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<p>Dimitris,</p>
<p>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?<br>
</p>
<p>cheers,</p>
<p>Andreas<br>
</p>
<blockquote type="cite" cite="mid:08a63bd2-00c7-96cb-f0b5-7f57fb4f0df5@utas.edu.au">
<p><br>
</p>
<p><br>
</p>
<p><b>without '-devel'</b><br>
</p>
<p>bash-4.1$ ../../../tools/genmake2 -mods=../code -rootdir=../../../ -mpi -of ../../../tools/build_options/linux_amd64_ifort<br>
<br>
GENMAKE :<br>
<br>
A program for GENerating MAKEfiles for the MITgcm project.<br>
For a quick list of options, use "genmake2 -h"<br>
or for more detail see the Developer's HOWTO manual at:<br>
<a class="moz-txt-link-freetext" href="http://mitgcm.org/public/docs.html" moz-do-not-send="true">
http://mitgcm.org/public/docs.html</a><br>
<br>
=== Processing options files and arguments ===<br>
getting local config information: none found<br>
getting OPTFILE information:<br>
using OPTFILE="../../../tools/build_options/linux_amd64_ifort"<br>
getting AD_OPTFILE information:<br>
using AD_OPTFILE="../../..//tools/adjoint_options/adjoint_default"<br>
check makedepend (local: 0, system: 0, 0)<br>
Turning on MPI cpp macros<br>
<br>
=== Checking system libraries ===<br>
Do we have the system() command using mpif77... yes<br>
Do we have the fdate() command using mpif77... yes<br>
Do we have the etime() command using mpif77... yes<br>
Can we call simple C routines (here, "cloc()") using mpif77... yes<br>
Can we unlimit the stack size using mpif77... yes<br>
Can we register a signal handler using mpif77... yes<br>
Can we use stat() through C calls... yes<br>
Can we create NetCDF-enabled binaries... yes<br>
Can we create LAPACK-enabled binaries... no<br>
Can we call FLUSH intrinsic subroutine... yes<br>
<br>
=== Setting defaults ===<br>
Adding MODS directories: ../code <br>
Making source files in eesupp from templates<br>
Making source files in pkg/exch2 from templates<br>
Making source files in pkg/regrid from templates<br>
<br>
=== Determining package settings ===<br>
getting package dependency info from ../../..//pkg/pkg_depend<br>
getting package groups info from ../../..//pkg/pkg_groups<br>
checking list of packages to compile:<br>
using PKG_LIST="../code/packages.conf"<br>
before group expansion packages are: gfd diagnostics timeave obcs kpp<br>
replacing "gfd" with: mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor<br>
after group expansion packages are: mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor diagnostics timeave obcs kpp<br>
applying DISABLE settings<br>
applying ENABLE settings<br>
packages are: debug diagnostics generic_advdiff kpp mdsio mom_common mom_fluxform mom_vecinv monitor obcs rw timeave<br>
applying package dependency rules<br>
packages are: debug diagnostics generic_advdiff kpp mdsio mom_common mom_fluxform mom_vecinv monitor obcs rw timeave<br>
Adding STANDARDDIRS='eesupp model'<br>
Searching for *OPTIONS.h files in order to warn about the presence<br>
of "#define "-type statements that are no longer allowed:<br>
found CPP_OPTIONS="./CPP_OPTIONS.h"<br>
found CPP_EEOPTIONS="./CPP_EEOPTIONS.h"<br>
Creating the list of files for the adjoint compiler.<br>
<br>
=== Creating the Makefile ===<br>
setting INCLUDES<br>
Determining the list of source and include files<br>
Writing makefile: Makefile<br>
Add the source list for AD code generation<br>
Making list of "exceptions" that need ".p" files<br>
Making list of NOOPTFILES<br>
Add rules for links<br>
Adding makedepend marker<br>
<br>
=== Done ===</p>
<p><b>with "-devel"</b><br>
</p>
<p>bash-4.1$ ../../../tools/genmake2 -devel -mods=../code -rootdir=../../../ -mpi -of ../../../tools/build_options/linux_amd64_ifort<br>
<br>
GENMAKE :<br>
<br>
A program for GENerating MAKEfiles for the MITgcm project.<br>
For a quick list of options, use "genmake2 -h"<br>
or for more detail see the Developer's HOWTO manual at:<br>
<a class="moz-txt-link-freetext" href="http://mitgcm.org/public/docs.html" moz-do-not-send="true">
http://mitgcm.org/public/docs.html</a><br>
<br>
=== Processing options files and arguments ===<br>
getting local config information: none found<br>
getting OPTFILE information:<br>
using OPTFILE="../../../tools/build_options/linux_amd64_ifort"<br>
getting AD_OPTFILE information:<br>
using AD_OPTFILE="../../..//tools/adjoint_options/adjoint_default"<br>
check makedepend (local: 0, system: 0, 0)<br>
Turning on MPI cpp macros<br>
<br>
=== Checking system libraries ===<br>
Do we have the system() command using mpif77... yes<br>
Do we have the fdate() command using mpif77... yes<br>
Do we have the etime() command using mpif77... yes<br>
Can we call simple C routines (here, "cloc()") using mpif77... yes<br>
Can we unlimit the stack size using mpif77... yes<br>
Can we register a signal handler using mpif77... yes<br>
Can we use stat() through C calls... yes<br>
Can we create NetCDF-enabled binaries... no<br>
Can we create LAPACK-enabled binaries... no<br>
Can we call FLUSH intrinsic subroutine... no<br>
<br>
=== Setting defaults ===<br>
Adding MODS directories: ../code <br>
Making source files in eesupp from templates<br>
Making source files in pkg/exch2 from templates<br>
Making source files in pkg/regrid from templates<br>
<br>
=== Determining package settings ===<br>
getting package dependency info from ../../..//pkg/pkg_depend<br>
getting package groups info from ../../..//pkg/pkg_groups<br>
checking list of packages to compile:<br>
using PKG_LIST="../code/packages.conf"<br>
before group expansion packages are: gfd diagnostics timeave obcs kpp<br>
replacing "gfd" with: mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor<br>
after group expansion packages are: mom_common mom_fluxform mom_vecinv generic_advdiff debug mdsio rw monitor diagnostics timeave obcs kpp<br>
applying DISABLE settings<br>
applying ENABLE settings<br>
packages are: debug diagnostics generic_advdiff kpp mdsio mom_common mom_fluxform mom_vecinv monitor obcs rw timeave<br>
applying package dependency rules<br>
packages are: debug diagnostics generic_advdiff kpp mdsio mom_common mom_fluxform mom_vecinv monitor obcs rw timeave<br>
Adding STANDARDDIRS='eesupp model'<br>
Searching for *OPTIONS.h files in order to warn about the presence<br>
of "#define "-type statements that are no longer allowed:<br>
found CPP_OPTIONS="./CPP_OPTIONS.h"<br>
found CPP_EEOPTIONS="./CPP_EEOPTIONS.h"<br>
Creating the list of files for the adjoint compiler.<br>
<br>
=== Creating the Makefile ===<br>
setting INCLUDES<br>
Determining the list of source and include files<br>
Writing makefile: Makefile<br>
Add the source list for AD code generation<br>
Making list of "exceptions" that need ".p" files<br>
Making list of NOOPTFILES<br>
Add rules for links<br>
Adding makedepend marker<br>
<br>
=== Done ===<br>
<br>
</p>
<br>
<div class="moz-cite-prefix">On 21/05/18 09:27, Dimitris Menemenlis wrote:<br>
</div>
<blockquote type="cite" cite="mid:0CF8F6E6-8150-40C0-A5B2-34CA88117D9E@gmail.com">
<div class="">Try generating the Makefile using “genmake2 -devel …”</div>
<div class="">Most build_options files contain the required flags pre-set</div>
<div class="">for array-bound checks, etc., when using the “devel" option.</div>
<div class="">But if you are using stock code, this is probably not the problem.</div>
<div class="">Did you try Patrick’s suggestions?</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">Dimitris Menemenlis </div>
<div><br class="">
<blockquote type="cite" class="">
<div class="">On May 20, 2018, at 4:07 PM, Andreas Klocker <<a href="mailto:Andreas.Klocker@utas.edu.au" class="" moz-do-not-send="true">Andreas.Klocker@utas.edu.au</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div text="#000000" bgcolor="#FFFFFF" class="">
<p class="">Dimitris,</p>
<p class="">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.</p>
<p class="">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.</p>
<p class="">How do I compile and link with array-bound checks turned on? I haven't tried that before...</p>
<p class="">cheers,</p>
<p class="">Andreas</p>
<div class=""><br class="">
</div>
</div>
</div>
</blockquote>
</div>
</div>
<br>
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</blockquote>
<br>
<pre class="moz-signature" cols="72">--
===============================================================
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: <a class="moz-txt-link-freetext" href="http://www.utas.edu.au/profiles/staff/imas/andreas-klocker" moz-do-not-send="true">http://www.utas.edu.au/profiles/staff/imas/andreas-klocker</a>
skype: andiklocker
===============================================================</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
===============================================================
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: <a class="moz-txt-link-freetext" href="http://www.utas.edu.au/profiles/staff/imas/andreas-klocker">http://www.utas.edu.au/profiles/staff/imas/andreas-klocker</a>
skype: andiklocker
===============================================================</pre>
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