[MITgcm-support] segmentation fault

Andreas Klocker andreas.klocker at utas.edu.au
Sun May 20 19:46:19 EDT 2018 

Dimitris,

I tried that...see below. Why do I get so many more issues, such as netcdf not working, if I use '-devel'?

I'm trying Patrick's suggestions now.

A>



without '-devel'

bash-4.1$ ../../../tools/genmake2 -mods=../code -rootdir=../../../ -mpi -of ../../../tools/build_options/linux_amd64_ifort

GENMAKE :

A program for GENerating MAKEfiles for the MITgcm project.
   For a quick list of options, use "genmake2 -h"
or for more detail see the Developer's HOWTO manual at:
   http://mitgcm.org/public/docs.html

===  Processing options files and arguments  ===
  getting local config information:  none found
  getting OPTFILE information:
    using OPTFILE="../../../tools/build_options/linux_amd64_ifort"
  getting AD_OPTFILE information:
    using AD_OPTFILE="../../..//tools/adjoint_options/adjoint_default"
  check makedepend (local: 0, system: 0, 0)
  Turning on MPI cpp macros

===  Checking system libraries  ===
  Do we have the system() command using mpif77...  yes
  Do we have the fdate() command using mpif77...  yes
  Do we have the etime() command using mpif77...  yes
  Can we call simple C routines (here, "cloc()") using mpif77...  yes
  Can we unlimit the stack size using mpif77...  yes
  Can we register a signal handler using mpif77...  yes
  Can we use stat() through C calls...  yes
  Can we create NetCDF-enabled binaries...  yes
  Can we create LAPACK-enabled binaries...  no
  Can we call FLUSH intrinsic subroutine...  yes

===  Setting defaults  ===
  Adding MODS directories: ../code
  Making source files in eesupp from templates
  Making source files in pkg/exch2 from templates
  Making source files in pkg/regrid from templates

===  Determining package settings  ===
  getting package dependency info from  ../../..//pkg/pkg_depend
  getting package groups info from      ../../..//pkg/pkg_groups
  checking list of packages to compile:
    using PKG_LIST="../code/packages.conf"
    before group expansion packages are: gfd diagnostics timeave obcs kpp
    replacing "gfd" with:  mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor
    after group expansion packages are:  mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor diagnostics timeave obcs kpp
  applying DISABLE settings
  applying ENABLE settings
    packages are:  debug diagnostics generic_advdiff kpp mdsio mom_common mom_fluxform mom_vecinv monitor obcs rw timeave
  applying package dependency rules
    packages are:  debug diagnostics generic_advdiff kpp mdsio mom_common mom_fluxform mom_vecinv monitor obcs rw timeave
  Adding STANDARDDIRS='eesupp model'
  Searching for *OPTIONS.h files in order to warn about the presence
    of "#define "-type statements that are no longer allowed:
    found CPP_OPTIONS="./CPP_OPTIONS.h"
    found CPP_EEOPTIONS="./CPP_EEOPTIONS.h"
  Creating the list of files for the adjoint compiler.

===  Creating the Makefile  ===
  setting INCLUDES
  Determining the list of source and include files
  Writing makefile: Makefile
  Add the source list for AD code generation
  Making list of "exceptions" that need ".p" files
  Making list of NOOPTFILES
  Add rules for links
  Adding makedepend marker

===  Done  ===

with "-devel"

bash-4.1$ ../../../tools/genmake2 -devel -mods=../code -rootdir=../../../ -mpi -of ../../../tools/build_options/linux_amd64_ifort

GENMAKE :

A program for GENerating MAKEfiles for the MITgcm project.
   For a quick list of options, use "genmake2 -h"
or for more detail see the Developer's HOWTO manual at:
   http://mitgcm.org/public/docs.html

===  Processing options files and arguments  ===
  getting local config information:  none found
  getting OPTFILE information:
    using OPTFILE="../../../tools/build_options/linux_amd64_ifort"
  getting AD_OPTFILE information:
    using AD_OPTFILE="../../..//tools/adjoint_options/adjoint_default"
  check makedepend (local: 0, system: 0, 0)
  Turning on MPI cpp macros

===  Checking system libraries  ===
  Do we have the system() command using mpif77...  yes
  Do we have the fdate() command using mpif77...  yes
  Do we have the etime() command using mpif77...  yes
  Can we call simple C routines (here, "cloc()") using mpif77...  yes
  Can we unlimit the stack size using mpif77...  yes
  Can we register a signal handler using mpif77...  yes
  Can we use stat() through C calls...  yes
  Can we create NetCDF-enabled binaries...  no
  Can we create LAPACK-enabled binaries...  no
  Can we call FLUSH intrinsic subroutine...  no

===  Setting defaults  ===
  Adding MODS directories: ../code
  Making source files in eesupp from templates
  Making source files in pkg/exch2 from templates
  Making source files in pkg/regrid from templates

===  Determining package settings  ===
  getting package dependency info from  ../../..//pkg/pkg_depend
  getting package groups info from      ../../..//pkg/pkg_groups
  checking list of packages to compile:
    using PKG_LIST="../code/packages.conf"
    before group expansion packages are: gfd diagnostics timeave obcs kpp
    replacing "gfd" with:  mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor
    after group expansion packages are:  mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor diagnostics timeave obcs kpp
  applying DISABLE settings
  applying ENABLE settings
    packages are:  debug diagnostics generic_advdiff kpp mdsio mom_common mom_fluxform mom_vecinv monitor obcs rw timeave
  applying package dependency rules
    packages are:  debug diagnostics generic_advdiff kpp mdsio mom_common mom_fluxform mom_vecinv monitor obcs rw timeave
  Adding STANDARDDIRS='eesupp model'
  Searching for *OPTIONS.h files in order to warn about the presence
    of "#define "-type statements that are no longer allowed:
    found CPP_OPTIONS="./CPP_OPTIONS.h"
    found CPP_EEOPTIONS="./CPP_EEOPTIONS.h"
  Creating the list of files for the adjoint compiler.

===  Creating the Makefile  ===
  setting INCLUDES
  Determining the list of source and include files
  Writing makefile: Makefile
  Add the source list for AD code generation
  Making list of "exceptions" that need ".p" files
  Making list of NOOPTFILES
  Add rules for links
  Adding makedepend marker

===  Done  ===


On 21/05/18 09:27, Dimitris Menemenlis wrote:
Try generating the Makefile using “genmake2 -devel …”
Most build_options files contain the required flags pre-set
for array-bound checks, etc., when using the “devel" option.
But if you are using stock code, this is probably not the problem.
Did you try Patrick’s suggestions?

Dimitris Menemenlis

On May 20, 2018, at 4:07 PM, Andreas Klocker <Andreas.Klocker at utas.edu.au<mailto:Andreas.Klocker at utas.edu.au>> wrote:


Dimitris,

I've done many runs with obcs cut-out from a global setup, but never had this issue before. So I don't think other setups would help me much, but they might be of use to others.

My code directory is pretty simple, there's hardly anything changed in there and the same code directory (apart from changes in the size of the vertical grid) have been used successfully before.

How do I compile and link with array-bound checks turned on? I haven't tried that before...

cheers,

Andreas




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--
===============================================================
Dr. Andreas Klocker
Physical Oceanographer

ARC Centre of Excellence for Climate System Science
&
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University of Tasmania
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Battery Point, TAS
7004 Australia

M:     +61 437 870 182
W:     http://www.utas.edu.au/profiles/staff/imas/andreas-klocker
skype: andiklocker
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