ToDo-List

Documentation

Responsibilities for PALM-internal workshop 2016 are marked in red color

Page (e. g. wiki/doc/app/userint)	What to do?	Name
wiki/doc/tec/developerrules	Write reference document for code formatting and programming rules / programmer guidelines	Siggi
wiki/doc/app/jobcontrol	Restructure mrun documentation
wiki/doc/tec/mbuild	Description of mbuild
wiki/doc/tec/subjob	Description of subjob
to be created	Create descriptive page for "Model Steering"
wiki/doc/app/...	Navigation for documentation pages (Steering of interactive/batch runs)
wiki/doc/tec/1d_model	Description of 1d model
wiki/doc/tec/cloud_physics	Description of cloud physics module
wiki/doc/app/examples/turbinf	Update description about usage of turbulent inflow	Tobias
wiki/doc	Update of page "Documentation"
<page>	complete explanations for PALM error messages	all, if there is time to spare
<page>	Links from manual to tutorial
<page>	Write descriptions for exercises 6-14 (divide all exercises into Tutorial exercises and Advanced exercises), Advanced examples->Research project examples
gallery	Update the gallery (new images from research projects)
wiki/Help/FAQ	Extend FAQ list
...	List the literature on which the applied methods and approaches (physical and numerical) are based on and set links to this list wherever references are made
wiki/doc/	Description of statistical methods (computation of fluxes and variances, horizontal averaging, etc.)
wiki/doc#Modelformulation	Transfer contents from the PALM paper (Maronga et al. 2015) to the trac system	Hiwi
<page>	Write documentation for wind turbine parametrization code	Björn Witha
wiki/doc/tec/lsm	Write documentation for land surface model	Björn
wiki/doc/tec/radiation	Write documentation for radiation models	Björn
wiki/doc/tec/bc	Write documentation for new treatment of the constant flux layer	Björn
wiki/doc/tec/ocean	density in formulas need to be corrected: in-situ density is used in the buoyancy and energy production term, potential density is only used to calculate stability (Brunt-Vaisala frequency for calculating the mixing length). This error was made in the Maronga et al.(2015) paper as well!

PALM seminar improvements (for 2017)

Item	What to do?	Name
Lecture handouts	Separate binding for lectures and exercises
Name tags	Name tags for participants. Provide PALM T-Shirts and/or name tags for lecturers / exercise advisors
Exercise solutions	After some time into the exercise sessions, participants should receive solutions for the input files in order to be able to produce and analyse some results
Group photo
Exercises	Reduce the runtime of the exercises and test the computational time with gfortran as participants often use this compiler on their noteboeoks.
Parameter file inconsistencies	Settings for data output are not consistent within the parameter file. For example, 3d/2d/pr output variables are explicitly declared, but timeseries are always the same (confusing for users). Also, differentiation between data_output and data_output_pr is confusing. A possible solution would be to use data_output exlusively and include profiles, e.g. for pt this then would read "pt", "pt_xy", "pt_pr", etc.
Default FFT solver	The default is currently "system-specific", but on some notebooks of the user there was no FFT library available. The default should thus be changed to the Temperton FFT
dt_dots	Description in the documentation should be revised (default value)
data output steering	User find it confusing that they have to specify the data output in the parameter file (e.g. for xy and 3d output) and then switch data output on AGAIN in the mrun call. Maybe we can find a more convenient solution?
mrungui	So far we have not used the mrungui within the seminar, although it might be quite convenient tool for users.
...

Source Code

Program parts	What to do?	Name
mrun, subjob, mbuild	Translate German comments to English	Siggi r1289
mrun	restructure / simplify / remove the parameter-file check	Björn
	develop new GUI for parameter file generation
	develop an installation script (using cmake mechanism	Helge
PALM code, OpenACC	completion of single-GPU porting	Siggi
PALM code, OpenACC	re-evaluation of the MPI-GPU-version
PALM code, OpenACC	implement CUDA-aware MPI
mrun, subjob	allow batch-job-directives (e.g. PBS) and execution commands (mpiexec, aprun, etc.) to be configured using entries in .mrun.config	Siggi
mrun, subjob, mbuild	cleaning	Siggi
PALM code	code clearing and restructuring following programmer guidelines of DWD/DMI	all
	- use KIND parameter for defining single/double precision instead of compiler options (e.g. -r8)	all r1354
	- select from modules only those variables really required, using the ONLY attribute	all r1324
	- describe variables in the declaration statements	all
	- review MODULE concept and extend it to other parts of the code (canopy model, coupling, ). This should include swap_timelevel.f90	Farah (canopy) r1484, Björn
	- move initialization from init_3d_model to the respective modules
PALM code	output progress messages on terminal or to the job protocol (see Helges progress bars)	Siggi, Helge r1402
	finish implementation of FFT/ALLTOALL overlapping	Ketelsen, Siggi r1306
	finish implementation of prognostic_equation/SENDRECV overlapping
<page>	Avoid collecting of 2D data on PE0 (topography data, surface coupling layer), maybe using co-array FORTRAN
	Implement flux limiter for Wicker-Skamarock	Matthias, Lennart postponed due to inherent optimization drawbacks
<page>	Implement RRTMG radiation model	Björn
<page>	Subgrid-scale saturation fluctuation for Lagrangian cloud model	Fabian
	Implement new particle data structure in LPM	Fabian
	Implement logarithmic interpolation of particle velocities near the surface	Matthias r1315
	Separate equation for passive scalar (multiple scalars?)	to be done in MOSAIK
	Modification of random number generator to allow better parallelization	Helge
	implementation of a tracbot, which automatically runs and checks examples in case of any code changes
	implement SGS model from Igor Esau	to be done in MOSAIK
	implement a soil model (similar to DALES?)	Björn
calc_spectra	check and update the internal calculation of spectra	Matthias (check)
	improve output of standard timeseries: L is defined as Obukhov-length for dry air; should also be defined for moist air; output of buoyancy flux w"vpt"0	Björn
data_output	implement output of hydrostatic pressure	Björn, Helge
data_output	implement output of scalar and momentum fluxes calculated by temporal EC
	implement random number generation for ensemble runs	Helge, Björn
	implement new boundary condition for cases where the grid spacing is in the order of the roughness length
	increase limit for some identifier strings (e.g. length of variable names is very limited)	Björn
PALM code	implement anelastic approximation	Helge
	implementation of viscous topography
PALM code	Use NetCDF instead of ASCII for topography data	to be done in MOSAIK
PALM code	Update GPL	all r1310
PALM code	Allow runs for >= 10000 cores	Björn, Siggi
PALM code	Create temporary job sub-directories via mrun (does not work properly with the FORTRAN system call function)
PALM code	Discuss the treatment of package parameters, regarding their appearance in read_var_list and write_var_list. Discuss the general treatment / separation of inipar and d3par parameters.	all
Example runs	Modify the "building" example run (example_building_p3d), since topography is allowed with WS-scheme
PALM code	For reference_state='horizontal_average' round the averaged profile (e.g. 3.3 digits) to make runs repeatable
PALM code	Add description for all variables/quantities used in PALM according to doxygen syntax
PALM code	Avoid repeating code blocks in data_output routines and use subroutines instead
PALM code	Avoid unnecessary grid checks when using multi grid solver	??
PALM code, topography	remove bug which appears for complex topography; the current workaround is to filter the topography apriori, but this doesn't help in case of topography on coarse-grid MG levels; filter may have to be applied within PALM code directly
PALM code	Remove unnecessary tail and dvrp code from Lagrangian particle model	Fabian
PALM code	Substitute some mathematical descriptions of processes in Lagrangian cloud model by more appropriate parameterizations (terminal velocities in lpm_advec and lpm_collision_kernels)	Fabian
PALM code	Implement Johannes' splitting and merging algorithm for Lagrangian particles	Fabian, Johannes
PALM code	Implement random velocity perturbations for Lagrangian droplets; make simple random number generator available for general usage	Fabian
PALM code	Unification of bulk cloud microphysics (i.e., delete calc_precipitation, calc_liquid_water, impact_of_latent_heat and introduce these processes to the microphysics subroutine)	Fabian
PALM code	Implement and homogenize output of cloud-physical variables derived from bulk and Lagrangian cloud physics (e.g., qc, ql, qr, lpt, pt)	Fabian
PALM code/ documentation	Change the name specific humidity to mixing ratio! We don't compute specific humidities.	Fabian
data_output	In profile output define zu and zw only once instead of define a vertical dimension for each individual variable (e.g. zpt, zw"u, zw"v, ...)
data_output	When calculating vertical cross sections averaged along x or y, leave out topography
data_output	Do not output ghost points
PALM code	Separate option "cyclic_fill" from restart run to avoid unwanted effects (e.g. surface heat flux value in namelist of a run using "cyclic_fill" will always be overwritten by the value used in the precursor run).
PALM code	Change mass flux correction from addition to multiplication	Tobias
PALM code	Integrate wind turbine parametrization code into the default code	Björn Witha
PALM code	define dimensions of data_output, data_output_pr, etc. as variables (avoid fixed numbers in code)
PALM code	Implement synthetic turbulence generation method	Tobias
mrun / ?	put INPUT and USER_CODE folder under revision control (git) with automatic updates whenever a job is sent
PALM code	Revision of large-scale forcing / nudging implementation including input data format. In this course, allow for using the mechanism to initialize PALM with explicit vertical profiles without further large-scale forcing or nudging	could be done within MOSAIK
PALM code	Particle code: unify allocation of particle arrays within lpm_droplet_collision, lpm_droplet_condensation, ... (REAL(wp), DIMENSION(:), ALLOCATABLE or REAL(wp), DIMENSION(prt_count(k,j,i)))	Fabian
PALM code	Use only one Magnus formula within the code (not several as in microphysics.f90, lpm_droplet_condensation.f90, calc_liquid_water.f90, land_surface_model.f90)	Fabian
PALM code	Implement PALM error messages in parallel random number generator module
mrun / data output	Use same cycle number for all output files
PALM code	Review summation of "1E-5_wp" in lines 164/167 in diffusivities.f90 (r2119), see ticket:393
data_output	Make use of already implemented 'long_name' attribute of variables, i.e. give possibility to assign a long_name for user defined variables
data_output	Set missing values/fill values inside topography and define these missing values as attributes in NetCDF file.
mrun, .mrun.config	allow for a different name and directory for the "job_queue" folder
PALM code	optimise calculation of npex and npey in init_pegrid, such that a working (and efficient) processor topology will be found if it exists	Katrin

Code performance

	define setups for scaling / benchmark runs	Björn, Siggi, Fabian
	carry out runs to determine PALM's weak/strong scaling behaviour + parallel efficiency, this might be good to be carried out during the test phase of the HLRNIII-Hannover-complex	?
<page>	<what>	<name>

Ticket system

Revision number

Add possibility to enter revision number in ticket header, currently only PALM version is available

Farah

Tools

-	new plotting tool to replace palmplot	Christoph + Hiwi
-	new tool to find possible model grid configurations	HiWi?
watchdog	Debugging: runs on two hosts at the same time, add on/off switches for each host, add "do you really want to cancel job hannover.1234567 ?"-button	Björn