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Porting of master (120) to lawrencium LR2 partition. #2

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Porting of master (120) to lawrencium LR2 partition. #2

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fc94f00
Porting of master (120) to lawrencium LR2 partition. Minor bug fix in…
Jan 11, 2016
4116012
Updates and fixes, porting to Lawrencium LR2
rgknox Jan 12, 2016
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9 changes: 9 additions & 0 deletions cime/machines/config_batch.xml
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Expand Up @@ -94,6 +94,15 @@
</directives>
</batch_system>

<batch_system MACH="lawrencium-lr2" version="x.y">
<directives>
<directive>--partition=lr2</directive>
<directive>--account={{ project }}</directive>
<directive>--exclusive</directive>
</directives>
</batch_system>


<!-- edison is PBS -->
<batch_system MACH="edison" version="x.y">
<directives>
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6 changes: 6 additions & 0 deletions cime/machines/config_compilers.xml
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Expand Up @@ -475,6 +475,12 @@ for mct, etc.
<ADD_GPTL_CPPDEFS> -DHAVE_PAPI </ADD_GPTL_CPPDEFS>
</compiler>

<compiler COMPILER="intel" MACH="lawrencium-lr2">
<ADD_SLIBS> -lnetcdff -lnetcdf -mkl</ADD_SLIBS>
<GPTL_CPPDEFS> -DHAVE_VPRINTF -DHAVE_GETTIMEOFDAY </GPTL_CPPDEFS>
</compiler>


<compiler COMPILER="gnu" MACH="yellowstone">
<LAPACK_LIBDIR> /glade/apps/opt/lib </LAPACK_LIBDIR>
<PIO_TYPENAME>netcdf</PIO_TYPENAME>
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66 changes: 66 additions & 0 deletions cime/machines/config_machines.xml
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Expand Up @@ -305,6 +305,72 @@
</mpirun>
</machine>

<machine MACH="lawrencium-lr2">
<DESC>Lawrencium LR2 cluster at LBL, OS is Linux (intel), batch system is SLURM</DESC>
<OS>LINUX</OS>
<COMPILERS>intel</COMPILERS>
<MPILIBS>openmpi,mpi-serial</MPILIBS>
<CESMSCRATCHROOT>/global/scratch/$ENV{USER}</CESMSCRATCHROOT>
<RUNDIR>$CESMSCRATCHROOT/$CASE/run</RUNDIR>
<EXEROOT>$CESMSCRATCHROOT/$CASE/bld</EXEROOT>
<DIN_LOC_ROOT>/global/scratch/$ENV{USER}/cesm_input_datasets/</DIN_LOC_ROOT>
<DIN_LOC_ROOT_CLMFORC>/global/scratch/$ENV{USER}/cesm_input_datasets/atm/datm7</DIN_LOC_ROOT_CLMFORC>
<DOUT_S_ROOT>$CESMSCRATCHROOT/cesm_archive/$CASE</DOUT_S_ROOT>
<DOUT_L_MSROOT>csm/$CASE</DOUT_L_MSROOT>
<CCSM_BASELINE>$CESMSCRATCHROOT/cesm_baselines</CCSM_BASELINE>
<CCSM_CPRNC>/$CESMSCRATCHROOT/cesm_tools/cprnc/cprnc</CCSM_CPRNC>
<BATCHQUERY>squeue</BATCHQUERY>
<BATCHREDIRECT></BATCHREDIRECT>
<BATCHSUBMIT>sbatch</BATCHSUBMIT>
<SUPPORTED_BY>jnjohnson at lbl dot gov and rgknox at same</SUPPORTED_BY>
<GMAKE_J>12</GMAKE_J>
<MAX_TASKS_PER_NODE>12</MAX_TASKS_PER_NODE>
<PROJECT_REQUIRED>TRUE</PROJECT_REQUIRED>
<batch_system type="slurm" version="2.0">
<queues>
<queue walltimemin="0" walltimemax="72:00:00" jobmin="0" jobmax="64" default="true">lr_normal</queue>
</queues>
<walltimes>
<walltime default="true">00:59:00</walltime>
</walltimes>
</batch_system>
<mpirun mpilib="mpi-serial">
<executable>mpirun</executable>
<arguments>
<arg name="num_tasks">-np {{ num_tasks }}</arg>
<arg name="tasks_per_node"> -npernode {{ tasks_per_node }}</arg>
</arguments>
</mpirun>
<mpirun mpilib="default">
<executable>mpirun</executable>
<arguments>
<arg name="num_tasks">-np {{ num_tasks }}</arg>
<arg name="tasks_per_node"> -npernode {{ tasks_per_node }}</arg>
</arguments>
</mpirun>
<!-- <module_system type="module">
<init_path lang="sh">/etc/profile.d/modules.sh</init_path>
<init_path lang="csh">/etc/profile.d/modules.csh</init_path>
<init_path lang="perl">/usr/Modules/init/perl.pm</init_path>
<cmd_path lang="sh">module</cmd_path>
<cmd_path lang="csh">module</cmd_path>
<cmd_path lang="perl">/usr/Modules/bin/modulecmd perl</cmd_path>
<modules>
<command name="purge"/>
<command name="load">cmake</command>
<command name="load">perl xml-libxml switch</command>
</modules>
<modules compiler="intel">
<command name="load">intel/2015.0.090</command>
<command name="load">openmpi</command>
<command name="load">mkl</command>
<command name="load">netcdf/4.3.2-intel-p</command>
</modules>
</module_system> -->
</machine>



<machine MACH="edison">
<DESC>NERSC XC30, os is CNL, 24 pes/node, batch system is PBS</DESC>
<COMPILERS>intel,gnu,cray</COMPILERS>
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37 changes: 37 additions & 0 deletions cime/machines/env_mach_specific.lawrencium-lr2
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@@ -0,0 +1,37 @@
#! /bin/csh -f

set CESM_REPO = `./xmlquery CCSM_REPOTAG -value`
if($status == 0) then
set COMPILER = `./xmlquery COMPILER -value`
set MPILIB = `./xmlquery MPILIB -value`
set DEBUG = `./xmlquery DEBUG -value`
set OS = `./xmlquery OS -value`
set PROFILE_PAPI_ENABLE = `./xmlquery PROFILE_PAPI_ENABLE -value`
set PROJECT = `./xmlquery PROJECT -value`
else
echo $0 using settings from environment:
endif
echo "COMPILER=$COMPILER"
echo "MPILIB=$MPILIB"
echo "DEBUG=$DEBUG"
echo "OS=$OS"
echo "PROJECT=$PROJECT"

source /etc/profile.d/modules.csh
module purge
module load cmake
module load perl xml-libxml switch

if ( $COMPILER == "intel" ) then
module load intel/2015.0.090
module load openmpi
module load netcdf/4.3.2-intel-p
module load mkl
endif

setenv NETCDF_PATH $NETCDF_DIR
#-------------------------------------------------------------------------------

limit coredumpsize 1000000
limit stacksize unlimited

2 changes: 1 addition & 1 deletion components/clm/src/ED/biogeochem/EDGrowthFunctionsMod.F90
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Expand Up @@ -140,7 +140,7 @@ real(r8) function tree_lai( cohort_in )

if( cohort_in%status_coh == 2 ) then ! are the leaves on?
slat = 1000.0_r8 * pftcon%slatop(cohort_in%pft) ! m2/g to m2/kg
cohort_in%c_area = c_area(cohort_in) ! call the tree area
cohort_in%c_area = c_area(cohort_in) ! call the tree area
leafc_per_unitarea = cohort_in%bl/(cohort_in%c_area/cohort_in%n) !KgC/m2
if(leafc_per_unitarea > 0.0_r8)then
tree_lai = leafc_per_unitarea * slat !kg/m2 * m2/kg = unitless LAI
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4 changes: 4 additions & 0 deletions components/clm/src/ED/main/EDInitMod.F90
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Expand Up @@ -335,6 +335,8 @@ subroutine init_cohorts( patch_in )

do pft = 1,numpft_ed !FIX(RF,032414) - turning off veg dynamics

if(EDecophyscon%initd(pft)>1.0E-7) then

allocate(temp_cohort) ! temporary cohort

temp_cohort%pft = pft
Expand Down Expand Up @@ -378,6 +380,8 @@ subroutine init_cohorts( patch_in )

deallocate(temp_cohort) ! get rid of temporary cohort

endif

enddo !numpft

call fuse_cohorts(patch_in)
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2 changes: 1 addition & 1 deletion components/clm/src/ED/main/EDTypesMod.F90
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Expand Up @@ -34,7 +34,7 @@ module EDTypesMod
integer , parameter :: SENES = 10 ! Window of time over which we track temp for cold sensecence (days)
real(r8), parameter :: DINC_ED = 1.0_r8 ! size of LAI bins.
integer , parameter :: N_DIST_TYPES = 2 ! number of disturbance types (mortality, fire)
integer , parameter :: numpft_ed = 2 ! number of PFTs used in ED.
integer , parameter :: numpft_ed = 10 ! number of PFTs used in ED.

! SPITFIRE
integer , parameter :: NLSC = 5 ! number carbon compartments in above ground litter array
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