Running `MESH` on Ubuntu

[kasra-keshavarz]

Documentation suggestion

More of a documentation suggestion, as @roalva82 and I have been trying to compile MESH on Ubuntu VMs (WSL + Multipass). Here is the workflow we used to compile with gcc stack:

Serial version:

$ sudo apt update
$ sudo apt install gcc build-essential gfortran libnetcdff-dev
$ make gfortran netcdf # in MESH's source code directory

MPI version:

$ sudo apt install libopenmpi-dev openmpi-bin libnetcdf-mpi-dev libnetcdff-dev
$ make mpi_gcc netcdf

Does MESH need the parallel capability for the NetCDF library? If yes, there should be some adjustments with the library names installed to have it compile properly.

I have used Ubuntu 20.04.6 LTS, and the software stack on its package repositories. The gcc used is 9.4.0.

@roalva82 have compiled on Ubuntu 22.04 with gcc 11.4.0 and the software stack available on 22.04's remote repositories.

[mee067]

I do not think MESH I/O is parallelized irrespective of the file format and therefore it won't need the parallelized netcdf library.

Mohamed Ahmed had issues trying to compile with gcc 13 and had to downgrade - just to note. He would have the details.

[kasra-keshavarz]

Just out of curiosity, I compiled MESH r1860 using gfortran/gcc v13.2.0 and it compiled without any issues. I don't think here is the right topic, but it would be nice to see the issue he is facing, and report it here.

Here are the specs:

Ubuntu 23.10
gfortran/gcc v13.2.0
MESH r1860

Here is NetCDF details:

$ nf-config --all

This netCDF-Fortran 4.5.4 has been built with the following features: 

  --cc        -> gcc
  --cflags    -> -I/usr/include -Wdate-time -D_FORTIFY_SOURCE=2

  --fc        -> gfortran
  --fflags    -> -I/usr/include -I/usr/include
  --flibs     -> -L/usr/lib/aarch64-linux-gnu -lnetcdff -Wl,-Bsymbolic-functions -flto=auto -ffat-lto-objects -flto=auto -Wl,-z,relro -Wl,-z,now -lnetcdf -lnetcdf -lm 
  --has-f90   -> 
  --has-f03   -> yes

  --has-nc2   -> yes
  --has-nc4   -> yes

  --prefix    -> /usr
  --includedir-> /usr/include
  --version   -> netCDF-Fortran 4.5.4
$ nc-config --all

This netCDF 4.9.2 has been built with the following features: 

  --cc            -> /usr/bin/cc
  --cflags        -> -I/usr/include -I/usr/include/hdf5/serial
  --libs          -> -L/usr/lib/aarch64-linux-gnu -L/usr/lib/aarch64-linux-gnu/hdf5/serial -lnetcdf
  --static        -> -lhdf5_hl -lhdf5 -lcrypto -lcurl -lpthread -lsz -lz -ldl -lm -lxml2

  --has-dap          -> yes
  --has-dap2         -> yes
  --has-dap4         -> yes
  --has-nc2          -> yes
  --has-nc4          -> yes
  --has-hdf5         -> yes
  --has-hdf4         -> no
  --has-logging      -> no
  --has-pnetcdf      -> no
  --has-szlib        -> no
  --has-cdf5         -> yes
  --has-parallel4    -> no
  --has-parallel     -> no
  --has-nczarr       -> yes
  --has-zstd         -> yes
  --has-benchmarks   -> no
  --has-multifilters -> no
  --has-stdfilters   -> deflate szip bz2
  --has-quantize     -> no

  --prefix        -> /usr
  --includedir    -> /usr/include
  --libdir        -> /usr/lib/aarch64-linux-gnu
  --plugindir     -> 
  --version       -> netCDF 4.9.2

[kasra-keshavarz]

Copying him here, just in case @MIsmlAhmed

[MIsmlAhmed]

That was for an older MESH version (1813, I think).

[kasra-keshavarz]

Thank you @MIsmlAhmed, an MVCE would be great to us started fixing it. I'll try on my end later today.

[dprincz]

MESH does not require parallel libraries of NetCDF.