SCORPIO 1.9.0
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Install Walk-through

Downloading Source

The SCORPIO library source can be download from github.

git clone https://github.com/E3SM-Project/scorpio.git

Prerequisites

The SCORPIO library requires a working C/C++ and Fortran compiler and an MPI library (e.g. MPICH). SCORPIO uses CMake for configuring the source, so the CMake software package needs to be available on the system. Since SCORPIO uses low level I/O libraries for I/O either NetCDF or PnetCDF libraries need to be installed on the system. SCORPIO includes support for NetCDF, PnetCDF, HDF5 and ADIOS2 I/O libraries.

Building and Installing

SCORPIO has been built using multiple compilers and installed on a variety of supercomputers. To enable support for the NetCDF library specify the path to the NetCDF C and Fortran installations using NetCDF_C_PATH and NetCDF_Fortran_PATH configuration options. To enable support for the PnetCDF library specify the path to the library via the PnetCDF_PATH configuration option. Similarly to enable support for the HDF5 library specify the install path of the HDF5 library using the HDF5_PATH configuration option. To enable support for ADIOS2 ensure that the environment variable ADIOS2_DIR is set to the ADIOS2 install directory. On some machines where compression support is enabled ADIOS2 and HDF5 might depend on paths to the compression libraries. For example to add support for compression using Blosc2 in ADIOS2 and HDF5 set the environment variable Blosc2_DIR to the Blosc2 library install directory. The compiler (or compiler wrapper) used for the build can be set by setting the environment variables CC, CXX and FC for the C, Fortran and C++ compilers. The library is configured by running cmake (CMake configure) and built using make. Please see the instructions below on how to build and install SCORPIO on some of the commonly used machines (Please note that the modules installed on these machines may change after machine updates).

  • Aurora : Aurora is a 10,624-node HPE Cray-Ex based system with 21,248 Intel Xeon CPUs at the ALCF (Argonne Leadership Computing Facility at Argonne National Laboratory). The system supports a 230 PB DAOS file system and a 100 PB Lustre file system.
  • Frontier : Frontier is a 9408-node supercomputer with 9408 AMD EPYC CPUs at the OLCF (Oak Ridge Leadership Computing Facility at Oak Ridge National Laboratory). The system supports a 679 PB Lustre file system.
  • Perlmutter : Perlmutter is a 3072-node supercomputer (CPU partition) with 6144 AMD EPYC CPUs at NERSC (National Energy Research Scientific Computing Center at Lawrence Berkeley National Laboratory). The system supports a 44 PB Lustre file system.
  • Linux : A generic Linux desktop/laptop

Aurora

The E3SM project has installed modules for NetCDF, PnetCDF and ADIOS2 libraries on Aurora. To use these modules, 

module use /lus/flare/projects/E3SMinput/soft/modulefiles

On Aurora the modules include support for NetCDF, PnetCDF, HDF5 and ADIOS2 I/O libraries.

  1. Modules

    Modules loaded for dependent software libraries depend on the compiler. The modules listed below are for the Intel OneAPI compiler.

    • Intel OneAPI compiler

      %> module use /lus/flare/projects/E3SMinput/soft/modulefiles
      %> module load cmake/3.31.8
      %> module load oneapi/release/2025.2.0
      %> module load netcdf/4.9.3c-4.6.2f
      %> module load pnetcdf/1.14.0
      %> module load adios2/2.10.2
      %> module load hdf5/1.14.6

  2. Environment Variables

    Set the CC, CXX, FC environment variables to point to the compiler wrappers. Set Blosc2_DIR, ADIOS2_DIR environment variables to point to the Blosc2 and ADIOS2 install directories. 

        CC=mpicc
    CXX=mpicxx
    FC=mpif90
    Blosc2_DIR=$BLOSC2_ROOT
    ADIOS2_DIR=$ADIOS2_ROOT

  3. Downloading & Building the library

    The script below downloads (clones) the SCORPIO library and builds it 

    
#!/bin/bash
source /usr/share/lmod/lmod/init/sh
module use /lus/flare/projects/E3SMinput/soft/modulefiles
module load cmake/3.31.8
module load oneapi/release/2025.2.0
module load netcdf/4.9.3c-4.6.2f
module load pnetcdf/1.14.0
module load adios2/2.10.2
module load hdf5/1.14.6

export Blosc2_DIR=$BLOSC2_ROOT
export ADIOS2_DIR=$ADIOS2_ROOT
export HDF5_PATH=$HDF5_ROOT

export LIBOMPTARGET_DEBUG=0
export OMP_TARGET_OFFLOAD=DISABLED
export MPIR_CVAR_ENABLE_GPU=0

export CC=mpicc
export CXX=mpicxx
export FC=mpifort
export F77=mpifort

git clone https://github.com/E3SM-Project/scorpio.git
cd scorpio
mkdir scorpio_build
cd scorpio_build

cmake \
-DPIO_BUILD_STATIC_LIBS=TRUE \
-DWITH_ADIOS2:BOOL=TRUE \
-DWITH_HDF5:BOOL=TRUE \
-DWITH_PNETCDF:BOOL=TRUE \
-DPIO_USE_MALLOC:BOOL=ON \
-DPIO_BUILD_TESTS:BOOL=ON \
-DPIO_ENABLE_EXAMPLES:BOOL=ON \
-DPIO_ENABLE_TESTS:BOOL=ON \
-DPIO_ENABLE_TIMING:BOOL=ON \
-DPnetCDF_PATH=$PNETCDF_PATH \
-DNetCDF_C_PATH=$NETCDF_PATH \
-DNetCDF_Fortran_PATH=$NETCDF_PATH \
-DHDF5_PATH=$HDF5_PATH \
-LH \
.. |& tee configure.log

make -j4 |& tee make.log

Frontier

On Frontier the modules below include support for NetCDF, PnetCDF, HDF5 and ADIOS2 I/O libraries.

  1. Modules

    Modules loaded for dependent software libraries depend on the compiler. The modules listed below are for the GNU compiler.

    • Cray Programming environment + GNU compiler

      %> module reset
      %> module load Core/25.03
      %> module load PrgEnv-gnu
      %> module load cpe/24.11
      %> module load libunwind/1.8.1 cray-python/3.11.7
      %> module load subversion git cmake
      %> module load cray-hdf5-parallel/1.14.3.3
      %> module load cray-netcdf-hdf5parallel/4.9.0.15
      %> module load cray-parallel-netcdf/1.12.3.15
      %> module load adios2/2.10.2-mpi

  2. Environment Variables

    Set the CC, CXX, FC environment variables to point to the compiler wrappers. Set ADIOS2_DIR environment variable to point to the ADIOS2 install directory. 

        CC=cc
    CXX=CC
    FC=ftn
    ADIOS2_DIR=$OLCF_ADIOS2_ROOT

  3. Downloading & Building the library

    The script below downloads (clones) the SCORPIO library and builds it 

    
#!/bin/bash
source /opt/cray/pe/lmod/lmod/init/sh
module reset
module load Core/25.03
module load PrgEnv-gnu
module load cpe/24.11
module load libunwind/1.8.1
module load cray-python/3.11.7
module load subversion
module load git
module load cmake
module load cray-hdf5-parallel/1.14.3.3
module load cray-netcdf-hdf5parallel/4.9.0.15
module load cray-parallel-netcdf/1.12.3.15
module load adios2/2.10.2-mpi

export NETCDF_PATH=$NETCDF_DIR
export PNETCDF_PATH=$PNETCDF_DIR
export ADIOS2_DIR=$OLCF_ADIOS2_ROOT

export CC=cc
export CXX=CC
export FC=ftn
export F77=ftn

git clone https://github.com/E3SM-Project/scorpio.git
cd scorpio
mkdir scorpio_build
cd scorpio_build

cmake \
-DPIO_BUILD_STATIC_LIBS=TRUE \
-DWITH_PNETCDF:BOOL=TRUE \
-DWITH_ADIOS2:BOOL=ON \
-DADIOS_BP2NC_TEST=ON \
-DPIO_ENABLE_FORTRAN:BOOL=ON \
-DPIO_USE_MALLOC:BOOL=ON \
-DPIO_BUILD_TESTS:BOOL=ON \
-DPIO_ENABLE_EXAMPLES:BOOL=ON \
-DPIO_ENABLE_TESTS:BOOL=ON \
-DPIO_ENABLE_TIMING:BOOL=ON \
-DPLATFORM:STRING=linux-gnu \
-DPnetCDF_PATH=$PNETCDF_PATH \
-DNetCDF_C_PATH=$NETCDF_PATH \
-DNetCDF_Fortran_PATH=$NETCDF_PATH \
-LH \
.. |& tee configure.log

make -j4 |& tee make.log

Perlmutter

On Perlmutter the modules below include support for NetCDF and PnetCDF I/O libraries.

  1. Modules

    Modules loaded for dependent software libraries depend on the compiler. The modules listed below are for the Intel compiler.

    • Cray Programming environment + Intel compiler

      %> module reset
      %> module load PrgEnv-intel/8.5.0
      %> module load intel/2024.1.0
      %> module load craype-accel-host
      %> module load craype/2.7.32
      %> module load cray-mpich/8.1.30
      %> module load cray-hdf5-parallel/1.12.2.9
      %> module load cray-netcdf-hdf5parallel/4.9.0.9
      %> module load cray-parallel-netcdf/1.12.3.13
      %> module load cmake/3.30.2

  2. Environment Variables

    Set the CC, CXX, FC environment variables to point to the compiler wrappers. 

        CC=cc
    CXX=CC
    FC=ftn

  3. Downloading & Building the library

    The script below downloads (clones) the SCORPIO library and builds it 

    
#!/bin/bash

source /usr/share/lmod/8.3.1/init/sh
module reset

module load PrgEnv-intel/8.5.0
module load intel/2024.1.0

module load craype-accel-host
module load craype/2.7.32
module load cray-mpich/8.1.30
module load cray-hdf5-parallel/1.12.2.9
module load cray-netcdf-hdf5parallel/4.9.0.9
module load cray-parallel-netcdf/1.12.3.13
module load cmake/3.30.2

export CC=cc
export CXX=CC
export F77=ftn
export FC=ftn

git clone https://github.com/E3SM-Project/scorpio.git
cd scorpio
mkdir scorpio_build
cd scorpio_build

cmake \
-DNetCDF_PATH=${CRAY_NETCDF_HDF5PARALLEL_PREFIX} \
-DPnetCDF_PATH=${CRAY_PARALLEL_NETCDF_PREFIX} \
-LH \
.. |& tee configure.log

make -j 4 |& tee make.log

Linux Desktop

On a Linux desktop install an MPI library and the PnetCDF or NetCDF library.

  1. Installing dependencies

    1. Download and install the MPICH library (Or an MPI library of your choice)
    2. Download and install the PnetCDF library

  2. Environment Variables

    Set the CC, CXX, FC environment variables to point to the MPICH (MPI library) compiler wrappers. 

        CC=mpicc
    CXX=mpicxx
    FC=mpif90

  3. Downloading & Building the library

    Assuming MPICH and PnetCDF libraries were installed in /usr/local/mpich/4.2.3/install and /usr/local/pnetcdf/1.14.0/install respectively, the script below downloads (clones) the SCORPIO library and builds it 

    
#!/bin/bash

export PATH=/usr/local/mpich/4.2.3/install/bin:$PATH
export PNETCDF_PATH=/usr/local/pnetcdf/1.14.0/install

export CC=mpicc
export CXX=mpicxx
export FC=mpif90

git clone https://github.com/E3SM-Project/scorpio.git
cd scorpio
mkdir scorpio_build
cd scorpio_build

cmake \
-DPIO_BUILD_STATIC_LIBS=TRUE \
-DWITH_PNETCDF:BOOL=TRUE \
-DPIO_ENABLE_FORTRAN:BOOL=ON \
-DPIO_USE_MALLOC:BOOL=ON \
-DPIO_BUILD_TESTS:BOOL=ON \
-DPIO_ENABLE_EXAMPLES:BOOL=ON \
-DPIO_ENABLE_TESTS:BOOL=ON \
-DPIO_ENABLE_TIMING:BOOL=ON \
-DPLATFORM:STRING=linux-gnu \
-DPnetCDF_PATH=$PNETCDF_PATH \
-LH \
.. |& tee configure.log

make -j4 |& tee make.log

Building and running examples

Once the library is built you can build SCORPIO examples (In the SCORPIO_SOURCE/examples directory) using the examples target 

make -j 4 examples

The examples can be run using the mpiexec (or the appropriate MPI program launcher) command.

Building and running tests

After building the library you can build SCORPIO tests using the tests target 

make -j 4 tests

On machines with a batch job scheduler (Aurora, Frontier, Perlmutter) refer to the appropriate user manual for information on how to run programs in batch jobs. The tests can be run from the build directory using the test target or using the CMake test driver ctest (from the command line on a Linux desktop and within a batch job on machines using a batch job scheduler) 

make test

or 

ctest

Last updated: 11-17-2025

Generated on Wed Nov 19 2025 11:01:53 for SCORPIO by doxygen 1.9.8