Difference between revisions of "HPC:Manual Software Install"

From HPC wiki
 
(7 intermediate revisions by 2 users not shown)
Line 1: Line 1:
 
This page describes how software can be installed in a user's own home (or lab's project directory)
 
This page describes how software can be installed in a user's own home (or lab's project directory)
 
=== Other Pages ===
 
*[[HPC:Main_Page|HPC Main Page]]
 
*[[HPC:Login|Connecting to the PMACS cluster]]
 
*[[HPC:User_Guide|User Guide]]
 
*[[HPC:Software|Available Software]]
 
*[[HPC:Archive System|PMACS Archive System]]
 
 
 
 
=== Manually Installing Software in home directories ===
 
=== Manually Installing Software in home directories ===
  
 
Installing software in home directories is allowed. The following example shows how to install a program (from source) like R in a home directory.  
 
Installing software in home directories is allowed. The following example shows how to install a program (from source) like R in a home directory.  
  
'''Note 1: All the steps below must be done in an interactive session! If not, the installation will fail.'''
+
'''Note 1: All the steps below must be done in an interactive session, not on the head node, consign.pmacs.upenn.edu! Else, the installation will fail.'''
  
 
'''Note 2:''' The example below describes how to install the software to $HOME/bin. If an alternative location is preferred, the configure/make install steps can be altered such that the program is installed the desired location.   
 
'''Note 2:''' The example below describes how to install the software to $HOME/bin. If an alternative location is preferred, the configure/make install steps can be altered such that the program is installed the desired location.   
  
 
==== Installation ====  
 
==== Installation ====  
 +
First, from the head node, launch an interactive session:
 +
<pre>
 +
$ bsub -Is bash
 +
</pre>
 +
  
First download the source and untar it into a directory:
+
Then, download the source and untar it into a directory:
  
 
<pre>
 
<pre>
Line 39: Line 35:
 
</pre>
 
</pre>
  
You can either change the "--prefx=$HOME/" to something different or run the "make install" step as "make install DESTDIR=<path_to_new_location"
+
R is now installed in a directory called "bin" inside your home directory ($HOME/bin). If an alternate location is preferred, change either the "--prefx=$HOME/" to something different or run the "make install" step as "make install DESTDIR=<path_to_new_location"
 +
 
 +
==== Use ====
 +
 
 +
Once installed the program can either be run interactively or non-interactively, based on the application.
 +
 
 +
The above example installation will install the program under $HOME/bin. To run this program in an interactive session:
 +
 
 +
<pre>
 +
$ $HOME/bin/R --version
 +
 
 +
$ $HOME/bin/R
 +
 
 +
</pre>
 +
 
 +
To run an Rscript using this version of R, include "$HOME/bin/Rscript" (without quotes) in your job script.
 +
 
 +
=== Other Pages ===
 +
----
 +
<div class="mw-collapsible mw-collapsed">
 +
*[[HPC:Main_Page|HPC Main Page]]
 +
*[[HPC:User_Guide|User Guide]]
 +
*[[HPC:Software|Available Software]]
 +
</div>

Latest revision as of 15:15, 13 August 2019

This page describes how software can be installed in a user's own home (or lab's project directory)

Manually Installing Software in home directories

Installing software in home directories is allowed. The following example shows how to install a program (from source) like R in a home directory.

Note 1: All the steps below must be done in an interactive session, not on the head node, consign.pmacs.upenn.edu! Else, the installation will fail.

Note 2: The example below describes how to install the software to $HOME/bin. If an alternative location is preferred, the configure/make install steps can be altered such that the program is installed the desired location.

Installation

First, from the head node, launch an interactive session:

$ bsub -Is bash


Then, download the source and untar it into a directory:

$ wget https://cran.r-project.org/src/base/R-3/R-3.2.2.tar.gz

$ tar zxvf R-3.2.2.tar.gz

Compile and install the program in the desired location:

$ cd R-3.2.2/

$ ./configure --prefix=$HOME/

$ make

$ make install

R is now installed in a directory called "bin" inside your home directory ($HOME/bin). If an alternate location is preferred, change either the "--prefx=$HOME/" to something different or run the "make install" step as "make install DESTDIR=<path_to_new_location"

Use

Once installed the program can either be run interactively or non-interactively, based on the application.

The above example installation will install the program under $HOME/bin. To run this program in an interactive session:

$ $HOME/bin/R --version

$ $HOME/bin/R 

To run an Rscript using this version of R, include "$HOME/bin/Rscript" (without quotes) in your job script.

Other Pages