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Software management

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

Considerations

  1. Find a suitable location and directory structure for serveral versions of the same library/code
  2. Manage the user environment to be able to access the correct version automatically
  3. 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
  • pandoc/introduction-to-vsc/04_module_environment/01_modules.txt
  • Last modified: 2024/10/24 10:28
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