Common GEOS-Chem error messages

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Here is a list of some commonly-encountered GEOS-Chem error messages.

Error when reading the "restart_gprod_aprod" file

Eric Leibensperger ( wrote:

I am trying to run GEOS-Chem and have encountered and error. The log file gives me this:
  GEOS-CHEM ERROR: No matches found for file restart_gprod_aprod.2001070100!
  STOP at READ_BPCH2 (bpch2_mod.f)!
I have the aerosol restart file (with the same name) in my ~/testrun/runs/run.v7-04-12/ folder. Is it looking for it elsewhere? I get an additional message in the log.error file, but I think that it is possibily the result of not being able to find the file above:
  ******  FORTRAN RUN-TIME SYSTEM  ******
  Error 1183:  deallocating an unallocated allocatable array
  Location:  the DEALLOCATE statement at line 4933 of "carbon_mod.f"
Any thoughts would be appreciated. Sorry to bother you with this!

Philippe Le Sager ( replied:

You must rewrite your restart_gprod_aprod.YYYYMMDDHH so that the date in the filename is the same as the one in the datablock header.
I wrote a routine to do that: ~phs/IDL/dvpt/various_rewrite/

NOTE: The file will be released in the next GAMAP version.

--Bob Yantosca 13:35, 1 April 2008 (EDT)

Exit Status

If you submit a job to the PBS Queue, the exit status will tell you a little bit about what happened. The exit status code is in the email that you will get back from the PBS server:

 PBS Job Id: 6015.altix
 Job Name:
 Execution terminated

Jobs that finish normally should have an exit status of 0. In the above example, we have an exit status of 1, which means that the job encountered some kind of error (either a compilation error or a run-time error).

A common exit status number is 143. This means that your job has exceeded the wall-clock time limit of the queue. The solution is to restart your job in a queue with a longer time limit.

Segmentation Fault

A segmentation fault may mean:

  • You have gone outside the declared bounds of an array
  • You are trying to access an ALLOCATABLE array that hasn't been allocated yet
  • You are trying to read data from a file into an array of the wrong dimensions

Example 1

Here is segmentation fault caused by the code trying read data from a file into an array which is too small to contain the data. This error was detected on the Altix platform. The output comes from the IDB debugger.

 Thread received signal SEGV
 stopped at [<opaque> for_read_seq_xmit(...) 0x40000000006b6500] 
 Information:  An <opaque> type was presented during execution of 
 the previous command.  For complete type information on this symbol,
 recompilation of the program will be necessary.  Consult the compiler
 man pages for details on producing full symbol table information using   
 the '-g' (and '-gall' for cxx) flags.

Example 2

The same error message as in Example 1 has also been known to occur on Altix when a variable that has not been initialized is passed to a subroutine or function:

 CALL MYSUB( I )   ! I is uninitialized!
 DO I = 1, IIPAR 

The solution to the problem is as follows:

 DO I = 1, IIPAR 
    CALL MYSUB( I )  ! Put the MYSUB call in the I-loop!

Bus Error

A bus error usually means that you are trying to call a subroutine with the wrong number of arguments.

On SGI, you usually will only get a bus error if you call a subroutine with too many, rather than too few arguments. Other behaviors are platform and compiler dependent.

Compilation Errors

Sometimes you might encounter a weird error during GEOS-Chem compilation. Here is an example.

Example: Fatal Error on Altix

The following error, which resulted on the Altix platform using Intel "ifort" v9 compiler:

 ifort: error: /opt/intel/fc/9.0/bin/fpp: core dumped
 ifort: error: Fatal error in /opt/intel/fc/9.0/bin/fpp, 
 terminated by unknown signal(139)
 make: *** [transport_mod.o] Error 1

was caused by an omitted " in an #include declaration, i.e.

 #     include "CMN_DIAG

Adding the closing " fixed the problem.