Locally Installing Software on the Cluster¶
- This guide will allow you to install software that isn't already available on the cluster by extracting a tarfile. To see what software is available on the cluster, run
Installing the Tarfile¶
- Log in to the cluster normally.
- Start by using
wgetfollowed by the link to a tarfile (also referred to as a Gzipped source tarball) to download it.
- Extract the tarfile with
tar zxvffollowed by the full name of the tarfile (including the extension)
cdinto the directory generated by the step above.
lsto check, if there is not already a configure file, you can generate one with
- Run the ./configure file with a prefix to the directory you'd like to install it to:
./configure --prefix=/some/other/directory. You can use
pwdto find the current directory you are in if that is your desired location. This step may produce a large amount of output.
maketo start the build process. This will also produce a large amount of output.
- Optional: you can run
make testto make sure everything works. Note that this will take a long time, so if you believe that the software you are downloading is reliable, you can skip this.
- Finally, use
make installto finish up, generating a lot more output.
- Once this is complete you have successfully installed the software.
Using the Installed Software¶
- If you want to begin using the software right away, you must specify the full path to the software. To find the full path you can navigate to the directory where the executable is and run
pwd. The full path is the output from
/ExecutableName(replace ExecutableName with the name of your executable file).
- If you want to set the executable to run with a simpler command, you can set up an alias by using
alias <Short Keyword>=<Full Path Name>.
An alias will only last for the span of the session. You will have to create the alias again if you log in again to the cluster.
Turning Installed Software into a Private Module¶
Currently, we only provide instructions for creating private modules on RHEL6.
- Please visit the Create Private Modules section under the Module Guide page.
- For this example, we will be extracting a tarfile containing Python 3.5.0.
- We start with
[svemuri8@login-s1 ~]$ wget https://www.python.org/ftp/python/3.5.0/Python-3.5.0.tgz --2019-06-12 14:13:13-- https://www.python.org/ftp/python/3.5.0/Python-3.5.0.tgz Resolving www.python.org... 22.214.171.124, 2a04:4e42:2c::223 Connecting to www.python.org|126.96.36.199|:443... connected. HTTP request sent, awaiting response... 200 OK Length: 20053428 (19M) [application/octet-stream] Saving to: `Python-3.5.0.tgz' 100%[=================================================================================================================================>] 20,053,428 53.0M/s in 0.4s 2019-06-12 14:13:15 (53.0 MB/s) - `Python-3.5.0.tgz' saved [20053428/20053428]
- Next, we extract the tarfile:
[svemuri8@login-s1 ~]$ tar zxvf Python-3.5.0.tgz
- There will now be a directory called Python-3.5.0
- cd into the directory:
[svemuri8@login-s1 ~]$ cd Python-3.5.0
- We can find the current directory with
[svemuri8@login-s4 Python-3.5.0]$ pwd /nv/hp16/svemuri8/Python-3.5.0
- Next we run
- Then the
- And then the
lsnow will show that there is a python executable among many other files in the directory.
- To run the python executable, we can simply specify the path and use python however we'd like:
[svemuri8@login-s4 Python-3.5.0]$ /nv/hp16/svemuri8/Python-3.5.0/python -V Python 3.5.0 [svemuri8@login-s4 Python-3.5.0]$ /nv/hp16/svemuri8/Python-3.5.0/python Python 3.5.0 (default, Jun 12 2019, 15:13:10) [GCC 4.4.7 20120313 (Red Hat 4.4.7-16)] on linux Type "help", "copyright", "credits" or "license" for more information. >>> print ("Hello World!") Hello World! >>> + Stopped /nv/hp16/svemuri8/Python-3.5.0/python [svemuri8@login-s4 Python-3.5.0]$
- To make it run with just
python, we'll set up an alias:
[svemuri8@login-s4 Python-3.5.0]$ alias python=/nv/hp16/svemuri8/Python-3.5.0/python [svemuri8@login-s4 Python-3.5.0]$ python Python 3.5.0 (default, Jun 12 2019, 15:13:10) [GCC 4.4.7 20120313 (Red Hat 4.4.7-16)] on linux Type "help", "copyright", "credits" or "license" for more information. >>>