Put CLM on BU servers

[tonygardella]

CLM works on the pecan VM put not on BU servers yet. Related to #352

[tonygardella]

Found that ".../clm4_5_1_r085/scripts/ccsm_utils/Machines/config_machines.xml" explicitly points to "/home/carya/..."

[tonygardella]

Getting a different error now:

CASE directory is: /projectnb/dietzelab/pecan.models/clm45/models/clm4_5_1_r085/scripts/US-UMB_I1850CLM45CN

CASE exeroot is: /projectnb/dietzelab/pecan.models/clm45/models/clm4_5_1_r085/run/US-UMB_I1850CLM45CN

CASE rundir is: /projectnb/dietzelab/pecan.models/clm45/models/clm4_5_1_r085/run/US-UMB_I1850CLM45CN/run

point data making NOT requested!  Make sure they exist
./create_newcase --case US-UMB_I1850CLM45CN --mach ubuntu --compset I1850CLM45CN --res CLM_USRDAT --compiler gnu --mpilib mpi-serial
grep: write error: Broken pipe
US-UMB_I1850CLM45CN created.  See create_newcase.log for details
CLM module options: -phys clm4_5 -bgc cn

Creating Macros file for ubuntu
/projectnb/dietzelab/pecan.models/clm45/models/clm4_5_1_r085/scripts/ccsm_utils/Machines/config_compilers.xml gnu ubuntu
Creating batch script US-UMB_I1850CLM45CN.run
1
1
Locking file env_mach_pes.xml
Creating user_nl_xxx files for components and cpl
Running preview_namelist script
 infile is /projectnb/dietzelab/pecan.models/clm45/models/clm4_5_1_r085/scripts/US-UMB_I1850CLM45CN/Buildconf/cplconf/cesm_namelist
CLM configure done.
Warning : CLM build-namelist::CLMBuildNamelist::process_namelist_commandline_clm_usr_name() : setting clm_usr_name -- but did NOT find any user datasets: 1x1pt_US-UMB

CLM adding use_case 1850_control defaults for var 'sim_year' with val '1850'
CLM adding use_case 1850_control defaults for var 'sim_year_range' with val 'constant'
CLM adding use_case 1850_control defaults for var 'stream_year_first_ndep' with val '1850'
CLM adding use_case 1850_control defaults for var 'stream_year_first_popdens' with val '1850'
CLM adding use_case 1850_control defaults for var 'stream_year_last_ndep' with val '1850'
CLM adding use_case 1850_control defaults for var 'stream_year_last_popdens' with val '1850'
CLM adding use_case 1850_control defaults for var 'use_case_desc' with val 'Conditions to simulate 1850 land-use'
See ./CaseDoc for component namelists
If an old case build already exists, might want to run US-UMB_I1850CLM45CN.clean_build before building
CESM US-UMB_I1850CLM45CN clean_build FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
 CESM BUILDNML SCRIPT STARTING
 - To prestage restarts, untar a restart.tar file into /projectnb/dietzelab/pecan.models/clm45/models/clm4_5_1_r085/run/US-UMB_I1850CLM45CN/run
 infile is /projectnb/dietzelab/pecan.models/clm45/models/clm4_5_1_r085/scripts/US-UMB_I1850CLM45CN/Buildconf/cplconf/cesm_namelist
CLM configure done.
Warning : CLM build-namelist::CLMBuildNamelist::process_namelist_commandline_clm_usr_name() : setting clm_usr_name -- but did NOT find any user datasets: 1x1pt_US-UMB

CLM adding use_case 1850_control defaults for var 'sim_year' with val '1850'
CLM adding use_case 1850_control defaults for var 'sim_year_range' with val 'constant'
CLM adding use_case 1850_control defaults for var 'stream_year_first_ndep' with val '1850'
CLM adding use_case 1850_control defaults for var 'stream_year_first_popdens' with val '1850'
CLM adding use_case 1850_control defaults for var 'stream_year_last_ndep' with val '1850'
CLM adding use_case 1850_control defaults for var 'stream_year_last_popdens' with val '1850'
CLM adding use_case 1850_control defaults for var 'use_case_desc' with val 'Conditions to simulate 1850 land-use'
 CESM BUILDNML SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
-------------------------------------------------------------------------
 CESM PRESTAGE SCRIPT STARTING
 - Case input data directory, DIN_LOC_ROOT, is /projectnb/dietzelab/pecan.models/clm45/models/ccsm_inputdata
 - Checking the existence of input datasets in DIN_LOC_ROOT
 CESM PRESTAGE SCRIPT HAS FINISHED SUCCESSFULLY
-------------------------------------------------------------------------
-------------------------------------------------------------------------
 CESM BUILDEXE SCRIPT STARTING
rm: No match.
 COMPILER is gnu
 - Build Libraries: mct gptl pio csm_share
Tue Jan 12 14:43:37 EST 2016 /projectnb/dietzelab/pecan.models/clm45/clm4_5_1_r085/run/US-UMB_I1850CLM45CN/bld/gnu/mpi-serial/nodebug/nothreads/mct.bldlog.160112-144334
ERROR: buildlib.mct failed, see /projectnb/dietzelab/pecan.models/clm45/clm4_5_1_r085/run/US-UMB_I1850CLM45CN/bld/gnu/mpi-serial/nodebug/nothreads/mct.bldlog.160112-144334
ERROR: cat /projectnb/dietzelab/pecan.models/clm45/clm4_5_1_r085/run/US-UMB_I1850CLM45CN/bld/gnu/mpi-serial/nodebug/nothreads/mct.bldlog.160112-144334
/projectnb/dietzelab/pecan.models/clm45/models/clm4_5_1_r085/scripts/US-UMB_I1850CLM45CN
Your job 2183486 ("US-UMB_I1850CLM45CN.run") has been submitted

I'll take a closer look at the config_machines.xml file again and then the files suggested in the error. I'll probably have to ping Dan about this.

[mdietze]

Part of this issue might be because the BU server isn't ubuntu, but CentOS, but this script has a setting for --mach ubuntu. Are there alternative options supported for --mach? If there's not CentOS, Red Hat is probably close enough, or perhaps some generic linux. Just a shot in the dark and possibly wrong

The first error listed, grep: write error: Broken pipe, should be something that you can track down within create_newcase

[tonygardella]

The 'ubuntu' is just an alias for the machine settings. The template given for machine configurations looked like the following block and I used the settings that Dan made for the VM, only changing the paths. The OS was set to "Linux".

<machine MACH="userdefined">
        <DESC>User Defined Machine</DESC>                                 <!-- can be anything -->
        <OS>USERDEFINED_required_macros</OS>                              <!-- LINUX,Darwin,CNL,AIX,BGL,BGP -->
        <COMPILERS>intel,ibm,pgi,pathscale,gnu,cray,lahey</COMPILERS>     <!-- intel,ibm,pgi,pathscale,gnu,cray,lahey -->
        <MPILIBS>openmpi,mpich,mpt,mpt,ibm,mpi-serial</MPILIBS>                <!-- openmpi, mpich, ibm, mpi-serial -->
        <CESMSCRATCHROOT>USERDEFINED_required_build</CESMSCRATCHROOT>                     <!-- complete path to the 'scratch' directory -->
        <RUNDIR>USERDEFINED_required_build</RUNDIR>                       <!-- complete path to the run directory -->
        <EXEROOT>USERDEFINED_required_build</EXEROOT>                     <!-- complete path to the build directory -->
        <DIN_LOC_ROOT>USERDEFINED_required_build</DIN_LOC_ROOT>           <!-- complete path to the inputdata directory -->
        <DIN_LOC_ROOT_CLMFORC>USERDEFINED_optional_build</DIN_LOC_ROOT_CLMFORC> <!-- path to the optional forcing data for CLM (for CRUNCEP forcing) -->
        <DOUT_S>FALSE</DOUT_S>                                            <!-- logical for short term archiving -->
        <DOUT_S_ROOT>USERDEFINED_optional_run</DOUT_S_ROOT>               <!-- complete path to a short term archiving directory -->
        <DOUT_L_MSROOT>USERDEFINED_optional_run</DOUT_L_MSROOT>           <!-- complete path to a long term archiving directory -->
        <CCSM_BASELINE>USERDEFINED_optional_run</CCSM_BASELINE>           <!-- where the cesm testing scripts write and read baseline results -->
        <CCSM_CPRNC>USERDEFINED_optional_test</CCSM_CPRNC>                <!-- path to the cprnc tool used to compare netcdf history files in testing -->
        <BATCHQUERY>USERDEFINED_optional_run</BATCHQUERY>
        <BATCHSUBMIT>USERDEFINED_optional_run</BATCHSUBMIT>
        <SUPPORTED_BY>USERDEFINED_optional</SUPPORTED_BY>
        <GMAKE_J>1</GMAKE_J>
        <MAX_TASKS_PER_NODE>USERDEFINED_required_build</MAX_TASKS_PER_NODE>
</machine>

Dan had written a custom setting for this to work on the VM, so I'll double check with him if I edited things correctly.

The grep: write error seems to always show up, even when I got CLM on the VM. I'll look into it briefly, but I think the machine settings need to be looked at closer.

[tonygardella]

I've copied and transferred the run that succeeded on the VM to the pecan2 and geo servers. The path on pecan2: /fs/data5/pecan.models/clm45/clm45.VM.version The path on geo: /projectnb/dietzelab/pecan.models/clm45/clm45.VM.version

[tonygardella]

Checklist for getting a ref_case onto BU servers:

• [ ] create_newcase -case pecan -compset ICLM45BGC -res f45_g37 -mach yellowstone -c
• [ ] ./case.setup
• [ ] ./case.build

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