Difference between revisions of "Isis tutorial installing"

Latest revision as of 08:53, 22 May 2020

Getting ISIS

Installing ISIS and all the modules it depends on, is not a trivial task.

We therefore provide a complete isis environment that is pre-installed in a so-called 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.

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.

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

sudo apt-get install singularity-container

On other Linux versions different commands are required.

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.,

mkdir xray
cd xray
wget https://www.sternwarte.uni-erlangen.de/isis/isis-singularity.img

you can then launch the singularity environment as follows:

cd xray
singularity run isis-singularity.img

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

Setup for Windows

For older windows machines:

Install singularity using the instructions 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

Follow the instructions above.

For Windows 10: follow the instructions 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 isis MacOS installation instructions, then 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

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 the instructions here.

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 ====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].
+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'''.
+For older windows machines:
-* 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=====
+* 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
-* 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=====
+* Follow the instructions above.
-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.
+For Windows 10:
+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=====
+* 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]]