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Hi, I'm using RhessysIOinR with Rhessys 6.0 with one of the examples in GitHub (ws_hja) and when I run the script I get:
[1] Output files with prefix patch_sim alerady exist in out/ and will be overwritten.
[1] "New def files written for file defs/veg_p300_shrub.def"
[1] "New hdr file written : worldfiles/ws/ws_1.hdr"
[1] "Tec file has been written"
[1] "----------------- Run 1 of 1 -----------------"
[1] Command line echo: /home/maria/rhessys_git/rhessys_git/rhessys/rhessys6.0 -w worldfiles/p300.world -whdr worldfiles/ws/ws_1.hdr -t tecfiles/p300.tec -r flowtables/p300.flow -st 1941 10 1 1 -ed 1998 10 1 1 -pre out//patch_sim -s 2.000000 2.000000 -sv 2.000000 2.000000 -svalt 1.000000 1.000000 -gw 0.200000 0.200000 -b -h -z -g -p -c
Segmentation fault (core dumped)
user system elapsed
0.037 0.005 0.225

I've been days stucked with it, Can anybody help me please?

library(RHESSysIOinR)
setwd("/mnt/hgfs/Ubuntu/nice0416/")
rh_path = file.path("/usr/local/bin/rhessys7.4")
input_rhessys = IOin_rhessys_input(
version = rh_path,
tec_file = "tecfiles/tec.test",
world_file = "worldfiles/ParWorld/adh.world",
world_hdr_prefix = "adh",
flowtable = "flowtables/adh.flow",
start = "2010 6 20 1",
end = "2011 10 1 1",
output_folder = "out/",
output_prefix = "adh",
commandline_options = c("-g")
)
input_tec_data = IOin_tec_std(start = "2010 6 20 1",
end = "2011 10 1 1",
output_state = TRUE)
input_hdr = IOin_hdr(
basin = "defs/basin.def",
hillslope = "defs/hill.def",
zone = "defs/zone.def",
soil = c("defs/soil_sandyloam.def", "defs/soil_clay.def", "defs/soil_loam.def","defs/soil_loamysand.def","defs/soil_sandyclayloam.def","defs/soil_siltyloam.def"),
landuse = c("defs/lu_undev.def","defs/lu_agriculture.def"),
stratum = c("defs/veg_douglasfir.def","defs/veg_deciduous.def","defs/veg_eucalypt.def","defs/veg_evergreen.def","defs/veg_grass.def","defs/veg_shrub.def"),
basestations = "clim/adh_base"
)
filter2 = build_output_filter(
timestep = "daily",
output_format = "csv",
output_path = "/out",
output_filename = "basin_daily",
spatial_level = "basin",
spatial_ID = as.integer("1"),
variables = "patch.streamflow"
)

output_filter = IOin_output_filters(filter2, file_name = "tecfiles/test_output_filter.yml")
n=5
input_def_pars_monte_carlo = IOin_def_pars_simple(
list("defs/soil_sandyloam.def", "m", runif(n, 0.1, 1)),
list("defs/soil_sandyloam.def", "Ksat_0", runif(n, 0.1, 2000)),
list("defs/soil_sandyloam.def", "m_z", runif(n, 0.1, 1)),
list("defs/soil_sandyloam.def", "pore_size_index", runif(n, 0.01, 1)),
list("defs/soil_sandyloam.def", "psi_air_entry",runif(n, 0.1, 3)),
list("defs/soil_sandyloam.def", "sat_to_gw_coeff", runif(n, 0, .7)),
list("defs/hill.def", "gw_loss_coeff", runif(n, 0, .7))
)

run_rhessys_multi(
input_rhessys = input_rhessys,
hdr_files = input_hdr,
tec_data = input_tec_data,
def_pars = input_def_pars_monte_carlo,
output_filter = output_filter
)
The above shows my entire code

Good afternoon,

I am working using RHESSysIOinR in a watershed of 70 km2,

I could compile rhessys 7.4 and I created my worldfile and flowtable,

However, when I use run_rhessys_single I have this message:

===== Beginning RHESSysIO file writing =====

===== Wrote hdr file 'worldfiles/waterford/waterford.hdr' =====
===== Wrote tec file =====

===== Finished RHESSysIO file writing =====

Command line echo: bash -c "rh_dev/rhessys//rhessys7.4 -w worldfiles/waterford.world -whdr worldfiles/waterford/waterford.hdr -t tecfiles/w8TC.tec -r flowtables/waterford.flow -st 1998 10 1 1 -ed 2000 10 1 1 -pre out//waterford -g -b"

===== Beginning RHESSys Simulation =====

added new parameter, adjust the num_variables in phys_constants.h
added new parameter, adjust the num_variables in phys_constants.h
added new parameter, adjust the num_variables in phys_constants.h
added new parameter, adjust the num_variables in phys_constants.h
added new parameter, adjust the num_variables in phys_constants.h
added new parameter, adjust the num_variables in phys_constants.h
.
.
.
NULL

Also when I created my worldfile/flowtable file there were some warnings :

Warning messages:
1: In getProjectionRef(x, OVERRIDE_PROJ_DATUM_WITH_TOWGS84 = OVERRIDE_PROJ_DATUM_WITH_TOWGS84, ... :
Discarded datum Not_specified_based_on_GRS_1980_ellipsoid in Proj4 definition: +proj=longlat +ellps=GRS80 +no_defs
2: In getProjectionRef(x, OVERRIDE_PROJ_DATUM_WITH_TOWGS84 = OVERRIDE_PROJ_DATUM_WITH_TOWGS84, ... :
Discarded datum Not_specified_based_on_GRS_1980_ellipsoid in Proj4 definition: +proj=longlat +ellps=GRS80 +no_defs
3: In getProjectionRef(x, OVERRIDE_PROJ_DATUM_WITH_TOWGS84 = OVERRIDE_PROJ_DATUM_WITH_TOWGS84, ... :
Discarded datum Not_specified_based_on_GRS_1980_ellipsoid in Proj4 definition: +proj=longlat +ellps=GRS80 +no_defs

I wonder if that's the problem.
Or if you have an idea why RHESSysIO did not recognize my data,

Thank you,

Able to run RHESSys within R environment but unable to run with output filtering

when included filter is used error that returns is
"Error: syntax error, unexpected DOT, expecting PATH_SPEC or FILENAME_SPEC, for token: |.|
construct_output_filter failed with error: output_filter_parser returned with an error."

when a custom filter that was created is used what is returned is
"Error: syntax error, unexpected IDENTIFIER, expecting PATH_SPEC or FILENAME_SPEC, for token: |test|
construct_output_filter failed with error: output_filter_parser returned with an error."

output_path is "test/" for the custom filter but other combinations of "test","/test/","./test/" have been applied.

RHESSys is being run via Windows in R

The code doesn't allow both a preexisting parameter table to be used in addition to searching other parameters. This can come up in multi-step calibrations. In my case, I calibrated subsurface parameters and identified the top parameter set. I wanted to bring this parameter set in from a preexisting table and further calibrate fire effect parameters.

A solution will allow both methods to be used but will require some error checking in case both methods refer to the same parameter.

currently there are many other packages used in rhessysIOinR, they're included in the imports in the description, but that doesn't attach the packages for use, currently you have to attach all the packages along with RHESSysIOinR but I think we should be able to get around this. It looks like right now it explicitly refers to the functions via :: so i'm not sure why you need to load the other packages, maybe just missing :: for some functions?

This issue makes it difficult to use awk for overwriting def files

Able to run test RHESSysPreprocess Script.

Attempting to run script with real world data.

Right after the Finished reading in maps message I get a 100% completion bar and a bar that hangs up at 50%, right after this I get the message "Error: C stack usage 7969812 is too close to the limit"

I have checked my files and they all work with R 5.18. They have been converted to tif files and the only map that has been modified is the topidx map to remove missing data within bounds of the world map.

Any ideas on what is causing the issue?

R doesn't seem to be able to terminate when RHESSys has been called.

Will,

I am thinking of moving the output filter file name to IOin_rhessys_input. I think this would make the usage more consistent with the other inputs (like the tec file) and would simplify the IOin_output_filter structure.

For example, if an existing output_filter was being used, then a path name in IOin_rhessys_input is all that would be need. If a new output filter is desired, then the path name in IOin_rhessys_input would be specified but an output_filter argument would be added.

Any thoughts or objections?

Ryan

Hi, I'm trying to generate the climatic sequence inputs to use RHESSysIOinR but I keep geting this message: FATAL ERROR: in construct_clim_sequence end date beyond end of clim sequence. I'm using the vignette from here: https://rdrr.io/github/RHESSys/RHESSysIOinR/src/vignettes/sample_inputs_simple.R, and the data from the study cases uploaded here in GitHub. Can anyone help me to generate the climatic inputs?
Thank you!

Hi, I want to know if it needs R / rstudio under Mac OS or Linux system to run theRHESSysIOinR. Can it run in Windows 10 system?

Thank you!

Attempting to run RHESSysIOinR on a windows machine with WSL installed. I have had success in running older versions (5.18) via RHESSysIOinR by swapping out the files in the rh_dev folder to the older 5.18 files.

I have not had success in running the most recent version of RHESSys via RHESSysIOinR. The test code provided which is titled "test-single_run.R" downloads from the develop branch but both this branch and the master branch give the same error.

Version 7.3 is the current version that is downloaded and compiled. 7.4 on develop.

"8 warnings generated.
cd output_filter/parser &&
bison --report=none -d output_filter_parser.y &&
flex output_filter_parser.l
/bin/sh: 2: bison: not found
make: *** [makefile:1080: output_filter/parser/output_filter_parser.tab.c] Error 127
make: Leaving directory '/mnt/c/Users/Carlos/Documents/R/win-library/4.0/RHESSysIOinR/extdata/rh_dev/rhessys'

Command line echo: wsl make -C rh_dev//rhessys -f makefile
RHESSys objects removed after compilation

-------------------- End compile_rhessys.R --------------------
Warning message:
In compile_rhessys(location = "rh_dev/") :
Make probably failed, returned: 2"

Are there any modifications to be made when attempting to run newer versions of RHESSys via RHESSysIOinR?

Need to create an alternative approach for assigning parameter names in the get_parameter_sets function that accounts for duplicate parameter names from multiple canopies. Current approach adds a ".1" to the second parameter listed in the parameter_change_list that is passed to run_rhessys.

Can select_output_variables.R be rewritten so that setwd() isn't needed?