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mpi_netcdf_installer

Scripts to download and install all the libraries needed for NetCDF

WARNING: You use this set of scripts at your own risk! It was written and configured for use in a small number of MIT computing environments, and has not been widely tested.

You will need the following environment variables:

  • NETCDF_HOME: This is where the bin, include, and lib folders will be installed. It must NOT already exist
  • NETCDF_FORTRAN_HOME: This must be the same as $NETCDF_HOME
  • CC: A working C compiler, e.g. icc or gcc
  • FC: A working Fortran compiler, e.g. ifort or gfortran
  • CXX: A working C++ compiler, e.g. icpc or g++
  • MPI_ROOT: The root directory for your MPI installation. See the note below!

If you already have a working MPI implementation, then $MPI_ROOT/bin/mpicc should exist. In this case you can skip Step 2 below. If you do NOT yet have a working MPI installation, then you will need to run Step 2 and you still need to set a value for MPI_ROOT (i.e. it should be where you will want your MPI implementation to be installed). In all cases, CC, FC, and CXX should be set to the serial compilers and NOT to MPI wrappers such as mpicc!

Installation:

There are three steps. Steps 2a and 2b are for systems where you do not yet have a working MPI installation. Step 3 then handles the actual installation of NetCDF. If you already have a working MPI installation, you can skip straight to Step 3.

Step 1: Downloading the source files

If you do not already have the directory "src_all" in this directory, run

./mpi_netcdf.sh -d

This will download the necessary source files into the directory "src_all". Use this if you need to run the installer on a node which does not have access to the internet.

Step 2: Installing an MPI implementation

If the user does NOT have a working MPI installation, this package comes with some (albeit only lightly-tested) scripts which can attempt to do so for them. This comes in two steps. The first is to install the OpenUCX communication framework, which replaced the "openib" transport layer in OpenMPI v4+.

Step 2a: Installing OpenUCX v1.8.1

As long as your compilers are correctly set up in the environment (ie "CC=gcc" or "CC=icc" and so on), you can start the OpenUCX build process by running

./ucx_build.sh /path/to/target/dir

with your desired target directory inserted as required. Once OpenUCX is installed, be sure to modify you PATH and LD_LIBRARY_PATH variables as suggested (and to do so in the bashrc file you will be using to build and run your MPI applications).

A note on OpenMPI and OpenUCX versions: There are two specific version clashes which are known to cause issues. Firstly, OpenMPI 4.0.2 does not work with versions of OpenUCX v1.7+, but this bug is resolved with OpenMPI 4.0.3. Secondly, versions of OpenUCX prior to v1.7 appear to have an issue where certain floating point exceptions result in an incomplete traceback, complicating debug. It is therefore STRONGLY recommened that you use OpenUCX v1.7+ with OpenMPI 4.0.3+. This script downloads and installs OpenMPI 4.0.4 with OpenUCX v1.8.1, which should avoid both of these issues and has been successfully tested with GCHPctm v12.9.0.

Step 2b: Installing OpenMPI v4.x.x

At this point, you must have the following additional environment variables set up:

  • MPI_ROOT: This is equivalent to your MPI "prefix" and must point to where you want your bin, include, and lib directories

You should also check that the command "ucx_info" works from anywhere. Otherwise, you only need your compiler environment variables defined (CC, FC, CXX). Now, run

./openmpi_build.sh

This should automatically install OpenMPI v4.x.x to the MPI_ROOT directory.

Step 3: Installing NetCDF

Standard installation

In theory, NetCDF can be installed immediately, simply by running:

./mpi_netcdf.sh

Select "y" for "Force MPI compilers", and provide a workable temporary directory (e.g. $HOME/tmp) when requested. Otherwise just follow the on-screen prompts. The installer will take the following steps:

  • Check which libraries are already installed (currently only curl is checked)
  • Install each of the following in order, if not found:
    • curl
    • zlib
    • szip
    • HDF-5
    • NetCDF-C
    • NetCDF-Fortran

Note: this process can take a while! If successful, this will end with a message recommending changes to your PATH and LD_LIBRARY_PATH, as well as a message about how to remove the temporary directory which was used to build the source code.

Advanced options

The user can choose to avoid installing one or more of the libraries above with the argument "-s" ("skip"). For example, if the user has a functioning copy of the curl and zlib libraries on their LD_LIBRARY_PATH, they can invoke the build process with

./mpi_netcdf -s curl,zlib

The argument to "-s" must be a comma-seperated list, made up of the values (on the left) below:

  • curl : curl
  • zlib : zlib
  • szip : szip
  • hdf : HDF-5
  • netcdf-c : NetCDF-C
  • netcdf-fortran : NetCDF-Fortran

Note that, for curl, this should not be necessary - presence of the curl library should be automatically detected. The user can also choose to skip automatic library detection by providing the "-f" ("force") argument. Combining these two arguments enables the user to force the installation of any combination of arguments.