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s# unidata/nctests - Regression Testing

This project contains the dockerfiles for two images, unidata/nctests and unidata/ncabi. The documentaiton below relates to nctests. Documentation for ncabi is forthcoming.

Overview

This docker image is used to perform spot-tests on Unidata netCDF packages. It can be used to test code repositories remotely or locally. See Examples for various command-line recipes for using this package.

When this docker container is run, it will check out the following packages from the Unidata github site:

  • netcdf-c
  • netcdf-fortran
  • netcdf-cxx4
  • netcdf-java
  • netcdf4-python
  • NetCDF Operators (NCO)

Each package will be built and tested. This way, we can see if any changes in netcdf-c break anything which depends on it (netcdf-fortran and netcdf-cxx4).

Available Compilers

The docker containers will let you use the following compilers:

  • gcc and g++
  • clang and clang++
  • mpicc (from mpich package)
  • intelone (x86_64 only).

These are controlled via the USE_CC and USE_CXX environmental variables.

Containers

The following containers/systems are available:

  • Ubuntu (64-bit)
    • serial (for serial tests)
    • parallel (for parallel tests)

These are specified by changing the USE_CC environmental variable, gcc by default.

NetCDF Operators (NCO)

From the NCO website:

The NCO toolkit manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5. It exploits the geophysical expressivity of many CF (Climate & Forecast) metadata conventions, the flexible description of physical dimensions translated by UDUnits, the network transparency of OPeNDAP, the storage features (e.g., compression, chunking, groups) of HDF (the Hierarchical Data Format), and many powerful mathematical and statistical algorithms of GSL (the GNU Scientific Library). NCO is fast, powerful, and free.

NCO integration adds additional regression testing.

Specifying an Alternative netcdf-c Branch

You can specify an alternative branch for netcdf-c than main using the following syntax.

$ docker run -e CBRANCH="branch name" unidata/nctests

Working with local copies instead of pulling from GitHub

It is possible to use local directories instead of pulling from github. You do this by mounting your local git directory to the root of the docker image filesystem, e.g.

$ docker run -v $(pwd)/netcdf-c:/netcdf-c unidata/nctests

When the image runs, it will check for the existence of /netcdf-c, /netcdf-fortran, /netcdf-cxx4 and /netcdf4-python. If they exist, the image will clone from these instead of pulling from GitHub.

Note: Because it is cloning from a 'local' directory, it is important that you have that local directory already on the branch you want to analyze. You will still need to set the appropriate Environmental Variable, however, if you want the build to be properly labelled for the CDash Dashboard.

Environmental Variables/Options

The following environmental variables can be used to control the behavior at runtime.

  • CMD - Run an alternative command. Options for this are help.
  • USEDASH - Set to any non-TRUE value to disable using the remote dashboard.
  • HELP - If non-zero, the help information will be printed to standard out.

Branch Control

  • CBRANCH - Git branch for netcdf-c
  • FBRANCH - Git branch for netcdf-fortran
  • CXXBRANCH - Git branch for netcdf-cxx4
  • JAVABRANCH - Git branch for netcdf-java
    • Default: maint-5.x
    • JDKVER - Version of OpenJDK to run for tests. Default: 17
      • Minimum version: 17.
  • PBRANCH - Git branch for netcdf4-python
  • NCOBRANCH - Git branch for NCO.
    • Default: 4.5.4.

Select HDF Version to Use

  • H4VER - Set to version you want to use. Default: None
    • Note: This versions < 4.3.0 do not work on arm architecture.
    • Note: If empty, no HDF4 tests are run.
  • H5VER - Set to the version you want to use. Default: 1.14.6
    • Introduced in version 1.9.3.
    • If non-empty, the specified HDF5 version will be downloaded, compiled and installed at runtime instead of using the pre-built version.
      • Example: -e HDF5SRC="1.14.6"
  • H5PACKAGE - If TRUE, install via package manager instead of from source.

Select AWS-S3-SDK

USES3INT takes precedence over USES3SDK

  • USES3INT - Set TRUE to use Internal interface. Default: FALSE
  • USES3SDK - Set TRUE to use AWS-S3-SDK. Default: FALSE
  • S3SDKVER - Version of AWS-S3-SDK to download and compile. Default: main

Compiler Option

  • USE_CC - C language compiler to use.
    • gcc - Default
    • clang
    • mpicc
      • MPICHVER - Version of MPICH to use. Options are default or numeric version, e.g. 4.2.0.
  • USE_CXX - C++ language compiler to use.
    • g++ - Default
    • clang++

Note that these options are currently only honored by the serial and serial32 images. How they function with the parallel images is TBD.

CFlags for CMake, autotools-based builds.

  • CMAKE_COPTS - CMake options for netcdf-c
  • CMAKE_FOPTS - CMake options for netcdf-fortran
  • CMAKE_CXXOPTS - CMake options for netcdf-cxx4
  • AC_COPTS - Autoconf options for netcdf-c
  • AC_FOPTS - Autoconf options for netcdf-fortran
  • AC_CXXOPTS - Autoconf options for netcdf-cxx4

Which Tests to run

  • RUNC - Set to OFF, FALSE, anything but TRUE, to disable running netcdf-c tests. NetCDF-C is still downloaded, compiled and installed.
  • RUNF - Set to OFF, FALSE, anything but TRUE, to disable running netcdf-fortran tests.
  • RUNCXX - Set to OFF, FALSE, anything but TRUE, to disable running netcdf-cxx4 tests.
  • RUNJAVA - Set to Non-TRUE to disable.
  • RUNP - Set to OFF, FALSE, anything but TRUE, to disable running netcdf4-python tests.
  • RUNNCO - Set to OFF, FALSE, anything but TRUE, to disable running NCO tests.

Build Systems to use

  • USE_BUILDSYSTEM - 'Defaults to 'cmake'. Options are cmake, autotools, both.
  • DISTCHECK - Default to FALSE. Requires USE_BUILDSYSTEM to be autotools or both. Runs make distcheck after make check.

Documentation generation

In order to build documentation for netcdf-c and netcdf-fortran, you must specify either or both of the variables below to TRUE or ON, and also create a volume mapping to /docs in the container, e.g. -v [path on host]:/docs.

  • CDOCS - Default: FALSE
  • FDOCS - Default: FALSE
  • CDOCS_DEV - Default: FALSE
  • FDOCS_DEV - Default: FALSE

Advanced Options

  • NCOMAKETEST - ADVANCED Default to FALSE. When TRUE, run make test for the NCO package and parse the output for Unidata-related output.
  • TESTPROC - ADVANCED Default to 1. Defines the number of processors to use when building and testing.
  • TESTPROC_FORTRAN - ADVANCED Default to 1. Defines the number of processors to use when building and testing.
  • USE_LOCAL_CP - ADVANCED Default to FALSE. Uses cp instead of git clone. This is required in particular circumstances and when a test image uses an older version of git that will not work with shallow copies.
  • ENABLE_C_MEMCHECK - ADVANCED NetCDF-C only Turns on the following options when running the C tests: -fsanitize=address -fno-omit-frame-pointer
  • FORTRAN_SERIAL_BUILD - ADVANCED NetCDF-Fortran only Forces TESTPROC to 1 for netCDF-Fortran.

Examples

Important Information for the Examples

For these examples, we will assume you are working on a command line, and located in the root netcdf-c directory, such that $(pwd) resolves to /location/to/root/netcdf/directory.

The following command line options will be used repeatedly, so I will explain them here. For a full explanation of docker command line arguments, see https://docs.docker.com/reference/commandline/cli/.

  • --rm: clean up the docker image after it exits.
  • -it: Run as an interactive shell. This allows us to ctrl-c a running docker instance.
  • -v: Mount a local volume to the docker image.
  • -e: Set an environmental variable.

See the section on environmental variables for a complete list of variables understood by unidata/nctests.

- Show the help file

This will show you the help file for the docker image.

$ docker run --rm -it -e CMD=help unidata/nctests

- Run a docker container interactively

This will put you into the shell for the docker container. Note that any changes you make will not persist once you exit.

$ docker run --rm -it --entrypoint /bin/bash unidata/nctests

- Run all tests (standard use case)

$ docker run --rm -it unidata/nctests

- Run all tests (standard use case) using clang instead of gcc

$ docker run --rm -it -e USE_CC=clang -e USE_CXX=clang++ unidata/nctests

- Run all tests against a specific branch

$ docker run --rm -it -e CBRANCH=working unidata/nctests

- Turn off DAP tests by passing in a cmake variable

$ docker run --rm -it -e COPTS="-DNETCDF_ENABLE_DAP=OFF" unidata/nctests

- Run all of the tests but do not use the remote dashboard

$ docker run --rm -it -e USEDASH=OFF unidata/nctests

- Run the tests against a local copy of the netcdf-c git repository instead of pulling from GitHub

Note that you will not switch branches inside the docker container when running like this; you must make sure your local repository (that you're at the root of, remember?) is on the branch you want to analyze.

$ docker run --rm -it -v $(pwd):/netcdf-c unidata/nctests

- Run the tests against a local copy, and disable the fortran, c++ and remote dashboard.

$ docker run --rm -it -v $(pwd):/netcdf-c -e USEDASH=OFF -e RUNF=OFF -e RUNCXX=OFF unidata/nctests

- Run the NetCDF-C tests using Autootools instead of CMake, and repeat the build twice.

$ docker run --rm -it -e USE_BUILDSYSTEM=both -e CREPS=2 unidata/nctests

Running non-serial tests

$ docker run --rm -it -e USE_BUILDSYSTEM=cmake -e USE_CC=mpicc unidata/nctests

Running Java tests with internal data and ctest repeats 3 times to try to get success.

$ docker run --rm -it -e CBRANCH=v4.9.2 -e RUNF=OFF -e CTEST_REPEAT=3 -e RUNJAVA=TRUE -v /path/to/cdmUnitTest:/share/testdata/cdmUnitTest -v ./results:/results unidata/nctests