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E3SM-Project / scorpio

A high-level Parallel I/O Library for structured grid applications
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Software for Caching Output and Reads for Parallel I/O (SCORPIO)

A high-level Parallel I/O Library for structured grid applications. This library was derived from the Parallel I/O library.

Website

For complete documentation, see the HTML documentation in the docs/html directory.

Nightly Tests

The results of our nightly tests on multiple platforms can be found on our cdash site at http://my.cdash.org/index.php?project=E3SM_SCORPIO.

Dependencies

SCORPIO can use NetCDF (version 4.3.3+), PnetCDF (version 1.6.0+) or ADIOS (version 2.6.0+) for I/O.

Ideally, the NetCDF version should be built with MPI, which requires that it be linked with an MPI-enabled version of HDF5. Optionally, NetCDF can be built with DAP support, which introduces a dependency on CURL. Additionally, HDF5, itself, introduces dependencies on LIBZ and (optionally) SZIP.

Configuring with CMake

To configure the build, SCORPIO requires CMake version 2.8.12+. The typical configuration with CMake can be done as follows:

CC=mpicc CXX=mpicxx FC=mpif90 cmake [-DOPTION1=value1 -DOPTION2=value2 ...] /path/to/pio/source

where mpicc, mpicxx and mpif90 are the appropriate MPI-enabled compiler wrappers for your system.

The OPTIONS section typically should consist of pointers to the install locations for various dependencies, assuming these dependencies are not located in canonical search locations.

For each dependency XXX, one can specify the location of its installation path with the CMake variable XXX_PATH. If the C and Fortran libraries for the dependency are installed in different locations (such as can be done with NetCDF), then you can specify individually XXX_C_PATH and XXX_Fortran_PATH. Hence, you can specify the locations of both NetCDF-C and NetCDF-Fortran, as well as PnetCDF, with the following CMake configuration line:

CC=mpicc CXX=mpicxx FC=mpif90 cmake -DNetCDF_C_PATH=/path/to/netcdf-c \
                         -DNetCDF_Fortran_PATH=/path/to/netcdf-fortran \
                         -DPnetCDF_PATH=/path/to/pnetcdf \
                         /path/to/pio/source

This works for the dependencies: NetCDF, PnetCDF, HDF5, LIBZ, SZIP.

Additional CMake Options

Additional configuration options can be specified on the command line.

The PIO_ENABLE_TIMING option can be set to ON or OFF to enable or disable the use of GPTL timing in the SCORPIO libraries. This feature requires the GPTL C library for the SCORPIO C library and the GPTL Fortran library with the perf_mod.mod and perf_utils.mod interface modules. If these GPTL libraries are already installed on the system, the user can point SCORPIO to the location of these libraries with the GPTL_PATH variable (or, individually, GPTL_C_PATH and GPTL_Fortran_Perf_PATH variables). However, if these GPTL libraries are not installed on the system, and GPTL cannot be found, then SCORPIO will build its own internal version of GPTL.

If PnetCDF is not installed on the system, the user can disable its use by setting -DWITH_PNETCDF=OFF. This will disable the search for PnetCDF on the system and disable the use of PnetCDF from within SCORPIO.

NetCDF is optional if PnetCDF is used, and the user can disable its use by setting -DWITH_NETCDF=OFF. This will disable the search for NetCDF on the system and disable the use of NetCDF from within SCORPIO.

ADIOS is another I/O library supported by SCORPIO, and the user can enable it by setting -DWITH_ADIOS2=ON. The path to the ADIOS install location needs to be specified by setting the ADIOS2_DIR environment variable to the install path.

If the user wishes to disable the SCORPIO tests, then the user can set the variable -DPIO_ENABLE_TESTS=OFF. This will entirely disable the CTest testing suite, as well as remove all of the test build targets.

If you wish to install SCORPIO in a safe location for use later with other software, you may set the CMAKE_INSTALL_PREFIX variable to point to the desired install location.

Building

Once you have successfully configured SCORPIO with CMake in a build directory. From within the build directory, build SCORPIO with:

make

This will build the pioc and piof libraries.

Testing

If you desire to do testing, and PIO_ENABLE_TESTS=ON (which is the default setting), you may build the test executables with:

make tests

Once the tests have been built, you may run tests with:

ctest

If you have not run make tests before you run ctest, then you will see all of the tests fail.

Alternatively, you may build the test executables and then run tests immediately with:

make check

(similar to the typical make check Autotools target).

NOTE: It is important to note that these tests are designed to run in parallel. If you are on one of the supported supercomputing platforms (i.e., NERSC, NWSC, ALCF, etc.), then the ctest command will assume that the tests will be run in an appropriately configured and scheduled parallel job. This can be done by requesting an interactive session from the login nodes and then running ctest from within the interactive terminal. Alternatively, this can be done by running the ctest command from a job submission script. It is important to understand, however, that ctest itself will preface all of the test executable commands with the appropriate mpirun/mpiexec/runjob/etc. Hence, you should not further preface the ctest command with these MPI launchers.

Installing

Once you have built the SCORPIO libraries, you may install them in the location specified by the CMAKE_INSTALL_PREFIX. To do this, simply type:

make install

If the internal GPTL libraries were built (because GPTL could not be found and the PIO_ENABLE_TIMING variable is set to ON), then these libraries will be installed with SCORPIO.