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Nicolas Le Corre
Nov 9, 2016, 10:35:48 AM11/9/16
to connectivity-modeling-system-club
Hello everyone,
I'm a fairly new user of CMS (which a fantastic tool!! Thank you to the developpers), but I've been able to run it with all the modules at off, or with the vertical matrix switched on. To go a step further in modeling shrimp larvae, I'd like to use the buoyancy, but I'm not sure to understand everything about this module.
It says in the manual that both temperature and salinity are required, and sometimes that it requires density and temperature. Using Hycom data for the moment (with getdata), I've only access to temperature and salinity. So I've tried in several ways, but I am always ending with a seg fault. From what I understand in the manual, CMS (because he is so smart!) is able to use temp and salinity to calculate density. Is there something you could advice/explain me about this module to make it work:
different data files for each variables (u, v, temp in separate files)?
do I have to provide density myself?
Do I need to activate another module?
Also, another remark/question: is it "normal" (is it only me?) that CMS is not able to manage nest data files (downloaded from getdata) if there are temperature and salinity in it, even if it is not using it (passive transportation).
PS: If needed, I join my test nest file below and I am currently using these modules:
1) intel/16 2) openmpi/intel/1.8 3) netcdf/intel/4.2 4) ncview/2.1.1
.
Thanks in advance for your help.
Nicolas
&nest_input
xaxis= "Longitude"
yaxis= "Latitude"
zaxis= "Depth"
taxis= "MT"
xstart=270
xend=275
ystart=24
yend=26
zstart=0
zend=100.00
zaxis_positive_direction= "down"
tstart_yy=2010
tstart_mm=9
tstart_dd=1
tend_yy=2010
tend_mm=9
tend_dd=7
time_step=86400
time_units= "days"
jdate_yy=1900
jdate_mm=12
jdate_dd=31
lon_name= "Longitude"
lat_name= "Latitude"
depth_name= "Depth"
depth_conversion_factor=1
time_name= "MT"
uvel_name= "u"
vvel_name= "v"
wvel_name= ""
wvel_positive_direction = ""
velocity_conversion_factor=1
dens_name= ""
temp_name= "temperature"
saln_name= "salinity"
ssh_name= ""
angle_file=""
fill_value=1.2676506E30
agrid=.true.
orthogrid=.true.
$end
Claire PARIS
Nov 9, 2016, 1:11:51 PM11/9/16
to Nicolas Le Corre, connectivity-modeling-system-club
Bonjour Nicolas,
Let me answer your questions below and explain the buoyancy module. Please note that the buoyancy module is designed for the egg stage. If you want to use for the shrimp an egg stage and then a larval stage, you can use the mass spawning module.
More below.
Cheers,
On Nov 9, 2016, at 10:35 AM, Nicolas Le Corre <nleco...@gmail.com> wrote:Hello everyone,I'm a fairly new user of CMS (which a fantastic tool!! Thank you to the developpers), but I've been able to run it with all the modules at off, or with the vertical matrix switched on. To go a step further in modeling shrimp larvae, I'd like to use the buoyancy, but I'm not sure to understand everything about this module.It says in the manual that both temperature and salinity are required, and sometimes that it requires density and temperature. Using Hycom data for the moment (with getdata), I've only access to temperature and salinity. So I've tried in several ways, but I am always ending with a seg fault. From what I understand in the manual, CMS (because he is so smart!) is able to use temp and salinity to calculate density. Is there something you could advice/explain me about this module to make it work:different data files for each variables (u, v, temp in separate files)?
No the nest files need to include all the variables, u,v,w, S, T
do I have to provide density myself?
Yes. You need to provide a range of densities for the initial conditions. For this, you need to have a “buoyancy” file in the input directory and turn “Buoyancy” “true” in ibm.nml
The buoyancy input file should have the following structure:
4
432000 864000 1728000 2160000
1010 1015 1020 1027
1012 1017 1022 1029
0.00025 0.00020 0.00015 0.00010
0.00027 0.00022 0.00017 0.00012
* Line 1 = number of columns, which represents the time steps at each the eggs’ properties will be changed
* Line 2 = time (in seconds) that each property column is valid
* Lines 3 and 4 = lower and upper boundaries of the particle density (kg/m^3 )
* Lines 5 and 6 = lower and upper boundaries of the particle diameter range (meters)
To simulate the transport not considering a range of values, simply add the same values for the lower and upper boundary. To use the same values for all time steps, create a file with one column, with a time interval equal to your simulation maximum time, e.g.
1
2160000
1010
1010
0.00010
0.00010
Do I need to activate another module?
No
Also, another remark/question: is it "normal" (is it only me?) that CMS is not able to manage nest data files (downloaded from getdata) if there are temperature and salinity in it, even if it is not using it (passive transportation).
No, it should work. The nest file is OK, except that problem you need the vertical velocity “w". The equation for the terminal velocity Vt is shown in Paris et al. (2013) page 49, equation (1).
Hope this helps,
Claire
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Nicolas Le Corre
Nov 10, 2016, 9:26:28 AM11/10/16
to Claire PARIS, connectivity-modeling-system-club
Merci Claire.
Sorry for the previous two messages, I rewrite it in one message to be clearer on the CMS group
I'm thinking about using the mass spawning module later, but I'm trying first to run the buoyancy module and be sure to understand it.
So, I guess one of the problem came from the missing w velocity, I did not understand that it was required (and it ia not available with all the simulations). I've added it to my nest file and w is now downloaded by getgata with T and S.
However, each time I have T and S variables in my nest files, whether buoyancy flag is on or off, the CMS give the error below. However CMS is running with u,v and w variables perfectly. It seems really to be related to these T and S variables, but I am not sure about how CMS is handling it.
cms: putget.c:4081: getNCvx_float_float: Assertion `value != ((void *)0)' failed.
forrtl: error (76): Abort trap signal
Image PC Routine Line Source
cms 000000000050B175 Unknown Unknown Unknown
cms 0000000000508D97 Unknown Unknown Unknown
cms 00000000004BF1A4 Unknown Unknown Unknown
cms 00000000004BEFB6 Unknown Unknown Unknown
cms 0000000000462886 Unknown Unknown Unknown
cms 0000000000466C78 Unknown Unknown Unknown
libpthread.so.0 0000003CF720F7E0 Unknown Unknown Unknown
libc.so.6 0000003CF6A325E5 Unknown Unknown Unknown
libc.so.6 0000003CF6A33DC5 Unknown Unknown Unknown
libc.so.6 0000003CF6A2B70E Unknown Unknown Unknown
libc.so.6 0000003CF6A2B7D0 Unknown Unknown Unknown
libnetcdf.so.7 00007F8F340B33C8 Unknown Unknown Unknown
libnetcdf.so.7 00007F8F340B20E7 Unknown Unknown Unknown
libnetcdf.so.7 00007F8F3409E1E6 Unknown Unknown Unknown
libnetcdf.so.7 00007F8F3409C05D Unknown Unknown Unknown
libnetcdff.so.5 00007F8F33BED2C0 Unknown Unknown Unknown
libnetcdff.so.5 00007F8F33C48775 Unknown Unknown Unknown
cms 000000000040E1F9 Unknown Unknown Unknown
cms 000000000042F400 Unknown Unknown Unknown
cms 00000000004209F8 Unknown Unknown Unknown
cms 000000000044C701 Unknown Unknown Unknown
cms 000000000040A2DE Unknown Unknown Unknown
libc.so.6 0000003CF6A1ED1D Unknown Unknown Unknown
cms 000000000040A1E9 Unknown Unknown Unknown
Aborted (core dumped)
Which I've tracked to the getphysical data nc
I've tried to run this nest file (after downloading data with getdata):
wvel_name= "w_velocity"
wvel_positive_direction = "upward"
velocity_conversion_factor=1
dens_name= ""
temp_name= "temperature"
saln_name= "salinity"
ssh_name= ""
angle_file=""
fill_value=1.2676506E30
agrid=.true.
orthogrid=.true.
$end
With this runconf:
&runconf
!====================================================================!
nnests = 1
timeMax = 432000
timestep = 86400
outputFreq = 86400
releaseFilename = "releaseFile"
!====================================================================!
!Turbulence Module
turb = .true.
horDiff = 2 !horizontal diffusivity
vertDiff = 0.5 !vertical diffusivity
turbTimestep = 86400 !in seconds
!====================================================================!
!Periodic Boundary Condition
periodicbc = .false.
!====================================================================!
!Landmask Boundary Condition
avoidcoast = .false.
!====================================================================!
!Backward Tracking Module
backward = .false.
!====================================================================!
!Output files in ASCII instead of netCDF
ascii = .false.
!====================================================================!
!Flag for putting particles back in the ocean when they go through the
!uppermost depth level
upperlevelsurface = .true.
!====================================================================!
!Flag for looping through the velocity fields
loopfiles = .false.
loopfilesstartyear = 1980
loopfilesstartmonth = 1
loopfilesstartday = 5
loopfilesendyear = 2006
loopfilesendmonth = 12
loopfilesendday = 29
!====================================================================!
!Options for restarting
restartfromfile = .false.
restartwritefreq = 18640000
!====================================================================!
!Options for mixed layer physics
mixedlayerphysics = .false.
mixedlayerwmax = 0.1
!====================================================================!
&end
and
and this buoyancy file (even if think CMS did not reach it) :
2
216000 432000
1010 1027
1012 1029
0.00025 0.00010
0.00027 0.00012
Sorry for the multiple messages,
Best,
Nicolas
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Nicolas Le Corre
Nov 17, 2016, 3:50:45 PM11/17/16
to connectivity-modeling-system-club
Hello everyone,
Just to let you know that I don't have this problem of T & S anymore. I've downloaded the new version released by Claire today and Temperature and salinity don't create errors anymore.
Not sure what was the problem. I noticed the new flag -limf in the mpi compiler of the new version, but not sure it is related to this former problem.
Thanks for your help.
Nicolas
Marika Galanidi
Nov 18, 2016, 1:28:09 AM11/18/16
to connectivity-modeling-system-club
Hi Nicolas,
I am glad to hear your problem is solved. In my case, even though I also downloaded the new version last night, the problems still persist. I still could not pinpoint the source of the problem, I think it may be some regridding issue but I don't understand why it happens with some of the files in the download and not with others (inspecting the files with gdal doens't reveal any differences). Anyhow, i am now trying to download from the hycom server and create the cms-required format manually.
All the best
Marika
Jeffrel Hermias
May 10, 2017, 10:12:10 PM5/10/17
to connectivity-modeling-system-club
Hi Nicolas. I've read this post and you were able to run the vertical migration file. i've tried running only the buoyancy module and it perfectly works. however, i tried running the ibio module (vertical migration) and the con_file_1 don't seem to give me an output. It's size is actually 0 and I already fix all the ibiotimestep and timestep issues but still my con_file_1 is 0 when turning the ibio module. I was wondering where is the issue in it. Probably the z values, or the "upward" or "downward" directions of w and all that. Hope you can give me insights. Thank you so much!
Nicolas Le Corre
May 11, 2017, 9:27:49 AM5/11/17
to Jeffrel Hermias, connectivity-modeling-system-club
Hello,
I'm not sure of what you've done previously. So here are a few questions:
- Have you ever used the polygon module before? The CMS will give you connectivity results only if you've used polygons (see the guide for that).
- Have you check in your trajectory result file if the depth of your particles has changed over time?
From there, we might be able to help you with that issue.
Best,
Nicolas
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Gilbert Nightray
Oct 23, 2018, 5:40:32 PM10/23/18
to connectivity-modeling-system-club
Hello, I'm trying to use the buoyancy module but, I'm downloading my data from the HYCOM (the Global data) so... it doesn't have velocity in w... It can't run without this, right?
Robin F
Oct 23, 2018, 5:50:58 PM10/23/18
to Gilbert Nightray, connectivity-modeling-system-club
Hi Gilbert,
Have you tried to run it without w before posting your question? Because it should work. Let us know if it doesn’t, however.
> Le 23 oct. 2018 à 17:40, Gilbert Nightray <gilbni...@gmail.com> a écrit :
>
> Hello, I'm trying to use the buoyancy module but, I'm downloading my data from the HYCOM (the Global data) so... it doesn't have velocity in w... It can't run without this, right?
--
Robin Faillettaz, Ph.D
——————————————————————
Postdoctoral Research Fellow
University of Miami
Rosenstiel School of Marine & Atmospheric Science
4600 Rickenbacker Causeway, Miami, FL 33149-1098, USA
Tel: (US) +1-702-910-0380; (FR) +33-6-84-91-43-33
Robin.Fa...@gmail.com
Robin.Fa...@univ-lille1.fr
Have you tried to run it without w before posting your question? Because it should work. Let us know if it doesn’t, however.
> Le 23 oct. 2018 à 17:40, Gilbert Nightray <gilbni...@gmail.com> a écrit :
>
> Hello, I'm trying to use the buoyancy module but, I'm downloading my data from the HYCOM (the Global data) so... it doesn't have velocity in w... It can't run without this, right?
Robin Faillettaz, Ph.D
——————————————————————
Postdoctoral Research Fellow
University of Miami
Rosenstiel School of Marine & Atmospheric Science
4600 Rickenbacker Causeway, Miami, FL 33149-1098, USA
Tel: (US) +1-702-910-0380; (FR) +33-6-84-91-43-33
Robin.Fa...@gmail.com
Robin.Fa...@univ-lille1.fr
bexeross
Oct 24, 2018, 2:31:08 AM10/24/18
to connectivity-modeling-system-club
Also it is possible to generate the W velocities from the U and V velocities based on the continuity equation (this is not perfect but it is something). I have a script somewhere that does this, I'll search it out and put it in the "postprocessing scripts & tips" thread.
All the best,
Bex
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