Ingest_cm1

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Ingest_cm1 is a Fortran module to abstract access to model output files from George Bryan's CM1 cloud model.

The current version of this module supports access to GrADS style files with one output file per timestep or one output file per timestep per MPI node; HDF5 output.

These represent files created by the following options in the CM1 namelist.input file (GRADS, GRADSMPI):

output_format = 1
output_filetpe = 2 or 3

And for HDF data:

output_format = 3, 4, 5
output_filetype = 3

NOTE: Support for the native tiled output is not yet implemented. You must untile the output with the included python script.

Future output format support is expected for NetCDF4 and native MPI tiled HDF output.

GETTING THE SOFTWARE

Download a current snapshot of ingest_cm1 with:

git clone https://github.com/cwebster2/ingest_cm1.git

INSTALLING

A Fortran 2003 compiler is required to build this software. If using GNU gfortran, use of version 4.8 or later is required due to the use of allocatable arrays of polymorphic types. Intel ifort should work but is untested, as are other fortran compilers.

IngestCM1 uses cmake to generate makefiles and you have a few options when building. The default options are to build a static library without HDF5 support and install into ingest_cm1's directory. To use this default, from the ingest_cm1 directory, do:

cmake .

To enable HDF5 support, use:

cmake . -DWITH_HDF5=1

If your HDF5 library is not found, you can specify a search path with the HDF5_ROOT environment variable.

HDF5_ROOT="/path/to/hdf5" cmake . -DWITH_HDF5=1

If your HDF5 library is built with cmake support, you can try this instead:

cmake . -DWITH_HDF5_CMAKE

To build a shared library instead of a static library, add the flag -DBUILD_SHARED_LIBS=1 flag to cmake and to change the installation location, e.g. /usr/local, use -DCMAKE_INSTALL_PREFIX:PATH=/usr/local. An example of all of the above is:

HDF5_ROOT="/path/to/hdf5" cmake . -DWITH_HDF5=1 -DBUILD_SHARED_LIBS=1 -DCMAKE_INSTALL_PREFIX:PATH=/usr

which will generate makefiles to build a shared library, install into /usr/lib and /usr/include and include HDF5 support.

To build and install ingest_cm1 do:

make
make install

USING

The cm1_dataset front end

The cm1_dataset front-end is able to load a dataset with multiple grids spread across multiple files. This paradigm assumes the output style of CM1 where there are 4 grids each for scalar, u, v, and w variables. Within each grid the output may be a single file per timestep, a single file for all timesteps or a file for each MPI rank at each timestep. This is defined by the dsettype variable below.

The procedures below are all part of the cm1_dataset derived type in module ingest_cm1.

open_dataset

integer function open_dataset(self, dsetpath, dsetbasename, dsettype, grids, nodex, nodey)
   class(cm1_dataset) :: self
   character(len=*), intent(in) :: dsetpath
   character(len=*), intent(in) :: dsetbasename
   integer, intent(in)          :: dsettype
   character, dimension(:)      :: grids
   integer, optional :: nodex, nodey

This opens the dataset located at dsetpath with basename dsetbasename.
dsettype is one of GRADS, GRADSMPI, GRADSSINGLE, or HDF. grids is an array of grids to open, e.g. ['s', 'u', 'v', 'w'] for a full dataset or ['s'] if only the scalar grid is desired. The variables nodex and nodey are only used for the GRADSMPI dsettype. These are the same values used in the namelist.input for the MPI run.

close_dataset

integer function close_dataset(self)
   class(cm1_dataset) :: self

This closes the dataset.

Reading data

There are three versions of read that return 2d, 3d and slices of 3d fields.

read_3d

integer function read(self, time, grid, varname, Field3D)
   implicit none
   class(cm1_dataset) :: self
   integer            :: time, gridno
   character          :: grid
   character(len=*)   :: varname
   real, dimension(:,:,:) :: Field3D

This function returns the 3d variable Field3D for the variable varname on grid grid at time time. It returns 1 on success and 0 on failure.

read_3d_slice

integer function read(self, time, grid, varname, Field3D, ib, ie, jb, je, kb, ke)
   implicit none
   class(cm1_dataset) :: self
   integer            :: time, gridno, ib, ie, jb, je, kb, ke
   character          :: grid
   character(len=*)   :: varname
   real, dimension(:,:,:) :: Field3D

This function works just as read_3d but returns a slice of the full variable. If the full 3D variable is FullField3D, then this returns Field3D = FullField3D(ib:ie, jb:je, kb:ke). Returns 1 on sucess and 0 on failure.

read_2d

integer function read(self, time, grid, varname, Field2D)
   implicit none
   class(cm1_dataset) :: self
   integer            :: time, gridno
   character          :: grid
   character(len=*)   :: varname
   real, dimension(:,:) :: Field2D

This function returns the 2d variable Field2D for the variable varname on grid grid at time time. It returns 1 on success and 0 on failure.

Accessing grid information

get_nx, get_ny, get_nz, get_nt

integer function get_nx(self, grid)
   implicit none
   class(cm1_dataset) :: self
   character          :: grid

These get dimensions of the specified grid grid.

get_x, get_y, get_z, get_t

function get_x(self, grid, cm1err) result(x)
   implicit none
   class(cm1_dataset) :: self
   character          :: grid
   integer            :: gridno
   logical, optional  :: cm1err
   real, dimension(:), allocatable :: x

These get the mesh of grid grid along the specified dimension

Example

use ingest_cm1
implicit none
type(cm1_dataset) :: cm1
integer :: status, nx, ny, nz
real, allocatable :: theta(:,:,:)

! this opens a GRADS dataset with variables at u, v, w and s points.
status = cm1%open_dataset('/path/to/dataset', 'cm1out', GRADS, ['s','u','v','w'])

! get array dimensions for the s grid
nx = cm1%get_nx('s')
ny = cm1%get_ny('s')
nz = cm1%get_nz('s')

! get a variable theta on grid 's' at time 900
allocate(theta(nx,ny,nz)
status = cm1%read(900, 's', 'th', theta)

! do stuff here

status = cm1%close_dataset()

The backend classes

You may also use the backend classes directly. These all derive from type cm1_base and each implements a specific file backend. The interface is similar to that of ingest_cm1. See the derived type and the base type for details.

Contributing

The easiest way to contribute is to fork the repository on github and submit pull requests. I'm open to all contributions from bugfixes to enhacements specific to your workflow use-case. Contributed code is licensed under the BSD license and you will attributed.

Author

Contributors as of 26 Oct 2015

  • Casey Webster (cwebster2)

License

Copyright (c) 2015, Casey Webster All rights reserved.

Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met:

1 Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer.

2 Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution.

3 Neither the name of the copyright holder nor the names of its contributors may be used to endorse or promote products derived from this software without specific prior written permission.

THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

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  • Casey Webster

    Casey Webster @wxCasey

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    8 months, 3 weeks ago

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    Casey Webster @wxCasey

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    Casey Webster @wxCasey

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