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Initialisation failed

Hello dear all,
I am a beginner with Ichthyop and I am trying to run Ichthyop 3.3 with ROMS 3D configuration. I have hourly outputs from ROMS during 2 months.
However I do not know what am I setting up wrong. I gues that might be something with the setting up in the very beggining of it, since it does not even start the simullation. I get the following message:
ichthyop[info] ===== Simulation started =====
ichthyop[info] [Simulation] Run 1 / 1
ichthyop[info] [Simulation] Initialising...
ichthyop[severe] Index: 0, Size: 0 | java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
ichthyop[severe] [Simulation] Initialisation failed (performing: SETUP)
In the attachments you will find my configuration file.
Thank you in advance,
Clarissa
 

Ichthyop version: 
Ichthyop 3.3alpha
Hydrodynamic dataset: 
ROMS Rutgers
Java version: 
Java SE 8
Operating system: 
Ubuntu

Hi dear all,
I retried to start Ichthyop 3.3. with a new configuration file, however I still get some initialization error in the SETUP.  And now I have tried to run Ichthyop from the terminal. I have 2 situations.
1. Running without setting up a path to my grid file, it gets me the following error:
ichthyop[info] Opened configuration file /home/clarissa/Ichthyop/ichthyop-3.3/cfg/2017_11_17_roms3d_Ichthy03.xml
ichthyop[info] ===== Simulation started =====
ichthyop[info] ++++ Run 1 / 1
ichthyop[info] Setting up...
ichthyop[info] {Dataset} Open /home/clarissa/Results/swa12ext_I02/swa12ext_Ichthy_avg_2008_jan.nc
ichthyop[severe] An error occured while running the simulation | java.lang.NullPointerException
  org.previmer.ichthyop.dataset.RomsCommon.readConstantField(RomsCommon.java:202)
  org.previmer.ichthyop.dataset.Roms3dCommon.readConstantField(Roms3dCommon.java:301)
  org.previmer.ichthyop.dataset.RomsCommon.setUp(RomsCommon.java:164)
  org.previmer.ichthyop.dataset.Roms3dCommon.setUp(Roms3dCommon.java:216)
  org.previmer.ichthyop.manager.DatasetManager.setupPerformed(DatasetManager.java:73)
  org.previmer.ichthyop.manager.SimulationManager.fireSetupPerformed(SimulationManager.java:386)
  org.previmer.ichthyop.manager.SimulationManager.setup(SimulationManager.java:341)
  org.previmer.ichthyop.IchthyopBatch.run(IchthyopBatch.java:50)
  java.lang.Thread.run(Thread.java:748)
2. When I set up a path to my grid file, it says the directory is invalid, however I do not understand why.
ichthyop[info] Opened configuration file /home/clarissa/Ichthyop/ichthyop-3.3/cfg/2017_11_17_roms3d_Ichthy03.xml
ichthyop[info] ===== Simulation started =====
ichthyop[info] ++++ Run 1 / 1
ichthyop[info] Setting up...
ichthyop[info] {Dataset} Open /home/clarissa/Results/swa12ext_I02/swa12ext_Ichthy_avg_2008_jan.nc
ichthyop[severe] An error occured while running the simulation | java.io.IOException: {Dataset} /home/clarissa/Ich/swa12ext_grd.nc is not a valid directory.
  org.previmer.ichthyop.dataset.Roms3dDataset.openDataset(Roms3dDataset.java:64)
  org.previmer.ichthyop.dataset.RomsCommon.setUp(RomsCommon.java:160)
  org.previmer.ichthyop.dataset.Roms3dCommon.setUp(Roms3dCommon.java:216)
  org.previmer.ichthyop.manager.DatasetManager.setupPerformed(DatasetManager.java:73)
  org.previmer.ichthyop.manager.SimulationManager.fireSetupPerformed(SimulationManager.java:386)
  org.previmer.ichthyop.manager.SimulationManager.setup(SimulationManager.java:341)
  org.previmer.ichthyop.IchthyopBatch.run(IchthyopBatch.java:50)
  java.lang.Thread.run(Thread.java:748)
I am sorry if this is very basic, but I hope you can help me.
Thank you for your attention.
Clarissa

Hi Clarrisa.

Could you please send me your grid file? And eventually (if not too heavy) your data file?

So that I can try to reproduce and solve the error.

Thanks

Nicolas

Hi Nicolas,
Thank you for your repply. In the attachtments you have my grid file (swa12ext_grd.nc.zip). Unfortunatetly my data file is too heavy, but I am attatching the content of the netcdf, in case it helps. Please let me know if I can give you any other information.
 
Thank you,
Clarissa

Hi Clarisse

I was not able to fully check since my initialisation fails because of missing dataset.

However, I may have found the issue. The error is due to the fact that the code interpreted your grid_file entry as a directory, and not as a file.

Can you please try to re-run the model but by using the following jar file and tell me if it worked?

https://filesender.renater.fr/?s=download&token=66890e83-d78e-db8f-9a83-...

If so, I will put this corrected version into the Download page.

Thanks

Nicolas

Hi Nicolas,
I have tryed to re-run with the new jar you have sent, however a new error is reported. Below is what it reports:
ichthyop[info] ===== Simulation started =====
ichthyop[info] [Simulation] Run 1 / 1
ichthyop[info] [Simulation] Initialising...
ichthyop[info] {Dataset} Open /home/clarissa/Results/swa12ext_I02/swa12ext_Ichthy_avg_2008_jan.nc
ichthyop[severe] NetcdfDataset.openFile: location is null | java.io.IOException: NetcdfDataset.openFile: location is null
ichthyop[severe] [Simulation] Initialisation failed (performing: SETUP)
 
Thank you,
Clarissa

Hi Clarissa

I found this new error, which is due to a mistake I made in the correction.

But this should do it now:

https://filesender.renater.fr/?s=download&token=e2b0d499-1aec-1248-1499-...

I advise you to put the absolute grid path (grid_file setting), to be sure that it works.

Let me know if it works now (I tried on some Roms data I have, it seemed to work).

Nicolas

Hi Nicolas,
It seems to be working now.
I have a another question, how does Ichthyop handles regions (release or recruitment) that have land in it, as isles for example?
Thank you very much for your attention! =)
All the best,
Clarissa

Hi Clarissa

Good news if it is working. Considering release and recruitment zones, land cells are not considered. For instance, if you release 100 cells in your ares, these 100 cells will be put randomly on water cells.

Nicolas

Hi Nicolas,
Thank you!

Ok! I understood that land cells will not be considered. But is there a minimum size for the areas that Ichthyop considers to be aceptable to release or recruit particles? For example, the area cannot be smaller than 2 grid points.
Clarissa

Hi,
I also have a similar issue with version 3.3. I have a separate ROMS grid file and getting the "not a valid directory error" when trying to simulate:

ichthyop[info] [Simulation] Initialising...

ichthyop[info] {Dataset} Open K:\testCTROMS\merged.nc

ichthyop[severe] {Dataset} coral_grd.nc is not a valid directory. | java.io.IOException: {Dataset} coral_grd.nc is not a valid directory.

ichthyop[severe] [Simulation] Initialisation failed (performing: SETUP)

 

I tried putting in the full path but also got the same error.

 

Can I also get a copy of the update jar file you sent to Clarrisa?

 

Thanks!

 

Rollan

 

 

Hi Rollan

Here is a link to the program. Tell me if it did work for you. If so, I will put this new version on the website.

https://filesender.renater.fr/?s=download&token=0c4aedeb-1abe-0b8c-fdfa-...

Nicolas

Hi Nicolas,
Thanks for the file. I tried it but go tthis error instead: 
ichthyop[severe] {Dataset} coral_grd_SRTM_v17.nc is not a valid file. | java.io.IOException: {Dataset} coral_grd_SRTM_v17.nc is not a valid file.
Anyway, I decided to append the grid file to the daily NC file and after encountering a few more errors (related to time conversion), I finally got it to run!!
Rollan 

Hello Rollan

Good news if you were able to manage some solutions. However, could you please send me (through dropbox or anything alike) your configuration, grid and forcing files (even with only one time step)?

So that I can try to understand why what I proposed didn't work.

Thanks a lot.

Nicolas

sure. Where do I send it?

Hi Rollan

You can send it either here or via Dropbox

Hi Nicolas,
It's seem that I'm having the same problem with grd file. Could you send the new version that you sent to Clarissa and Rollan. The links exposed here in the discussion has expired.
Thanks in advance,
Luciana

In my ROMS output data. Lon, lat and mask are archivied in a separate grid file. So, I indicated the grid file in the hidden grid file parameter. But, the program identified this file as a directory.. similar with the error described by Clarissa and Rollan. 
ichthyop[info] ===== Simulation started =====
ichthyop[info] [Simulation] Run 1 / 1
ichthyop[info] [Simulation] Initialising...
ichthyop[info] {Dataset} Open /media/luciana/invernos/v5_85_01i/avg/sao12tbc_luciana_avg_20920701.nc
ichthyop[severe] {Dataset} /media/luciana/invernos/v5_85_01i/avg/sao12tbc_luciana_grd.nc is not a valid directory. | java.io.IOException: {Dataset} /media/luciana/invernos/v5_85_01i/avg/sao12tbc_luciana_grd.nc is not a valid directory.
ichthyop[severe] [Simulation] Initialisation failed (performing: SETUP)
Attached here I send the content of netcdf files: grd and avg file.
 

Hi Luciana

I have added the nwe jar file to the "Download" section.

Nicolas