Newer
Older
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
Environment and Modules
=======================
### Environment Customization
After logging in, you may want to configure the environment. Write your
preferred path definitions, aliases, functions and module loads in the
.bashrc file
`
# ./bashrc
# Source global definitions
if [ -f /etc/bashrc ]; then
. /etc/bashrc
fi
# User specific aliases and functions
alias qs='qstat -a'
module load PrgEnv-gnu
# Display informations to standard output - only in interactive ssh session
if [ -n "$SSH_TTY" ]
then
module list # Display loaded modules
fi
`
Do not run commands outputing to standard output (echo, module list,
etc) in .bashrc for non-interactive SSH sessions. It breaks fundamental
functionality (scp, PBS) of your account! Take care for SSH session
interactivity for such commands as
stated in the previous example.
in the previous example.
### Application Modules
In order to configure your shell for running particular application on
Anselm we use Module package interface.
The modules set up the application paths, library paths and environment
variables for running particular application.
We have also second modules repository. This modules repository is
created using tool called EasyBuild. On Salomon cluster, all modules
will be build by this tool. If you want to use software from this
modules repository, please follow instructions in section [Application
Modules
Path Expansion](environment-and-modules.html#EasyBuild).
The modules may be loaded, unloaded and switched, according to momentary
needs.
To check available modules use
`
$ module avail
`
To load a module, for example the octave module use
`
$ module load octave
`
loading the octave module will set up paths and environment variables of
your active shell such that you are ready to run the octave software
To check loaded modules use
`
$ module list
`
To unload a module, for example the octave module use
`
$ module unload octave
`
Learn more on modules by reading the module man page
`
$ man module
`
Following modules set up the development environment
PrgEnv-gnu sets up the GNU development environment in conjunction with
the bullx MPI library
PrgEnv-intel sets up the INTEL development environment in conjunction
with the Intel MPI library
### Application Modules Path Expansion
All application modules on Salomon cluster (and further) will be build
using tool called
[EasyBuild](http://hpcugent.github.io/easybuild/ "EasyBuild").
In case that you want to use some applications that are build by
EasyBuild already, you have to modify your MODULEPATH environment
variable.
`
export MODULEPATH=$MODULEPATH:/apps/easybuild/modules/all/
`
This command expands your searched paths to modules. You can also add
this command to the .bashrc file to expand paths permanently. After this
command, you can use same commands to list/add/remove modules as is
described above.