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Software libraries (generic)

The MeluXina User Software environment offers many software libraries that can be used in your C/C++, Fortran, Python and other applications. This page showcases how you can use them when building your application.

First you will need to activate the corresponding environment module with module load <library/version>.

The modules populate your shell's environment with several variables, one of which is called EBROOT<LIBRARYNAME>.

You may use env | grep EBROOT to see all the variables that appear once a module is loaded, note that any dependencies of the module will also create this type of entries.

The EBROOT* variable contains the library's installation path, and can be used in your commands and scripts ($EBROOT<NAME>) to point to specific folders available underneath and link your application to the library (e.g. $EBROOT<NAME>/lib, $EBROOT<NAME>/include, etc.).

It is preferred to use the variable as the reference to the installation path, instead of hard-coding the full path, which may change.

We provide two different examples for data management and GPU-accelerated libraries:

  • HDF5 for file format and data model management
  • cuDNN is the NVIDIA Deep Neural Network for forward and backward convolution, pooling and normalization.

Example using HDF5

EasyBuild module description

HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of data-types, and is designed for flexible and efficient I/O and for high volume and complex data.

Available HDF5 versions

Check the available versions on MeluXina with module command:

module avail HDF5
Terminal output example
------------------------- /apps/USE/easybuild/release/latest/modules/all --------------------------
HDF5/1.10.7-gompi-2020b     HDF5/1.12.0-gompi-2020b
HDF5/1.10.7-gompic-2020b    HDF5/1.12.1-gompi-2020b (L,D)

Where:
L:  Module is loaded
D:  Default Module

For example, in the MeluXina 2021.2 software stack you will find:

HDF5 - serial MPI(OpenMPI) - parallel
HDF5/1.10.7-gompi-2020b
HDF5/1.10.7-gompic-2020b (CUDA)
HDF5/1.12.0-gompi-2020b
HDF5/1.12.1-gompi-2020b

Compilation of code using HDF5 library

Load a serial or MPI-parallel build of HDF5 in order to compile your program:

module load HDF5/1.12.1-gompi-2020b

The EBROOTHDF5 and HDF5_DIR environment variables are then populated in your shell's environment and point to the HDF5 installation dir:

echo $EBROOTHDF5
Terminal output example
/apps/USE/easybuild/release/2021.2/software/HDF5/1.12.1-gompi-2020b/

You can now compile your C/C++/Fortran code (e.g. writedata.cpp) step by step, using the MPI C++ compiler wrapper:

mpicxx -c -I/$EBROOTHDF5/include writedata.cpp

and then link HDF5 library:

mpicxx -o writedata writedata.o -L$EBROOTHDF5/lib -lhdf5_cpp -lhdf5

Note that HDF5 contains helper utilities that can be used to compile in a single step:

h5c++ -o writedata writedata.cpp

Example using cuDNN

EasyBuild module description

The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks.

Available HDF5 versions

Check the available versions on MeluXina with module command:

module avail cuDNN
Terminal output example
-------------------------- /apps/USE/easybuild/release/latest/modules/all --------------------------
   cuDNN/8.0.4.30-CUDA-11.1.1    cuDNN/8.2.1.32-CUDA-11.3.1
   cuDNN/8.1.1.33-CUDA-11.2.2    cuDNN/8.2.2.26-CUDA-11.4.1 (L,D)

   Where:
    L:  Module is loaded
    D:  Default Module

For example, in the MeluXina 2021.2 software stack you will find:

cuDNN/8.0.4.30-CUDA-11.1.1 
cuDNN/8.1.1.33-CUDA-11.2.2    
cuDNN/8.2.1.32-CUDA-11.3.1
cuDNN/8.2.2.26-CUDA-11.4.1

Compilation of code using cuDNN library

Load one of the available version in order to compile your program:

module load cuDNN/8.2.2.26-CUDA-11.4.1

The EBROOTCUDNN environment variables are then populated in your shell's environment and point to the cuDNN installation dir:

echo $EBROOTCUDNN
Terminal output example
/apps/USE/easybuild/release/2021.2/software/cuDNN/8.2.2.26-CUDA-11.4.1

You can now compile your cuda code (e.g. pooling.cu) step by step, using CUDA compiler:

nvcc -c -I/$EBROOTCUDNN/include pooling.cpp

and then link cuDNN library:

nvcc -o pooling pooling.o -L$EBROOTCUDNN/lib -lcudnn -lcudnn_static