Difference between revisions of "Common GEOS-Chem error messages"
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NetCDF: HDF error
Then this usually means
Then this usually means trying to read corrupted . The quickest solution is to re-download the netCDF file from the original source.
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:11, 2 January 2019 (UTC)
--[[User:Bmy|Bob Yantosca]] ([[User talk:Bmy|talk]]) 21:11, 2 January 2019 (UTC)
Revision as of 21:12, 2 January 2019
Here is a list of some commonly-encountered GEOS-Chem error messages. Also be sure to visit our Machine issues and portability wiki page for a list of compiler-specific issues.
- 1 Overview
- 2 Compile-time warnings and errors
- 3 Compile-time errors caused by compiler bugs
- 4 Run-time crashes and abnormal exits
- 4.1 Errors reading the GEOS-Chem restart file
- 4.2 HEMCO Error: Cannot find file for current simulation time
- 4.3 List-directed I/O syntax error
- 4.4 NetCDF: HDF Error
- 4.5 UCX not defined at compile time
- 4.6 No output scheduled on last day of run
- 4.7 HEMCO Run Error
- 4.8 HEMCO time stamps may be wrong
- 4.9 Allocation error
- 4.10 Permission denied error
- 4.11 Floating invalid or floating-point exception error
- 4.12 N_/L2_/L2-cutoff JXTRA error
- 4.13 KPP "Step size too small" error
- 4.14 Mixed file access modes error
- 4.15 Negative tracer found in WETDEP
- 5 Segmentation faults
- 6 Other memory-related errors
Compile-time warnings and errors
In this section we discuss some compilation warnings that you may encounter.
- Warnings are not generally fatal—GEOS-Chem will usually continue to compile while an informational message is displayed.
- Errors, on the other hand, will halt the GEOS-Chem compilation process.
Error in opening the compiled module file
RnPbBe_mod.F(118): error #7002: Error in opening the compiled module file. Check INCLUDE paths. [CHEMGRID_MOD] USE CHEMGRID_MOD, ONLY : ITS_IN_THE_STRATMESO ----------^ RnPbBe_mod.F(118): error #6580: Name in only-list does not exist. [ITS_IN_THE_STRATMESO] USE CHEMGRID_MOD, ONLY : ITS_IN_THE_STRATMESO -------------------------------------^ compilation aborted for RnPbBe_mod.F (code 1)
This error message usually indicates indicates a typo in the Makefile dependencies section. For example, the above error was caused by this Makefile code
rnpbbe_mod.o : RnPbBe_mod.F \ chemgrid_mod.o diag_mod.o \ hco_interface_mod.o
because the capitalization of the object file name did not exactly correspond to the source code file name. The compilation process died with the above error because it was expecting to find a module file named RnPbBe_mod.o but could not.
Module file cannot be read
If you should encounter this type of error:
ifort -cpp -w -O2 -auto -noalign -convert big_endian -openmp -Dmultitask -c time_mod.f 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] USE JULDAY_MOD, ONLY : JULDAY, CALDATE
Then this means that you are trying to link to previously-created *.mod files that were generated by a different compiler. Making clean and re-compiling from scratch should solve this problem.
--Bob Y. 13:39, 1 July 2008 (EDT)
Intel Fortran 17 compilation error (also can happen with GNU Fortran)
If you are using GEOS-Chem v10-01 with the Intel Fortran Compiler version 17 (or with any recent version of the GNU Fortran compiler) then you might encounter the above error. These newer compilers are much stricter in their interpretations of the Fortran standard, and thus do not like the way that a couple of routines in the NcdfUtil and HEMCO/ folders have been written.
The best way to solve this error is to upgrade to the GEOS-Chem v11-01 public release. In this version, the offending code has been rewritten in such a way that it is compatible with the newest versions of the Intel Fortran Compiler and GNU Fortran Compiler. For complete instructions on how to downloaad GEOS-Chem v11-01, please visit the GEOS-Chem Online User's Guide.
For more information about this bug, please see this post on our Intel Fortran Compiler wiki page.
f77: command not found
/bin/bash: f77: command not found ... make: Leaving directory 'merra2_05x0625_CH4_na' ../Makefile_header.mk:321: *** "Select a compiler: COMPILER=ifort, COMPILER=pgi, COMPILER=gfortran". Stop. make: *** [all] Error 2 make: *** [mp] Error 2
The above error happens when GEOS-Chem cannot determine the name of your Fortran compiler. To fix this issue, make sure to specify the proper Unix environment variables in your .bashrc or .cshrc startup script. For complete instructions, please see our Environment variables that specify compiler names wiki post.
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 this post on the software.intel.com site for a full explanation.
--Bob Y. 15:32, 22 August 2012 (EDT)
GNU Fortran internal compiler error
f951: internal compiler error: in read_module, at fortran/module.c:5090 0x6251ee read_module ../.././gcc/fortran/module.c:5090 0x6251ee gfc_use_module ../.././gcc/fortran/module.c:6980 0x626896 gfc_use_modules() ../.././gcc/fortran/module.c:7104 ... etc ... Please submit a full bug report, with preprocessed source if appropriate. Please include the complete backtrace with any bug report. See <http://gcc.gnu.org/bugs.html> for instructions. make: *** [flexchem_mod.o] Error 1 make: *** Waiting for unfinished jobs....
If you should encounter an error similar to the one shown above when using the GNU Fortran compiler, the easiest solution is to rebuild GEOS-Chem from scratch.
which will remove all previously compiled modules and object files. If you are compiling from a GEOS-Chem run directory, you can also type:
which will also remove any output files generated by GEOS-Chem. (Use this option with caution!)
Compile-time errors caused by compiler bugs
A few GEOS-Chem errors have been traced to bugs in the compiler that was used to build the GEOS-Chem executable. For your convenience, we have collated a list of these issues. Please see our our Known issues caused by compiler bugs wiki page for more information.
Failed in XMAP_R4R4 error
If you are using the Intel Fortran Compiler 15, then you may encounter an error such as this:
forrtl: severe (408): fort: (2): Subscript #1 of the array LON2 has value 1 which is greater than the upper bound of -1 Image PC Routine Line Source libifcoremt.so.5 00002B9EFA2188D3 Unknown Unknown Unknown geos.mp 00000000011FCE35 regrid_a2a_mod_mp 1914 regrid_a2a_mod.F90 libiomp5.so 00002B9EFB70A8A3 Unknown Unknown Unknown
Solution: If you are using array-out-of-bounds checking, make sure to compile GEOS-Chem with these flags: BOUNDS=y DEBUG=y. For more information, see this post on our HEMCO wiki page.
Seg fault in HEMCO with Intel Fortran 12, 13, or 14
forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source ... geos 0000000000ADDCF4 hcoio_dataread_mo 2810 hcoio_dataread_mod.F90 geos 0000000000AD84DE hcoio_dataread_mo 2499 hcoio_dataread_mod.F90 geos 0000000000AB8971 hco_readlist_mod_ 438 hco_readlist_mod.F90 geos 0000000000AB8398 hco_readlist_mod_ 267 hco_readlist_mod.F90 geos 0000000000AA99A6 hco_driver_mod_mp 138 hco_driver_mod.F90 geos 0000000000844C07 hcoi_gc_main_mod_ 546 hcoi_gc_main_mod.F90 geos 0000000000801A2E emissions_mod_mp_ 172 emissions_mod.F90 geos 00000000006720B7 MAIN__ 834 main.F
For a workaround, please see this post on our HEMCO wiki page.
Run-time crashes and abnormal exits
In this section, we provide information about some commonly-reported run-time errors that cause GEOS-Chem to halt executing.
Errors reading the GEOS-Chem restart file
Please see the following posts for more information about errors that may occur when reading GEOS-Chem restart files:
HEMCO Error: Cannot find file for current simulation time
If you see an error such as this in your HEMCO.log file:
HEMCO ERROR: Cannot find file for current simulation time: ./GEOSChem.Restart.17120701_0000z.nc4 - Cannot get field SPC_NO. Please check file name and time (incl. time range flag) in the config. file
Then this can have a couple of causes:
- HEMCO cannot find the file because it is missing on disk.
- HEMCO will try to look back in time starting with the current year and going all the way back to the year 1712 or 1713. So if you see 1712 or 1713 in the error message, that is a tip-off that the file is missing.
- HEMCO cannot find an expected variable name within a file.
List-directed I/O syntax error
The above error message indicates that the simulation crashed at line 871 in GeosCore/input_mod.F. This means there was an issue while reading the input.geos file (located in the run directory). For example, GEOS-Chem might have expected numeric input, but instead a character was read from input.geos, thus causing a read error. This type of error can occur the input.geos corresponds to a version of GEOS-Chem that is different from yours.
This error is not limited to input.geos; it can happen for any text file that is being read from disk (both in GEOS-Chem and in any other Fortran programs you may write).
NetCDF: HDF Error
If you should encounter this error message:
NetCDF: HDF error
Then this usually means GEOS-Chem was trying to read an incomplete or corrupted netCDF file. The quickest solution is to re-download the netCDF file from the original source.
UCX not defined at compile time
This error may occur if you are compiling GEOS-Chem (v11-01 and prior versions) and directly from the source code directory and not a run directory. Whenever you compile GEOS-Chem in the source code directory, you must remember to use the following Makefile options:
CHEM=Standard UCX=y # Standard simulation (used for benchmarking GC) CHEM=UCX UCX=y # UCX simulation (i.e. Standard simulation w/o SOA species)
To avoid these errors, we STRONGLY RECOMMEND that you always compile GEOS-Chem from a run directory. This will ensure that the Makefile switches relevant to your simulation will always be activated. For more information, please see these wiki posts:
NOTE: In GEOS-Chem v11-02 and higher versions, the Makefile option UCX=y will automatically be set whenever you select CHEM=Standard or CHEM=UCX.
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 OUTPUT MENU section of the input.geos file on the GEOS-Chem wiki.
HEMCO Run Error
Errors messages containing "HCO" originate in the HEMCO emissions component. For example:
=============================================================================== GEOS-CHEM ERROR: HCO_RUN STOP at HCOI_GC_RUN (hcoi_gc_main_mod.F90) ===============================================================================
Additional helpful diagnostic information can be found in the HEMCO log file, which is usually named HEMCO.log.
Updated error message for v11-01
In GEOS-Chem v11-01 and higher versions, additional text instructs the user to also check the HEMCO log file.
=============================================================================== GEOS-CHEM ERROR: HCO_RUN HEMCO ERROR: Please check the HEMCO log file for error messages! STOP at HCOI_GC_RUN (GeosCore/hcoi_gc_main_mod.F90) ===============================================================================
HEMCO time stamps may be wrong
HEMCO reads the files but gives zero emissions and shows the following time step error: HEMCO WARNING: ncdf reference year is prior to 1901 - time stamps may be wrong! --> LOCATION: GET_TIMEIDX (hco_read_std_mod.F90)
Lizzie Lundgren wrote:
That HEMCO error occurs if the reference time for the netCDF file time dimension is prior to 1901. If you do ncdump –c filename you will be able to see the metadata for the time dimension as well as the time variable values. The time units should include the reference date.
You can get around this issue by changing the reference time within the file. You can do this with CDO (climate data operators) using the setreftime command.
Here is a bash script example (by GCST member Melissa Sulprizio) that updates the calendar and reference time for all files ending in *.nc within a directory. Support team member developed this for a user very recently who ran into the same issue. In that case the first file was for Jan 1, 1950, so that was made the new reference time. I would recommend doing the same for your dataset so that the first time variable value would be 0. This script also compresses the file which we recommend doing.
#!/bin/bash for file in *nc; do echo "Processing $file" cdo setcalendar,standard $file tmp.nc mv tmp.nc $file cdo setreftime,1950-01-01,0 $file tmp.nc mv tmp.nc $file nccopy -d1 -c "time/1" $file tmp.nc mv tmp.nc $file done
After you update the file you can then again do ncdump –c filename to check the time dimension. For the case above it looks like this after processing.
double time(time) ; time:standard_name = "time" ; time:long_name = "time" ; time:bounds = "time_bnds" ; time:units = "days since 1950-01-01 00:00:00" ; time:calendar = "standard" ; . . . time = 0, 31, 59, 90, 120, 151, 181, 212, 243, 273, 304, 334, 365, 396, 424, 455, 485, 516, 546, 577, 608, 638, 669, 699, 730, 761, 790, 821, 851, 882, 912, 943, 974, 1004, 1035, 1065, 1096, 1127, 1155, 1186, 1216, 1247, etc
If your GEOS-Chem simulation dies with this error output:
=============================================================================== GEOS-CHEM ERROR: Allocation error in array: MY_ARRAY STOP at alloc_err.f ===============================================================================
then this means that you do not have enough memory to run your simulation. This type of error can frequently occur if you are running a full-chemistry simulation at the 2° x 2.5° global grid, or one of the 0.5° x 0.666° nested grids. You may need to tell your queuing system to make more memory available for your GEOS-Chem simulation. Ask your IT staff for details.
Permission denied error
If you receive this error:
v11-01.run: Permission denied.
after having submitted a run script to a queue system (such as SLURM or Grid Engine), then doublecheck the Unix permissions of your v11-01.run 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 v11-01.run
and then re-submit the script to the queue system.
Floating invalid or floating-point exception error
You can check for several common floating-point math errors by compiling with the FPEX=y option. This will halt the simulation with an error message such as:
forrtl: error (65): floating invalid # Error message from Intel Fortran Compiler Floating point exception (core dumped) # Error message from GNU Fortran Compiler
This error typically means that a division-by-zero occurred, or a NaN value was encountered in one of your variables.
A common way to prevent these types of errors is to ensure "safe" divisions (i.e. to make sure that the denominator is nonzero). You can do this manually with an IF statement, or use the routines SAFE_DIV or IS_SAFE_DIV in GeosCore/error_mod.F.
N_/L2_/L2-cutoff JXTRA error
NOTE: This issue was resolved in v11-01d.
---> DATE: 2013/11/13 GMT: 19:00 X-HRS: 307.000 - Found all 44 GEOS-FP A1 met fields for 2013/11/13 19:30 N_/L2_/L2-cutoff JXTRA: 601 96 0.00 N_/L2_/L2-cutoff JXTRA: 601 96 0.00 ... run dies later with NaN's in chemistry ...
If you are using a version of GEOS-Chem prior to v11-01d, then you might have experienced this error, where a simulation using GEOS-FP or MERRA met fields dies in the chemistry solver after many such "JXTRA" warnings are printed to the log file.
This error has been attributed to a bug in the GEOS-FP and MERRA convection module, and was resolved in v11-01d. Upgrading to the GEOS-Chem v11-01 public release code or (patching your GEOS-Chem v10-01 code with this fix) will solve the issue.
KPP "Step size too small" error
The following abnormal exit from the KPP chemical solver:
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 ... 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 manually adjust the convergence criteria in the GEOS-Chem code to fix this condition.
--Bob Y. 11:30, 9 November 2010 (EST)
Mixed file access modes error
This error is particular to the Intel Fortran Compiler. You might encounter this in conjunction with the ND49 timeseries diagnostic.
According to the Intel website:
severe (31): Mixed file access modes FOR$IOS_MIXFILACC. An attempt was made to use any of the following combinations: * Formatted and unformatted operations on the same unit * An invalid combination of access modes on a unit, such as direct and sequential * An Intel® Fortran RTL I/O statement on a logical unit that was opened by a program coded in another language
Here are a few suggestions to try if you haven’t already:
- Make sure you don’t already have a ND49 file in the location that you’re writing. In other words, make sure GEOS-Chem isn’t trying to write to a file that already exists.
- Do “make realclean”, recompile, and run again to see if the error is persistent.
- Are you using an out-of-the-box version of the code or a modified version? If the latter, do you still get this error with a “clean” copy of the code?
- Is there a particular READ/WRITE format statement that is causing the problem? You could try compiling with BOUNDS=y TRACEBACK=y FPE=y DEBUG=y and running in totalview (do “module load totalview” first on Odyssey) to locate the problematic line.
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/ 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:
- Values of F_PRIME > 1 in routine WETDEP
- Negative tracer due to negative RH values in the met field data
- Negative tracer in routine WETDEP
- Negative tracer in routine WETDEP #2
- 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 tracer_mod.f) 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.
--Bob Y. 12:50, 15 July 2011 (EDT)
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 Intel Fortran Compiler error messages. You may get a slightly different error message if you are using a different compiler (such as GNU Fortran).
If you compiled GEOS-Chem with the 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:
Traceback error stack
NOTE: TRACEBACK=yes is turned on by default in v11-01 and higher versions.
When GEOS-Chem is compiled with the TRACEBACK=yes option, it will print out an error stack, which includes the list of routines that were called when the error occurred and the line at which the error occurred.
An error stack is included below:
forrtl: severe (174): SIGSEGV, segmentation fault occurred Image PC Routine Line Source libintlc.so.5 00002ACA46B91961 Unknown Unknown Unknown libintlc.so.5 00002ACA46B900B7 Unknown Unknown Unknown libnetcdff.so.5 00002ACA4473D682 Unknown Unknown Unknown libnetcdff.so.5 00002ACA4473D4D6 Unknown Unknown Unknown libnetcdff.so.5 00002ACA4471DD4C Unknown Unknown Unknown libnetcdff.so.5 00002ACA44721DB8 Unknown Unknown Unknown libpthread.so.0 00000031A0A0F710 Unknown Unknown Unknown geos.mp 000000000175FF79 hco_interface_mod 341 hco_interface_mod.F90 geos.mp 00000000005F1F47 carbon_mod_mp_emi 5490 carbon_mod.F geos.mp 00000000016EAF33 emissions_mod_mp_ 206 emissions_mod.F90 geos.mp 00000000010BB119 MAIN__ 1383 main.F geos.mp 000000000040370E Unknown Unknown Unknown libc.so.6 00000031A061ED5D Unknown Unknown Unknown geos.mp 0000000000403619 Unknown Unknown Unknown
The top line with a valid routine and line number printed is the location of the error. In this case, there is an issue in hco_interface_mod.F at line 341. You may also choose to step back through the routines to determine what went wrong. Again, in this case, the problematic routine in hco_interface_mod.F90 was called from carbon_mod.F (line 5490), etc. It may be useful to recompile and rerun GEOS-Chem with additional debug options turned on (e.g. BOUNDS=yes, FPE-yes) to determine the cause of the error. For more information, see our GEOS-Chem coding and debugging wiki page.
Most often, a segmentation fault indicates an 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 BOUNDS=yes option will turn on Array Out-of-Bounds error checking. The TRACEBACK=yes option will print out the Error Stack, as described above. 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 grep 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.
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.
--Bob Y. 15:57, 22 June 2012 (EDT)
Finally, a segmentation fault can happen if GEOS-Chem uses up all of the available 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 COMMON block
- variables that are NOT declared with the SAVE attribute
- variables that are NOT declared as an ALLOCATABLE array
- variables that are NOT declared as a POINTER 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 .cshrc file:
limit stacksize unlimited
or .bashrc file:
ulimit -s unlimited
If you encounter a SIGSEGV(174) 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.
--Bob Y. 15:57, 22 June 2012 (EDT)
forrtl: error (76): IOT trap signal
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 .cshrc
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.
Bob Yantosca replied:
- I found 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 Resetting the stack size for Linux.
--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° x 2.5° or finer. (Many users have reported that this error does not occur at 4° x 5° 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 glibc 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:
- Setting stacksize for the Intel Fortran Compiler (aka "IFORT")
- Setting stacksize for the PGI Compiler
- Setting stacksize for the Sun Studio compiler
--Bob Y. 16:07, 14 December 2010 (EST)
Bad GEOS-4 A6 met data causing segmentation fault
Please see this post about bad GEOS-4 A6 met data causing a segmentation fault in GEOS-Chem simulations.
--Bob Y. 15:19, 16 February 2010 (EST)
The errors listed below, which occur infrequently, are related to invalid memory operations. These can especially occur with
A bus error means that you are trying to reference memory that cannot possibly be there. The website StackOverflow.com has a definition of bus error and how it differs from a segmentation fault.
One cause of a bus error can be if you are trying to call a subroutine with the wrong number of arguments (i.e. usually too many arguments).
--Bob Y. 12:27, 19 October 2012 (EDT)
Dwarf subprogram entry error
The error message:
Dwarf subprogram entry L_ROUTINE-NAME__LINE-NUMBER__par_loop2_2_576 has high_pc < low_pc. This warning will not be repeated for other occurrences.
can occur when you try to use a pointer variable that is unassociated (i.e. that is not currently pointing to any other variable) from within an OpenMP parallel loop, where:
- ROUTINE-NAME is the name of the routine where the error occurred, and
- LINE-NUMBER is the line where the error occurred.
We recently discovered that this error can be caused if you have a pointer declaration such as this:
TYPE(Species), POINTER :: ThisSpc => NULL()
where the pointer
ThisSpc is later used to point to another variable from within an OpenMP parallel loop. As it turns out, the above declaration statement will inadvertently cause pointer
ThisSpc to be declared with the SAVE attribute. This can cause a segmentation fault, because all pointers used within an OpenMP parallel region must be created and destroyed on the same thread.
This type of problem can usually be fixed by removing the nullification from the declaration statement. In other words, you can rewrite the above line of code with:
TYPE(Species), POINTER :: ThisSpc . . . ThisSpc => NULL()
For more information, please see this article.
IFORT error: Relocation truncated to fit
Please see this wiki post on our Intel Fortran Compiler page which describes how to work around an Relocation truncated to fit error message.
--Bob Y. 10:46, 24 February 2012 (EST)
IFORT error: Out of memory asking for NNNNN
This is not a common error message, but it may occur if you are compiling a version of GEOS-Chem for a high-resolution horizontal grid, or with one of the available microphysics packages (i,e. APM or TOMAS). Please see this wiki post on our Intel Fortran Compiler page which describes this error in detail.
--Bob Y. 10:42, 26 July 2013 (EDT)
Memory error: "munmap_chunk: invalid pointer"
The following error is not common but can happen:
|Error||*** glibc detected *** ./geos: munmap_chunk(): invalid pointer: 0x00000000059aac30 ***|
|Explanation||This happens when the pointer passed to (C-library language routine free(), which is called from Fortran routine NULLIFY()) is not valid or has been modified somehow. I don't really know the details here. The bottom line is that the pointer passed to free() must be the same as returned by (C-library routines) malloc(), realloc() and their friends.
The free() function frees the memory space pointed to by ptr, which must have been returned by a previous call to malloc(), calloc() or realloc(). Otherwise, or if free(ptr) has already been called before, undefined behavior occurs. If ptr is NULL, no operation is performed. GNU 2012-05-10 MALLOC(3)
|Simpler explanation||This can happen if you are trying to deallocate or nullify a pointer variable that has already been deallocated or modified.|
Memory error: "free: invalid size"
The following error is not common but can happen:
|Error||*** Error in `./geos': free(): invalid size: 0x000000000662e090 ***|
|Explanation||It means that you have a memory error. You may be trying to free a pointer that wasn't allocated (or delete an object that wasn't created) or you may be trying to nullify/delete such an object more than once. You may be overflowing a buffer or otherwise writing to memory to which you shouldn't be writing, causing heap corruption.
Any number of programming errors can cause this problem. You need to use a debugger, get a backtrace, and see what your program is doing when the error occurs. If that fails and you determine you have corrupted the heap at some previous point in time, you may be in for some painful debugging (it may not be too painful if the project is small enough that you can tackle it piece by piece).
Memory error: "double free or corruption"
The following error is not common, but can occur under some circumstances:
|Error||*** glibc detected *** ./geos: double free or corruption (out):|
|Explanation||There are at least two possible situations:
For the first one I strongly suggest NULL-ing all deleted pointers.
You have [some] options:
Three basic rules:
Combination of these three works quite well.