Software management

Software management

Article written by Markus Stöhr (VSC Team) <html><br></html>(last update 2017-10-09 by ms).

Considerations

Find a suitable location and directory structure for serveral versions of the same library/code
Manage the user environment to be able to access the correct version automatically
Manage different software stacks, e.g. use different compiler(-version) or different library versions to build another library (–> 1.)

Location of compiled software

mountpoint
└── processor architecture
    │
    └── glibc (C-library) of OS
        │   
        └── processor type
            │   
            └──program name
               │   
               └──program version

/opt/sw
└── x86_64
    │   
    └── glibc-2.17
        │   
        └── ivybridge-ep
            │   
            └──hdf5
               │   
               └──1.8.18-MPI

Details of hdf5/1.8.18-MPI

tree -d -L 5 /opt/sw/x86_64/glibc-2.17/ivybridge-ep/hdf5/1.8.18-MPI

/opt/sw/x86_64/glibc-2.17/ivybridge-ep/hdf5/1.8.18-MPI
├── gcc
│   └── 5.3
│       └── intel-mpi
│           └── 5
│               ├── bin
│               ├── include
│               ├── lib
│               └── share
└── intel
    ├── 15
    │   └── intel-mpi
    │       └── 5
    │           ├── bin
    │           ├── include
    │           ├── lib
    │           └── share
    ├── 16
    │   └── intel-mpi
    │       └── 5
    │           ├── bin
    │           ├── include
    │           ├── lib
    │           └── share
    └── 17
        └── intel-mpi
            └── 2017
                ├── bin
                ├── include
                ├── lib
                └── share

Software used for compiling is reflected in the directory structure

Environment Modules

environment: global variables available to current and all sub-shells (‘env’/ ‘set’ )
http://modules.sourceforge.net/
module: all modifications (set and prepend to variables) in the user environment necessary for using a piece of software
handles additional software, which is not installed to default system paths
makes different versions of one piece of software available
prerequisites: loading a module may require loading other modules before

module avail

shows available modules.
searches paths given by MODULEPATH

own modules can be added by extending MODULEPATH
If multiple modules with the same name/version are present in different directories, the first found by MODULEPATH will be used.

two parts:
- software name (directory)
- version (file with definitions)

ls /opt/sw/Modules/Libraries/hdf5
1.6.10  1.8.14      1.8.14-SERIAL  1.8.18      1.8.18-SERIAL
1.8.12  1.8.14-MPI  1.8.16         1.8.18-MPI

module load <modulename>

[markus@l33 ~]$ module load hdf5/1.8.18-MPI

You are not meeting the prereq of this module. Currently loaded modules:
None

The following modules combinations can be loaded:
(1): module load intel/15 intel-mpi/5 hdf5/1.8.18-MPI
(2): module load intel/16 intel-mpi/5 hdf5/1.8.18-MPI
(3): module load gcc/5.3 intel-mpi/5 hdf5/1.8.18-MPI
(4): module load intel/17 intel-mpi/2017 hdf5/1.8.18-MPI

Do copy and paste:

module load intel/16 intel-mpi/5 hdf5/1.8.18-MPI

module list

list currently loaded modules

module purge

remove all loaded modules;
recommended in job scripts before loading any modules (reproducibility)

module remove <modulename> <modulename> ...

removes a list of modules

module show  <modulename>

shows the variables added to your environment by a module

module show hdf5/1.8.18-MPI
/opt/sw/Modules/Libraries/hdf5/1.8.18-MPI:

conflict         hdf5 
setenv           VSC_HDF5_ROOT      /opt/sw/x86_64/glibc-2.17/ivybridge-ep/hdf5/1.8.18-MPI/intel/16/intel-mpi/5 

prepend-path     CPATH                  $VSC_HDF5_ROOT/include 
prepend-path     INCLUDE                $VSC_HDF5_ROOT/include 
setenv           VSC_HDF5_INCLUDE       $VSC_HDF5_ROOT/include 

prepend-path     LD_LIBRARY_PATH        $VSC_HDF5_ROOT/lib 
prepend-path     LIBRARY_PATH           $VSC_HDF5_ROOT/lib 
setenv           VSC_HDF5_LIB           $VSC_HDF5_ROOT/lib 

prepend-path     PATH                   $VSC_HDF5_ROOT/bin 
setenv           VSC_HDF5_BIN           $VSC_HDF5_ROOT/bin 

setenv           VSC_HDF5_VERSION_MAJOR 1 
setenv           VSC_HDF5_VERSION_MINOR 8 
setenv           VSC_HDF5_VERSION_MICRO 18-MPI 
setenv           VSC_HDF5_VERSION 1.8 
-------------------------------------------------------------------

Exercises

look at your user environment:

env
env |grep PATH
echo $PATH |tr ':' '\n'
echo $LD_LIBRARY_PATH |tr ':' '\n'
echo $MODULEPATH |tr ':' '\n'

inspect the contents of the directories in MODULEPATH
look at directory structure of installed software, e.g.:

tree -d /opt/sw/x86_64/glibc-2.17/ivybridge-ep/hdf5

try the module commands

module avail
module load hdf5/1.8.18-MPI #follow instructions in shell!
module list 
module show hdf5/1.8.18-MPI
module purge

compare PATH and LD_LIBRARY_PATH before and after loading a module

Adding own gnuplot module

setup your own modules directory and a directory for gnuplot

mkdir ${HOME}/mymodules
mkdir ${HOME}/mymodules/gnuplot

prepend own module directory to MODULEPATH:

export MODULEPATH=${HOME}/mymodules:$MODULEPATH

create module file: ${HOME}/mymodules/gnuplot/5.0.5:

#%Module
set inst_base $env(HOME)/mysoftware/gnuplot/5.0.5

prepend-path PATH $inst_base/bin
prepend-path LD_LIBRARY_PATH $inst_base/lib
append-path CPATH $inst_base/include
setenv MYVAR test1234

Exercises

check how module is loaded by default VSC-3 modules

module avail 2>&1  | less #search for gnuplot; use '/' within less for searching
module load gnuplot/5.0.5
module show gnuplot/5.0.5

create own module environment as described on previous slide, create a directory within your training sub-folder
check again, how the module is loaded.

Simple example

eg. from HDF5:

EXAMPLE=$VSC_HDF5_ROOT/share/hdf5_examples/c/ph5example.c

Compile using Intel C Compiler (file):

module purge
module load intel/16 \
    intel-mpi/5 hdf5/1.8.18-MPI

cp $EXAMPLE .
mpiicc -lhdf5 ph5example.c -o ph5example

Compile using Gnu C Compiler (file):

module purge
module load gcc/5.3 \
    intel-mpi/5 hdf5/1.8.18-MPI

cp $EXAMPLE .
mpicc -lhdf5 ph5example.c -o ph5example

If needed add e.g. include directory explicitly:

mpiicc -I$VSC_HDF5_INCLUDE -lhdf5 ph5example.c -o ph5example

Compiler names

Hint:

mpiifort
mpifort
mpicc
mpiicc

Table of Contents

Software management

Considerations

Location of compiled software

Details of hdf5/1.8.18-MPI

Environment Modules

Exercises

Adding own gnuplot module

Exercises

Simple example

Compiler names