Notation: lines beginning with a
$you should enter at the terminal, which typically ends with a$(but don't enter an additional$).
The research computing staff maintain a lot of software on discovery, but it is not all compatible with each other (there are different versions of the same software, for example) so it is not all available all of the time by default - you have to choose which you want to load. These are organized in modules.
List the available modules:
$ module avail
As you can see, there are a lot, including quantum chemistry packages, molecular dynamics packages, specialized compilers, matlab, etc. See for example there are five versions of python and five of anaconda:
anaconda2/2018.12
anaconda2/2.7
anaconda3/2018.12
anaconda3/3.6
anaconda3/3.7
Some modules allow you to find out more about them by typing module whatis <name>, for example:
$ module whatis gaussian
This will tell you about it, and crucially, a list of the prerequisites, in the correct order.
These contain compilers and libraries that the software you want was compiled against, and are needed for it to run.
It suggests putting these module load commands in your .bashrc file, which we will get to
in the next tutorial. For now, we will just type them by hand.
But before you do that, let's see what python you will get without loading the modules.
There may be several programs called
python and when you type python the computer has to pick one of them to run.
The way it does this is by searching through all the directories listed in your $PATH until it finds one containing
an executable called python, and runs that.
I can see my current $PATH by typing echo $PATH:
$ echo $PATH
/shared/centos7/discovery/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin
The which program is a helpful command that tells you which executable program will
be run when you ask for a given program. ie. which is the first directory in your $PATH
that contains an executable with the requested name. For example:
$ which python
/usr/bin/python
To see what version this is:
$ python -V
Python 2.7.5
Let's see if there's a python3 program:
$ which python3
/usr/bin/which: no python3 in (/shared/centos7/discovery/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)
This is telling us that there is no executable called python3 in any of the directories listed in the $PATH. If I were to try executing it, it would fail:
$ python3
-bash: python3: command not found
Likewise, there is no program called conda and trying to run it will fail:
$ which conda
/usr/bin/which: no conda in (/shared/centos7/discovery/bin:/usr/lib64/qt-3.3/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin)
$ conda
-bash: conda: command not found
Now let's load the acaconda modules we found out about earlier.
When we did module whatis anoconda3/3.7 there were no pre-requisite modules listed, so we can just load this one on its own:
$ module load anaconda3/3.7
And try again:
$ which python
/shared/centos7/anaconda3/3.7/bin/python
The default python is now Python 3 from the anaconda distribution:
$ python -V
Python 3.7.0
Now we can execute it, type some python commands, and get the results. Press control-D to quit it when you're done:
$ python
Python 3.7.0 (default, Jun 28 2018, 13:15:42)
[GCC 7.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> print("Hello, World!")
Hello, World!
>>>
You learned in section 7 of the UNIX tutorial how to compile UNIX software packages but if you want some new software installed, it's often easiest to ask the friendly folks at [email protected] to install it for you as a new module, rather than trying to configure and compile it yourself. Especially if you think it'll be useful for other people.
When loading a new module remember to always use module whatis to find out what the
prerequisites are. If you want to run several programs at the same time, and aren't sure
what order to load the combined list of prerequisites in, try a few sensible combinations
then ask [email protected] for help!
Next: 3. Editing your .bashrc