Troubleshooting

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There are some recurrent errors that people encounter when compiling/working with DINEOF. Here is a little list (with solutions):
There are some recurrent errors that people encounter when compiling/working with DINEOF. Here is a little list (with solutions):
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  * EXTERNAL          ETIME
  * EXTERNAL          ETIME
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=== Only mssing values with netCDF files ===
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When using netCDF files, please use the missing_value or _FillValue with a real number (float) and not with NaN (though this is now tolerated in netCDF files it is not yet implemented in DINEOF and can result in interpretations of your file having no data)
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=== Integer overflow when running the small example ===
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You get the following error when you run the small example.
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Fortran runtime error: Integer overflow when calculating the amount of memory to allocate.
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Note that the data files of the small example are in "big endian". You have to leave the format to "big_endian" in the Makefile to run the small example. You can only use another format when you create yourself the data set.

Latest revision as of 09:29, 9 September 2014

There are some recurrent errors that people encounter when compiling/working with DINEOF. Here is a little list (with solutions):

Contents

"Segmentation fault"

When compiling with ifort, you may encounter a "segmentation fault" error when running DINEOF. Something like this:

 ****************************************************
  Numerical data read
  You entered the values:
  number of EOF modes you want to compute           2
  maximal size for the Krylov subspace           8
  
  You asked not to  normalise of the input matrices
  
  The right and left EOFs will be written in directory Output/
  
 ****************************************************
 You entered filenames seacoos2005.avhrr
                      seacoos2005.avhrr.mask
 Data error in UINQUIRE, not a conform file: "seacoos2005.avhrr".
 Segmentation fault

The problem appears to be that ifort allocates too few stack memory by default. If you type the following command in a terminal:

ulimit -s 1000000

That may solve the problem (the number needs to be a very high number, whatever you choose)

"Error = -3"

Another common problem is when you start to see this message appear in the screen when you run DINEOF:

 Error with _saupd, info =           -3
 Check documentation in _saupd 

This one is also simple to solve: you need to specify in dineof.init the number of modes to be calculated (nev), and the Kryvlov space (ncv), which need to be smaller than the temporal size of your data, AND, ncv > nev+5. If one or both of these conditions is not met, the above message will appear.


"Error = -8"

A less common problem:

Error with _saupd, info =           -8                                       
Check documentation in _saupd           

This problem is related to the filtering of the time covariance matrix: if the time vector is not well written (i.e., the values are not all distinct), the filtering cannot be made properly. As the time is in simple precision, even if the values are distinct, they can be read as identical values.

Here is an example of a time vector which lead to the problem:

ncdump -v time bstot_mumm.nc
data:                                                               
time = 731582, 731582.020833333, 731582.041666667, 731582.0625,

Solutions:

  • Deactivate the filtering (B_DIFF option in file ppdef.h)
  • Write the time in double precision

netCDF compilation error

In some systems, the fortran part of netCDF is in a separate netcdf library, called "netcdff". In those, it is needed to add -lnetcdff (two f's) before the -lnetcdf option, in the compilation command:

-lnetcdff -lnetcdf

If you use the DINEOF Makefile, this means to add this option to the "DINEOF_LIBRARIES" variable:

DINEOF_LIBRARIES =  -L/usr/lib -larpack  -llapack  -lblas  -lnetcdff -lnetcdf

of the compilation file (Linux-gfortran.mk, etc)

DINEOF compilation error due to ARPACK

If, when compiling DINEOF, you find the following error:

/home/user/ARPACK/libarpack.a(second.o): In function `second_':
second.f:(.text+0x16): undefined reference to `etime_'
collect2: ld returned 1 exit status
make: *** [dineof] Error 1

you will need to edit file 'second.f' located in your $HOME/ARPACK folder. There, you should comment the following line by adding an asterisk at the beginning:

EXTERNAL           ETIME

becomes:

* EXTERNAL           ETIME

Only mssing values with netCDF files

When using netCDF files, please use the missing_value or _FillValue with a real number (float) and not with NaN (though this is now tolerated in netCDF files it is not yet implemented in DINEOF and can result in interpretations of your file having no data)


Integer overflow when running the small example

You get the following error when you run the small example.

Fortran runtime error: Integer overflow when calculating the amount of memory to allocate. 

Note that the data files of the small example are in "big endian". You have to leave the format to "big_endian" in the Makefile to run the small example. You can only use another format when you create yourself the data set.

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