Skip to end of metadata
Go to start of metadata

On O2, users can compile and install software in their /home directories or shared directories (e.g. /n/groups , /n/dataX ) where you have write permission. In general, during the configure step, --prefix can be set to a directory where you have write access to install the software to that directory. Software installs via binary files do not need to be compiled, only uncompressed.

Quick Start

1) Download (wget or curl) or sFTP upload software source files (usually a tar.gz) to a write-accessible directory (like /home/mfk8) from an interactive shell (not "login0X").

Interactive shell:

mfk8@login02:~$ srun --pty -p interactive -t 0-12:00 /bin/bash 

wget or curl software from an FTP or HTTP URL:

mfk8@compute-a-01-01:~$ wget ftp://someURL.tar.gz

2) Unpack file using tar from an interactive shell (please do not compile on shell login servers, denoted "loginX")

If the file is a tar.gz, unpack tarball:

mfk8@compute-a-01-01:~$ tar -zxvf yourtarfile.tar.gz

If the file is just .gz, unpack:

mfk8@compute-a-01-01:~$ gunzip yourgzipfile.gz

This creates a directory for the software with its contents.

3) Change to the directory created during the unpack, view README or install guide. This may indicate what compilers/libraries are needed to install. Check out module spider for available compilers and libraries.

mfk8@compute-a-01-01:~$ cd newsoftwarefolder
mfk8@compute-a-01-01:~/newsoftware$ less README

4) Load the compiler and any libraries necessary, as found in README, and make sure to specify --prefix or whatever the equivalent flag is if specified in the README:

mfk8@compute-a-01-01:~/newsoftwarefolder$ module load gcc/6.2.0
mfk8@compute-a-01-01:~/newsoftwarefolder$ ./configure --prefix=/home/mfk8/newsoftwarefolder

5) Usually run make then make install (check README/install notes)

mfk8@compute-a-01-01:~/newsoftwarefolder$ make
mfk8@compute-a-01-01:~/newsoftwarefolder$ make install

6) Software executables are generally now in a "bin" folder.  You can add (prepend) these to your $PATH environment variable like so, to make them accessible simply by name:

mfk8@compute-a-01-01:~/newsoftwarefolder$ export PATH=/home/mfk8/newsoftwarefolder/bin:$PATH

If you download and install software into your /home or other directory, you are generally expected to adhere to any software license agreement. If you have questions about this or need help deploying a license, please feel encouraged to contact HMS Research Computing.

  • No labels