Search found 55 matches

by jordanschnell
Mon Sep 28, 2020 3:49 pm
Forum: Gas Chemistry and KPP
Topic: Compilation failed: buffer overflow detected using KPP
Replies: 1
Views: 4

Re: Compilation failed: buffer overflow detected using KPP

Hi,

This seems to be a memory issue. Are you compiling on the command line? Can you provide the compile with additional memory?

Jordan
by jordanschnell
Mon Sep 28, 2020 3:45 pm
Forum: WRF-Chem Bug Reports
Topic: Segfault somewhere in Henry's law coefficient definition
Replies: 9
Views: 66

Re: Segfault somewhere in Henry's law coefficient definition

Hi Lukas,

I do not, but of course please let us know if you find anything else! Thanks.

Jordan
by jordanschnell
Wed Sep 23, 2020 7:10 pm
Forum: WRF-Chem Bug Reports
Topic: Plumerise bug
Replies: 7
Views: 88

Re: Plumerise bug

Hi Neeldip, Great to hear that this is working - It's likely aem_so4 is all zero in rsl.out.0000 because there are no bb emissions on that tile (i.e., how WRF decomposes the domain). Can you please do a grep on all of the rsl.out.* files to see if this was the issue? If so, I'd like to submit a pull...
by jordanschnell
Wed Sep 23, 2020 2:47 pm
Forum: WRF-Chem Bug Reports
Topic: Segfault somewhere in Henry's law coefficient definition
Replies: 9
Views: 66

Re: Segfault somewhere in Henry's law coefficient definition

Hi Lukas,

The PR looks great - I'll get it approved and it will be in the next release. Thank YOU for your help.

Jordan
by jordanschnell
Tue Sep 22, 2020 4:49 pm
Forum: Running
Topic: Program stops in FTUV module with anthropogenic file after running a few hours
Replies: 18
Views: 629

Re: Program stops in FTUV module with anthropogenic file after running a few hours

Hi Xin, Are you saying the problem is fixed or it is still hanging with anthro input? I don't see anything wrong with your namelist. As for the wrfbiochemi file, In the past I've always just created one for all 12 months, but I don't know how that could be related to your anthro_emis files. Have you...
by jordanschnell
Tue Sep 22, 2020 4:41 pm
Forum: WRF-Chem Bug Reports
Topic: Segfault somewhere in Henry's law coefficient definition
Replies: 9
Views: 66

Re: Segfault somewhere in Henry's law coefficient definition

Hi Lukas, Yes, a check and fatal call here would probably be best. If you are comfortable modifying the code, it would be most helpful if you submitted a pull request for this issue to the WRF github. You can find the template in your WRF installation: WRF/.github/PULL_REQUEST_TEMPLATE. Essentially ...
by jordanschnell
Tue Sep 22, 2020 4:02 pm
Forum: WRF-Chem Bug Reports
Topic: Segfault somewhere in Henry's law coefficient definition
Replies: 9
Views: 66

Re: Segfault somewhere in Henry's law coefficient definition

Hi Lukas,

You are indeed correct. Numgas is set = 0 in module_input_chem_data.F As you can see, this chemistry option only includes GHGs and so you should set gas_drydep_opt = 0.

Jordan
by jordanschnell
Fri Sep 18, 2020 10:28 pm
Forum: Running
Topic: real.exe invalid parent id for domain 2
Replies: 8
Views: 42

Re: real.exe invalid parent id for domain 2

Hi Paul, That is unfortunate - I don't think this is the issue, but you still have several places that need changed: Change this: auxinput6_inname = 'wrfbiochemi_d01','wrfbiochemi_d01', auxinput7_inname = 'wrffirechemi_d<domain>','wrffirechemi_d<domain>', auxinput8_inname = 'wrfchemi_gocart_bg_d<dom...
by jordanschnell
Fri Sep 18, 2020 3:02 pm
Forum: WRF-Chem Bug Reports
Topic: Plumerise bug
Replies: 7
Views: 88

Re: Plumerise bug

Very interesting - I assume the other sulfate bins are also elevated? I've looked at the routines that add biomass burning emissions for Mosaic (module_mosaic_addemiss.F), and may have found something - In the fire select loop, this is defined: aem_so4 = bburn_mosaic_f(n)*ebu(i,k,j,p_ebu_sulf) Howev...
by jordanschnell
Thu Sep 17, 2020 10:22 pm
Forum: Running
Topic: real.exe invalid parent id for domain 2
Replies: 8
Views: 42

Re: real.exe invalid parent id for domain 2

Hi Paul, It's looks to be a problem with your reading your namelist. In namelist.output, it has MAX_DOM = 1.  I've just relooked at your namelist.wps, and its possible you need to change parent_id = 1, 1, 2. If you run metgrid with a namelist.wps max_dom = 2 instead of 3, does that change anything? ...
by jordanschnell
Thu Sep 17, 2020 7:55 pm
Forum: Running
Topic: real.exe invalid parent id for domain 2
Replies: 8
Views: 42

Re: real.exe invalid parent id for domain 2

Hi Paul, Ok - does running real produce a namelist.output? If so, can you attach it? Also for the namelist options with d<domain>, you only need one value, as <domain> takes care of it. these nml options are also not within a block: auxinput13_inname = 'wrfchemv_d<domain>', 'wrfchemv_d<domain>', aux...
by jordanschnell
Thu Sep 17, 2020 5:29 pm
Forum: WRF-Chem Bug Reports
Topic: Plumerise bug
Replies: 7
Views: 88

Re: Plumerise bug

Hi, Are you seeing elevated concentrations of any other species? The plumerise calculations should operate/transport all species the same way. To me that suggests a problem with chemistry or the emissions. Can you verify the magnitude of your SO2 fire emissions is within a reasonable value? Is this ...
by jordanschnell
Thu Sep 17, 2020 2:24 pm
Forum: Running
Topic: real.exe invalid parent id for domain 2
Replies: 8
Views: 42

Re: real.exe invalid parent id for domain 2

Hi,

One thing I notice is that the namelist option: sfcp_to_sfcp is not held within the &domains. Another thing to try is to set parent_id = 1, 1.

Jordan
by jordanschnell
Mon Sep 14, 2020 8:09 pm
Forum: Running
Topic: FATAL CALLED: STOP: activate before 48000
Replies: 2
Views: 33

Re: FATAL CALLED: STOP: activate before 48000

Hi Pramod, The problem is that you have cfl errors: d01 2017-06-28_01:01:30 5051 points exceeded cfl=2 in domain d01 at time 2017-06-28_01:01:30 hours d01 2017-06-28_01:01:30 MAX AT i,j,k: 44 157 59 vert_cfl,w,d(eta)= 7.311847 12.04821 4.1962974E-03 d01 2017-06-28_01:01:30 66 points exceeded cfl=2 i...
by jordanschnell
Mon Sep 14, 2020 7:50 pm
Forum: WRF-Chem Bug Reports
Topic: Segfault somewhere in Henry's law coefficient definition
Replies: 9
Views: 66

Re: Segfault somewhere in Henry's law coefficient definition

Hi Lukas, Is your error occurring during the compile or the model run? If the latter, please delete chem/module_dep_simple.o and chem/module_dep_simple.mod, uncomment the FCDEBUG flags, and recompile. If the compile doesn't catch the problem, hopefully it will be discovered at runtime. Please also a...
by jordanschnell
Thu Sep 10, 2020 8:58 pm
Forum: General
Topic: WRF_VPRM have no negative value in CO2_BIO and CO2_OCE
Replies: 1
Views: 42

Re: WRF_VPRM have no negative value in CO2_BIO and CO2_OCE

Hi,

I believe these quantities are concentrations, so cannot be zero. Are you interested in the fluxes? e.g., see this line in module_ghg_fluxes.F

chem(i,1,j,p_co2_bio)= chem(i,1,j,p_co2_bio) + conv_rho* (eghg_bio(i,1,j,p_ebio_gee) + eghg_bio(i,1,j,p_ebio_res)) ! both uptake and release

Jordan
by jordanschnell
Thu Sep 10, 2020 8:48 pm
Forum: Emissions
Topic: Code for reading emission files
Replies: 7
Views: 207

Re: Code for reading emission files

Hi Soroush, Everything looks fine with the registry. After you changed the registry, did you perform a ./clean -a ? That is required any time the registry is changed. Otherwise, can you attach your full compile log, and if the compile aborted for a specific program, please also attach that file (.F)...
by jordanschnell
Thu Sep 10, 2020 7:42 pm
Forum: Chemistry-meteorology Interactions
Topic: Aerosol wet deposition output
Replies: 1
Views: 51

Re: Aerosol wet deposition output

Hi Neeldip, I'm not familiar with MOSAIC, but it looks like you need to extract it from the array "qsrflx" which is computed in the subroutine wetscav_cbmz_mosaic. Within module_wetscav_driver.F, note how the accumulated wet deposition is calculated for other species. You should be able to add your ...
by jordanschnell
Thu Sep 10, 2020 7:26 pm
Forum: Emissions
Topic: Code for reading emission files
Replies: 7
Views: 207

Re: Code for reading emission files

Hi Soroush, Can you attach your registry.chem? And did you also add the species as a state variable in the emis_ant array? For example, see emissions of so2: state real e_so2 i+jf emis_ant 1 Z i5r "E_SO2" "EMISSIONS" "mol km^-2 hr^-1" Jordan
by jordanschnell
Tue Sep 01, 2020 4:33 pm
Forum: General
Topic: WRF Chem v4 user guide
Replies: 2
Views: 92

Re: WRF Chem v4 user guide

Hi, Unfortunately there is not yet an updated user guide, however, most changes between 3.9 and 4.2 have been modest - at least on the chem side of things. You can see a list of documented changes here: https://github.com/wrf-model/WRF/releases and chem-specific pull requests here: https://github.co...
by jordanschnell
Thu Aug 27, 2020 4:06 pm
Forum: Chemistry-meteorology Interactions
Topic: Error with ACM2 pbl
Replies: 4
Views: 103

Re: Error with ACM2 pbl

Hi, ndepvel looks to be an integer that describes how many (n) species deposition velocities (depvel) will be calculated for. I don't quite understand the reason for the error/catch of ndepvel vs. num_vert_mix. My advice would be once you find out what number you need for ndepvel (either numgas or n...
by jordanschnell
Wed Aug 26, 2020 3:28 pm
Forum: Chemistry-meteorology Interactions
Topic: Error with ACM2 pbl
Replies: 4
Views: 103

Re: Error with ACM2 pbl

Hi, Your error is coming from this block of code in chemics_init.F ! Set the num_vert_mix variable if using ACM num_vert_mix = 0 IF ( config_flags%bl_pbl_physics == ACMPBLSCHEME ) THEN mix_select: SELECT CASE(config_flags%chem_opt) CASE (RADM2SORG_AQ, RADM2SORG_AQCHEM, RACMSORG_AQ, RACMSORG_AQCHEM_K...
by jordanschnell
Wed Aug 26, 2020 3:18 pm
Forum: Running
Topic: WRFChem with NETCDF4
Replies: 2
Views: 94

Re: WRFChem with NETCDF4

Hi,

I assume you have compiled with NETCDF4? And your netcdf installation also supports NETCDF4? Can you attach your configure.wrf and your rsl.error?

Jordan
by jordanschnell
Fri Aug 21, 2020 3:01 pm
Forum: Running
Topic: MPI_ABORT was invoked
Replies: 1
Views: 73

Re: MPI_ABORT was invoked

Hi,

This could be caused by a whole range of issues - Is this the first time you are using this executable? Can you attach some relevant files including your namelist.input, rsl.out.0000, and rsl.error.0000? You can also try using srun instead of mpirun.

Jordan
by jordanschnell
Wed Aug 19, 2020 4:59 pm
Forum: WRF-Chem Bug Reports
Topic: Bug with nesting
Replies: 3
Views: 186

Re: Bug with nesting

Hi Senghor, A couple questions - do all of your rsl.errors/outs end the same way? I see that you are using 72 processors to run real - Do you get the same error if you used far fewer procs (e.g., 1, 2, 4, or 8)? Your domain is not especially large so it shouldn't take too long on fewer cores. Please...

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