`Segmentation fault` on *nemogcm.f90* running GYRE_PISCES

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#1

Dear all,

Hello, I am a beginner and I met some problems when running test case.
I’m trying to set up a configuration with GYRE_PISCES (TOP wasn’t compiled for speed).
I encounter this problem. I think it is related with the initialization of the NEMO.
Does anyone know how to fix it?

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

Backtrace for this error:
#0  0x7f7efb9e3d21 in ???
#1  0x7f7efb9e2ef5 in ???
#2  0x7f7efb68820f in ???
#3  0x7f7efbcf732b in ???
#4  0x55c4fcacb1ff in ???
#5  0x55c4fc6c0736 in ???
#6  0x55c4fc88830e in ???
#7  0x55c4fc48a7ac in ???
#8  0x55c4fbe2fa0c in __nemogcm_MOD_nemo_init
	at /media/cmlws/Data1/[user]/NEMO/r4.0.6/cfgs/GYRE_testing/BLD/ppsrc/nemo/nemogcm.f90:269
#9  0x55c4fbe329fd in __nemogcm_MOD_nemo_gcm
	at /media/cmlws/Data1/[user]/NEMO/r4.0.6/cfgs/GYRE_testing/BLD/ppsrc/nemo/nemogcm.f90:165
#10  0x55c4fbe2df61 in nemo
	at /media/cmlws/Data1/[user]/NEMO/r4.0.6/cfgs/GYRE_testing/WORK/nemo.f90:18
#11  0x55c4fbe2df9a in main
	at /media/cmlws/Data1/[user]/NEMO/r4.0.6/cfgs/GYRE_testing/WORK/nemo.f90:11

===================================================================================
=   BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES
=   PID 1671418 RUNNING AT cmlws
=   EXIT CODE: 139
=   CLEANING UP REMAINING PROCESSES
=   YOU CAN IGNORE THE BELOW CLEANUP MESSAGES
===================================================================================
YOUR APPLICATION TERMINATED WITH THE EXIT STRING: Segmentation fault (signal 11)
This typically refers to a problem with your application.
Please see the FAQ page for debugging suggestions

For information my arch file:

%NCDF_HOME           /home/[user]/anaconda3
%HDF5_HOME           /home/[user]/anaconda3
%XIOS_HOME           /media/cmlws/Data1/[user]/xios-2.5
%OASIS_HOME          /not/defined

%NCDF_INC            -I%NCDF_HOME/include -I%HDF5_HOME/include
%NCDF_LIB            -L%NCDF_HOME/lib -lnetcdff -lnetcdf -lstdc++
%XIOS_INC            -I%XIOS_HOME/inc
%XIOS_LIB            -L%XIOS_HOME/lib -lxios -L/usr/lib/gcc/x86_64-linux-gnu/9 -lstdc++

%OASIS_INC           -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
%OASIS_LIB           -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip

%CPP                 /usr/bin/cpp-9
%CPPFLAGS            -P -traditional

%FC                  /usr/bin/mpif90
%FCFLAGS             -fdefault-real-8 -funroll-all-loops -cpp -fcray-pointer -ffree-line-length-none -g -O0 -fbacktrace
%FFLAGS              %FCFLAGS
#%LD                  /usr/bin/mpif90 -Wl,-rpath=$HOME/INSTALL/lib:/usr/lib
%LD                  /usr/bin/mpif90
%LDFLAGS             -L/usr/lib/x86_64-linux-gnu
%FPPFLAGS            -P -C -traditional
%AR                  ar
%ARFLAGS             -rs
%MK                  make
%USER_INC            %XIOS_INC %OASIS_INC %NCDF_INC
%USER_LIB            %XIOS_LIB %OASIS_LIB %NCDF_LIB

%CC                  cc
%CFLAGS              -O0 -fbacktrace

Thank you in advance.

Best regards,

Hwa-Jin Choi

#2

Hei Jin,

What do you mean by “TOP was not compiled for speed” ? Can you run GYRE without PISCES ?

Cheers,

Robinson

#3

Did you have a look at ocean.output? Do you see the E R R O R flag?
What is the contents of the line 269 of …/r4.0.6/cfgs/GYRE_testing/BLD/ppsrc/nemo/nemogcm.f90 ?

Sébastien

#4

Robinson,

I’m sorry. I stand corrected.
In /cfgs/GYRE_PISCES/cpp_GYRE_PISCES.fcm, I replaced key_top with key_nosignedzero. I referred to this site.
https://nemo-related.readthedocs.io/en/latest/compilation_notes/nemo40.html
Thank you for your interest.

Best regards,

Hwa-Jin

#5

@smasson

Thank you for your advices.
I can’t find the file… maybe I guess it wasn’t created.
Can you tell me where the ocean.output is located?

The content of the line 269 of nemogcm.f90 is about the IF( lk_oasis ) THEN

SUBROUTINE nemo_init
      !!----------------------------------------------------------------------
      !!                     ***  ROUTINE nemo_init  ***
      !!
      !! ** Purpose :   initialization of the NEMO GCM
      !!----------------------------------------------------------------------
      INTEGER ::   ios, ilocal_comm   ! local integers
      !!
      NAMELIST/namctl/ ln_ctl   , sn_cfctl, nn_print, nn_ictls, nn_ictle,   &
         &             nn_isplt , nn_jsplt, nn_jctls, nn_jctle,             &
         &             ln_timing, ln_diacfl
      NAMELIST/namcfg/ ln_read_cfg, cn_domcfg, ln_closea, ln_write_cfg, cn_domcfg_out, ln_use_jattr
      !!----------------------------------------------------------------------
      !
      cxios_context = 'nemo'
      !
      !                             !-------------------------------------------------!
      !                             !     set communicator & select the local rank    !
      !                             !  must be done as soon as possible to get narea  !
      !                             !-------------------------------------------------!
      !
      IF( Agrif_Root() ) THEN
         IF( lk_oasis ) THEN
            CALL cpl_init( "oceanx", ilocal_comm )                               ! nemo local communicator given by oasis
            CALL xios_initialize( "not used"       , local_comm =ilocal_comm )   ! send nemo communicator to xios
         ELSE
            CALL xios_initialize( "for_xios_mpi_id", return_comm=ilocal_comm )   ! nemo local communicator given by xios
         ENDIF
      ENDIF

Is there any way to fix this problem?
Thank you again for your time.

Best regards,

Hwa-Jin

#6

Very strange…
The error appears at the early beginning at the simulation. almost nothing has been done. It looks like the code was not properly compiled.
lk_oasis should be defined and initialized to .false. in …/r4.0.6/cfgs/GYRE_testing/BLD/ppsrc/nemo/sbc_oce.f90. Do you see this line:

LOGICAL , PUBLIC ::   lk_oasis = .FALSE.
#7

Smasson

Thanks to your comment, I rechecked the compiled code.
I was suspicious of installation of xios, so I reinstalled xios, the segment fault error was passed.
I think the xios and NEMO weren’t configured to be consistent with the compilers.
Thanks for your help :grinning:

Hwa-Jin