Difference between revisions of "Load modules"
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To load a software module, use <code>module load</code>. In the example below, we will use Python 3. | To load a software module, use <code>module load</code>. In the example below, we will use Python 3. | ||
| − | + | Initially, Python 3 is not loaded and therefore not available for use. We can test this by using the command <code>which</code> that looks for programs the same way that Bash does. We can use it to tell us where a particular piece of software is stored. | |
[me@nodelogin01~]$ which python3 | [me@nodelogin01~]$ which python3 | ||
/usr/bin/which: no python3 in (/cm/shared/apps/slurm/18.08.4/sbin:/cm/shared/apps/slurm/18.08.4/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.local/bin:/home/me/bin) | /usr/bin/which: no python3 in (/cm/shared/apps/slurm/18.08.4/sbin:/cm/shared/apps/slurm/18.08.4/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.local/bin:/home/me/bin) | ||
| Line 9: | Line 9: | ||
[me@nodelogin01 ~]$ module load Python/3.7.2-GCCcore-8.2.0 | [me@nodelogin01 ~]$ module load Python/3.7.2-GCCcore-8.2.0 | ||
[me@nodelogin01 ~]$ which python3 | [me@nodelogin01 ~]$ which python3 | ||
| − | /cm/shared/easybuild/software/Python/3.7. | + | /cm/shared/easybuild/software/Python/3.7.4-GCCcore-8.3.0/bin/python3 |
| − | + | So what just happened? To understand the output, first we need to understand the nature of the <code>$PATH</code> environment variable. <code>$PATH</code> is a special environment variable that controls where a Linux ''operating system'' (OS) looks for software. Specifically <code>$PATH</code> is a list of directories (separated by <code>:</code>) that the OS searches through for a command. As with all environment variables, we can print it using <code>echo</code>. | |
[me@nodelogin01 ~]$ echo $PATH | [me@nodelogin01 ~]$ echo $PATH | ||
| + | /cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/XZ/5.2.4-GCCcore- 8.2.0/bin:/cm/shared/easybuild/software/SQLite/3.27.2-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/Tcl/8.6.9-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/libreadline/8.0-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/ncurses/6.1-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/bzip2/1.0.6- GCCcore-8.2.0/bin:/cm/shared/easybuild/software/GCCcore/8.2.0/bin:/cm/shared/apps/slurm/19.05.1/sbin:/cm/shared/apps/slurm/19.05.1/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.local/bin:/home/me/bin | ||
| − | + | You will notice a similarity to the output of the <code>which</code> command. In this case, there’s only one difference: the <code>/cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin</code> directory at the beginning. | |
| − | + | ||
| + | When we used <code>module load Python/3.7.2-GCCcore-8.2.0</code>, it added this directory to the beginning of our <code>$PATH</code>. Let us examine what is there: | ||
| − | + | [me@nodelogin01 ~]$ ls /cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin | |
| − | + | 2to3 futurize pip pytest python3-config rst2odt_prepstyles.py sphinx-apidoc | |
| − | + | 2to3-3.7 idle3 pip3 py.test pyvenv rst2odt.py sphinx-autogen | |
| − | + | chardetect idle3.7 pip3.7 python pyvenv-3.7 rst2pseudoxml.py sphinx-build | |
| − | + | cygdb netaddr pybabel python3 rst2html4.py rst2s5.py sphinx-quickstart | |
| − | + | cython nosetests __pycache__ python3.7 rst2html5.py rst2xetex.py tabulate | |
| − | + | cythonize nosetests-3.7 pydoc3 python3.7-config rst2html.py rst2xml.py virtualenv | |
| − | + | easy_install pasteurize pydoc3.7 python3.7m rst2latex.py rstpep2html.py wheel | |
| − | + | easy_install-3.7 pbr pygmentize python3.7m-config rst2man.py runxlrd.py | |
| − | + | ||
| + | <br />Taking this to its conclusion, <code>module load</code> adds software to your <code>$PATH</code>. It “loads” software. | ||
| + | |||
| + | A special note on this, <code>module load</code> will also load required software dependencies. If you compare the output below with what you had when you first logged in to ALICE, you will notice several other modules have been load automatically, because the Python module depends on them. | ||
| − | + | [me@nodelogin01 ~]$ module list | |
| + | Currently Loaded Modules: | ||
| + | 1) shared 5) GCCcore/8.2.0 9) libreadline/8.0-GCCcore-8.2.0 13) GMP/6.1.2-GCCcore-8.2.0 | ||
| + | 2) DefaultModules 6) bzip2/1.0.6-GCCcore-8.2.0 10) Tcl/8.6.9-GCCcore-8.2.0 14) libffi/3.2.1-GCCcore-8.2.0 | ||
| + | 3) gcc/8.2.0 7) zlib/1.2.11-GCCcore-8.2.0 11) SQLite/3.27.2-GCCcore-8.2.0 15) Python/3.7.2-GCCcore-8.2.0 | ||
| + | 4) slurm/19.05.1 8) ncurses/6.1-GCCcore-8.2.0 12) XZ/5.2.4-GCCcore-8.2.0 | ||
| − | + | Also a note of warning: When you load several modules, it is possible that their dependencies can cause conflicts and problems later on. It is best to always check what other modules have been automatically loaded. | |
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Latest revision as of 08:57, 2 September 2020
Load modules
To load a software module, use module load. In the example below, we will use Python 3.
Initially, Python 3 is not loaded and therefore not available for use. We can test this by using the command which that looks for programs the same way that Bash does. We can use it to tell us where a particular piece of software is stored.
[me@nodelogin01~]$ which python3 /usr/bin/which: no python3 in (/cm/shared/apps/slurm/18.08.4/sbin:/cm/shared/apps/slurm/18.08.4/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.local/bin:/home/me/bin)
We can load the python3 command with module load:
[me@nodelogin01 ~]$ module load Python/3.7.2-GCCcore-8.2.0 [me@nodelogin01 ~]$ which python3 /cm/shared/easybuild/software/Python/3.7.4-GCCcore-8.3.0/bin/python3
So what just happened? To understand the output, first we need to understand the nature of the $PATH environment variable. $PATH is a special environment variable that controls where a Linux operating system (OS) looks for software. Specifically $PATH is a list of directories (separated by :) that the OS searches through for a command. As with all environment variables, we can print it using echo.
[me@nodelogin01 ~]$ echo $PATH /cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/XZ/5.2.4-GCCcore- 8.2.0/bin:/cm/shared/easybuild/software/SQLite/3.27.2-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/Tcl/8.6.9-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/libreadline/8.0-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/ncurses/6.1-GCCcore-8.2.0/bin:/cm/shared/easybuild/software/bzip2/1.0.6- GCCcore-8.2.0/bin:/cm/shared/easybuild/software/GCCcore/8.2.0/bin:/cm/shared/apps/slurm/19.05.1/sbin:/cm/shared/apps/slurm/19.05.1/bin:/cm/local/apps/gcc/8.2.0/bin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/me/.local/bin:/home/me/bin
You will notice a similarity to the output of the which command. In this case, there’s only one difference: the /cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin directory at the beginning.
When we used module load Python/3.7.2-GCCcore-8.2.0, it added this directory to the beginning of our $PATH. Let us examine what is there:
[me@nodelogin01 ~]$ ls /cm/shared/easybuild/software/Python/3.7.2-GCCcore-8.2.0/bin 2to3 futurize pip pytest python3-config rst2odt_prepstyles.py sphinx-apidoc 2to3-3.7 idle3 pip3 py.test pyvenv rst2odt.py sphinx-autogen chardetect idle3.7 pip3.7 python pyvenv-3.7 rst2pseudoxml.py sphinx-build cygdb netaddr pybabel python3 rst2html4.py rst2s5.py sphinx-quickstart cython nosetests __pycache__ python3.7 rst2html5.py rst2xetex.py tabulate cythonize nosetests-3.7 pydoc3 python3.7-config rst2html.py rst2xml.py virtualenv easy_install pasteurize pydoc3.7 python3.7m rst2latex.py rstpep2html.py wheel easy_install-3.7 pbr pygmentize python3.7m-config rst2man.py runxlrd.py
Taking this to its conclusion, module load adds software to your $PATH. It “loads” software.
A special note on this, module load will also load required software dependencies. If you compare the output below with what you had when you first logged in to ALICE, you will notice several other modules have been load automatically, because the Python module depends on them.
[me@nodelogin01 ~]$ module list
Currently Loaded Modules:
1) shared 5) GCCcore/8.2.0 9) libreadline/8.0-GCCcore-8.2.0 13) GMP/6.1.2-GCCcore-8.2.0
2) DefaultModules 6) bzip2/1.0.6-GCCcore-8.2.0 10) Tcl/8.6.9-GCCcore-8.2.0 14) libffi/3.2.1-GCCcore-8.2.0
3) gcc/8.2.0 7) zlib/1.2.11-GCCcore-8.2.0 11) SQLite/3.27.2-GCCcore-8.2.0 15) Python/3.7.2-GCCcore-8.2.0
4) slurm/19.05.1 8) ncurses/6.1-GCCcore-8.2.0 12) XZ/5.2.4-GCCcore-8.2.0
Also a note of warning: When you load several modules, it is possible that their dependencies can cause conflicts and problems later on. It is best to always check what other modules have been automatically loaded.