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Merge wolf and conejo changes, commit '19fe5678', into andre-ed-clm-16x
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conflict in BatchUtils.pm

Test suite: ed - yellowstone gnu, intel, pgi
Test baseline: none
Test status: all tests pass
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@bandre-ucar
bandre-ucar committed Jun 23, 2016
2 parents 09ae271 + 19fe567 commit 6cd649e
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Showing 7 changed files with 227 additions and 6 deletions.
43 changes: 42 additions & 1 deletion cime/cime_config/cesm/machines/config_batch.xml
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Expand Up @@ -22,8 +22,33 @@
<directive name=""></directive>
</directives>
</batch_system>

<batch_system type="none" version="x.y">
<batch_query args=""></batch_query>
<batch_submit></batch_submit>
<batch_redirect></batch_redirect>
<batch_directive></batch_directive>
<directives>
<directive name=""></directive>
</directives>
</batch_system>

<batch_system MACH="wolf" version="x.y">
<batch_directive>#MSUB</batch_directive>
<directives>
<directive>-l nodes={{ num_nodes }}:ppn={{ tasks_per_node }}</directive>
</directives>
</batch_system>

<batch_system MACH="conejo" version="x.y">
<batch_directive>#MSUB</batch_directive>
<directives>
<directive>-l nodes={{ num_nodes }}:ppn={{ tasks_per_node }}</directive>
</directives>
</batch_system>


<batch_system type="cobalt" version="x.y">
<batch_system type="cobalt" version="x.y">
<batch_query>qstat</batch_query>
<batch_submit>bash</batch_submit>
<batch_directive></batch_directive>
Expand All @@ -38,6 +63,22 @@
<arg flag="--mode script"/>
</submit_args>
</batch_system>

<batch_system type="moab" version="x.y">
<batch_query>showq</batch_query>
<batch_submit>msub </batch_submit>
<batch_directive>#MSUB</batch_directive>
<jobid_pattern>(\d+)$</jobid_pattern>
<depend_string> -W depend=afterok:jobid</depend_string>
<directives>
<directive> -N {{ job_id }}</directive>
<directive> -l walltime={{ wall_time }}</directive>
<directive> -j oe </directive>
<directive default="n"> -r {{ rerunnable }} </directive>
<directive default="ae" > -m {{ mail_options }} </directive>
<directive default="/bin/bash" > -S {{ shell }}</directive>
</directives>
</batch_system>

<batch_system type="lsf" version="9.1">
<batch_query args=" -w" >bjobs</batch_query>
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64 changes: 64 additions & 0 deletions cime/cime_config/cesm/machines/config_compilers.xml
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Expand Up @@ -302,6 +302,70 @@ for mct, etc.
<ADD_FFLAGS MPILIB="mpi-serial"> -mcmodel medium </ADD_FFLAGS>
</compiler>

<compiler MACH="conejo" COMPILER="intel">
<MPICC>mpicc</MPICC>
<MPIFC>mpif90</MPIFC>
<MPICXX>mpic++</MPICXX>
<SFC>ifort</SFC>
<SCC>icc</SCC>
<SCXX>icpc</SCXX>
<ADD_SLIBS>$(shell $(NETCDF_PATH)/bin/nf-config --flibs) -llapack -lblas</ADD_SLIBS>
<GPTL_CPPDEFS> -DHAVE_VPRINTF -DHAVE_GETTIMEOFDAY </GPTL_CPPDEFS>
<TRILINOS_PATH>$(TRILINOS_PATH)</TRILINOS_PATH>
<ADD_SLIBS MPILIB="mpich"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="mpich2"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="mpt"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="openmpi"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="mvapich"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="impi"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="mpi-serial"> -mkl </ADD_SLIBS>
</compiler>

<compiler MACH="conejo" COMPILER="gnu">
<MPICC>mpicc</MPICC>
<MPIFC>mpif90</MPIFC>
<MPICXX>mpic++</MPICXX>
<SFC>gfortran</SFC>
<SCC>gcc</SCC>
<SCXX>g++</SCXX>
<ADD_SLIBS>$(shell $(NETCDF_PATH)/bin/nf-config --flibs) -llapack -lblas</ADD_SLIBS>
<CXX_LIBS>-lstdc++ -lmpi_cxx</CXX_LIBS>
<TRILINOS_PATH>$(TRILINOS_PATH)</TRILINOS_PATH>
<ALBANY_PATH>$(ALBANY_PATH)</ALBANY_PATH>
</compiler>

<compiler MACH="wolf" COMPILER="intel">
<MPICC>mpicc</MPICC>
<MPIFC>mpif90</MPIFC>
<MPICXX>mpic++</MPICXX>
<SFC>ifort</SFC>
<SCC>icc</SCC>
<SCXX>icpc</SCXX>
<ADD_SLIBS>$(shell $(NETCDF_PATH)/bin/nf-config --flibs) -llapack -lblas</ADD_SLIBS>
<TRILINOS_PATH>$(TRILINOS_PATH)</TRILINOS_PATH>
<ADD_SLIBS MPILIB="mpich"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="mpich2"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="mpt"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="openmpi"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="mvapich"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="impi"> -mkl=cluster </ADD_SLIBS>
<ADD_SLIBS MPILIB="mpi-serial"> -mkl </ADD_SLIBS>
</compiler>

<compiler MACH="wolf" COMPILER="gnu">
<MPICC>mpicc</MPICC>
<MPIFC>mpif90</MPIFC>
<MPICXX>mpic++</MPICXX>
<SFC>gfortran</SFC>
<SCC>gcc</SCC>
<SCXX>g++</SCXX>
<ADD_SLIBS>$(shell $(NETCDF_PATH)/bin/nf-config --flibs) -llapack -lblas</ADD_SLIBS>
<CXX_LIBS>-lstdc++ -lmpi_cxx</CXX_LIBS>
<TRILINOS_PATH>$(TRILINOS_PATH)</TRILINOS_PATH>
<ALBANY_PATH>$(ALBANY_PATH)</ALBANY_PATH>
</compiler>


<compiler COMPILER="intelmic">
<!-- http://software.intel.com/en-us/articles/intel-composer-xe/ -->
<ADD_CPPDEFS> -DFORTRANUNDERSCORE -DNO_R16</ADD_CPPDEFS>
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7 changes: 6 additions & 1 deletion cime/utils/perl5lib/Batch/BatchUtils.pm
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Expand Up @@ -212,7 +212,12 @@ sub submitSingleJob()

eval {
open (my $RUN, "-|", $runcmd) or $logger->logdie ("job submission failed, $!");
$output = <$RUN>;
#X# $output = <$RUN>;
foreach (<$RUN>) {
chomp;
print "$_\n";
$output .= $_;
}
close $RUN or $logger->logdie( "job submission failed: |$?|, |$!|");
};
my $exitstatus = ($?>>8);
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104 changes: 104 additions & 0 deletions cime/utils/perl5lib/t/mocks_ModuleLoader/config_machines.xml
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Expand Up @@ -91,6 +91,110 @@
<MAX_TASKS_PER_NODE>USERDEFINED_required_build</MAX_TASKS_PER_NODE>
</machine>

<machine MACH="wolf">
<DESC>LANL Linux Cluster, 16 pes/node, batch system Moab</DESC>
<NODENAME_REGEX>wolf</NODENAME_REGEX>
<TESTS>acme_developer</TESTS>
<COMPILERS>intel,gnu</COMPILERS>
<MPILIBS>openmpi,mvapich,mpi-serial</MPILIBS>
<OS>LINUX</OS>
<RUNDIR>/lustre/scratch1/turquoise/$ENV{USER}/ACME/cases/$CASE/run</RUNDIR>
<EXEROOT>/lustre/scratch1/turquoise/$ENV{USER}/ACME/cases/$CASE/bld</EXEROOT>
<DIN_LOC_ROOT>/lustre/scratch1/turquoise/$ENV{USER}/ACME/input_data</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/lustre/scratch1/turquoise/$ENV{USER}/ACME/input_data/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>/lustre/scratch1/turquoise/$ENV{USER}/ACME/archive/$CASE</DOUT_S_ROOT>
<DOUT_L_MSROOT>UNSET</DOUT_L_MSROOT>
<CCSM_BASELINE>/lustre/scratch1/turquoise/$ENV{USER}/ACME/input_data/ccsm_baselines</CCSM_BASELINE>
<CESMSCRATCHROOT>/lustre/scratch1/turquoise/$ENV{USER}/ACME</CESMSCRATCHROOT>
<CCSM_CPRNC>/turquoise/usr/projects/climate/SHARED_CLIMATE/software/wolf/cprnc/v0.40/cprnc</CCSM_CPRNC>
<BATCHQUERY>mshow</BATCHQUERY>
<BATCHSUBMIT>msub</BATCHSUBMIT>
<BATCHREDIRECT></BATCHREDIRECT>
<batch_system type="moab" version="x.y">
<walltimes>
<walltime default="true">00:30:00</walltime>
<walltime ccsm_estcost="1">00:30:00</walltime>
<walltime ccsm_estcost="3">00:30:00</walltime>
</walltimes>
</batch_system>
<mpirun mpilib="default">
<executable>mpirun</executable>
<arguments>
<arg name="num_tasks"> -n {{ num_tasks }}</arg>
</arguments>
</mpirun>
<mpirun mpilib="openmpi">
<executable>mpirun</executable>
<arguments>
<arg name="num_tasks"> -n {{ num_tasks }}</arg>
</arguments>
</mpirun>
<mpirun mpilib="mvapich">
<executable>srun</executable>
<arguments>
<arg name="num_tasks"> -n {{ num_tasks }}</arg>
</arguments>
</mpirun>
<mpirun mpilib="mpi-serial">
<executable></executable>
</mpirun>
<GMAKE_J>4</GMAKE_J>
<MAX_TASKS_PER_NODE>16</MAX_TASKS_PER_NODE>
<SUPPORTED_BY>jacobsen.douglas -at- gmail.com</SUPPORTED_BY>
</machine>

<machine MACH="conejo">
<DESC>LANL Linux Cluster, 8 pes/node, batch system Moab</DESC>
<COMPILERS>intel,gnu</COMPILERS>
<MPILIBS>openmpi,mvapich,mpi-serial</MPILIBS>
<OS>LINUX</OS>
<RUNDIR>/lustre/scratch1/turquoise/$ENV{USER}/ACME/cases/$CASE/run</RUNDIR>
<EXEROOT>/lustre/scratch1/turquoise/$ENV{USER}/ACME/cases/$CASE/bld</EXEROOT>
<DIN_LOC_ROOT>/usr/projects/cesm/input_data</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/usr/projects/cesm/input_data/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>/lustre/scratch1/turquoise/$ENV{USER}/ACME/archive/$CASE</DOUT_S_ROOT>
<DOUT_L_MSROOT>UNSET</DOUT_L_MSROOT>
<CCSM_BASELINE>/usr/projects/cesm/input_data/ccsm_baselines</CCSM_BASELINE>
<CESMSCRATCHROOT>/lustre/scratch1/turquoise/$ENV{USER}/ACME</CESMSCRATCHROOT>
<CCSM_CPRNC>/turquoise/usr/projects/climate/SHARED_CLIMATE/software/wolf/cprnc/v0.40/cprnc</CCSM_CPRNC>
<BATCHQUERY>mshow</BATCHQUERY>
<BATCHSUBMIT>msub</BATCHSUBMIT>
<BATCHREDIRECT></BATCHREDIRECT>
<batch_system type="moab" version="x.y">
<walltimes>
<walltime default="true">00:30:00</walltime>
<walltime ccsm_estcost="1">00:30:00</walltime>
<walltime ccsm_estcost="3">00:30:00</walltime>
</walltimes>
</batch_system>
<mpirun mpilib="default">
<executable>mpirun</executable>
<arguments>
<arg name="num_tasks"> -n {{ num_tasks }}</arg>
</arguments>
</mpirun>
<mpirun mpilib="openmpi">
<executable>mpirun</executable>
<arguments>
<arg name="num_tasks"> -n {{ num_tasks }}</arg>
</arguments>
</mpirun>
<mpirun mpilib="mvapich">
<executable>srun</executable>
<arguments>
<arg name="num_tasks"> -n {{ num_tasks }}</arg>
</arguments>
</mpirun>
<mpirun mpilib="mpi-serial">
<executable></executable>
</mpirun>
<GMAKE_J>4</GMAKE_J>
<MAX_TASKS_PER_NODE>8</MAX_TASKS_PER_NODE>
<SUPPORTED_BY>jacobsen.douglas -at- gmail.com</SUPPORTED_BY>
</machine>



<machine MACH="babbage">
<DESC>NERSC , 16 pes/node, batch system is PBS</DESC>
<OS>LINUX</OS>
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6 changes: 4 additions & 2 deletions components/clm/src/ED/biogeochem/EDGrowthFunctionsMod.F90
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Expand Up @@ -350,8 +350,10 @@ subroutine mortality_rates( cohort_in,cmort,hmort,bmort )
real(r8) :: frac ! relativised stored carbohydrate

! 'Background' mortality (can vary as a function of density as in ED1.0 and ED2.0, but doesn't here for tractability)
bmort = 0.014_r8

! bmort = EDecophyscon%b_mort(cohort_in%pft) !0.014_r8
! RGK:/CX HOLDING OFF ON SENS-ANALYSIS UNTIL MACHINE CONFIGS SQUARED AWAY
bmort = 0.014_r8

! Proxy for hydraulic failure induced mortality.
if(cohort_in%patchptr%btran_ft(cohort_in%pft) <= 0.000001_r8)then
hmort = ED_val_stress_mort
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4 changes: 2 additions & 2 deletions components/clm/src/ED/biogeochem/EDPhysiologyMod.F90
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Expand Up @@ -309,13 +309,13 @@ subroutine phenology( currentSite, ed_phenology_inst, temperature_inst, watersta
a = -68.0_r8
b = 638.0_r8
c = -0.001_r8
coldday = 5.0_r8
coldday = 5.0_r8 !ed_ph_chiltemp

mindayson = 30

!Parameters from SDGVM model of senesence
ncolddayslim = 5
cold_t = 7.5_r8
cold_t = 7.5_r8 ! ed_ph_coldtemp

t = udata%time_period
temp_in_C = t_veg24(currentSite%oldest_patch%clm_pno-1) - tfrz
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5 changes: 5 additions & 0 deletions components/clm/src/ED/main/EDPftvarcon.F90
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Expand Up @@ -38,6 +38,7 @@ module EDPftvarcon
real(r8) :: clone_alloc (0:mxpft) ! fraction of carbon balance allocated to clonal reproduction.
real(r8) :: seed_alloc (0:mxpft) ! fraction of carbon balance allocated to seeds.
real(r8) :: sapwood_ratio (0:mxpft) ! amount of sapwood per unit leaf carbon and m of height. gC/gC/m
real(r8) :: dbh2h_m (0:mxpft) ! allocation parameter m from dbh to height
end type EDPftvarcon_type

type(EDPftvarcon_type), public :: EDPftvarcon_inst
Expand Down Expand Up @@ -131,6 +132,10 @@ subroutine EDpftconrd( ncid )

call ncd_io('sapwood_ratio',EDPftvarcon_inst%sapwood_ratio, 'read', ncid, readvar=readv)
if ( .not. readv) call endrun(trim(subname)// ' ERROR : error in reading in pft data')

! HOLDING ON SEW ENSITIVITY-ANALYSIS PARAMETERS UNTIL MACHINE CONFIGS SET RGK/CX
! call ncd_io('dbh2h_m',EDPftvarcon_inst%dbh2h_m, 'read', ncid, readvar=readv)
! if ( .not. readv) call endrun(trim(subname)// ' ERROR : error in reading in pft data')

end subroutine EDpftconrd

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