[MITgcm-support] segmentation fault
Andreas Klocker
andreas.klocker at utas.edu.au
Sun May 27 22:04:07 EDT 2018
Dimitris,
Do you know why I get so many more issues, such as netcdf not working, if I use '-devel' with genmake 2? Could any of those cause a segmentation fault?
cheers,
Andreas
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
&
Institute for Marine and Antarctic Studies
University of Tasmania
20 Castray Esplanade
Battery Point, TAS
7004 Australia
M: +61 437 870 182
W: http://www.utas.edu.au/profiles/staff/imas/andreas-klocker
skype: andiklocker
===============================================================
--
===============================================================
Dr. Andreas Klocker
Physical Oceanographer
ARC Centre of Excellence for Climate System Science
&
Institute for Marine and Antarctic Studies
University of Tasmania
20 Castray Esplanade
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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