Amarel - Revision history

Wilkin: /* Python Jupyter notebook: */

2024-02-06T16:00:16Z

Python Jupyter notebook:

← Older revision		Revision as of 16:00, 6 February 2024
Line 338:		Line 338:
	# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. This '''conda''' environment built for DMCS_1 makes available many of the Python modules you are used to using.		# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. This '''conda''' environment built for DMCS_1 makes available many of the Python modules you are used to using.

	Click '''Launch''' and wait. This can take a couple minutes.		These settings are remembered the next time you access OnDemand.

			Click '''Launch''' and wait. This can take a couple minutes.

	You should see sub-window of the web page like this </br> [[Image:JupyterStarting.png\|600px]] </br></br>When the session is ready it changes to this: </br> [[Image:JupyterRunning.png\|600px]]		You should see sub-window of the web page like this </br> [[Image:JupyterStarting.png\|600px]] </br></br>When the session is ready it changes to this: </br> [[Image:JupyterRunning.png\|600px]]

Wilkin: /* Python Jupyter notebook: */

2024-02-06T15:58:28Z

Python Jupyter notebook:

← Older revision		Revision as of 15:58, 6 February 2024
Line 336:		Line 336:
	# For ''Slurm feature'' enter <span class="blue">cascadelake</span> so your session starts on our older nodes and does not interfere take the larger, faster cores being used by OMG		# For ''Slurm feature'' enter <span class="blue">cascadelake</span> so your session starts on our older nodes and does not interfere take the larger, faster cores being used by OMG
	# For ''conda path'' enter <span class="blue">/projects/dmcs_1/miniconda3</span>		# For ''conda path'' enter <span class="blue">/projects/dmcs_1/miniconda3</span>
	# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. ~~Click [[Media:Amarel Jupyter config.png \| here]]~~ to ~~see what the completed launch page looks like~~.		# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. This '''conda''' environment built for DMCS_1 makes available many of the Python modules you are used to using.

	Click '''Launch''' and wait. This can take a couple minutes.		Click '''Launch''' and wait. This can take a couple minutes.

	You should see sub-window of the web page like this </br> [[Image:JupyterStarting.png\|600px]] </br></br>When the session is ready it changes to this: </br> [[Image:JupyterRunning.png\|600px]]		You should see sub-window of the web page like this </br> [[Image:JupyterStarting.png\|600px]] </br></br>When the session is ready it changes to this: </br> [[Image:JupyterRunning.png\|600px]]
	# Start your notebook by clicking the '''Connect to Jupyter, Anaconda version 5.1.0''' button: (If this does not appear, check that you correctly entered the '''conda path''' and '''conda environment''' at step 3 above.) </br>[[Image:JupyterConnect.png\|400px]]
	# This should place you in a file browse window from which you can navigate to one of your existing Jupyter notebooks, or, to start a new Untitled notebook, select ''Python 3 (ipykernel)'' from the ''New'' pull-down menu on the right side of the page [[Image:NewPythonNotebook.png]]
	# Once your notebook is running, you can import the xroms package as you would any other toolbox, by entering '''<span style="font-family: monospace;">import xroms</span>''' then hold down the shift key and hit the return/enter key. You will see an asterisk ['''*'''] in the square brackets.
	~~# Once that asterisk changes to a '''1''', the xroms python module has been loaded.~~

	~~This~~ '''conda''' environment ~~built for DMCS_1 makes available many~~ of the ~~Python modules~~ you are ~~used~~ to ~~using~~.		Start your notebook by clicking the '''Connect to Jupyter, Anaconda version 5.1.0''' button: (If this does not appear, check that you correctly entered the '''conda path''' and '''conda environment''' at step 3 above.) </br>[[Image:JupyterConnect.png\|400px]]

			This should place you in a file browse window from which you can navigate to one of your existing Jupyter notebooks, or, to start a new Untitled notebook, select ''Python 3 (ipykernel)'' from the ''New'' pull-down menu on the right side of the page [[Image:NewPythonNotebook.png]]

			Once your notebook is running, you can import the xroms package as you would any other toolbox, by entering '''<span style="font-family: monospace;">import xroms</span>''' then hold down the shift key and hit the return/enter key. You will see an asterisk ['''*'''] in the square brackets.

			At present the '''<span style="font-family: monospace;">import</span>''' steps are quite slow ... 30 seconds ... so be patient and don't re-run those cells in your notebook if you don't have to.

	===Matlab:===		===Matlab:===

Wilkin: /* Python Jupyter notebook: */

2024-02-06T15:55:11Z

Python Jupyter notebook:

← Older revision		Revision as of 15:55, 6 February 2024
Line 337:		Line 337:
	# For ''conda path'' enter <span class="blue">/projects/dmcs_1/miniconda3</span>		# For ''conda path'' enter <span class="blue">/projects/dmcs_1/miniconda3</span>
	# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. Click [[Media:Amarel Jupyter config.png \| here]] to see what the completed launch page looks like.		# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. Click [[Media:Amarel Jupyter config.png \| here]] to see what the completed launch page looks like.
	# Click '''Launch''' and wait. This can take a couple minutes.
	# You should see sub-window of the web page like this </br> [[Image:JupyterStarting.png\|600px]] </br></br>When the session is ready it changes to this: </br> [[Image:JupyterRunning.png\|600px]]		Click '''Launch''' and wait. This can take a couple minutes.

			You should see sub-window of the web page like this </br> [[Image:JupyterStarting.png\|600px]] </br></br>When the session is ready it changes to this: </br> [[Image:JupyterRunning.png\|600px]]
	# Start your notebook by clicking the '''Connect to Jupyter, Anaconda version 5.1.0''' button: (If this does not appear, check that you correctly entered the '''conda path''' and '''conda environment''' at step 3 above.) </br>[[Image:JupyterConnect.png\|400px]]		# Start your notebook by clicking the '''Connect to Jupyter, Anaconda version 5.1.0''' button: (If this does not appear, check that you correctly entered the '''conda path''' and '''conda environment''' at step 3 above.) </br>[[Image:JupyterConnect.png\|400px]]
	# This should place you in a file browse window from which you can navigate to one of your existing Jupyter notebooks, or, to start a new Untitled notebook, select ''Python 3 (ipykernel)'' from the ''New'' pull-down menu on the right side of the page [[Image:NewPythonNotebook.png]]		# This should place you in a file browse window from which you can navigate to one of your existing Jupyter notebooks, or, to start a new Untitled notebook, select ''Python 3 (ipykernel)'' from the ''New'' pull-down menu on the right side of the page [[Image:NewPythonNotebook.png]]

Wilkin: /* Python Jupyter notebook: */

2024-02-06T15:54:38Z

Python Jupyter notebook:

← Older revision		Revision as of 15:54, 6 February 2024
Line 329:		Line 329:
	===Python Jupyter notebook:===		===Python Jupyter notebook:===
	# Select '''Personal Jupyter''' from the list on the left		# Select '''Personal Jupyter''' from the list on the left
	# Make your selection for '''number of hours''' your session can remain active (''e.g.'' <span class="blue">3 ~~hours~~</span>)		# Make your selection for '''number of hours''' your session can remain active (''e.g.'' <span class="blue">3</span>) hours
	# Set the '''number of cores''' to run on (I suggest <span class="blue">1</span> for now)		# Set the '''number of cores''' to run on (I suggest <span class="blue">1</span> for now)
	# Set '''memory''' (<span class="blue">8</span> GB is an OK choice)		# Set '''memory''' (<span class="blue">8</span> GB is an OK choice)

Wilkin: /* Python Jupyter notebook: */

2024-02-06T15:54:18Z

Python Jupyter notebook:

← Older revision		Revision as of 15:54, 6 February 2024
Line 329:		Line 329:
	===Python Jupyter notebook:===		===Python Jupyter notebook:===
	# Select '''Personal Jupyter''' from the list on the left		# Select '''Personal Jupyter''' from the list on the left
	# Make your selection for '''number of hours''' your session can remain active (''e.g.'' 3 hours)		# Make your selection for '''number of hours''' your session can remain active (''e.g.'' <span class="blue">3 hours</span>)
	# Set the '''number of cores''' to run on (I suggest 1 for now)		# Set the '''number of cores''' to run on (I suggest <span class="blue">1</span> for now)
	# Set '''memory''' (8 GB is an OK choice)		# Set '''memory''' (<span class="blue">8</span> GB is an OK choice)
	# For ''Partition'' enter ''e.g.'' <span class="blue">p_omg_1</span>		# For ''Partition'' enter ''e.g.'' <span class="blue">p_omg_1</span>
	# Leave ''Reservation'' blank		# Leave ''Reservation'' blank

Wilkin: /* Python Jupyter notebook: */

2024-02-06T15:53:27Z

Python Jupyter notebook:

← Older revision		Revision as of 15:53, 6 February 2024
Line 334:		Line 334:
	# For ''Partition'' enter ''e.g.'' <span class="blue">p_omg_1</span>		# For ''Partition'' enter ''e.g.'' <span class="blue">p_omg_1</span>
	# Leave ''Reservation'' blank		# Leave ''Reservation'' blank
	# For ''Slurm feature'' enter ''cascadelake'' so your session starts on our older nodes and does not interfere take the larger, faster cores being used by OMG		# For ''Slurm feature'' enter <span class="blue">cascadelake</span> so your session starts on our older nodes and does not interfere take the larger, faster cores being used by OMG
	# For ''conda path'' enter <span class="blue">/projects/dmcs_1/miniconda3</span>		# For ''conda path'' enter <span class="blue">/projects/dmcs_1/miniconda3</span>
	# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. Click [[Media:Amarel Jupyter config.png \| here]] to see what the completed launch page looks like.		# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. Click [[Media:Amarel Jupyter config.png \| here]] to see what the completed launch page looks like.

Wilkin: /* Python Jupyter notebook: */

2024-02-06T15:52:15Z

Python Jupyter notebook:

← Older revision		Revision as of 15:52, 6 February 2024
Line 329:		Line 329:
	===Python Jupyter notebook:===		===Python Jupyter notebook:===
	# Select '''Personal Jupyter''' from the list on the left		# Select '''Personal Jupyter''' from the list on the left
	# Make your ~~selections~~ for '''number of hours''' your session can remain active (''e.g.'' 3 hours), the '''number of cores''' to run on (1)~~, and~~ '''memory''' (8 GB is an OK choice)		# Make your selection for '''number of hours''' your session can remain active (''e.g.'' 3 hours)
	# For ''Partition'' enter ''e.g.'' <span class="blue">p_omg_1</span> ~~if you are in OMG.~~ Leave ''Reservation'' ~~and~~ ''Slurm feature'' ~~blank.~~ For ''conda path'' enter <span class="blue">/projects/dmcs_1/miniconda3</span> ~~and for~~ ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. Click [[Media:Amarel Jupyter config.png \| here]] to see what the completed launch page looks like.		# Set the '''number of cores''' to run on (I suggest 1 for now)
			# Set '''memory''' (8 GB is an OK choice)
			# For ''Partition'' enter ''e.g.'' <span class="blue">p_omg_1</span>
			# Leave ''Reservation'' blank
			# For ''Slurm feature'' enter ''cascadelake'' so your session starts on our older nodes and does not interfere take the larger, faster cores being used by OMG
			# For ''conda path'' enter <span class="blue">/projects/dmcs_1/miniconda3</span>
			# For ''conda environment'' enter <span class="blue">/projects/dmcs_1/sw/packages/xroms/py38</span>. Click [[Media:Amarel Jupyter config.png \| here]] to see what the completed launch page looks like.
	# Click '''Launch''' and wait. This can take a couple minutes.		# Click '''Launch''' and wait. This can take a couple minutes.
	# You should see sub-window of the web page like this </br> [[Image:JupyterStarting.png\|600px]] </br></br>When the session is ready it changes to this: </br> [[Image:JupyterRunning.png\|600px]]		# You should see sub-window of the web page like this </br> [[Image:JupyterStarting.png\|600px]] </br></br>When the session is ready it changes to this: </br> [[Image:JupyterRunning.png\|600px]]

Wilkin: /* Mac OS */

2024-01-30T21:02:40Z

Mac OS

← Older revision		Revision as of 21:02, 30 January 2024
Line 87:		Line 87:

	# If you are still connected to ''Amarel'', disconnect by entering '''exit'''		# If you are still connected to ''Amarel'', disconnect by entering '''exit'''
	# At the prompt for your local machine, enter '''<span style="font-family: monospace;">nano ~/.ssh/config</span>''' and paste the block below at the end of the file:<div class="box">Host amarel<br />Hostname amarel.rutgers.edu<br />HostKeyAlias amarel<br />User NetID</div> replacing <span class="blue">NetID</span> with your own NetID. Save and exit (Ctrl+o Ctrl+x). This allows you to type '''<span style="font-family: monospace;">ssh amarel</span>''' to connect instead of ssh ~~fakeuser~~@amarel.rutgers.edu.		# At the prompt for your local machine, enter '''<span style="font-family: monospace;">nano ~/.ssh/config</span>''' and paste the block below at the end of the file:<div class="box">Host amarel<br />Hostname amarel.rutgers.edu<br />HostKeyAlias amarel<br />User NetID</div> replacing <span class="blue">NetID</span> with your own NetID. Save and exit (Ctrl+o Ctrl+x). This allows you to type '''<span style="font-family: monospace;">ssh amarel</span>''' to connect instead of '''<span style="font-family: monospace;">ssh fakeruser@amarel.rutgers.edu</span>'''
	# Enter '''<span style="font-family: monospace;">ls ~/.ssh</span>'''. If there is a file listed called <span class="blue">id_rsa.pub</span> skip to 5		# Enter '''<span style="font-family: monospace;">ls ~/.ssh</span>'''. If there is a file listed called <span class="blue">id_rsa.pub</span> skip to 5
	# Enter '''<span style="font-family: monospace;">ssh-keygen -t rsa</span>''', then hit return to accept the default location, enter a passphase twice (or leave blank for no passphrase)		# Enter '''<span style="font-family: monospace;">ssh-keygen -t rsa</span>''', then hit return to accept the default location, enter a passphase twice (or we recommend you just leave it blank twice for no passphrase)
	# Copy the public portion of the key to ''Amarel'' by entering '''<span style="font-family: monospace;">scp ~/.ssh/id_rsa.pub amarel:.</span>'''		# Copy the public portion of the key to ''Amarel'' by entering '''<span style="font-family: monospace;">scp ~/.ssh/id_rsa.pub amarel:.</span>'''
	# SSH to ''Amarel'' ('''<span style="font-family: monospace;">ssh amarel</span>''') and check if you already have a .ssh folder:<div class="box">[rjdave@amarel1 ~]$ ls -l .ssh<br />total 33<br />-rw------- 1 rjdave rjdave 1069 Sep 8 2017 authorized_keys<br />-rw-r--r-- 1 rjdave rjdave 434 Jun 4 2021 config<br />-rw-r--r-- 1 rjdave rjdave 5992 Dec 2 13:47 known_hosts</div> You probably won't have all the files above but if you instead get the message '''<span style="font-family: monospace;"><div class="box">ls: cannot access .ssh: No such file or directory</span>'''</div>then enter the following command:</br>'''<span style="font-family: monospace;">mkdir .ssh && chmod 700 .ssh</span>'''. </br>These two commands (combined on one line) will create the .ssh folder and set the required permissions. Setting private user-only permissions ('''chmod 700 ...''') is important, because the system will not allow you to have your keys viewable by others users.		# SSH to ''Amarel'' ('''<span style="font-family: monospace;">ssh amarel</span>''') and check if you already have a .ssh folder:<div class="box">[rjdave@amarel1 ~]$ ls -l .ssh<br />total 33<br />-rw------- 1 rjdave rjdave 1069 Sep 8 2017 authorized_keys<br />-rw-r--r-- 1 rjdave rjdave 434 Jun 4 2021 config<br />-rw-r--r-- 1 rjdave rjdave 5992 Dec 2 13:47 known_hosts</div> You probably won't have all the files above but if you instead get the message '''<span style="font-family: monospace;"><div class="box">ls: cannot access .ssh: No such file or directory</span>'''</div>then enter the following command:</br>'''<span style="font-family: monospace;">mkdir .ssh && chmod 700 .ssh</span>'''. </br>These two commands (combined on one line) will create the .ssh folder and set the required permissions. Setting private user-only permissions ('''chmod 700 ...''') is important, because the system will not allow you to have your keys viewable by others users.

Wilkin: /* Mac OS */

2024-01-30T21:00:51Z

Mac OS

← Older revision		Revision as of 21:00, 30 January 2024
Line 87:		Line 87:

	# If you are still connected to ''Amarel'', disconnect by entering '''exit'''		# If you are still connected to ''Amarel'', disconnect by entering '''exit'''
	# At the prompt for your local machine, enter '''<span style="font-family: monospace;">nano ~/.ssh/config</span>''' and paste the block below at the end of the file:<div class="box">Host amarel<br />Hostname amarel.rutgers.edu<br />HostKeyAlias amarel<br />User NetID</div> replacing <span class="blue">NetID</span> with your own NetID. Save and exit (Ctrl+o Ctrl+x). This allows you to type '''<span style="font-family: monospace;">ssh amarel</span>''' to connect.		# At the prompt for your local machine, enter '''<span style="font-family: monospace;">nano ~/.ssh/config</span>''' and paste the block below at the end of the file:<div class="box">Host amarel<br />Hostname amarel.rutgers.edu<br />HostKeyAlias amarel<br />User NetID</div> replacing <span class="blue">NetID</span> with your own NetID. Save and exit (Ctrl+o Ctrl+x). This allows you to type '''<span style="font-family: monospace;">ssh amarel</span>''' to connect instead of ssh fakeuser@amarel.rutgers.edu.
	# Enter '''<span style="font-family: monospace;">ls ~/.ssh</span>'''. If there is a file listed called <span class="blue">id_rsa.pub</span> skip to 5		# Enter '''<span style="font-family: monospace;">ls ~/.ssh</span>'''. If there is a file listed called <span class="blue">id_rsa.pub</span> skip to 5
	# Enter '''<span style="font-family: monospace;">ssh-keygen -t rsa</span>''', then hit return to accept the default location, enter a passphase twice (or leave blank for no passphrase)		# Enter '''<span style="font-family: monospace;">ssh-keygen -t rsa</span>''', then hit return to accept the default location, enter a passphase twice (or leave blank for no passphrase)

Wilkin: /* Mac OS */

2024-01-30T20:57:07Z

Mac OS

← Older revision		Revision as of 20:57, 30 January 2024
Line 90:		Line 90:
	# Enter '''<span style="font-family: monospace;">ls ~/.ssh</span>'''. If there is a file listed called <span class="blue">id_rsa.pub</span> skip to 5		# Enter '''<span style="font-family: monospace;">ls ~/.ssh</span>'''. If there is a file listed called <span class="blue">id_rsa.pub</span> skip to 5
	# Enter '''<span style="font-family: monospace;">ssh-keygen -t rsa</span>''', then hit return to accept the default location, enter a passphase twice (or leave blank for no passphrase)		# Enter '''<span style="font-family: monospace;">ssh-keygen -t rsa</span>''', then hit return to accept the default location, enter a passphase twice (or leave blank for no passphrase)
	# Copy the public portion of the key to ''Amarel'' by entering ~~:<div class="box">scp ~/.ssh/id_rsa.pub amarel:.</div>~~		# Copy the public portion of the key to ''Amarel'' by entering '''<span style="font-family: monospace;">scp ~/.ssh/id_rsa.pub amarel:.</span>'''
	'''<span style="font-family: monospace;">scp ~/.ssh/id_rsa.pub amarel:.</span>'''
	# SSH to ''Amarel'' ('''<span style="font-family: monospace;">ssh amarel</span>''') and check if you already have a .ssh folder:<div class="box">[rjdave@amarel1 ~]$ ls -l .ssh<br />total 33<br />-rw------- 1 rjdave rjdave 1069 Sep 8 2017 authorized_keys<br />-rw-r--r-- 1 rjdave rjdave 434 Jun 4 2021 config<br />-rw-r--r-- 1 rjdave rjdave 5992 Dec 2 13:47 known_hosts</div> You probably won't have all the files above but if you instead get the message '''<span style="font-family: monospace;"><div class="box">ls: cannot access .ssh: No such file or directory</span>'''</div>then enter the following command:</br>'''<span style="font-family: monospace;">mkdir .ssh && chmod 700 .ssh</span>'''. </br>These two commands (combined on one line) will create the .ssh folder and set the required permissions. Setting private user-only permissions ('''chmod 700 ...''') is important, because the system will not allow you to have your keys viewable by others users.		# SSH to ''Amarel'' ('''<span style="font-family: monospace;">ssh amarel</span>''') and check if you already have a .ssh folder:<div class="box">[rjdave@amarel1 ~]$ ls -l .ssh<br />total 33<br />-rw------- 1 rjdave rjdave 1069 Sep 8 2017 authorized_keys<br />-rw-r--r-- 1 rjdave rjdave 434 Jun 4 2021 config<br />-rw-r--r-- 1 rjdave rjdave 5992 Dec 2 13:47 known_hosts</div> You probably won't have all the files above but if you instead get the message '''<span style="font-family: monospace;"><div class="box">ls: cannot access .ssh: No such file or directory</span>'''</div>then enter the following command:</br>'''<span style="font-family: monospace;">mkdir .ssh && chmod 700 .ssh</span>'''. </br>These two commands (combined on one line) will create the .ssh folder and set the required permissions. Setting private user-only permissions ('''chmod 700 ...''') is important, because the system will not allow you to have your keys viewable by others users.
	# Once you have a .ssh folder with the proper permissions, enter the following commands</br> '''<span style="font-family: monospace;">cat ~/id_rsa.pub >> ~/.ssh/authorized_keys && chmod 640 ~/.ssh/authorized_keys</span>'''</br>then exit back to your local machine and execute '''<span style="font-family: monospace;">ssh amarel</span>''' again. It should no longer ask for your password.		# Once you have a .ssh folder with the proper permissions, enter the following commands</br> '''<span style="font-family: monospace;">cat ~/id_rsa.pub >> ~/.ssh/authorized_keys && chmod 640 ~/.ssh/authorized_keys</span>'''</br>then exit back to your local machine and execute '''<span style="font-family: monospace;">ssh amarel</span>''' again. It should no longer ask for your password.