Newer
Older
Lmod is a modules tool, a modern alternative to the oudated & no longer actively maintained Tcl-based environment modules tool.
Detailed documentation on Lmod is available at [here](http://lmod.readthedocs.io).
!!! warning
All the new modules will be availabe in Lmod environment only.
Create folder or file `.lmod` into your home folder. Logout and login. New Lmod enviroment will be active now.
```bash
$ mkdir ~/.lmod
$ logout
Connection to login4.salomon.it4i.cz closed.
local~$ ssh vop999@login.it4i.cz
_____ _
/ ____| | |
| (___ __ _| | ___ _ __ ___ ___ _ __
\___ \ / _` | |/ _ \| '_ ` _ \ / _ \| '_ \
____) | (_| | | (_) | | | | | | (_) | | | |
|_____/ \__,_|_|\___/|_| |_| |_|\___/|_| |_|
http://www.it4i.cz/?lang=en
$
$ ml
No modules loaded
```
| Date | Action |
| ---------- | ---------------------- |
* significantly more responsive module commands, in particular module avail (ml av)
* easier to use interface
* module files can be written in either Tcl or Lua syntax (and both types of modules can be mixed together)
Below you will find more details and examples.
| ------------------------ | ---------------------------------------------------------------- |
| ml | module list |
| ml GCC/6.2.0-2.27 | module load GCC/6.2.0-2.27 |
| ml -GCC/6.2.0-2.27 | module unload GCC/6.2.0-2.27 |
| ml purge | module unload all modules |
| ml av | module avail |
| ml show GCC/6.2.0-2.27 | module show GCC |
| ml spider | gcc searches (case-insensitive) for gcc in all available modules |
| ml spider GCC/6.2.0-2.27 | show all information about the module GCC/6.2.0-2.27 |
| ml save mycollection | stores the currently loaded modules to a collection |
| ml restore mycollection | restores a previously stored collection of modules |
To get an overview of the currently loaded modules, use module list or ml (without specifying extra arguments).
```bash
$ ml
Currently Loaded Modules:
1) EasyBuild/3.0.0 (S) 2) lmod/7.2.2
Where:
S: Module is Sticky, requires --force to unload or purge
```
!!! tip
For more details on sticky modules, see the section on [ml purge](#resetting-by-unloading-all-modules).
To get an overview of all available modules, you can use ml avail or simply ml av:
---------------------------------------- /apps/modules/compiler ----------------------------------------------
GCC/5.2.0 GCCcore/6.2.0 (D) icc/2013.5.192 ifort/2013.5.192 LLVM/3.9.0-intel-2017.00 (D)
... ...
---------------------------------------- /apps/modules/devel -------------------------------------------------
Autoconf/2.69-foss-2015g CMake/3.0.0-intel-2016.01 M4/1.4.17-intel-2016.01 pkg-config/0.27.1-foss-2015g
Autoconf/2.69-foss-2016a CMake/3.3.1-foss-2015g M4/1.4.17-intel-2017.00 pkg-config/0.27.1-intel-2015b
... ...
In the current module naming scheme, each module name consists of two parts:
* the part before the first /, corresponding to the software name
* the remainder, corresponding to the software version, the compiler toolchain that was used to install the software, and a possible version suffix
The (D) indicates that this particular version of the module is the default, but we strongly recommend to not rely on this as the default can change at any point. Usuall, the default will point to the latest version available.
If you just provide a software name, for example gcc, it prints on overview of all available modules for GCC.
```bash
$ ml spider gcc
---------------------------------------------------------------------------------
GCC:
---------------------------------------------------------------------------------
Description:
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
Versions:
GCC/4.4.7-system
GCC/4.7.4
GCC/4.8.3
GCC/4.9.2-binutils-2.25
GCC/4.9.2
GCC/4.9.3-binutils-2.25
GCC/4.9.3
GCC/4.9.3-2.25
GCC/5.1.0-binutils-2.25
GCC/5.2.0
GCC/5.3.0-binutils-2.25
GCC/5.3.0-2.25
GCC/5.3.0-2.26
GCC/5.3.1-snapshot-20160419-2.25
GCC/5.4.0-2.26
GCC/6.2.0-2.27
Other possible modules matches:
GCCcore
---------------------------------------------------------------------------------
To find other possible module matches do:
module -r spider '.*GCC.*'
---------------------------------------------------------------------------------
For detailed information about a specific "GCC" module (including how to load the modules) use the module's full name.
For example:
$ module spider GCC/6.2.0-2.27
---------------------------------------------------------------------------------
```
!!! tip
If you use spider on a full module name like GCC/6.2.0-2.27 it will tell on which cluster(s) that module available:
```bash
$ module spider GCC/6.2.0-2.27
--------------------------------------------------------------------------------------------------------------
GCC: GCC/6.2.0-2.27
--------------------------------------------------------------------------------------------------------------
Description:
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
This module can be loaded directly: module load GCC/6.2.0-2.27
Help:
The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada,
as well as libraries for these languages (libstdc++, libgcj,...). - Homepage: http://gcc.gnu.org/
```
This tells you what the module contains and a URL to the homepage of the software.
## Available Modules for a Particular Software Package
To check which modules are available for a particular software package, you can provide the software name to ml av.
For example, to check which versions of git are available:
```bash
$ ml av git
-------------------------------------- /apps/modules/tools ----------------------------------------
git/2.8.0-GNU-4.9.3-2.25 git/2.8.0-intel-2017.00 git/2.9.0 git/2.9.2 git/2.11.0 (D)
Where:
D: Default Module
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
```
Lmod does a partial match on the module name, so sometimes you need to use / to indicate the end of the software name you are interested in:
```bash
$ ml av GCC/
------------------------------------------ /apps/modules/compiler -------------------------------------------
GCC/4.4.7-system GCC/4.8.3 GCC/4.9.2 GCC/4.9.3 GCC/5.1.0-binutils-2.25 GCC/5.3.0-binutils-2.25 GCC/5.3.0-2.26 GCC/5.4.0-2.26 GCC/4.7.4 GCC/4.9.2-binutils-2.25 GCC/4.9.3-binutils-2.25 GCC/4.9.3-2.25 GCC/5.2.0 GCC/5.3.0-2.25 GCC/6.2.0-2.27 (D)
Where:
D: Default Module
Use "module spider" to find all possible modules.
Use "module keyword key1 key2 ..." to search for all possible modules matching any of the "keys".
```
To see how a module would change the environment, use ml show:
help([[Python is a programming language that lets you work more quickly and integrate your systems more effectively. - Homepage: http://python.org/]])
whatis("Description: Python is a programming language that lets you work more quickly and integrate your systems more effectively. - Homepage: http://python.org/")
conflict("Python")
load("bzip2/1.0.6")
load("zlib/1.2.8")
load("libreadline/6.3")
load("ncurses/5.9")
load("SQLite/3.8.8.1")
load("Tk/8.6.3")
load("GMP/6.0.0a")
load("XZ/5.2.2")
prepend_path("CPATH","/apps/all/Python/3.5.2/include")
prepend_path("LD_LIBRARY_PATH","/apps/all/Python/3.5.2/lib")
prepend_path("LIBRARY_PATH","/apps/all/Python/3.5.2/lib")
prepend_path("MANPATH","/apps/all/Python/3.5.2/share/man")
prepend_path("PATH","/apps/all/Python/3.5.2/bin")
prepend_path("PKG_CONFIG_PATH","/apps/all/Python/3.5.2/lib/pkgconfig")
setenv("EBROOTPYTHON","/apps/all/Python/3.5.2")
setenv("EBVERSIONPYTHON","3.5.2")
setenv("EBDEVELPYTHON","/apps/all/Python/3.5.2/easybuild/Python-3.5.2-easybuild-devel")
setenv("EBEXTSLISTPYTHON","setuptools-20.1.1,pip-8.0.2,nose-1.3.7")
```
!!! tip
Note that both the direct changes to the environment as well as other modules that will be loaded are shown.
If you're not sure what all of this means: don't worry, you don't have to know, just try loading the module as try using the software.
The effectively apply the changes to the environment that are specified by a module, use ml and specify the name of the module.
For example, to set up your environment to use intel:
```bash
$ ml intel/2017.00
$ ml
Currently Loaded Modules:
1) GCCcore/5.4.0
2) binutils/2.26-GCCcore-5.4.0 (H)
3) icc/2017.0.098-GCC-5.4.0-2.26
4) ifort/2017.0.098-GCC-5.4.0-2.26
5) iccifort/2017.0.098-GCC-5.4.0-2.26
6) impi/2017.0.098-iccifort-2017.0.098-GCC-5.4.0-2.26
7) iimpi/2017.00-GCC-5.4.0-2.26
8) imkl/2017.0.098-iimpi-2017.00-GCC-5.4.0-2.26
9) intel/2017.00
Where:
H: Hidden Module
```
!!! tip
Note that even though we only loaded a single module, the output of ml shows that a whole bunch of modules were loaded, which are required dependencies for intel/2017.00.
It is important to note that **only modules that are compatible with each other can be loaded together. In particular, modules must be installed either with the same toolchain as the modules that** are already loaded, or with a compatible (sub)toolchain.
For example, once you have loaded one or more modules that were installed with the intel/2017.00 toolchain, all other modules that you load should have been installed with the same toolchain.
In addition, only **one single version** of each software package can be loaded at a particular time. For example, once you have the Python/3.5.2-intel-2017.00 module loaded, you can not load a different version of Python in the same session/job script, neither directly, nor indirectly as a dependency of another module you want to load.
To revert the changes to the environment that were made by a particular module, you can use ml -<modname>.
For example:
```bash
$ ml
Currently Loaded Modules:
1) EasyBuild/3.0.0 (S) 2) lmod/7.2.2
$ which gcc
/usr/bin/gcc
$ ml GCC/
$ ml
Currently Loaded Modules:
1) EasyBuild/3.0.0 (S) 2) lmod/7.2.2 3) GCCcore/6.2.0 4) binutils/2.27-GCCcore-6.2.0 (H) 5) GCC/6.2.0-2.27
$ which gcc
/apps/all/GCCcore/6.2.0/bin/gcc
$ ml -GCC
$ ml
Currently Loaded Modules:
1) EasyBuild/3.0.0 (S) 2) lmod/7.2.2 3) GCCcore/6.2.0 4) binutils/2.27-GCCcore-6.2.0 (H)
$ which gcc
/usr/bin/gcc
```
To reset your environment back to a clean state, you can use ml purge or ml purge --force:
```bash
$ ml
Currently Loaded Modules:
1) EasyBuild/3.0.0 (S) 2) lmod/7.2.2 3) GCCcore/6.2.0 4) binutils/2.27-GCCcore-6.2.0 (H)
$ ml purge
The following modules were not unloaded:
(Use "module --force purge" to unload all):
1) EasyBuild/3.0.0
$ ml
Currently Loaded Modules:
1) EasyBuild/3.0.0 (S)
$ ml purge --force
$ ml
No modules loaded
```
As such, you should not (re)load the cluster module anymore after running ml purge.
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
If you have a set of modules that you need to load often, you can save these in a collection (only works with Lmod).
First, load all the modules you need, for example:
```bash
ml intel/2017.00 Python/3.5.2-intel-2017.00
```
Now store them in a collection using ml save:
```bash
$ ml save my-collection
```
Later, for example in a job script, you can reload all these modules with ml restore:
```bash
$ ml restore my-collection
```
With ml savelist can you gets a list of all saved collections:
```bash
$ ml savelist
Named collection list:
1) my-collection
2) my-test-collection
```
To inspect a collection, use ml describe.
To remove a module collection, remove the corresponding entry in $HOME/.lmod.d.