diff --git a/cime/cime_config/cesm/machines/config_batch.xml b/cime/cime_config/cesm/machines/config_batch.xml index 7201b3ce98..c9597f3796 100644 --- a/cime/cime_config/cesm/machines/config_batch.xml +++ b/cime/cime_config/cesm/machines/config_batch.xml @@ -22,8 +22,33 @@ + + + + + + + + + + + + + #MSUB + + -l nodes={{ num_nodes }}:ppn={{ tasks_per_node }} + + + + + #MSUB + + -l nodes={{ num_nodes }}:ppn={{ tasks_per_node }} + + + - + qstat bash @@ -38,6 +63,22 @@ + + + showq + msub + #MSUB + (\d+)$ + -W depend=afterok:jobid + + -N {{ job_id }} + -l walltime={{ wall_time }} + -j oe + -r {{ rerunnable }} + -m {{ mail_options }} + -S {{ shell }} + + bjobs diff --git a/cime/cime_config/cesm/machines/config_compilers.xml b/cime/cime_config/cesm/machines/config_compilers.xml index a6096e1c24..4068571580 100644 --- a/cime/cime_config/cesm/machines/config_compilers.xml +++ b/cime/cime_config/cesm/machines/config_compilers.xml @@ -302,6 +302,70 @@ for mct, etc. -mcmodel medium + + mpicc + mpif90 + mpic++ + ifort + icc + icpc + $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -llapack -lblas + -DHAVE_VPRINTF -DHAVE_GETTIMEOFDAY + $(TRILINOS_PATH) + -mkl=cluster + -mkl=cluster + -mkl=cluster + -mkl=cluster + -mkl=cluster + -mkl=cluster + -mkl + + + + mpicc + mpif90 + mpic++ + gfortran + gcc + g++ + $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -llapack -lblas + -lstdc++ -lmpi_cxx + $(TRILINOS_PATH) + $(ALBANY_PATH) + + + + mpicc + mpif90 + mpic++ + ifort + icc + icpc + $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -llapack -lblas + $(TRILINOS_PATH) + -mkl=cluster + -mkl=cluster + -mkl=cluster + -mkl=cluster + -mkl=cluster + -mkl=cluster + -mkl + + + + mpicc + mpif90 + mpic++ + gfortran + gcc + g++ + $(shell $(NETCDF_PATH)/bin/nf-config --flibs) -llapack -lblas + -lstdc++ -lmpi_cxx + $(TRILINOS_PATH) + $(ALBANY_PATH) + + + -DFORTRANUNDERSCORE -DNO_R16 diff --git a/cime/utils/perl5lib/Batch/BatchUtils.pm b/cime/utils/perl5lib/Batch/BatchUtils.pm index eb728059ff..d8f8c52bd9 100755 --- a/cime/utils/perl5lib/Batch/BatchUtils.pm +++ b/cime/utils/perl5lib/Batch/BatchUtils.pm @@ -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); diff --git a/cime/utils/perl5lib/t/mocks_ModuleLoader/config_machines.xml b/cime/utils/perl5lib/t/mocks_ModuleLoader/config_machines.xml index 81f1298b61..d85ba3ba4b 100644 --- a/cime/utils/perl5lib/t/mocks_ModuleLoader/config_machines.xml +++ b/cime/utils/perl5lib/t/mocks_ModuleLoader/config_machines.xml @@ -91,6 +91,110 @@ USERDEFINED_required_build + + LANL Linux Cluster, 16 pes/node, batch system Moab + wolf + acme_developer + intel,gnu + openmpi,mvapich,mpi-serial + LINUX + /lustre/scratch1/turquoise/$ENV{USER}/ACME/cases/$CASE/run + /lustre/scratch1/turquoise/$ENV{USER}/ACME/cases/$CASE/bld + /lustre/scratch1/turquoise/$ENV{USER}/ACME/input_data + /lustre/scratch1/turquoise/$ENV{USER}/ACME/input_data/atm/datm7 + /lustre/scratch1/turquoise/$ENV{USER}/ACME/archive/$CASE + UNSET + /lustre/scratch1/turquoise/$ENV{USER}/ACME/input_data/ccsm_baselines + /lustre/scratch1/turquoise/$ENV{USER}/ACME + /turquoise/usr/projects/climate/SHARED_CLIMATE/software/wolf/cprnc/v0.40/cprnc + mshow + msub + + + + 00:30:00 + 00:30:00 + 00:30:00 + + + + mpirun + + -n {{ num_tasks }} + + + + mpirun + + -n {{ num_tasks }} + + + + srun + + -n {{ num_tasks }} + + + + + + 4 + 16 + jacobsen.douglas -at- gmail.com + + + + LANL Linux Cluster, 8 pes/node, batch system Moab + intel,gnu + openmpi,mvapich,mpi-serial + LINUX + /lustre/scratch1/turquoise/$ENV{USER}/ACME/cases/$CASE/run + /lustre/scratch1/turquoise/$ENV{USER}/ACME/cases/$CASE/bld + /usr/projects/cesm/input_data + /usr/projects/cesm/input_data/atm/datm7 + /lustre/scratch1/turquoise/$ENV{USER}/ACME/archive/$CASE + UNSET + /usr/projects/cesm/input_data/ccsm_baselines + /lustre/scratch1/turquoise/$ENV{USER}/ACME + /turquoise/usr/projects/climate/SHARED_CLIMATE/software/wolf/cprnc/v0.40/cprnc + mshow + msub + + + + 00:30:00 + 00:30:00 + 00:30:00 + + + + mpirun + + -n {{ num_tasks }} + + + + mpirun + + -n {{ num_tasks }} + + + + srun + + -n {{ num_tasks }} + + + + + + 4 + 8 + jacobsen.douglas -at- gmail.com + + + + NERSC , 16 pes/node, batch system is PBS LINUX diff --git a/components/clm/src/ED/biogeochem/EDGrowthFunctionsMod.F90 b/components/clm/src/ED/biogeochem/EDGrowthFunctionsMod.F90 index 98925f1684..ea3dc4c71a 100755 --- a/components/clm/src/ED/biogeochem/EDGrowthFunctionsMod.F90 +++ b/components/clm/src/ED/biogeochem/EDGrowthFunctionsMod.F90 @@ -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 diff --git a/components/clm/src/ED/biogeochem/EDPhysiologyMod.F90 b/components/clm/src/ED/biogeochem/EDPhysiologyMod.F90 index b949c5fd76..e77e916883 100755 --- a/components/clm/src/ED/biogeochem/EDPhysiologyMod.F90 +++ b/components/clm/src/ED/biogeochem/EDPhysiologyMod.F90 @@ -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 diff --git a/components/clm/src/ED/main/EDPftvarcon.F90 b/components/clm/src/ED/main/EDPftvarcon.F90 index 421828a6ba..475ee7b1bb 100644 --- a/components/clm/src/ED/main/EDPftvarcon.F90 +++ b/components/clm/src/ED/main/EDPftvarcon.F90 @@ -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 @@ -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