Error in fit_model when running VAST for index standardization.R

[Rcaini]

Error in fit_model when running VAST for index standardization.R

Hi,I’m running the VAST for index standardization.R . When I running the code fit = fit_model( settings = settings, Lat_i = example$sampling_data[,'Lat'], Lon_i = example$sampling_data[,'Lon'], t_i = example$sampling_data[,'Year'], c_i = rep(0,nrow(example$sampling_data)), b_i = example$sampling_data[,'Catch_KG'], a_i = example$sampling_data[,'AreaSwept_km2'], v_i = example$sampling_data[,'Vessel'] ) I get this error:

Writing output from fit_model in directory: D:/xuexi/0321/VAST/

Making extrapolation-grid

Using strata All_areas For the UTM conversion, automatically detected zone 60.

Reducing extrapolation-grid from 34128 to 2000 cells for Region(s): User

Loaded from D:/xuexi/0321/VAST//Kmeans_extrapolation-2000.RData

Making spatial information

Loaded from D:/xuexi/0321/VAST//Kmeans_knots-200.RData Error in fmesher.read(prefix, "manifold") : File 'C:/Users/rcaini/AppData/Local/Temp/RtmpCcjNv7/fmesher253421e8657c.manifold' does not exist.

When you are available, could you kindly provide some suggestions to me? Thank you so much.

[James-Thorson-NOAA]

I remember seeing this on some NOAA machines, when the anti-virus would for some reason delete the "fmesher.exe" file used by INLA. could you provide more details about your machine and OS? And perhaps try re-installing INLA to see if that fixes it?

[Rcaini]

Thank you so much. I try re-installing INLA , but it doesn’t work. I’ll provide more details about my machine and OS. The CPU is Intel(R) Core(TM) i3-5005U CPU @2.00GHz 2.00GHz , the RAM is 4.00GB. My machine is a 64-bit operating system. When you are available, could you kindly provide some suggestions to me?

[James-Thorson-NOAA]

what does "doesn't work" mean about installing INLA?

I'm guessing that this will need to be sorted via some INLA Q&A resource, but happy to hear a bit more before closing the issue here.

[Rcaini]

Thank you so much. My machine have the"fmesher.exe" file. "doesn't work" means I try re-installing INLA , but the error still exists. Could you kindly provide some suggestions to me?

[Blevy2]

Hi @Rcaini ,

I have encountered the same error while working on a NOAA server. I just reinstalled INLA but the problem persists. Did you ever reach a resolution with this?

Thank you for your help,

Ben Levy

[James-Thorson-NOAA]

I'm sorry to hear that you both are having this problem, and also that I don't seem to have responded a year ago!

I've had this occur on my AFSC Virtual Machine (VM), and it seems to occur from the virus-protection software being overly aggressive and deleting the "fmesher.exe" file. In the cases I encountered personally, it was fixed by re-installing INLA.

@Blevy2 can you confirm that whether you can find the fmesher.exe file in its original location after encountering the error?

Obviously this is a bit into the software-install and INLA-support direction, so I can't promise a lot of expertise. but happy to keep discussing on this thread, and leaving it open.

[ChristineStawitz-NOAA]

I also found the related thread on the R-INLA google group you might want to peek through (although this is for Mac users)

https://groups.google.com/g/r-inla-discussion-group/c/4JVY4ZcyfH0

It seems like you can also run into this if you install INLA from Github instead of downloading the package directly.

[Blevy2]

Hi @James-Thorson-NOAA. It looks there are a bunch of fmesher files in the folder but not the one that my error is for nor the .exe file.

I received the error 'Error in fmesher.read(prefix, "manifold") : File '/tmp/RtmpupRlbm/fmesher7587a102cd257.manifold'

and when I look in that folder I see the folllowing:

[blevy@neptune READ-PDB-blevy2-MFS2]$ cd '/tmp/RtmpupRlbm'
[blevy@neptune RtmpupRlbm]$ ls 42f433224a554f45b04af58da88f4472.png fmesher7587a102cd257.input.s fmesher7587a102cd257.input.segm.bnd.grp fmesher7587a102cd257.input.segm.bnd.idx fmesher7587a2493630d.input.s fmesher7587a2493630d.input.segm.bnd.grp fmesher7587a2493630d.input.segm.bnd.idx libloc_177_62bf5716560c0e2b.rds

Unfortunately I am not able to install or remove packages myself on these servers right now. Any package change has to be carried out by IT by submitting a ticket. I asked them to reinstall INLA last week and I received notice it was reinstalled on Friday. Maybe the virus protection on the server already deleted the file(s) in the last week.

Thank you for pointing me to that thread @ChristineStawitz-NOAA . It sounds like the solution there also involved reinstalling the package so I may be out of luck with using VAST on these servers for now.