Installation and Dependencies

Dependencies

  1. The following dependencies are required for Nek5000
  • FORTRAN 77 compilers
  • C and C++ compilers
  • MPI
  1. The following dependencies are required for ADIOS2
  • CMake

In a super computer such as Dardel at PDC in Stockholm, loading the following modules is enough for compilation and execution:

module swap PrgEnv-cray PrgEnv-gnu
module load PDC
module load CMake/3.21.2
module swap craype-network-ofi craype-network-ucx
module swap cray-mpich cray-ucx
module load cray-mpich-ucx

Installation and Usage

Linking Nek5000 with ADIOS2

In this repository we include a Nek5000 version that has been modified for linking with the ADIOS2 library. For the sake of convenience, we have included a tested version of ADIOS2 under the /Nek5000/3rd_party/adios2 that can be easily installed by executing the install.sh script in the folder or at Nek5000 compile time (see sections below). If a user wish to use their own version of Nek5000, some files in the source need to be modified for the linking to occur. Such files can be readily checked and copied from the Nek5000 version shipped in this repository.

The following files were modified in the core:

The following files were added to the 3rd_party folder and contain the ADIOS2 subroutines.

Compiling Nek5000 with ADIOS2

Just as for any other used-defined function in Nek5000, 3 main files must be modified to be able to use the toolbox:

  1. compile_script
  2. makefile_usr.inc
  3. <casename>.usr

Templates of the modified files can be found at the DCTB and examples folders, however, a list of modifications to the files can be found by using the hyperlinks.

Having modified all the files accordingly, compilation follows by ensuring that the SIZE file is present in the folder and executing the command:

./compile_script --all

If ADIOS2 has not been compiled, the following message will prompt and ADIOS2 will be compiled:

compression requires ADIOS2 to be build before compilation of Nek5000
Turning to -build-dep mode
building 3rd-party dependencies

In this case, after the compilation of ADIOS2, Nek5000 will not automatically restart the compilation of the case, therefore after all the 3rd party libraries have been compiled, the user must run ./compile_script --all once again to compile the case. If the process is succesful, the executable Nek5000 and the folder config will be added to the compile sub-directory.

Running Nek5000 with ADIOS2

Prior to running, the behaviour of the compression toolbox can be modified by changing the runtime parameters that need to be included in the <casename>.par file. A template of the of the aditions to this file can be found in the DCTB and examples folder and a description of each parameter can be found following <casename>.par

To run Nek5000 it is necesary that the Nek5000 executable and the config folder are copied from the compilation folder to the run folder. Executing Nek5000 with the data compression toolbox enabled is as simple as executing, for example:

mpirun -n 4 ./nek5000