Module command

IPSL mesocenter ( spirit,spiritx and hal) uses module command for software initialization (Version 5.0.1)

Syntax:

module command could be now abbreviated in just ml

module (avail [product] | load product[/version] | list | switch product/version1 product/version2 | display product[/version] ...)

avail : list all known product and versions
help : display software information
load : initialize a product in his default version if no version is specified
list : list already loaded product and version
switch : changing the version of already loaded product
purge : unload product
display : display help and show which environment variables are modified
save : _ Save current module list to collection_
restore: Restore module list from collection or file

more information with module help command

Product could be a compiler, a library or a software

Sample

user@spirit1:~$ module avail
------------------------ /usr/share/modules/modulefiles ------------------------
dot  module-git  module-info  modules  null  use.own  
--------------- /net/nfs/tools/meso-u20/modules-spack/Compilers ----------------
gcc/9.4.0   gcc/11.2.0        intel/2021.4.0  nvhpc/21.9  
gcc/10.3.0  intel/19.0.8.324  nvhpc/20.11     
--------------- /net/nfs/tools/meso-u20/modules-spack/Libraries ----------------
armadillo/10.5.0             netcdf-c/4.7.4-mpi                    
blis/0.8.1                   netcdf-c/4.7.4-parallel-netcdf        
blitz/1.0.2                  netcdf-c/4.7.4-serial                 
eccodes/2.21.0               netcdf-fortran/4.5.3                  
eccodes/2.21.0-openmp        netcdf-fortran/4.5.3-mpi              
eccodes/2.21.0-pthreads      netcdf-fortran/4.5.3-parallel-netcdf  
eccodes/2.21.0-serial        netcdf-fortran/4.5.3-serial           
flexiblas/3.0.4              openblas/0.3.14                       
hdf5/1.8.22                  openblas/0.3.14-openmp                
hdf5/1.8.22-mpi              openblas/0.3.14-pthreads              
hdf5/1.8.22-serial           openblas/0.3.14-serial                
hdf5/1.10.7                  openblas/0.3.17                       
hdf5/1.10.7-mpi              openblas/0.3.17-openmp                
hdf5/1.10.7-serial           openblas/0.3.17-pthreads              
intel-mkl/2020.4.304         openblas/0.3.17-serial                
intel-mkl/2020.4.304-openmp  openmpi/4.0.7                         
intel-mkl/2020.4.304-serial  parallel-netcdf/1.12.2                
intel-mkl/2020.4.304-tbb     ucx/1.11.2                            
jasper/2.0.32                valgrind/3.17.0-mpi                   
netcdf-c/4.7.4               
---------------- /net/nfs/tools/meso-u20/modules-spack/Products ----------------
cdo/1.9.10   ferret/7.6.0    idl/8.2       matlab/2021b  parallel/20200822  
cylc/6.11.4  git-lfs/2.11.0  julia/1.6.3   nco/4.9.3     R/4.0.5            
cylc/7.9.5   git/2.31.1      matlab/2019b  nco/5.0.1     singularity/3.9.5  
cylc/8.0rc1  idl/6.4         matlab/2020b  nvtop/1.2.2   
----------------- /net/nfs/tools/meso-u20/modules-spack/Python -----------------
anaconda3-py/2020.11  pytorch-ignite/0.4.3         pytorch/1.10.1    
anaconda3-py/2021.11  pytorch-ignite/0.4.8         tensorflow/2.2.0  
catboost/0.24.4       pytorch-lightning/1.1.8-gpu  tensorflow/2.4.1  
catboost/1.0.4        pytorch-lightning/1.5.10     tensorflow/2.6.3  
jax/0.3.1             pytorch/1.7.1                tensorflow/2.7.0  
lightgbm/3.3.2-cpu    pytorch/1.8.2-lts            xgboost/1.5.2

Using module

user@spirit1:~$ module list
No Modulefiles Currently Loaded.
user@spirit1:~$ gfortran --version
GNU Fortran (Ubuntu 9.4.0-1ubuntu1~20.04.1) 9.4.0

user@spirit1:~$ module load gcc/10.3.0 
user@spirit1:~$ gfortran --version
GNU Fortran (Spack GCC) 10.3.0

user@spirit1:~$ type matlab
-bash: type: matlab: not found
user@spirit1:~$ module avail matlab
---------------- /net/nfs/tools/meso-u20/modules-spack/Products ----------------
matlab/2019b  matlab/2020b  matlab/2021b  
user@spirit1:~$ module load matlab/2021b 
user@spirit1:~$ type matlab
matlab is /net/nfs/tools/matlab/2021b/matlab

Compilers and libraries modules

how to load libraries module

Default compiler is OS compiler (gcc 9.4.0)
if no compiler is loaded before loading a library, default compiler will be used

user@spirit1:~$ module list
No Modulefiles Currently Loaded.
user@spirit1:~$ module load openmpi/4.0.7 
Loading openmpi/4.0.7
  Loading requirement: gcc/9.4.0
user@spirit1:~$ type mpifort
mpifort is /net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/openmpi/4.0.7-gcc-9.4.0-v4soq3vs5n5rex3gszzs7ffvud66aceh/bin/mpifort

* if a compiler is already loaded , library will be loaded for this compiler

user@spirit1:~$ module list
Currently Loaded Modulefiles:
 1) intel/19.0.8.324  
user@spirit1:~$ module load netcdf-fortran/4.5.3
user@spirit1:~$ module load netcdf-fortran/4.5.3
user@spirit1:~$ type nf-config
nf-config est /net/nfs/tools/u20/22.3/PrgEnv/intel/linux-ubuntu20.04-zen2/netcdf-fortran/4.5.3-intel-19.0.8.324-friscs3w2oeb73gbl37h4ae7p43fp2gh/bin/nf-config

you could see over compiler name and version in path

you can switch a compiler module and all already loaded library module are automatically switched for the new compiler

user@spirit1:~$ module load gcc/10.3.0 eccodes/2.21.0 openmpi/4.0.7 netcdf-fortran/4.5.3 jasper/2.0.32 
user@spirit1:~$ module list
Currently Loaded Modulefiles:
 1) gcc/10.3.0   2) eccodes/2.21.0   3) openmpi/4.0.7   4) netcdf-fortran/4.5.3   5) jasper/2.0.32  
user@spirit1:~$ module switch gcc/10.3.0 intel/2021.4.0 
Switching from gcc/10.3.0 to intel/2021.4.0
  Unloading dependent: jasper/2.0.32 netcdf-fortran/4.5.3 openmpi/4.0.7 eccodes/2.21.0
  Reloading dependent: eccodes/2.21.0 openmpi/4.0.7 netcdf-fortran/4.5.3 jasper/2.0.32

to see which compiler is supported by a module (some are not supported by all compiler)

module help module_name/version

user@spirit1:~$ module help jasper
-------------------------------------------------------------------
Module Specific Help for /net/nfs/tools/meso-u20/modules/Libraries/jasper/2.0.32:

Library for manipulating JPEG-2000 images
Available software environment(s):
- gcc/9.4.0
- gcc/10.3.0
- gcc/11.2.0
- intel/19.0.8.324
- intel/2021.4.0

If you want to use this module with another software environment,
please contact the support team.

mailto: meso-support@ipsl.fr
-------------------------------------------------------------------

Module collection

you have the possibilty to save a list of module as a collection and restore them

user@spirit1:~$ ml purge
user@spirit1:~$ ml list
No Modulefiles Currently Loaded.
user@spirit1:~$ ml load intel/2021.4.0 netcdf-fortran/4.5.3-mpi netcdf-c/4.7.4-mpi hdf5/1.10.7-mpi openmpi/4.0.7
user@spirit1:~$ ml list
Currently Loaded Modulefiles:
 1) intel/2021.4.0   2) netcdf-fortran/4.5.3-mpi   3) netcdf-c/4.7.4-mpi   4) hdf5/1.10.7-mpi   5) openmpi/4.0.7  
user@spirit1:~$ ml save my-intel-env
user@spirit1:~$ ml purge 
user@spirit1:~$ ml list
No Modulefiles Currently Loaded.
user@spirit1:~$ ml restore my-intel-env
Loading intel/2021.4.0
Loading netcdf-fortran/4.5.3-mpi
Loading netcdf-c/4.7.4-mpi
Loading hdf5/1.10.7-mpi
Loading openmpi/4.0.7

finding include and libs needed to compile my soft

some tools have their own compile command that do this for you:
- openmpi ( mpicc mpifort mpif90 mpif77)
- hdf5 ( h5cc h5fc)
some tools have their own utility to find include and libraries
- netcdf-fortran ( nf-config --flibs | nf-config --fflags)
- netcdf ( nc-config --libs | nc-config --cflags)
- this could be used in script to compile
FFLAGS="$(nf-config --fflags)"

LDFLAGS="$(nf-config --flibs)"
- this could be use in Makefile also
INC_CDF=$(shell nf-config --fflags)

LIB_CDF=$(shell nf-config --flibs)

user@spirit1:~$ ml load netcdf-fortran
Loading netcdf-fortran/4.5.3-serial
  Loading requirement: gcc/9.4.0
user@spirit1:~$ nf-config --flibs
-L/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/netcdf-fortran/4.5.3-gcc-9.4.0-qljspmfrwblkxd5x6vz6ksij4xfjohfo/lib -lnetcdff
user@spirit1:~$ nf-config --fflags
-I/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/netcdf-fortran/4.5.3-gcc-9.4.0-qljspmfrwblkxd5x6vz6ksij4xfjohfo/include -I/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/netcdf-fortran/4.5.3-gcc-9.4.0-qljspmfrwblkxd5x6vz6ksij4xfjohfo/include

all our libraries packages support pkg-config method
- pkg-config --libs library_name
- pkg-config --cflags library_name
- this could be used in script to compile
  
  FFLAGS="$(pkg-config --cflags library_name)"
  
  LDFLAGS="$(pkg-config --libs library_name )"
- this could be use in Makefile also
  
  MY_INC=$(shell pkg-config --cflags library_name)
  
  MY_LIB=$(shell pkg-config --libs library_name)

user@spirit1:~$ module load jasper
user@spirit1:~$ pkg-config --libs jasper
-L/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/jasper/2.0.32-gcc-9.4.0-n4jakgxec5pawylyyrxtnr3t47qizcp3/lib -ljasper
user@spirit1:~$ pkg-config --cflags jasper
-I/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/jasper/2.0.32-gcc-9.4.0-n4jakgxec5pawylyyrxtnr3t47qizcp3/include/jasper -I/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/jasper/2.0.32-gcc-9.4.0-n4jakgxec5pawylyyrxtnr3t47qizcp3/include

all our libraries packages have an environment variable <Product_name_UpperCase>_ROOT
- include could be find in <Product_name_UpperCase>_ROOT/include
- libs could be find in <Product_name_UpperCase>_ROOT/lib

user@spirit1:~$ module load openblas/0.3.17
Loading openblas/0.3.17
  Loading requirement: gcc/9.4.0
user@spirit1:~$ env |grep ROOT
OPENBLAS_ROOT=/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/openblas/0.3.17-gcc-9.4.0-ies6zv7vdu7wxgx5pqjaxxftzqxcm3o3

All our packages prepend the library path in LD_LIBRARY_PATH environment variable

finding what is modified in my environment when I load a module

For this use the module display command

user@spirit1:~$ module load hdf5/1.8.22-mpi
Loading hdf5/1.8.22-mpi
  Loading requirement: gcc/9.4.0
user@spirit1:~$ module display hdf5/1.8.22-mpi
-------------------------------------------------------------------
/net/nfs/tools/meso-u20/modules/Libraries/hdf5/1.8.22-mpi:

module-whatis   {HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. }
prereq          gcc/9.4.0 gcc/10.3.0 gcc/11.2.0 intel/19.0.8.324 intel/2021.4.0 nvhpc/20.11 nvhpc/21.9
conflict        hdf5
prepend-path    LD_LIBRARY_PATH /net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/hdf5/1.8.22-gcc-9.4.0-xaqnfhyk3sphx4jt6kycvqjhgxagtgev/lib
prepend-path    PATH /net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/hdf5/1.8.22-gcc-9.4.0-xaqnfhyk3sphx4jt6kycvqjhgxagtgev/bin
prepend-path    PKG_CONFIG_PATH /net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/hdf5/1.8.22-gcc-9.4.0-xaqnfhyk3sphx4jt6kycvqjhgxagtgev/lib/pkgconfig
prepend-path    CMAKE_PREFIX_PATH /net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/hdf5/1.8.22-gcc-9.4.0-xaqnfhyk3sphx4jt6kycvqjhgxagtgev/
setenv          HDF5_ROOT /net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/hdf5/1.8.22-gcc-9.4.0-xaqnfhyk3sphx4jt6kycvqjhgxagtgev

Available software environment(s):
- gcc/9.4.0
- gcc/10.3.0
- gcc/11.2.0
- intel/19.0.8.324
- intel/2021.4.0
- nvhpc/20.11
- nvhpc/21.9

If you want to use this module with another software environment,
please contact the support team.

mailto: meso-support@ipsl.fr
-------------------------------------------------------------------

finding which option have been used to compile the librairies in the module

From the module display command you have the path to the source module files

All compilation FLAGS for the software are in comment in the source module files for each compiler

user@spirit1:~$ head /net/nfs/tools/meso-u20/modules/Libraries/hdf5/1.8.22-mpi
#%Module1.0
# generated : 2022/03/25-07:06:54
#
## Module file created by spack (https://github.com/spack/spack) on 2022-03-25 06:20:23.500576
##
## hdf5@1.8.22%gcc@9.4.0~cxx+fortran+hl~ipo~java+mpi+shared+szip~threadsafe+tools api=default build_type=RelWithDebInfo arch=linux-ubuntu20.04-zen2/xaqnfhy
##
## Configure options: -DALLOW_UNSUPPORTED:BOOL=ON -DHDF5_BUILD_EXAMPLES:BOOL=OFF -DBUILD_TESTING:BOOL=ON -DHDF5_ENABLE_Z_LIB_SUPPORT:BOOL=ON -DHDF5_ENABLE_SZIP_SUPPORT:BOOL=ON -DHDF5_ENABLE_SZIP_ENCODING:BOOL=ON -DBUILD_SHARED_LIBS:BOOL=ON -DONLY_SHARED_LIBS:BOOL=OFF -DHDF5_ENABLE_PARALLEL:BOOL=ON -DHDF5_ENABLE_THREADSAFE:BOOL=OFF -DHDF5_BUILD_HL_LIB:BOOL=ON -DHDF5_BUILD_CPP_LIB:BOOL=OFF -DHDF5_BUILD_FORTRAN:BOOL=ON -DHDF5_BUILD_JAVA:BOOL=OFF -DHDF5_BUILD_TOOLS:BOOL=ON -DCMAKE_C_COMPILER:STRING=/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/openmpi/4.0.7-gcc-9.4.0-v4soq3vs5n5rex3gszzs7ffvud66aceh/bin/mpicc -DCMAKE_Fortran_COMPILER:STRING=/net/nfs/tools/u20/22.3/PrgEnv/gcc/linux-ubuntu20.04-zen2/openmpi/4.0.7-gcc-9.4.0-v4soq3vs5n5rex3gszzs7ffvud66aceh/bin/mpif90
##
## Module file created by spack (https://github.com/spack/spack) on 2022-03-25 06:20:23.478368