Isis tutorial installing - Revision history

Wilms at 06:53, 22 May 2020

2020-05-22T06:53:17Z

← Older revision		Revision as of 08:53, 22 May 2020
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	For Windows 10:		For Windows 10:
	follow the instructions [[Install ISIS on Windows 10\|at this link]]. This is fairly advanced, however.		follow the instructions [[Install ISIS on Windows 10\|at this link]]. This is fairly advanced, however.

			=====Setup for Mac =====

			Apple systems claim they are Unix, but they really are not fully compatible to Unix standards. What is worse, there are two different eco systems available for MacOS if you want to compile your own software. And often, only one of them works. If you feel adventurous, you can install the prerequisites on the [https://space.mit.edu/ASC/isis/mac_install.html isis MacOS installation instructions], then [https://heasarc.gsfc.nasa.gov/lheasoft/install.html install HEASoft] (you need to use the source installation), and then go back and install isis.

			If you are not experienced in compiling and installing your own software on MacOS, this is not recommended, however, and it is better to ask for an account at the observatory (see below).

	=====Working on Remeis observatory computers=====		=====Working on Remeis observatory computers=====

Wilms: /* Setup for Windows */

2020-05-20T16:42:41Z

Setup for Windows

← Older revision		Revision as of 18:42, 20 May 2020
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	=====Setup for Windows =====		=====Setup for Windows =====

			For older windows machines:

	* Install singularity using the instructions [https://sylabs.io/guides/3.5/user-guide/# on the singularity homepage]. This is a somewhat involved process, but doable in principle if you are ok with computers. If the instructions don't		* Install singularity using the instructions [https://sylabs.io/guides/3.5/user-guide/# on the singularity homepage]. This is a somewhat involved process, but doable in principle if you are ok with computers. If the instructions don't
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	* Follow the instructions above.		* Follow the instructions above.

	~~(an alternative is currently being prepared - watch this place)~~

			For Windows 10:
			follow the instructions [[Install ISIS on Windows 10\|at this link]]. This is fairly advanced, however.

	=====Working on Remeis observatory computers=====		=====Working on Remeis observatory computers=====

Wilms: revision 2020

2020-05-19T13:06:15Z

revision 2020

← Older revision		Revision as of 15:06, 19 May 2020
Line 2:		Line 2:
	====Getting ISIS====		====Getting ISIS====
	Installing ISIS and all the modules it depends on, is not a trivial task.		Installing ISIS and all the modules it depends on, is not a trivial task.
	~~We therefore provide a complete VirtualBox diskimage that contains a full operating system and all required software ready for use.~~

	~~VirtualBox is~~ a ~~software~~ that ~~allows to simulate a complete PC including CPU, memory, disks, etc., i.e. it creates~~ a [~~http~~://en.~~wikipedia~~.~~org~~/~~wiki~~/~~Virtual_machine virtual machine~~].		We therefore provide a complete isis environment that is pre-installed in a so-called [https://sylabs.io/guides/3.5/user-guide/# singularity environment]. Singularity runs very well under Linux and can also be installed under windows, although this is a bit more complex, which is why we also offer an alternative. Note that you will need about 4 GB of disk space for the installation.

	~~=====Setup=====~~		If you do not have enough disk space available or if you are not happy/comfortable with installing software on your computer, we also have an option to run the tutorials on machines at the observatory.
	* If you do not ~~already~~ have ~~VirtualBox installed, [http://www.virtualbox.org~~/ ~~download] and install it. VirtualBox is available for Windows~~, ~~Linux, Mac OS X, and Solaris~~.

			=====Setup for Linux =====
			* Install singularity. How you do this depends on the flavor of Linux that you have installed. On ubuntu systems, this is as easy as executing

	* The VirtualBox diskimage containing all required software for the exercises is available for [http://pulsar.sternwarte.uni-~~erlangen.de/kreykenbohm/XrayLab.vdi.gz download]. However, the disk image is huge: even in compressed state, it is about 4.5GB.~~		sudo apt-get install singularity-container
	* To use the disk image, you first need to uncompress the compressed image. Your disk should have plenty free space available: the uncompressed diskimage has a size of about 12GB. However, depending on how much data you install ~~in your virtual machine, the required disk space can grow beyond 50GB.~~
	* Start up VirtualBox

	~~[[File:Vb_new~~.~~png]]~~		On other Linux versions different commands are required.

	~~Note: depending on your operating system, the layout and labeling of the buttons might differ a bit.~~		* Create a working directory for the lecture and download the singularity image for isis and the other tools required for the tutorial from https://www.sternwarte.uni-erlangen.de/isis/isis-singularity.img , e.g.,
	* Create a ~~new virtual machine by clicking on '''New'''. You will be greeted by~~ the ~~"New Virtual Machine Wizard" which helps you to set up~~ the ~~new virtual machine. Click '''Next'''.~~
	* Enter an appropriate name for ~~the virtual machine, e.g. '''XLab'''.~~
	* Select '''Linux''' as operating system type, and ~~'''Ubuntu (64 Bit)''' as version. Click '''Next'''.~~
	* Select how much memory your virtual machine should have. 2 GB is a decent choice, however, you should '''not''' select more than 50% of actual amount of memory of your PC. For example, if your laptop has 2 GB of RAM, you should not attribute more than 1 GB to the ~~virtual machine. Click '''Next'''.~~
	* Select the ~~virtual hard disk to use~~: ~~select '''Use existing harddisk''' and click on the folder icon. A new window opens.~~
	* The new window allows to navigate through the folders of your PC. ~~Locate and select the disk image you previously downloaded~~. ~~Click '''Open'''~~.
	* The window closes and the chosen disk image is shown. ~~Click '''Next'''~~.
	* A summary of your selections is shown. ~~If everything is ok~~, ~~click '''Create'''.~~
	* The main window now lists your freshly created virtual machine

	~~[[File~~:~~Vb2~~.~~png]]~~		mkdir xray
	* in principle, your virtual machine is ready for use. ~~However, your virtual machine is currently only a stand~~-~~alone system~~. ~~You will not be able to transfer data in or out of your virtual machine like any PC that is not connected to a network.~~		cd xray
	* the easiest way to transfer data between your host PC and your virtual machine is a '''shared folder''', i.e. a folder that is visible to your host PC and the virtual machine.		wget https://www.sternwarte.uni-erlangen.de/isis/isis-singularity.img
	* Make sure that your virtual machine is powered down.
	* Create a new folder on your host computer, for example "vbox_shared".
	* In the VirtualBox main window, click on '''Shared Folders''' in the panel on the right side. A warning message may pop up which you can safely ignore.
	* A new window appears that shows all shared folders currently available (there should be none).

	~~[[File~~:~~Vb4.png]]~~		* you can then launch the singularity environment as follows:
	* Click on the folder icon with the green plus sign		cd xray
	* Select the previously created folder and give it the name "'''transfer'''". Do not choose a different name!		singularity run isis-singularity.img
	* Check the '''Auto-~~Mount''' box and click '''Ok'''~~.
	* Click '''Ok'''

			This brings you into an environment that contains most of the relevant X-ray astronomical software, such as, e.g., fv (which you might want to use to display X-ray astronomical data files). You then launch isis by typing '''isis''':

			isis

	=====~~Usage~~=====		=====Setup for Windows =====

	* ~~when you have set up~~ the ~~virtual machine, start it by clicking on ''' Start'''~~.		* Install singularity using the instructions [https://sylabs.io/guides/3.5/user-guide/# on the singularity homepage]. This is a somewhat involved process, but doable in principle if you are ok with computers. If the instructions don't
	* You may be presented with one or more Info boxes, which you can safely ignore.
	* VirtualBox will boot the ~~virtual machine and after a few moments greet you with the Linux login screen~~.
	* The account for your virtual machine has already been set up, you can log in with the username '''xraylab''' and the corresponding password '''Roentgen'''.
	* a ~~lot of your work will be done in a '''terminal'''~~, ~~i.e. by entering commands via keyboard.~~
	* To transfer data from your host system, copy the data into the shared folder you created above. The shared folder will show up in ~~your virtual box under /transfer. To transfer data from your virtual box to the host PC, simply copy the data into /transfer.~~
	* When you are ~~done~~ with ~~your work, you need to shutdown your virtual machine: if you are logged in, right-click on the desktop background and select '''Leave'''.~~
	* A window pops up: select '''Turn Off computer'''. Your virtual machine will shut down. ~~Once the virtual machine has powered down completely,~~ the ~~main window shows the state of the virtual machine as~~ '~~''Powered Off'''.~~
	* You can now quit VirtualBox.

	~~=====Important Notes=====~~		* Follow the instructions above.
	* ~~when running a virtual machine, '''never''' simply quit VirtualBox, or kill~~ the ~~window. '''This may damage the virtual disk image and it therefore may become unusable'''.~~
	* also '''never''' simply shutoff your host PC. This also may damage the virtual diskimage.

	~~=====Alternatives to the Virtual Box solution=====~~		(an alternative is currently being prepared - watch this place)

	If you do not have enough disk space on your computer, contact Ingo Kreykenbohm at the email address given out in the lecture and ask him to create an account on the Remeis computers for you.
			=====Working on Remeis observatory computers=====

			* If you do not have enough disk space on your computer or do not want to install things locally, contact Ingo Kreykenbohm at the email address given out in the lecture and ask him to create an account on the Remeis computers for you.

			* To work on the computers from home, once you have the Remeis account, install the X2go remote desktop environment, following [https://www.sternwarte.uni-erlangen.de/wiki/index.php/X2Go_Remote_Desktop the instructions here].


	[[Category:Isis / Slang]]		[[Category:Isis / Slang]]

Niu: Created page with " ====Getting ISIS==== Installing ISIS and all the modules it depends on, is not a trivial task. We therefore provide a complete VirtualBox diskimage that contains a full oper..."

2018-04-12T12:37:54Z

Created page with " ====Getting ISIS==== Installing ISIS and all the modules it depends on, is not a trivial task. We therefore provide a complete VirtualBox diskimage that contains a full oper..."

New page

====Getting ISIS====
Installing ISIS and all the modules it depends on, is not a trivial task.
We therefore provide a complete VirtualBox diskimage that contains a full operating system and all required software ready for use.

VirtualBox is a software that allows to simulate a complete PC including CPU, memory, disks, etc., i.e. it creates a [http://en.wikipedia.org/wiki/Virtual_machine virtual machine].

=====Setup=====
* If you do not already have VirtualBox installed, [http://www.virtualbox.org/ download] and install it. VirtualBox is available for Windows, Linux, Mac OS X, and Solaris.

* The VirtualBox diskimage containing all required software for the exercises is available for [http://pulsar.sternwarte.uni-erlangen.de/kreykenbohm/XrayLab.vdi.gz download]. However, the disk image is huge: even in compressed state, it is about 4.5GB.
* To use the disk image, you first need to uncompress the compressed image. Your disk should have plenty free space available: the uncompressed diskimage has a size of about 12GB. However, depending on how much data you install in your virtual machine, the required disk space can grow beyond 50GB.
* Start up VirtualBox

[[File:Vb_new.png]]

Note: depending on your operating system, the layout and labeling of the buttons might differ a bit.
* Create a new virtual machine by clicking on '''New'''. You will be greeted by the "New Virtual Machine Wizard" which helps you to set up the new virtual machine. Click '''Next'''.
* Enter an appropriate name for the virtual machine, e.g. '''XLab'''.
* Select '''Linux''' as operating system type, and '''Ubuntu (64 Bit)''' as version. Click '''Next'''.
* Select how much memory your virtual machine should have. 2 GB is a decent choice, however, you should '''not''' select more than 50% of actual amount of memory of your PC. For example, if your laptop has 2 GB of RAM, you should not attribute more than 1 GB to the virtual machine. Click '''Next'''.
* Select the virtual hard disk to use: select '''Use existing harddisk''' and click on the folder icon. A new window opens.
* The new window allows to navigate through the folders of your PC. Locate and select the disk image you previously downloaded. Click '''Open'''.
* The window closes and the chosen disk image is shown. Click '''Next'''.
* A summary of your selections is shown. If everything is ok, click '''Create'''.
* The main window now lists your freshly created virtual machine

[[File:Vb2.png]]
* in principle, your virtual machine is ready for use. However, your virtual machine is currently only a stand-alone system. You will not be able to transfer data in or out of your virtual machine like any PC that is not connected to a network.
* the easiest way to transfer data between your host PC and your virtual machine is a '''shared folder''', i.e. a folder that is visible to your host PC and the virtual machine.
* Make sure that your virtual machine is powered down.
* Create a new folder on your host computer, for example "vbox_shared".
* In the VirtualBox main window, click on '''Shared Folders''' in the panel on the right side. A warning message may pop up which you can safely ignore.
* A new window appears that shows all shared folders currently available (there should be none).

[[File:Vb4.png]]
* Click on the folder icon with the green plus sign
* Select the previously created folder and give it the name "'''transfer'''". Do not choose a different name!
* Check the '''Auto-Mount''' box and click '''Ok'''.
* Click '''Ok'''

=====Usage=====

* when you have set up the virtual machine, start it by clicking on ''' Start'''.
* You may be presented with one or more Info boxes, which you can safely ignore.
* VirtualBox will boot the virtual machine and after a few moments greet you with the Linux login screen.
* The account for your virtual machine has already been set up, you can log in with the username '''xraylab''' and the corresponding password '''Roentgen'''.
* a lot of your work will be done in a '''terminal''', i.e. by entering commands via keyboard.
* To transfer data from your host system, copy the data into the shared folder you created above. The shared folder will show up in your virtual box under /transfer. To transfer data from your virtual box to the host PC, simply copy the data into /transfer.
* When you are done with your work, you need to shutdown your virtual machine: if you are logged in, right-click on the desktop background and select '''Leave'''.
* A window pops up: select '''Turn Off computer'''. Your virtual machine will shut down. Once the virtual machine has powered down completely, the main window shows the state of the virtual machine as '''Powered Off'''.
* You can now quit VirtualBox.

=====Important Notes=====
* when running a virtual machine, '''never''' simply quit VirtualBox, or kill the window. '''This may damage the virtual disk image and it therefore may become unusable'''.
* also '''never''' simply shutoff your host PC. This also may damage the virtual diskimage.

=====Alternatives to the Virtual Box solution=====

If you do not have enough disk space on your computer, contact Ingo Kreykenbohm at the email address given out in the lecture and ask him to create an account on the Remeis computers for you.

[[Category:Isis / Slang]]