NetCDF / Parallel-NetCDF

NetCDF (Network Common Data Form) and Parallel-NetCDF (PnetCDF) are available through the Spack package manager for scientific data storage and parallel I/O operations.

NetCDF provides comprehensive support for HDF5 backend, multiple compression formats, and both serial and parallel I/O. Both NetCDF-C and NetCDF-Fortran libraries are available.

Parallel-NetCDF (PnetCDF) is a high-performance I/O library optimized for parallel access to NetCDF files, featuring burst buffering and relaxed consistency semantics for improved performance in MPI applications.

NetCDF Quick Start

Note

For the value of ${SPACK_ROOT}, please refer to Spack Instances for the installation path.

# Modify this path accordingly
export SPACK_ROOT="/path/to/spack"

# Activate Spack environment
source "${SPACK_ROOT}/dist/bin/setup-env.sh" -y

# Load a supported compiler and MPI
module load intel-oneapi-compilers
module load intel-oneapi-mpi

# Check available NetCDF versions
module avail netcdf

# Load NetCDF-C
module load netcdf-c

# Load NetCDF-Fortran
module load netcdf-fortran

# Verify installation
nc-config --version
nf-config --version  # If Fortran loaded

Note

Module names may include a 7-digit hash suffix (e.g., netcdf-c/4.9.2-abc1234). You do NOT need to include this hash when loading - the version alone (e.g., 4.9.2) is sufficient.

Parallel NetCDF Quick Start

Note

For the value of ${SPACK_ROOT}, please refer to Spack Instances for the installation path.

# Modify this path accordingly
export SPACK_ROOT="/path/to/spack"

# Activate Spack environment
source "${SPACK_ROOT}/dist/bin/setup-env.sh" -y

# Load a supported compiler and MPI
module load intel-oneapi-compilers/2025
module load intel-oneapi-mpi/2021

# Check available Parallel NetCDF versions
module avail parallel-netcdf

# Load Parallel NetCDF
module load parallel-netcdf

# Verify installation
pnetcdf-config --version

Note

Module names may include a 7-digit hash suffix (e.g., parallel-netcdf/1.14.0-abc1234). You do NOT need to include this hash when loading - the version alone (e.g., 1.14.0) is sufficient.

Building with NetCDF

C Programs

# Export compiler and linker flags for Makefiles
export CC=mpicc
export CFLAGS="$(nc-config --cflags)"
export LDFLAGS="$(nc-config --libs)"

# Direct compilation example
$CC -o myprogram myprogram.c $CFLAGS $LDFLAGS

C++ Programs

# Export compiler and linker flags for Makefiles
export CXX=mpicxx
export CXXFLAGS="$(nc-config --cflags)"
export LDFLAGS="$(nc-config --libs)"

# Direct compilation example
$CXX -o myprogram myprogram.cpp $CXXFLAGS $LDFLAGS

Fortran Programs

# Export compiler and linker flags for Makefiles
export FC=mpifort
export FFLAGS="$(nf-config --fflags)"
export LDFLAGS="$(nf-config --flibs)"

# Direct compilation example
$FC -o myprogram myprogram.f90 $FFLAGS $LDFLAGS

Using Makefile

CC ?= mpicc
CXX ?= mpicxx
FC ?= mpifort

# Set NetCDF related flags
CFLAGS += $(shell nc-config --cflags)
CXXFLAGS += $(shell nc-config --cflags)
FFLAGS += $(shell nf-config --fflags)

LDFLAGS += $(shell nc-config --libs)
FLDFLAGS += $(shell nf-config --flibs)

# Build rule for C source files
.c.o:
     $(CC) $(CFLAGS) -c $< -o $@

# Build rule for C++ source files
.cpp.o:
     $(CXX) $(CXXFLAGS) -c $< -o $@

# Build rule for Fortran source files
.f90.o:
     $(FC) $(FFLAGS) -c $< -o $@

# Link example for a C program. For Fortran, use $(FC) and $(FLDFLAGS).
myprogram: myprogram.o
     $(CC) -o $@ $^ $(LDFLAGS)

Using CMake

Using FindNetCDF:

find_package(NetCDF REQUIRED)

target_link_libraries(myprogram PRIVATE netCDF::netcdf)

Using pkg-config in CMake:

find_package(PkgConfig REQUIRED)
pkg_check_modules(NETCDF REQUIRED IMPORTED_TARGET netcdf)

target_link_libraries(myprogram PRIVATE PkgConfig::NETCDF)

Using pkg-config

# Query flags for NetCDF-C
pkgconf --cflags --keep-system-cflags netcdf
pkgconf --libs --keep-system-libs netcdf

# Query flags for NetCDF-Fortran
pkgconf --cflags --keep-system-cflags netcdf-fortran
pkgconf --libs --keep-system-libs netcdf-fortran

# Use in compilation
export CC=mpicc
export CFLAGS="$(pkgconf --cflags --keep-system-cflags netcdf)"
export LDFLAGS="$(pkgconf --libs --keep-system-libs netcdf)"

Building with Parallel NetCDF

C Programs

# Export compiler and linker flags for Makefiles
export CC=mpicc
export CFLAGS="$(pnetcdf-config --cflags)"
export LDFLAGS="$(pnetcdf-config --libs)"

# Direct compilation example
$CC -o myprogram myprogram.c $CFLAGS $LDFLAGS

C++ Programs

# Export compiler and linker flags for Makefiles
export CXX=mpicxx
export CXXFLAGS="$(pnetcdf-config --cflags)"
export LDFLAGS="$(pnetcdf-config --libs)"

# Direct compilation example
$CXX -o myprogram myprogram.cpp $CXXFLAGS $LDFLAGS

Fortran Programs

# Export compiler and linker flags for Makefiles
export FC=mpifort
export FFLAGS="$(pnetcdf-config --fflags)"
export LDFLAGS="$(pnetcdf-config --flibs)"

# Direct compilation example
$FC -o myprogram myprogram.f90 $FFLAGS $LDFLAGS

Using Makefile

CC ?= mpicc
CXX ?= mpicxx
FC ?= mpifort

# Set Parallel NetCDF related flags
CFLAGS += $(shell pnetcdf-config --cflags)
CXXFLAGS += $(shell pnetcdf-config --cflags)
FFLAGS += $(shell pnetcdf-config --fflags)

LDFLAGS += $(shell pnetcdf-config --libs)
FLDFLAGS += $(shell pnetcdf-config --flibs)

# Build rule for C source files
.c.o:
     $(CC) $(CFLAGS) -c $< -o $@

# Build rule for C++ source files
.cpp.o:
     $(CXX) $(CXXFLAGS) -c $< -o $@

# Build rule for Fortran source files
.f90.o:
     $(FC) $(FFLAGS) -c $< -o $@

# Link example for a C program. For Fortran, use $(FC) and $(FLDFLAGS).
myprogram: myprogram.o
     $(CC) -o $@ $^ $(LDFLAGS)

Using pkg-config

# Query flags for Parallel NetCDF
pkgconf --cflags --keep-system-cflags pnetcdf
pkgconf --libs --keep-system-libs pnetcdf

# Use in compilation
export CC=mpicc
export CFLAGS="$(pkgconf --cflags --keep-system-cflags pnetcdf)"
export LDFLAGS="$(pkgconf --libs --keep-system-libs pnetcdf)"

Features Availability

NetCDF-C Features

Feature	Description	Enabled
Parallel I/O	MPI-based parallel file access	✓
NetCDF-4/HDF5 Format	Full NetCDF-4 and HDF5 backend support	✓
Parallel NetCDF (PnetCDF)	High-performance parallel I/O library	✓
Standard Filters	Compression filters: deflate, bz2, blosc, zstd	✓
ZSTD Compression	Modern compression algorithm	✓
SZIP Compression	Lossless compression support	✓
Multi-filters	Multiple compression filters support	✓
NetCDF-2 Classic Format	Legacy classic format support	✓
CDF-5 Format	Large variable support (>2GB)	✓
NCZarr	Cloud-optimized Zarr format support	✓
Logging	Debug and diagnostic logging	✓
HDF4 Format	Legacy HDF4 format support	✗
DAP2/DAP4 Protocol	Remote data access protocols	✗
Benchmarks	Performance benchmarking tools	✗

Parallel NetCDF Features

Feature	Description	Enabled
Burst Buffering	Improved I/O performance via buffering	✓
Erange Fill	Fill values for out-of-range errors	✓
Relax Coordinate Boundary	Relaxed coordinate boundary checking	✓
In-place Swap	Automatic byte-swapping	Auto
NetCDF-4 Format	NetCDF-4/HDF5 format support	✗
Thread-safe	Thread-safe operations	✗
Subfiling	Subfiling for improved parallel I/O	✗
ADIOS Integration	ADIOS I/O framework integration	✗
Profiling	Performance profiling support	✗
Debug Mode	Debug mode with additional checks	✗
Null-byte Header Padding	Header padding for alignment	✗

Support and Resources

NetCDF Documentation

• NetCDF-C Documentation

• NetCDF-Fortran Documentation

Parallel-NetCDF Documentation

• Parallel-NetCDF Official Site

• PnetCDF C Programming Interface Reference