uoa-eresearch/easierbuild

Build scripts and instructions for software on the NeSI Auckland cluster that is too hard to build with easybuild.

easierbuild

Build scripts and instructions for software on the NeSI Auckland cluster that is too hard to build with easybuild.

General notes

Private Modules

Private modules are useful for custom software builds and when admin privileges do not allow global installs. They can be setup in a project or home dir e.g:

/projects/uoa00035/privatemodules/HDF5/1.8.15-intel-2015a

To use modules in this location, execute module use /projects/uoa00035/privatemodules This is best placed in the ~/.bashrc

Building and testing with Intel

Building binaries is pretty straight forward, just load the appropriate Intel module and set the compiler flag e.g:

module load intel/2015a
export CC=$EBROOTICC/bin/icc
export CXX=$EBROOTICC/bin/icpc
export FC=$EBROOTIFORT/bin/ifort
export F77=$EBROOTIFORT/bin/ifort

./configure --prefix=/install/path
make

If you have MPI code to build, generally you would do something like this:

module load intel/2015a
export CC=$EBROOTIMPI/bin64/mpiicc
export MPICC=$EBROOTIMPI/bin64/mpiicc
export CXX=$EBROOTIMPI/bin64/mpiicpc
export MPICXX=$EBROOTIMPI/bin64/mpiicpc
export FC=$EBROOTIMPI/bin64/mpiifort
export F77=$EBROOTIMPI/bin64/mpiifort

./configure --prefix=/install/path
make

If you want to test Intel build MPI code, e.g if one of the make targets is 'check' you may encounter a problem with running mpiexec/mpirun, e.g:

... cannot connect to local mpd ...
1. no mpd is running on this host
2. an mpd is running but was started without a "console" (-n option)

This is because Intel MPI is not built against SLURM, so to make it work we need to reference mpiexec.hydra which is in $EBROOTIMPI/bin64.

So have a look to see where mpiexec/mpirun is being referenced and replace with mpiexec.hydra.

Then use an interactive session:

salloc -A uoa00035 --ntasks=8 -C avx --time=5:00:00

Next unset I_MPI_PMI_LIBRARY as this may cause some conflicts in access the correct MPI environment.

Now run the make check and hopefully it should work.