error trying to build AMIP CCSM scenario

[mmarcella@air-worldwide_com]

Hi all,I'm new to running/building CCSM.  Im trying to set up an AMIP run on an intel 64bit RHEL pgi machine...I am able to get through the first few steps, but I am now getting stuck on the getting the build script to compile properly (with an AMIP intel pgi test case).  I get the following error, which I trace back through the error logs and it looks like it cannot find a gcc or C compiler when I look at the config.log file and all the error messages below.  (although 'which gcc' definitely shows that I have it installed on the machine)Does anyone happen to know where/why my error may be occurring?  Any help would be greatly appreciated!   When I open the config file I see the following error(s):./configure  CC="mpicc" FC="mpif90" F90="mpif90" INCLUDEPATH="-I/usr/local/mpich-1.2.7p1-intel-3.2.02/include"checking for C compiler default output file name... configure: error: C compiler cannot create executables. When I open this config.log file it is alluding to, it looks mostly like it is just outputting my path and throws an error when it is look for the C compiler: configure:1663: checking for C compiler default output file nameconfigure:1666: mpicc  -I/home/i63639/netcdf/include  conftest.c –lnetcdf >&5gcc: –lnetcdf: No such file or directoryconfigure:1669: $? = 1configure: failed program was:| /* confdefs.h.  */|| #define PACKAGE_NAME "MCT"| #define PACKAGE_TARNAME "mct"| #define PACKAGE_VERSION "2.0"| #define PACKAGE_STRING "MCT 2.0"| #define PACKAGE_BUGREPORT ""| /* end confdefs.h.  */|| int| main ()| {||   ;|   return 0;| }configure:1708: error: C compiler cannot create executables 

 

[jedwards]

This error:gcc: –lnetcdf: No such file or directory Indicates that it can't find your netcdf lib.    You should have -L $NETCDF_PATH/lib in your LDFLAGS

 

[mmarcella@air-worldwide_com]

Hi jedwards,
Thanks for the response; much appreciated!  However, in my chsrc I do have my netcdf libs defined and they are located where the cshrc is looking (see below).  Is it possible that CESM or some program/script it is calling is hardcoded to look for the netcdf and other variables in a specific (other) location and is actually overriding my .cshrc file?  Or do I need to set the location of my netcdf locations somewhere else in the CCSM build?  My chsrc lines for netcdf env:#setenv NETCDF /usr/lib64setenv NETCDF /home/i63639/netcdfsetenv PATH ${PATH}:/usr/lib64setenv CPPFLAGS -I${NETCDF}/includesetenv LD_LIBRARY_PATH ${NETCDF}/libsetenv LDFLAGS -L${NETCDF}/libsetenv LIBS –lnetcdf 

 

[jedwards]

You shouldn't need to set these in your .cshrc.In your env_mach_specific.$HOST file try settingsetenv NETCDF_PATH /home/i63639/netcdfthat should be all that you need except that newer versions of netcdf also require -lnetcdff  

 

[mmarcella@air-worldwide_com]

Hi, Ok thank you! In my test case directory though, all I have is an env_mach_specific file.  Not a env_mach_specific.$HOST file.  Do I just need to edit the line in there that is commented out like such:#--- set env variables for Macros if neededsetenv NETCDF_PATH /home/i63639/netcdf Apologies for all the questions but brand new to CESM and compiling/building this model.  Thank you for your help and patience with this!

 

[jedwards]

The file scripts/ccsm_utils/Machines/env_mach_specific.$HOST is copied to env_mach_specific in your case directory.   So if you change it inenv_mach_specific you will change it only for your case.   Did you do the port to this machine, or did someone else?

 

[mmarcella@air-worldwide_com]

I ported/dl'ed CESM directly to this machine from the web.  I do understand how changing this specific file will only work for this test case, but that is fine for the time being.  Unfortunately though, even when I edited that file I still get the following error when I try to execute the build script, however I now feel like there is maybe a different error in the log file?:CCSM BUILDEXE SCRIPT STARTING - Build Libraries: mct pio csm_share Thu Dec 5 14:52:29 EST 2013 /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/mct.bldlog.131205-145144ERROR: mct.buildlib failed, see /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/mct.bldlog.131205-145144ERROR: cat /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/mct.bldlog.131205-145144Thu Dec 5 14:52:29 EST 2013 /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/mct.bldlog.131205-145144Copying source to CCSM EXEROOT...New build of MCTRunning configure...for OS=Linux MACH=generic_linux_pgicat: Filepath: No such file or directorycat: Srcfiles: No such file or directory/opt/cesm/scripts/F_AMIP_CN_PGI/Tools/mkSrcfiles > /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/Srcfilescp -f /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/Filepath /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/Deppath/opt/cesm/scripts/F_AMIP_CN_PGI/Tools/mkDepends Deppath Srcfiles > /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/Depends./configure  FC="mpif90" F90="mpif90" --host=Linuxconfigure: WARNING: If you wanted to set the --build type, don't use --host.    If a cross compiler is detected then cross compile mode will be used.checking for Linux-cc... nochecking for cc... ccchecking for C compiler default output file name... configure: error: C compiler cannot create executablesSee `config.log' for more details.gmake: *** [configure] Error 77cp: cannot stat `Makefile.conf': No such file or directoryMakefile:4: Makefile.conf: No such file or directorymake: *** No rule to make target `Makefile.conf'.  Stop.~                                                                

 

[jedwards]

See `config.log' for more details in directory /sffiles/mmarcella/cesm_scratch/F_AMIP_CN_PGI/mct/

 

[mmarcella@air-worldwide_com]

Hi jedwards,  I did and it is the same error message as before, as not being able to find -lnetcdf.  So Im guessing editing the env_mach_specific file did not work, or I did not edit it properly?