[MITgcm-support] netcdf problems when running genmake

Sat Aug 12 11:07:01 EDT 2017

Hi Andreas,

The problem is more serious than just netcdf. It seems that ifort
compiler is unusable since none of the simple test pass:
>   Do we have the system() command using ifort...  no
>   Do we have the fdate() command using ifort...  no
>   Do we have the etime() command using ifort...  no
>   Can we call simple C routines (here, "cloc()") using ifort... no

Are you sure the right module is loaded ? and you have access to a valid
intel licence ?

Cheers,
Jean-Michel

On Sat, Aug 12, 2017 at 01:25:26PM +1000, Andreas Klocker wrote:
> Hi guys,
> 
> Maybe someone can help...
> 
> I'm trying to use genmake (see below) before compiling the MITgcm.
> For some reason I don't understand it has some issues with netcdf
> (again, see the genmake message below). This only started to be a
> problem recently.
> 
> A colleague of mine, running the same checkpoint (62), with the same
> opt-file, on the same machine, same netcdf_root, with the same
> modules loaded, does not have that problem. The same problem also
> appears with an older checkpoint.
> 
> Is there any way I can get a more detailed error log pointing me
> towards this problem? Or has anyone got any hints which might help?
> Without a more detailed error message I'm not sure where to start
> looking...even though I assume it's something trivial...
> 
> cheers,
> 
> Andreas
> 
> 
> 
> 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
> Warning: ROOTDIR was not specified ; try using a local copy of
> MITgcm found at "../../.."
>   getting OPTFILE information:
>     using
> OPTFILE="../../../tools/build_options/linux_ia64_ifort+mpi_raijin"
>   getting AD_OPTFILE information:
>     using AD_OPTFILE="../../../tools/adjoint_options/adjoint_default"
> 
> ===  Checking system libraries  ===
>   Do we have the system() command using ifort...  no
>   Do we have the fdate() command using ifort...  no
>   Do we have the etime() command using ifort...  no
>   Can we call simple C routines (here, "cloc()") using ifort... no
>   Can we unlimit the stack size using ifort...  no
>   Can we register a signal handler using ifort...  no
>   Can we use stat() through C calls...  no
>   Can we create NetCDF-enabled binaries...  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 ptracers diagnostics
> timeave mnc obcs layers 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 ptracers
> diagnostics timeave mnc obcs layers kpp
>   applying DISABLE settings
>   applying ENABLE settings
>     packages are:  debug diagnostics generic_advdiff kpp layers
> mdsio mnc mom_common mom_fluxform mom_vecinv monitor obcs ptracers
> rw timeave
> *********************************************************************
> WARNING: the "mnc" package was enabled but tests failed to compile
>   NetCDF applications.  Please check that:
> 
>   1) NetCDF is correctly installed for this compiler and
>   2) the LIBS variable (within the "optfile") specifies the correct
>        NetCDF library to link against.
> 
>   Due to this failure, the "mnc" package is now DISABLED.
> *********************************************************************
>   applying package dependency rules
>     packages are: debug diagnostics generic_advdiff kpp layers mdsio
> mom_common mom_fluxform mom_vecinv monitor obcs ptracers 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  ===
> 
> -- 
> ===============================================================
> Dr. Andreas Klocker
> ARC Fellow (DECRA)
> 
> Institute for Marine and Antarctic Studies
> University of Tasmania
> 20 Castray Esplanade
> Battery Point, TAS
> 7004 Australia
> 
> M:     +61 437 870 182
> W:     https://sites.google.com/site/andreasoceanographywebsite
> skype: andiklocker
> ===============================================================
> 
> 
> 
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