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FATAL CALLED FROM FILE: <stdin> LINE: 187

V

VladimirSobral

New member
Hello

I'm a new user of the WRF just trying to be familiar with some routines.
On my personal laptop, I can run the model with one domain however with two domains this information shows up:

Domain # 1: dx = 10000.000 m
Domain # 2: dx = 3333.333 m
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: <stdin> LINE: 187
nesting requires either an MPI build or use of the -DSTUBMPI option
-------------------------------------------

Could anyone help me?

Thanks
 

Attachments

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Hi,
When you compiled WRF, did you choose the "basic" nesting option, or the "no nest" option? Are you running a real data case, or an idealized case? Can you attach your configure.wrf file? Thanks!
 
Hi,

I chose the basic nesting option and I'm running a real data case.
The configure.wrf file is attached.
Please let me inform some laptop settings
Laptop Dell
Processor: Intel(R) Core(TM) i7-4500U CPU @ 1.80GHz
Cores - 2
Threads - 4

Thank you for your reply.
 

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Apologies for the delay, and thank you for confirming that information.

1) Is it possible that you're in an environment that does not have the path set to find the MPI library?
2) Since you're on a Dell machine, are you in a Windows environment, or have you built a Linux parallel system on Windows?
 
kwerner said:
Apologies for the delay, and thank you for confirming that information.

1) Is it possible that you're in an environment that does not have the path set to find the MPI library?
2) Since you're on a Dell machine, are you in a Windows environment, or have you built a Linux parallel system on Windows?
Click to expand...
I agree with @kwerner I think the error is not exporting the environment variables needed for GNU.

Bash: 
#setting environment for WRF model to run
export LD_LIBRARY_PATH=/home/workhorse/WRF/Libs/NETCDF/lib:$LD_LIBRARY_PATH
export LD_LIBRARY_PATH=/home/workhorse/WRF/Libs/grib2/lib:$LD_LIBRARY_PATH
export PATH=/home/workhorse/WRF/Libs/MPICH/bin:$PATH
export PATH=/home/workhorse/WRF/Libs/grib2/lib:$PATH
Something similar to that above
 
Hi...

I am getting the same error.. but not sure what and how to fix it. I was able to run "mpirun -np 1 ./real.exe" but "rsl.error.0000" is file is not created.

Also, I noticed I have met_em.d02 files got created but I only see wrfbdy_d01. shouldn't I see d02 file also?

Please help!!



Capture3.JPG
 
Did you fix the issue? if so how?

VladimirSobral said:
Hello

I'm a new user of the WRF just trying to be familiar with some routines.
On my personal laptop, I can run the model with one domain however with two domains this information shows up:

Domain # 1: dx = 10000.000 m
Domain # 2: dx = 3333.333 m
-------------- FATAL CALLED ---------------
FATAL CALLED FROM FILE: <stdin> LINE: 187
nesting requires either an MPI build or use of the -DSTUBMPI option
-------------------------------------------

Could anyone help me?

Thanks
Click to expand...
 
Hi everyone

Thanks @kwerner and @William.Hatheway for your reply.
Regarding @kwerner's questions:

1) It is possible. However, I have written the paths suggested by @William.Hatheway and still couldn't run WRF.
2) I'm on a Dell machine in a Linux environment (Ubuntu).

So, I tried to recompile WRF using serial mode (instead of parallel). With this, I was able to run the model. However, I had a new problem after 2 days of simulation, as you can see below:

--------------------------------------------------------------------------------
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7fa5eb623960 in ???
#1 0x7fa5eb622ac5 in ???
#2 0x7fa5eb24251f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x55813de4c3f3 in ???
#4 0x55813de503d5 in ???
#5 0x55813de54cbd in ???
#6 0x55813d5751ef in ???
#7 0x55813d59d87d in ???
#8 0x55813cab59aa in ???
#9 0x55813c2ed5d7 in ???
#10 0x55813c10a8ba in ???
#11 0x55813b15c3f9 in ???
#12 0x55813b15ca89 in ???
#13 0x55813b0dda07 in ???
#14 0x55813b0dce8e in ???
#15 0x7fa5eb229d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#16 0x7fa5eb229e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#17 0x55813b0dcec4 in ???
#18 0xffffffffffffffff in ???
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 1 with PID 0 on node juliao-Inspiron-5437 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

Any suggestion?

Thank you
 
VladimirSobral said:
Hi everyone

Thanks @kwerner and @William.Hatheway for your reply.
Regarding @kwerner's questions:

1) It is possible. However, I have written the paths suggested by @William.Hatheway and still couldn't run WRF.
2) I'm on a Dell machine in a Linux environment (Ubuntu).

So, I tried to recompile WRF using serial mode (instead of parallel). With this, I was able to run the model. However, I had a new problem after 2 days of simulation, as you can see below:

--------------------------------------------------------------------------------
Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 0x7fa5eb623960 in ???
#1 0x7fa5eb622ac5 in ???
#2 0x7fa5eb24251f in ???
at ./signal/../sysdeps/unix/sysv/linux/x86_64/libc_sigaction.c:0
#3 0x55813de4c3f3 in ???
#4 0x55813de503d5 in ???
#5 0x55813de54cbd in ???
#6 0x55813d5751ef in ???
#7 0x55813d59d87d in ???
#8 0x55813cab59aa in ???
#9 0x55813c2ed5d7 in ???
#10 0x55813c10a8ba in ???
#11 0x55813b15c3f9 in ???
#12 0x55813b15ca89 in ???
#13 0x55813b0dda07 in ???
#14 0x55813b0dce8e in ???
#15 0x7fa5eb229d8f in __libc_start_call_main
at ../sysdeps/nptl/libc_start_call_main.h:58
#16 0x7fa5eb229e3f in __libc_start_main_impl
at ../csu/libc-start.c:392
#17 0x55813b0dcec4 in ???
#18 0xffffffffffffffff in ???
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpiexec noticed that process rank 1 with PID 0 on node juliao-Inspiron-5437 exited on signal 11 (Segmentation fault).
--------------------------------------------------------------------------

Any suggestion?

Thank you
Click to expand...
@VladimirSobral

did you make sure to change the paths to where the files are located?
 
@VladimirSobral
I'm glad you were able to get past your initial error. Since your new error is a different issue, will you please start a new thread to inquire about the issue? Thanks.
 
@William.Hatheway

Yes, I changed the paths according to your suggestion.
As I'm using a simple laptop with one processor, I assume that the serial mode is more appropriate to use in my run. But it's just an idea.
Thanks for your reply.
 
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