Difference between revisions of "Common GEOS-Chem error messages"

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Here is a list of some commonly-encountered GEOS-Chem error messages.  Also be sure to visit our [[Machine issues & portability]] wiki page for a list of compiler-specific issues.
+
#REDIRECT [[Guide to GEOS-Chem error messages]]
 
+
== File I/O errors ==
+
 
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=== A3 met fields not found ===
+
 
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If routine <tt>OPEN_A3_FIELDS</tt> (in <tt>a3_read_mod.f</tt>) returns a "file not found" error shortly after the start of your GEOS-Chem simulation, i.e.:
+
 
+
  $$ Finished Reading Linoz Data $$
+
 
+
===============================================================================
+
GEOS-CHEM I/O ERROR    29 in file unit    73
+
Encountered at routine:location open_a3_fields:1
+
+
Error  29: File not found
+
===============================================================================
+
      - CLEANUP: deallocating arrays now...
+
 
+
then this could indicate one of the following conditions:
+
 
+
==== Error caused by MEGAN biogenic emissions ====
+
 
+
MEGAN keeps a 10-day running average of temperature, and therefore requires that the the met field files for the 10 days prior to the start of the GEOS-Chem simulation be present on disk.
+
 
+
You can solve this error in one of two ways:
+
 
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# Make sure you have the previous 10 days (or better yet, the entire previous month!) of data prior to your GEOS-Chem simulation's starting date
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# Start your GEOS-Chem simulation at a later date
+
 
+
==== Error caused by not recompiling cleanly ====
+
 
+
This error may also indicate that you have attempted to [[Common_GEOS-Chem_error_messages#Error_computing_F_OF_PBL|change the resolution of GEOS-Chem without recompiling cleanly]].  Some parts of the GEOS-Chem code (object files, module files) may still be compiled for a different grid resolution.
+
 
+
You can usually fix this doing a
+
+
make realclean
+
 
+
command before recompiling the code.
+
 
+
--[[User:Bmy|Bob Y.]] 10:47, 15 November 2010 (EST)
+
 
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=== I/O Error #29 ===
+
 
+
This error indicates that GEOS-Chem cannot find the proper [[#A3 met fields not found|A3 met field file]].
+
 
+
'''''NOTE: Error #29 is specific to the [[Intel Fortran Compiler|IFORT compiler]].  If you are using a different compiler, then the I/O error number may differ.'''''
+
 
+
--[[User:Bmy|Bob Y.]] 15:30, 3 November 2010 (EDT)
+
 
+
=== Problem reading binary punch file ===
+
 
+
If you are having problems reading a binary punch file into GEOS-Chem, make sure that you have the [[Reading_binary_files_in_IDL#.22Big_Endian.22_vs._.22Little_Endian.22_byte_ordering|correct endian setting]] in your makefile.  These are:
+
 
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* Intel Fortran compiler (IFORT): <tt>-convert big_endian</tt>
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* PGI compiler: <tt>-byteswapio</tt>
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* Sun Studio compiler: <tt>-xfilebyteorder=big16:%all</tt>
+
 
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Most machines that use an Intel or AMD chipset are little-endian machines.  A few of the older architectures (e.g. Cray, SGI Origin) are big-endian.  Binary punch files are always big-endian (due to historical reasons), so you will need to tell your compiler to do the byte swapping manually.
+
 
+
The symptoms of such an error can be as follows:
+
 
+
'''''Daewon Byun wrote:'''''
+
 
+
:In the <tt>SUBROUTINE READ_BPCH2</tt>, It reads the <tt>FTI = CTM bin 02</tt>  fine, but then fails to read anything after. I dumped the IOUNIT and IO error code -- as you see TMP_TITLE is empty....
+
 
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    IUNIT, IOS, TMP_TITLE =            98          -1
+
 
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:Then the program stops at the
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    IF ( IOS /= 0 ) THEN
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      PRINT*, 'open_bpch2_for_read:2'
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      STOP
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    ENDIF
+
 
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:If I force to read further removing the "STOP", then I get (again, I tried to dump..)
+
 
+
    MODELNAME, LONRES, LATRES, HALFPOLAR, CENTER180 =  0.000000    0.000000      0        0
+
 
+
--[[User:Bmy|Bob Y.]] 09:57, 24 July 2008 (EDT)
+
 
+
=== Module file cannot be read ===
+
 
+
If you should encounter this type of error:
+
 
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ifort -cpp -w -O2 -auto -noalign -convert big_endian -openmp -Dmultitask -c time_mod.f
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fortcom: Error: time_mod.f, line 259: This module file was generated for a different
+
platform or by an incompatible compiler or compiler release. It cannot be read.  [JULDAY_MOD]
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      USE JULDAY_MOD, ONLY : JULDAY, CALDATE
+
 
+
Then this means that you are trying to link to previously-created <tt>*.mod</tt> files that were generated by a different compiler.  Making clean and re-compiling from scratch should solve this problem.
+
 
+
--[[User:Bmy|Bob Y.]] 13:39, 1 July 2008 (EDT)
+
 
+
=== 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 [[Secondary_organic_aerosols#The restart_gprod_aprod.YYYYMMDDhh file|aerosol restart file]] (with the same name) in my <tt>~/testrun/runs/run.v7-04-12/</tt> 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  ******
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  Error 1183:  deallocating an unallocated allocatable array
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  Location:  the DEALLOCATE statement at line 4933 of "carbon_mod.f"
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  Abort
+
 
+
:Any thoughts would be appreciated. Sorry to bother you with this!
+
:Eric
+
 
+
'''''Philippe Le Sager replied:'''''
+
 
+
:You must rewrite your <tt>restart_gprod_aprod.YYYYMMDDHH</tt> so that the date in the filename is the same as the one in the datablock header.
+
 
+
:I wrote a routine to do that: <tt>~phs/IDL/dvpt/various_rewrite/rewrite_agprod.pro</tt>
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:-Philippe
+
 
+
NOTE: The file rewrite_agprod.pro will be released in the next GAMAP version.
+
 
+
--[[User:Bmy|Bmy]] 15:59, 9 May 2008 (EDT)
+
 
+
==== For GEOS-Chem v8-03-01 and higher ====
+
 
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In GEOS-Chem v8-03-01 and higher, the <tt>restart_gprod_aprod.YYYYMMDDhh</tt> file has been renamed to <tt>soaprod.YYYYMMDDhh</tt>.  The [[#Error when reading the .22restart_gprod_aprod.22_file|above-described error]] can occur with the <tt>soaprod.YYYYMMDDhh</tt> file if the date in the file does not match the starting date of your simulation.
+
 
+
--[[User:Bmy|Bob Y.]] 13:10, 4 November 2010 (EDT)
+
 
+
=== File ann_mean_trop.geos5.* not found ===
+
 
+
If you are running a GEOS-5 simulation and get an error that says that GEOS-Chem cannot locate the <tt>ann_mean_trop.geos5.2x25</tt> or <tt>ann_mean_trop.geos5.4x5</tt> file, then make sure that the following option is set in your <tt>input.geos</tt> file. 
+
 
+
Use variable tropopause?: T
+
 
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Starting in version [[GEOS-Chem versions under development#v7-04-12|GEOS-Chem v7-04-12]], GEOS-Chem can now use a variable tropopause (i.e. chemistry is done up to the location of the actual tropopause as diagnosed from the met fields at any given timestep).  '''''You cannot use the annual mean tropopause for GEOS-5.''''' 
+
 
+
--[[User:Bmy|Bob Y.]] 15:18, 7 July 2008 (EDT)
+
 
+
=== Problem reading GEOS-4 TROPP files ===
+
 
+
Please see [[Dynamic tropopause#Problem reading GEOS-4 TROPP files|this wiki post]] for more information about a common problem that can occur if you using GEOS-4 meteorology with the [[Dynamic tropopause|dynamic tropopause]].
+
 
+
=== OPEN failure ===
+
 
+
If you are reading data from a binary punch file, and encounter this type of error:
+
 
+
  - ANTHRO_CARB_TBOND: Reading /as/group/geos/data/GEOS_1x1/historical_emissions_201203/BCOC/BCOC_anthsrce.2000.geos.1x1
+
  Error opening filename=
+
  ^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
+
  <AA><A6>B^@^@^@^@^@^@^@^@^@^@^@^@^@^@^@
+
===============================================================================
+
GEOS-CHEM I/O ERROR    30 in file unit    65
+
Encountered at routine:location open_bpch2_for_read:1
+
+
Error  30: OPEN failure
+
===============================================================================
+
 
+
Then recompile your code with the <tt>BOUNDS=yes</tt> option.  Chances are this is the side-effect of an [[Common GEOS-Chem error messages#Array-out-of-bounds error|array out-of-bounds error]] caused by your array being too small to hold the data that is being read in from disk.  Compiling with <tt>BOUNDS=yes</tt> and re-running should help you locate the problem, and you should get an error message such as:
+
 
+
forrtl: severe (408): fort: (2): Subscript #1 of the array ARRAY has value 73 which is greater than the upper bound of 72 
+
 
+
which will point you to the specific array where the problem is occurring.
+
 
+
--[[User:Bmy|Bob Y.]] 11:00, 8 March 2012 (EST)
+
 
+
== Crashes or abnormal exits ==
+
+
=== KPP "Step size too small" error ===
+
 
+
The following abnormal exit from the [[KPP solvers FAQ|KPP chemical solver]]:
+
 
+
    - PHYSPROC: Trop chemistry at 2006/07/01 00:00
+
Forced exit from Rosenbrock due to the following error:
+
--> Step size too small: T + 10*H = T or H < Roundoff
+
T=  3044.21151383269      and H=  1.281206877135470E-012
+
+
...
+
+
JLOOP, I, J, L        7231          31          51          1
+
Forced exit from Rosenbrock due to the following error:
+
--> Step size too small: T + 10*H = T or H < Roundoff
+
T=  3044.21151383269      and H=  1.281206877135470E-012
+
failed twice !!!
+
+
indicates that the chemistry could not converge to a solution in the given grid box.  Possible reasons for this could be:
+
 
+
# A particular tracer has numerically underflowed or overflowed.  This can happen especially in the aerosol chemistry and equilibrium routines, where many exponentials and logarithms are used in the algorithms.
+
# The restart file is not appropriate for the given simulation.  For example, if the restart file was created using the Synoz O3 flux boundary condtion, but you have turned on the Linoz stratospheric O3 chemistry, then this mismatch can cause the solver not to converge.  You can try switching to a restart file generated from a simulation with the same input options as the simulation that you wish to perform.
+
 
+
You may have to [[KPP_solvers_FAQ#How_do_I_choose_the_absolute_and_relative_tolerance.3F|manually adjust the convergence criteria]] in the GEOS-Chem code to fix this condition.
+
 
+
--[[User:Bmy|Bob Y.]] 11:30, 9 November 2010 (EST)
+
 
+
=== Permission denied error ===
+
 
+
If you receive this error:
+
 
+
Thu Nov  4 11:03:57 EDT 2010
+
run.geos: Permission denied.
+
 
+
after having submitted a [http://acmg.seas.harvard.edu/geos/doc/man/chapter_6.html#6.2.4 run script to a queue system] (such as SGE), then doublecheck the Unix permissions of your script.  If the script does not have the Unix "execute" permission then the queue system will not be able to run it.
+
 
+
Use the Unix chmod command to make your script executable
+
 
+
chmod 755 run.geos
+
 
+
and then re-submit the script to the queue system.
+
 
+
--[[User:Bmy|Bob Y.]] 10:26, 9 November 2010 (EST)
+
 
+
=== Error computing F_OF_PBL ===
+
 
+
'''''NOTE: The same error described below can cause GEOS-Chem to die elsewhere, and not just in the F_OF_PBL computation.'''''
+
 
+
If you should encounter this error (which occurs in routine <tt>COMPUTE_PBL_HEIGHT</tt> from <tt>pbl_mix_mod.f</tt>)
+
 
+
  bad sum at:            1          70  -1.00000000000000   
+
  bad sum at:            1          81  -1.00000000000000   
+
===============================================================================
+
GEOS-CHEM ERROR: Error in computing F_OF_PBL!
+
STOP at COMPUTE_PBL_HEIGHT ("pbl_mix_mod.f")
+
===============================================================================
+
 
+
===============================================================================
+
GEOS-CHEM ERROR: Error in computing F_OF_PBL!
+
STOP at COMPUTE_PBL_HEIGHT ("pbl_mix_mod.f")
+
===============================================================================
+
      - CLEANUP: deallocating arrays now...
+
  bad sum at:            1          48  -1.00000000000000   
+
  bad sum at:            1          59  -1.00000000000000   
+
  bad sum at:          73          46  -1.00000000000000   
+
 
+
you should check to see if your code was not recompiled cleanly.  Often this is a result of not doing a
+
 
+
make realclean
+
 
+
before trying to switch from 2&deg; x 2.5&deg; to 4&deg; x 5&deg; or vice versa in the <tt>define.h</tt> header file.  Often this type of error can be deduced by looking at the GEOS-Chem log file.  When this error occurs the resolution indicated at the top of the GEOS-Chem log file, e.g.:
+
 
+
*************  S T A R T I N G  2 x 2.5  G E O S--C H E M  *************
+
 
+
will not match the longitudes and latitudes as reported a little further down in the log file:
+
 
+
Grid box longitude centers [degrees]:
+
-180.000 -175.000 -170.000 -165.000 -160.000 -155.000 -150.000 -145.000
+
  ...
+
+
Grid box latitude centers [degrees]:
+
  -89.000  -86.000  -82.000  -78.000  -74.000  -70.000  -66.000  -62.000
+
  ...
+
 
+
--[[User:Bmy|Bob Y.]] 12:13, 25 October 2010 (EDT)
+
 
+
=== Negative tracer found in WETDEP ===
+
 
+
If your simulation encounters negative (or NaN) tracer concentrations in the WETDEP routine, then this can be an indication of a problem further upsteam, perhaps in the aerosol routines (highly probable if the tracer is SO4, SO4s, HNO3, SO2, or NH3). We have fixed some of these bugs by making the code more robust.  If you are using a GEOS-Chem version prior to v8-01-01, then you should get [ftp://ftp.as.harvard.edu/pub/geos-chem/patches/v8-01-01/ ftp://ftp.as.harvard.edu/pub/geos-chem/patches/v8-01-01/ these patches].  (These patches have been added to the standard GEOS-Chem code in versions higher than v8-01-01.) Please see the following links for more information:
+
 
+
*[[Wet_deposition#Values_of_F_PRIME_greater_than_1_in_WETDEP|Values of <tt>F_PRIME</tt> > 1 in routine <tt>WETDEP</tt>]]
+
*[[GEOS-5 issues#Small_negative_RH_value_in_20060206.a6.2x25_file|Negative tracer due to negative RH values in the met field data]]
+
*[[Wet deposition#Negative_tracer_in_routine_WETDEP|Negative tracer in routine WETDEP]]
+
*[[Wet deposition#Negative tracer in routine WETDEP .232|Negative tracer in routine WETDEP #2]]
+
*[[Aerosol_thermodynamical_equilibrium#Run_dies_in_RPMARES_unexpectedly|A bug in RPMARES]] was also leading to a crash in WETDEP.
+
 
+
If the fixes above do not solve your problem, you will need to debug. The first step is to use few calls to CHECK_STT (from <tt>tracer_mod.f</tt>) to isolate the part of the code where negative tracers are created. This can be done quite fast if the code dies early enough in the run.
+
 
+
--[[User:Bmy|Bob Y.]] 12:50, 15 July 2011 (EDT)
+
 
+
=== LISOPOH error ===
+
 
+
If you are running the [[Secondary organic aerosols|SOA simulation]] and encounter this error:
+
 
+
===============================================================================
+
GEOS-CHEM ERROR: LISOPOH needs to be defined for SOA!
+
STOP at chemdr.f
+
===============================================================================
+
 
+
Then this means that the species <tt>LISOPOH</tt> is not set to an active species in the chemical mechanism.  <tt>LISOPOH</tt> needs to be a turned off for the standard 43-tracer simulation, but turned on the SOA simulation.
+
 
+
To fix the error, change this line in your <tt>globchem.dat</tt> file from:
+
 
+
D LISOPOH            1.00 1.000E-20 1.000E-20 1.000E-20 1.000E-20
+
 
+
to
+
 
+
A LISOPOH            1.00 1.000E-20 1.000E-20 1.000E-20 1.000E-20
+
 
+
and then re-run GEOS-Chem.
+
 
+
--[[User:Bmy|Bob Y.]] 10:09, 26 August 2011 (EDT)
+
 
+
=== Fatal error in IFORT ===
+
 
+
The following error, which resulted on the Altix platform using Intel "ifort" v9.1 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.
+
 
+
=== Too many levels in photolysis code ===
+
 
+
Please see [[Photolysis mechanism#Too many levels in photolysis code|this discussion about the "Too many levels in photolysis code" error]] that can sometimes happen in the FAST-J photolysis code.
+
 
+
--[[User:Bmy|Bob Y.]] 11:09, 12 January 2010 (EST)
+
 
+
=== No output scheduled on last day of run ===
+
 
+
If you encounter this error at the start of your GEOS-Chem simulation:
+
 
+
==========================================================================
+
GEOS-CHEM ERROR: No output scheduled on last day of run!
+
STOP at IS_LAST_DAY_GOOD ("input_mod.f")
+
==========================================================================
+
 
+
This means that you have not told GEOS-Chem to save out diagnostic data on the day that your simulation ends.  GEOS-Chem adds this error check in order to prevent you from running a long simulation only to have no diagnostics printed out at the end of the run.
+
 
+
For more information on how to schedule diagnostic output in GEOS-Chem, please see the section entitled "[http://acmg.seas.harvard.edu/geos/doc/man/chapter_5.html#5.2.1.13 "the OUTPUT MENU section of the <tt>input.geos</tt> file"] in our GEOS-Chem Online Users' Guide.
+
 
+
--[[User:Bmy|Bob Y.]] 12:56, 15 July 2011 (EDT)
+
 
+
=== 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.
+
 
+
--[[User:Bmy|Bob Y.]] 13:01, 4 November 2010 (EDT)
+
 
+
== Segmentation faults ==
+
 
+
If your simulation dies with a '''segmentation fault''' error, this means that GEOS-Chem tried to access an invalid memory location.  We list several instances of segmentation faults below:
+
 
+
=== Severe(174) SIGSEGV error ===
+
 
+
'''''NOTE: In this section, we shall use the IFORT compiler error messages.  You may get a slightly different error message if you are using a different compiler (such as PGI).'''''
+
 
+
If you compiled GEOS-Chem with the [[Intel Fortran Compiler|IFORT compiler]], you may encounter the following error message:
+
 
+
forrtl: severe (174): SIGSEGV, segmentation fault occurred
+
 
+
This means that a segmentation fault (i.e. memory error) has occurred during your GEOS-Chem simulation.  This can be caused by:
+
 
+
==== Array-out-of-bounds error ====
+
 
+
Most often, a segmentation fault indicates an [[#Example 3|array out-of-bounds condition]].  To find out more information about where this error is occurring, recompile GEOS-Chem with the following Makefile options:
+
 
+
make realclean
+
make BOUNDS=yes TRACEBACK=yes
+
 
+
The <tt>BOUNDS=yes</tt> option will turn on '''Array Out-of-Bounds''' error checking.  The <tt>TRACEBACK=yes</tt> option will print out the '''Error Stack''', or a list of routines that were called, and the line at which the error occurred.  These options will provide more detailed error output.
+
 
+
After recompiling, you should receive an error message such as:
+
 
+
forrtl: severe (408): fort: (3): Subscript #1 of the array PBL_THICK has value -1000000 which is less than the lower bound of 1
+
 
+
This tells you that there is a problem with a certain array.  Use the Unix <tt>grep</tt> command to search for all instances of this array in the GEOS-Chem source code:
+
 
+
grep -i PBL_THICK *.f*
+
 
+
and search for the problem. 
+
 
+
NOTE: In the above example, we manually forced an out-of-bounds error with this line of code:
+
 
+
        !### FORCE OOB error for testing
+
        PBL_THICK(-1000000,J)  = BLTHIK
+
 
+
Removing this line will fix the error.
+
 
+
--[[User:Bmy|Bob Y.]] 15:57, 22 June 2012 (EDT)
+
 
+
==== Invalid memory access ====
+
 
+
A segmentation fault can also happen if GEOS-Chem makes an reference to a memory location that is invalid.  You may see an error message such as this:
+
 
+
severe (174): SIGSEGV, segmentation fault occurred
+
This message indicates that the program attempted an invalid memory reference.
+
Check the program for possible errors.
+
 
+
This can happen if you are trying to read data from a file into an array, but the array is too small to hold all of the data.  You can use a debugger (such as Totalview or IDB) to try to diagnose the situation.  You may receive an error message from the debugger similar to this one: 
+
 
+
  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.
+
 
+
Usually, increasing the size of the array (i.e. until it is large enough to contain all of the data) will fix this problem.
+
 
+
--[[User:Bmy|Bob Y.]] 15:57, 22 June 2012 (EDT)
+
 
+
==== Stack overflow ====
+
 
+
Finally, a segmentation fault can happen if GEOS-Chem uses up all of the available [http://en.wikipedia.org/wiki/Stack-based_memory_allocation stack memory] on your system.  The stack memory is a special part of the memory where short-term variables get stored. 
+
 
+
The compiler will typically place into the stack memory all local temporary variables, such as:
+
 
+
* variables that are local to a given subroutine
+
* variables that are NOT located within a <tt>COMMON</tt> block
+
* variables that are NOT declared with the <tt>SAVE</tt> attribute
+
* variables that are NOT declared as an <tt>ALLOCATABLE</tt> array
+
* variables that are NOT declared as a <tt>POINTER</tt> variable or array
+
 
+
Therefore, it is important to make sure that your computational environment is set up to use the maximum amount of stack memory.  You can do this by placing the following line in your <tt>.cshrc</tt> or <tt>.bashrc</tt> file:
+
 
+
limit stacksize unlimited
+
 
+
If you encounter a <tt>SIGSEGV(174)</tt> message due to a stacksize memory error, you may see the following error text:
+
 
+
severe (174): SIGSEGV, possible program stack overflow occurred
+
Program requirements exceed current stacksize resource limit.
+
 
+
--[[User:Bmy|Bob Y.]] 15:57, 22 June 2012 (EDT)
+
 
+
==== forrtl: error (76): IOT trap signal ====
+
 
+
'''''[mailto:xun@gps.caltech.edu Xun Jiang] wrote:'''''
+
 
+
:We met the following error message
+
 
+
    forrtl: severe (174): SIGSEGV, segmentation fault occurred
+
+
    Stack trace terminated abnormally.
+
    forrtl: error (76): IOT trap signal
+
+
    Note: The error appears after
+
    - RDSOIL: Reading
+
    Data/GEOS_2x2.5/soil_NOx_200203/climatprep2x25.dat
+
    ### MAIN: a DAILY DATA
+
 
+
:I have the following lines in <tt>.cshrc</tt>
+
 
+
    setenv KMP_STACKSIZE 329033024
+
    limit cputime    unlimited
+
    limit datasize    unlimited
+
    limit stacksize  unlimited
+
    limit filesize    unlimited
+
    limit memoryuse  unlimited
+
    limit descriptors unlimited
+
 
+
:However, it still doesn't work. Any suggestion is really appreciated.
+
 
+
'''''[mailto:yantosca@seas.harvard.edu Bob Yantosca] replied:'''''
+
 
+
:I found [http://xtechnotes.blogspot.com/2006/01/1001-most-idiotic-error-messages.html this internet post] which has an explanation:
+
 
+
    Cause:
+
    The stack size for child threads are overflowing.  The main stack size for the program
+
    is changed by the ulimit command (in Bash shell) or limit command (in C shell).
+
    However this environment variable does not set the size for the child thread stack size.
+
    Thus the child thread stack overflow.
+
+
    Solution:
+
    Set the environment variables to increase the child thread stack size.
+
+
    #for intel, using bash shell
+
    export KMP_STACKSIZE=500000000
+
+
    # for intel, using csh or tcsh shell
+
    setenv KMP_STACKSIZE 500000000
+
 
+
:For more information, please see our wiki post on [[Intel Fortran Compiler#Resetting stacksize for Linux|Resetting the stack size for Linux]].
+
 
+
--[[User:Bmy|Bob Y.]] 11:20, 26 June 2012 (EDT)
+
 
+
=== Segmentation fault encountered after TPCORE initialization ===
+
 
+
You may encounter a segmentation fault right after the following text is printed.
+
 
+
NASA-GSFC Tracer Transport Module successfully initialized
+
 
+
This error usually occurs when:
+
 
+
# You are running GEOS-Chem at sufficiently fine resolution, such as 2&deg; x 2.5&deg; or finer.  (Many users have reported that this error does not occur at 4&deg; x 5&deg; resolution.)
+
# You are using a large number of advected tracers.
+
# Both #1 and #2
+
 
+
If you are using the [[Intel Fortran Compiler]], the cause of this error can likely be traced to a known issue with the the <tt>glibc</tt> library.  This will cause GEOS-Chem to think that it has used up all of the available memory, when in fact there is plenty of memory still available.  However, you may also encounter this same error even if you have compiled GEOS-Chem with a different compiler.
+
 
+
You can usually correct this error by manually telling your system to use the maximum amount of stack memory when running GEOS-Chem.  For detailed instructions, please see the following links:
+
 
+
#[[Intel Fortran Compiler#Resetting stacksize for Linux|Setting stacksize for the Intel Fortran Compiler (aka "IFORT")]]
+
#[[Machine_issues_%26_portability#Setting_the_stacksize|Setting stacksize for the PGI Compiler]]
+
#[[Machine_issues_%26_portability#.22Not_enough_space.22_error_in_TPCORE|Setting stacksize for the Sun Studio compiler]]
+
 
+
--[[User:Bmy|Bob Y.]] 16:07, 14 December 2010 (EST)
+
 
+
=== Bad GEOS-4 A6 met data causing segmentation fault ===
+
 
+
Please see [[GMAO_GEOS-4#Bad GEOS-4 A6 met data causing segmentation fault|this post about bad GEOS-4 A6 met data causing a segmentation fault]] in GEOS-Chem simulations.
+
 
+
--[[User:Bmy|Bob Y.]] 15:19, 16 February 2010 (EST)
+
 
+
=== IFORT error: Relocation truncated to fit ===
+
 
+
Please see [[Intel Fortran Compiler#Relocation truncated to fit error|this wiki post on our Intel Fortran Compiler page]] which describes how to work around an <tt>Relocation truncated to fit</tt> error message.
+
 
+
--[[User:Bmy|Bob Y.]] 10:46, 24 February 2012 (EST)
+
 
+
== Compilation warnings ==
+
 
+
In this section we discuss some compilation warnings that you may encounter.  Warnings are not generally fatal&mdash;GEOS-Chem will usually continue to compile while an informational message is displayed.
+
 
+
=== Internal threshold was exceeded ===
+
 
+
This warning is specific to the [[Intel Fortran Compiler]].  It usually happens when you try to optimize a complex module or subroutine.  Please see [http://software.intel.com/en-us/articles/internal-threshold-was-exceeded this post on the software.intel.com site] for a full explanation.
+
 
+
--[[User:Bmy|Bob Y.]] 15:32, 22 August 2012 (EDT)
+

Latest revision as of 20:30, 14 June 2019