ms.northwestern.edu:5001

=== Copying data to diskstation via scp ===

You can use scp as you would use it for copying files to any other machine:
<pre>
scp LOCAL_FILES pergamon:
</pre>

=== Copying data to diskstation via rsync ===

You must specify your home folder, i.e., from your workstation do
<pre>
rsync -avz LOCAL_FILES pergamon:/volume1/homes/USERNAME
</pre>

=== Mounting your Synology folder on OS X ===

On your Mac, start Finder, select 'Go' and then 'Connect to Server'. In server address, enter:
<pre>
afp://pergamon.ms.northwestern.edu
</pre>
From the folders offered, select 'home'. This folder is now available in Finder under 'Shared: pergamon' and from the command line on your Mac via '/Volumes/home'.

As an alternative, you can also mount your folder via the WebDAV protocol. This works in the same way, except that you enter the following for the server address:
<pre>
https://pergamon.ms.northwestern.edu:5006
</pre>

Once the pergamon drive is mounted you can use it as a back up drive with Time Machine on a Mac OS. Simply chose the appropriate pergamon drive (e.g. home) in Time Machine and the backup should begin. Depending on the size of your disk the first backup might take up to two days. After the first backup the Time Machine will perform regular hourly backups whenever connected to the internet and pergamon is mounted. These bakups Time Machine will create a folder "xx.sparsebundle", where "xx" is your computer name, within which all backup files are kept. Note the standard quota per user is 1TB (as of June 2019) so you might want to delete old backups manually to avoid overfilling the drive. When restoring files the Time Machine will take more time to load as compared to having an USB backup drive which is due to bandwidth limitations of the network connection.

=== Accessing your Synology folder on your Linux workstation via WebDAV ===

On Ubuntu, open Nautilus (see e.g. https://www.synology.com/en-global/knowledgebase/tutorials/610#t2_3) and choose '''Connect to server'''. Then enter as ''Server Address'':
<pre>
davs://pergamon.ms.northwestern.edu:5006
</pre>

On openSuSE, open Dolphin (from launcher go to "Computer" and then "Network"). Then choose '''Add Network Folder'''. In the dialog box, enter:
* '''Name:''' Pergamon
* '''User:''' your username
* '''Server:''' pergamon.ms.northwestern.edu
* '''Port:''' 5006
* '''Folder:''' /
* Check '''Use encryption'''. It is possible that the port is then reset to 443. If this happens, change it back to 5006.

Then proceed via '''Save & Connect'''. You will receive a warning about the SSL certificate. Accept this.

=== Mounting your Synology folder on your Linux workstation via WebDAV ===

Prerequisite: the davfs driver must have been installed and configured, see below under 'Enabling davfs'. Then, as regular user, do
<pre>
mount /mnt/pergamon
</pre>

To unmount, do
<pre>
umount /mnt/pergamon
</pre>

This works well, but one problem I observed is that the creation time of folders copied TO the Synology folder is not preserved when using 'cp -p' or 'cp -a'. In principle this should be possible (they are preserved when using rsync), so this appears to be a bug.

=== Mounting your Synology folder on your Linux workstation via NFS ===

This is technically possible, but currently not enabled.

== Administration ==

=== Creating a new user ===

* On the Control Panel, select ''User'', ''Create''.

** Choose the same username as in NIS.

** '''Join groups''': Only ''users''.

** '''Assign shared folder permissions''': ''read/write'' to '''homes''', ''no access'' to all other folders.

** '''User quota settings''': 1000 GB.

** '''Assign application permissions''':

** '''User speed limit setting''': no limit.

* After this, log in as root, and change /etc/passwd, such that for the new users '''/sbin/nologin''' is replaced with '''/bin/sh'''

* Also, while logged in as root, do '''chmod og-rx /volume1/homes/newuser''' (where '''newuser''' is the new username)

=== Enabling davfs on Linux ===

These instructions are for openSuSE 13.1.

* Install davfs2 (see https://software.opensuse.org/package/davfs2)
* Add this line to '''/etc/fstab''':
<pre>
https://pergamon:5006 /mnt/pergamon davfs rw,noauto,user,file_mode=600,dir_mode=700 0 0
</pre>
* Create mount point:
<pre>
mkdir /mnt/pergamon
</pre>

Installation instructions for OpenSuSE Leap 15.0

2019-05-03T22:23:53Z

Tc387:

* If the installation program hangs almost right away on a PCI-related message, add the boot option "nomodeset" and retry.
* Do not 'upgrade' from an earlier version. Choose 'new install', but use extreme care not to interfere with existing scratch partitions.
* Select the following additional software categories:
** Console tools
** File server
* Unselect:
** Games
* Network configuration:
** Firewall enabled, SSH open
** Static IP address, subnet mask: 255.255.255.0
** DNS: 129.105.1.1, 129.105.49.1, 8.8.8.8
** Domain search: 'ms.northwestern.edu' and 'northwestern.edu'
** Gateway (under 'routing' tab): 129.105.92.1
* After install, in Software Management add:
** In "RPM groups" tab: gcc-fortran, gcc7-c++
** Via "Search" tab: motif, motif-devel, glibc-devel-static, lsb, ncftp, nethogs, pico, MozillaThunderbird, libreadline6, apcupsd, apcupsd-cgi, apcupsd-gui, vlc, emacs-auctex, xmgrace, libappindicator3-1, libgdk_pixbuf-2_0-0-32bit, libgtk-2_0-0-32bit, libxml2-2-32bit, lynx, mmv, readline-devel, xosview, xsane
* In YaST, Network Services:
** NIS client: Domain "el"; Server 129.105.92.12; Open Port in Firewall
** NSF client: Mount /home (options: defaults,rw) and /usr/local from ariadne (options: defaults)
** NTP configuration: Start NTP daemon now and on boot; add server 129.105.92.12
* Connect TO the new machine from ariadne, as root. This will add the host key to ~/.ssh/known_hosts. From there, copy it to /etc/ssh/ssh_known_hosts (still on ariadne). Also, between the hostname and the IP address, add the FQDN of the new machine, so that that is also associate with the same host key.
* Then, as root '''on the new machine''', do:
** ln -s /usr/local/etc/profile.local /etc
** ln -s /usr/local/etc/ssh/ssh_known_hosts /etc/ssh
** add the file /usr/local/etc/hosts_list to /etc/hosts
** scp nestor:/etc/motd /etc (and then edit this file to represent the new machine; "nvidia-smi" is a useful program to find the videocard installed)
** texconfig (and set default paper size to 'letter')
** in /etc/ssh/ssh_config set "ForwardX11 yes"
** in /etc/ssh/sshd_config confirm that "X11Forwarding" is set to "yes"
** in /etc/ssh/sshd_config change "#AuthorizedKeysFile" to ".ssh/authorized_keys2"
** scp telemachos:/root/.bashrc ~
** scp telemachos:/etc/hosts.allow /etc
** scp telemachos:/etc/hosts.deny /etc
* Install debugging software packages via YaST:
** In Software Repositories, enable openSUSE-Leap-15.0-Debug and openSUSE-Leap-15.0-Update-Debug.
** Go to Software Management, select glibc-debuginfo [NOTE: Does not seem to be available through these repositories]
* [[Setting up e-mail notifications for Linux Software RAID]].
* YaST -> Software: Online Update.
* Install Chrome:
** <nowiki>wget https://dl.google.com/linux/direct/google-chrome-stable_current_x86_64.rpm</nowiki>
** rpm -ivh google-chrome-stable_current_x86_64.rpm
** ln -s /usr/bin/google-chrome /usr/bin/chrome
* Install ffmpeg:
** Add packman repository (from command line): zypper addrepo -f <nowiki>http://packman.inode.at/suse/openSUSE_Leap_15.0/</nowiki> packman
** Go into Yast - Software Management. Remove "ffmpeg" and install "ffmpeg-3" from Packman repository (this is necessary to encode h.264 videos)
-----

* Add NVIDIA driver (follow the recommend method via "community repository" and the "zypper inr", followed by a reboot):
** http://en.opensuse.org/SDB:NVIDIA_drivers

* YaST -> Hardware -> Printer -> Printer via Network -> Connection Wizard -> TCP/JetDirect; after installation, configure default options via http://localhost:631

Tools

2019-03-23T16:21:26Z

Tc387: /* UNIX */

=== Data analysis tools ===

Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML.

* [[Autocorrelation]]
* [[Generic Analyzer]]
* [[Gnuplot]]
* [[Compressed data files]]

=== Programming ===
* [[Compiler notes]]
* [[Debugging]]
* [[Programming notes]]

=== Document processing ===

Ideally, we prepare manuscripts in [http://en.wikipedia.org/wiki/LaTeX LaTeX]. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word.

* [[Notes on using LaTeX for manuscripts]]
* [[Notes on using Microsoft Word for manuscripts]]

=== Job submission and scheduling ===
* [[Notes on Torque]]
* [[Notes on Maui]]

=== UNIX ===
* [http://www.linuxproblem.org/art_9.html Password-less login via ssh]
* Short version of password-less login: (1) go to your home folder (e.g. ariadne:~/ ). (2) type "ssh-keygen" and press the enter key a few times to leave all answers blank (unless you are prompted to override the existing key in which case you should type "yes"). (3) type "ssh-copy-id XX" , where "XX" is the server name or IP address you wish to ssh into and enter the password. You can repeat this step and add multiple addresses. (4) On servers running Open-SUSE (ariadne, minotaur, hydra) you should also copy the generated key to: "cp ~/.ssh.authorized_keys ~/.ssh/authorized_keys2 ". Re-login and voilà, no more password needed. The same procedure also works on a macOS. However, ssh-copy-id needs to be installed (e.g. via brew install ssh-copy-id) and step (4) should be skipped.
* [[Command-line interface on Linux/UNIX]]

=== Data visualization tools ===
In order to communicate our research effectively, it is often useful to visualize the data from simulations. Here are a set of tools for creating/editing images and videos.

===== Visualizing Dump Files =====

* [[VMD]]
* [[pymol]]

===== Handling image/video files =====

* [[FFmpeg]]

=== Miscellaneous ===
* [[Dropbox]]

Tools

2019-03-23T16:18:02Z

Tc387: /* UNIX */

=== Data analysis tools ===

Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML.

* [[Autocorrelation]]
* [[Generic Analyzer]]
* [[Gnuplot]]
* [[Compressed data files]]

=== Programming ===
* [[Compiler notes]]
* [[Debugging]]
* [[Programming notes]]

=== Document processing ===

Ideally, we prepare manuscripts in [http://en.wikipedia.org/wiki/LaTeX LaTeX]. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word.

* [[Notes on using LaTeX for manuscripts]]
* [[Notes on using Microsoft Word for manuscripts]]

=== Job submission and scheduling ===
* [[Notes on Torque]]
* [[Notes on Maui]]

=== UNIX ===
* [http://www.linuxproblem.org/art_9.html Password-less login via ssh]
* Short version of password-less login: (1) go to your home folder (e.g. ariadne:~/ ). (2) type "ssh-keygen" and press the enter key a few times to leave all answers blank (unless you are prompted to override the existing key in which case you should type "yes"). (3) type "ssh-copy-id XX" , where "XX" is the server name or IP address you wish to ssh into, you can repeat this step and add multiple addresses. (4) On servers running Open-SUSE (ariadne, minotaur, hydra) you should also copy the generated key to: "cp ~/.ssh.authorized_keys ~/.ssh/authorized_keys2 ". Re-login and voilà, no more password needed. The same procedure also works on a macOS. However, ssh-copy-id needs to be installed (e.g. via brew install ssh-copy-id) and step (4) should be skipped.
* [[Command-line interface on Linux/UNIX]]

=== Data visualization tools ===
In order to communicate our research effectively, it is often useful to visualize the data from simulations. Here are a set of tools for creating/editing images and videos.

===== Visualizing Dump Files =====

* [[VMD]]
* [[pymol]]

===== Handling image/video files =====

* [[FFmpeg]]

=== Miscellaneous ===
* [[Dropbox]]

Tools

2019-03-23T16:16:54Z

Tc387: /* UNIX */

=== Data analysis tools ===

Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML.

* [[Autocorrelation]]
* [[Generic Analyzer]]
* [[Gnuplot]]
* [[Compressed data files]]

=== Programming ===
* [[Compiler notes]]
* [[Debugging]]
* [[Programming notes]]

=== Document processing ===

Ideally, we prepare manuscripts in [http://en.wikipedia.org/wiki/LaTeX LaTeX]. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word.

* [[Notes on using LaTeX for manuscripts]]
* [[Notes on using Microsoft Word for manuscripts]]

=== Job submission and scheduling ===
* [[Notes on Torque]]
* [[Notes on Maui]]

=== UNIX ===
* [http://www.linuxproblem.org/art_9.html Password-less login via ssh]
* Short version of password-less login: (1) go to your home folder (e.g. ariadne:~/ ). (2) type "ssh-keygen" and press the enter key a few times to leave all answers blank (unless you are prompted to override the existing key in which case you should type "yes"). (3) type "ssh-copy-id XX" , where "XX" is the server name or IP address you wish to ssh into, you can repeat this step and add multiple addresses. (4) On servers running Open-SUSE (Ariadne, minotaur, hydra) you should also copy the generated key to: "cp ~/.ssh.authorized_keys ~/.ssh/authorized_keys2 ". Re-login and voilà, no more password needed. The same procedure also works on a macOS. However, ssh-copy-id needs to be installed (e.g. via brew install ssh-copy-id) and step (4) should be skipped.
* [[Command-line interface on Linux/UNIX]]

=== Data visualization tools ===
In order to communicate our research effectively, it is often useful to visualize the data from simulations. Here are a set of tools for creating/editing images and videos.

===== Visualizing Dump Files =====

* [[VMD]]
* [[pymol]]

===== Handling image/video files =====

* [[FFmpeg]]

=== Miscellaneous ===
* [[Dropbox]]

Tools

2019-03-23T16:15:54Z

Tc387: /* UNIX */

=== Data analysis tools ===

Computer simulations involve the use of a set of analysis tools. Here, we share notes and ideas on programs commonly used in the CSML.

* [[Autocorrelation]]
* [[Generic Analyzer]]
* [[Gnuplot]]
* [[Compressed data files]]

=== Programming ===
* [[Compiler notes]]
* [[Debugging]]
* [[Programming notes]]

=== Document processing ===

Ideally, we prepare manuscripts in [http://en.wikipedia.org/wiki/LaTeX LaTeX]. Occasionally, especially when collaborating with other research groups, it may be necessary to work in Microsoft Word.

* [[Notes on using LaTeX for manuscripts]]
* [[Notes on using Microsoft Word for manuscripts]]

=== Job submission and scheduling ===
* [[Notes on Torque]]
* [[Notes on Maui]]

=== UNIX ===
* [http://www.linuxproblem.org/art_9.html Password-less login via ssh]
* Short version of password-less login: (1) go to your home folder (e.g. ariadne:~/ ). (2) type "ssh-keygen" and press the enter key a few times to leave all answers blank (unless you are prompted to override the existing key in which case you should type "yes"). (3) type "ssh-copy-id XX" , where "XX" is the server name or IP address you wish to ssh into, you can repeat this step and add multiple addresses. (4) On servers running Open-SUSE (Ariadne, minotaur, hydra) you should also copy the generated key to: "cp ~/.ssh.authorized_keys ~/.ssh/authorized_keys2 ". Re-login and voilà, no more password needed.
The same procedure also works on a macOS. However, ssh-copy-id needs to be installed (e.g. via brew install ssh-copy-id) and step (4) should be skipped.
* [[Command-line interface on Linux/UNIX]]

=== Data visualization tools ===
In order to communicate our research effectively, it is often useful to visualize the data from simulations. Here are a set of tools for creating/editing images and videos.

===== Visualizing Dump Files =====

* [[VMD]]
* [[pymol]]

===== Handling image/video files =====

* [[FFmpeg]]

=== Miscellaneous ===
* [[Dropbox]]