Installing CCSM4
Under construction
As a group we have a set of source code located in /project/ccsm on the SciNET GPFS:
Each of the latest versions of the model will have a "_current" at the end of the model version to designate a link to the current subversion being used. These codes have been modified to run on SciNET: Status: Model -------- TCS --------- GPC CCSM3 --------- Yes --------- No CCSM4 --------- Yes --------- Yes CESM1 --------- Yes --------- Yes
If you prefer to install in your own user space directory (e.g. you don't have access to /project/ccsm) you can use the following instructions:
- DOWNLOAD SOURCE CODE AND DATA
Download the source code from http://www.ccsm.ucar.edu/models/ccsm4.0/ The CCSM4.0 User's Guide, available from the CCSM4 web site, gives instructions on getting the input data sets. There is new script check_input_data which checks whether the correct input data sets are available. The build script now calls check_input_data and downloads any missing data sets. Note that this means that the first time the build script is run it must be as an interactive job, not as a batch job, as the compute nodes do not have access to an external network. The directory that holds the input data is set in the variable DIN_LOC_ROOT_CSMDATA in config_machines.xml below.
- CREATE SPECIFIC FILES
In $CCSM4_DIR/scripts/ccsm_utils/Machines create the files Macros.tcs, env_machopts.tcs and mkbatch.tcs by copying the equivalent generic_linux_intel or bluefire (equivalent to TCS) files.
- EDIT Macros.tcs
- EDIT env_machopts.tcs
depending on which modules are loaded on GPC (TCS doesn't need this)
- --- set env variables for Macros if needed
#setenv NETCDF_PATH something setenv NETCDF_PATH something setenv NETCDF_MODS something
- EDIT mkbatch.tcs
You will need the following:
set mach = tcs
(copy and modify from bluefire or appropriate machine type)
setenv OMP_NUM_THREADS ${maxthrds}
#mpiexec -n ${maxtasks} ./ccsm.exe >&! ccsm.log.\$LID
mpirun -np ${maxtasks} ./ccsm.exe >&! ccsm.log.\$LID
The value of vmem will have to adjusted for each job.
- EDIT config_machines.xml
Replace the paths with paths to your own copy of the data and executable. Not all of the above may be necessary for all resolutions and compsets.
Here are the diff files for TCS:
diff --git a/Macros.bluefire b/Macros.tcs index 9643b77..1502c9b 100644 --- a/Macros.bluefire +++ b/Macros.tcs @@ -74,15 +74,15 @@ else
endif LD := $(FC)
-NETCDF_PATH := /usr/local -INC_NETCDF := $(NETCDF_PATH)/include -LIB_NETCDF := $(NETCDF_PATH)/lib -MOD_NETCDF := $(NETCDF_PATH)/include +NETCDF_PATH := $(SCINET_NETCDF_BASE) +INC_NETCDF := $(SCINET_NETCDF_PATH)/include +LIB_NETCDF := $(SCINET_NETCDF_PATH)/lib +MOD_NETCDF := $(SCINET_NETCDF_PATH)/include
INC_MPI := LIB_MPI :=
-PNETCDF_PATH := /contrib/parallel-netcdf-1.1.1svn -LIB_PNETCDF := $(PNETCDF_PATH)/lib +PNETCDF_PATH := $(SCINET_PNETCDF_BASE) +LIB_PNETCDF := $(SCINET_PNETCDF_LIB)
LAPACK_LIBDIR := /usr/local/lib CFLAGS := $(CPPDEFS) -q64 -O2
@@ -94,7 +94,8 @@ FLAGS_OPT := -O2 -qstrict -Q
LDFLAGS := -q64 -bdatapsize:64K -bstackpsize:64K -btextpsize:64K AR := ar MOD_SUFFIX := mod
-CONFIG_SHELL := /usr/local/bin/bash +CONFIG_SHELL := /usr/bin/bash +
#=============================================================================== # Override with user settings
[[File: diff --git a/mkbatch.bluefire b/mkbatch.tcs index c4a8e20..0e71df1 100755 --- a/mkbatch.bluefire +++ b/mkbatch.tcs @@ -1,6 +1,6 @@
#! /bin/tcsh -f
-set mach = bluefire +set mach = tcs
################################################################################# if ($PHASE == set_batch) then
@@ -42,14 +42,7 @@ endif
@ batchpes = ${nodes} * ${PES_PER_NODE}
./xmlchange -file env_mach_pes.xml -id BATCH_PES -val ${batchpes}
-if ($?ACCOUNT) then - set account_name = $ACCOUNT -else - set account_name = `grep -i "^${CCSMUSER}:" /etc/project.ncar | cut -f 1 -d "," | cut -f 2 -d ":" ` - if (-e ~/.ccsm_proj) then - set account_name = `head -1 ~/.ccsm_proj` - endif -endif +set account_name = $USER
if ($?QUEUE) then set queue_name = $QUEUE
@@ -57,7 +50,7 @@ else
set queue_name = regular endif
-set time_limit = "0:50" +set time_limit = "24:00"
if ($CCSM_ESTCOST > 0) set time_limit = "1:50" if ($CCSM_ESTCOST > 1) set time_limit = "4:00"
@@ -66,17 +59,31 @@ cat >! $CASEROOT/${CASE}.${mach}.run << EOF1
#============================================================================== # This is a CCSM coupled model Load Leveler batch job script for $mach #==============================================================================
-#BSUB -n $ntasks_tot -#BSUB -R "span[ptile=${ptile}]" -#BSUB -q ${queue_name} -#BSUB -N -#BSUB -x -#BSUB -a poe -#BSUB -o poe.stdout.%J -#BSUB -e poe.stderr.%J -#BSUB -J $CASE -#BSUB -W ${time_limit} -#BSUB -P ${account_name} +# @ shell = /usr/bin/tcsh +# @ output = poe.stdout.\$(jobid).\$(stepid) +# @ error = poe.stderr.\$(jobid).\$(stepid)
+# @ notification = never +# @ bulkxfer = yes +# @ environment = COPY_ALL +# @ node_usage = not_shared +# @ checkpoint = no +# @ class = verylong +# @ job_type = parallel +# @ job_name = $CASE +# @ wall_clock_limit = ${time_limit} +## @ node = 10 +## @ tasks_per_node = 1 +# @ task_geometry = {$task_geo} +# +## this is necessary in order to avoid core dumps for batch files +## which can cause the system to be overloaded +# ulimits +# @ core_limit = 0 +#===================================== +## necessary to force use of infiniband network for MPI traffic +# @ network.MPI = sn_all,not_shared,US,HIGH +#===================================== +# @ queue
setenv LSB_PJL_TASK_GEOMETRY "{$task_geo}"
setenv BIND_THRD_GEOMETRY "$thrd_geo"
@@ -99,11 +106,8 @@ echo "\`date\` -- CSM EXECUTION BEGINS HERE"
setenv NTHRDS \$BIND_THRD_GEOMETRY setenv MP_LABELIO yes
-if (\$USE_MPISERIAL == "FALSE") then - mpirun.lsf /contrib/bin/ccsm_launch /contrib/bin/job_memusage.exe ./ccsm.exe >&! ccsm.log.\$LID -else - /contrib/bin/job_memusage.exe ./ccsm.exe >&! ccsm.log.\$LID -endif + +/usr/bin/poe /project/ccsm/bin/ccsm_launch ./ccsm.exe >&! ccsm.log.\$LID
wait echo "\`date\` -- CSM EXECUTION HAS FINISHED"
@@ -130,7 +134,7 @@ endif
touch ${CASEROOT}/${CASE}.${mach}.l_archive
chmod 775 ${CASEROOT}/${CASE}.${mach}.l_archive
-set account_name = `grep -i "^${CCSMUSER}:" /etc/project.ncar | cut -f 1 -d "," | cut -f 2 -d ":" ` +set account_name = $USER
if (-e ~/.ccsm_proj) then set account_name = `head -1 ~/.ccsm_proj` endif
]]
[[File: diff --git a/config_machines.xml~ b/config_machines.xml index 97f2829..3b2c70a 100644 --- a/config_machines.xml~ +++ b/config_machines.xml @@ -2,6 +2,68 @@
<config_machines>
+<machine MACH="cryo" + DESC="Guido's i7 desktop (intel), 8 pes" + EXEROOT="/home/$CCSMUSER/cesm/exe/$CASE" + OBJROOT="$EXEROOT" + INCROOT="$EXEROOT/lib/include" + DIN_LOC_ROOT_CSMDATA="/home/guido/cesm/inputdata" + DIN_LOC_ROOT_CLMQIAN="/project/tss/atm_forcing.datm7.Qian.T62.c080727" + DOUT_S_ROOT="/home/$CCSMUSER/cesm/archive/$CASE" + DOUT_L_HTAR="FALSE" + DOUT_L_MSROOT="csm/$CASE" + CCSM_BASELINE="/fs/cgd/csm/ccsm_baselines" + CCSM_CPRNC="/fs/cgd/csm/tools/cprnc_64/cprnc" + OS="Linux" + BATCHQUERY="/usr/local/torque/bin/qstat" + BATCHSUBMIT="/usr/local/torque/bin/qsub" + GMAKE_J="1" + MAX_TASKS_PER_NODE="8" + MPISERIAL_SUPPORT="FALSE" /> + +<machine MACH="tcs" + DESC="U of T IBM p6, os is AIX, 32 pes/node, batch system is Moab/LoadLeveler, testing" + EXEROOT="/scratch/$CCSMUSER/$CASE" + OBJROOT="$EXEROOT" + LIBROOT="$EXEROOT/lib" + INCROOT="$EXEROOT/lib/include" + DIN_LOC_ROOT_CSMDATA="/project/ccsm/inputdata" + DIN_LOC_ROOT_CLMQIAN="/cgd/tss/atm_forcing.datm7.Qian.T62.c080727" + DOUT_S_ROOT="/scratch/$CCSMUSER/archive/$CASE" + DOUT_L_HTAR="TRUE" + DOUT_L_MSROOT="/project/peltier/$CCSMUSER/archive/$CASE" + CCSM_BASELINE="/project/ccsm" + CCSM_CPRNC="/home/guido/bin/cprnc" + OS="AIX" + BATCHQUERY="llq" + BATCHSUBMIT="llsubmit" + GMAKE_J="32" + MAX_TASKS_PER_NODE="64" + MPISERIAL_SUPPORT="TRUE" + PES_PER_NODE="32" /> +
+<machine MACH="gpc" + DESC="U of T iDataPlex intel cluster, os is linux, 8 pes/node, batch system is Moab/Torque, testing" + EXEROOT="/scratch/$CCSMUSER/$CASE" + OBJROOT="$EXEROOT" + LIBROOT="$EXEROOT/lib" + INCROOT="$EXEROOT/lib/include" + DIN_LOC_ROOT_CSMDATA="/project/ccsm/inputdata" + DIN_LOC_ROOT_CLMQIAN="/cgd/tss/atm_forcing.datm7.Qian.T62.c080727" + DOUT_S_ROOT="/scratch/$CCSMUSER/archive/$CASE" + DOUT_L_HTAR="TRUE" + DOUT_L_MSROOT="/project/peltier/$CCSMUSER/archive/$CASE" + CCSM_BASELINE="/project/ccsm" + CCSM_CPRNC="/home/guido/bin/cprnc" + OS="AIX" + BATCHQUERY="/opt/torque/bin/qstat" + BATCHSUBMIT="/opt/torque/bin/qsub" + GMAKE_J="1" + MAX_TASKS_PER_NODE="8" + MPISERIAL_SUPPORT="TRUE" + PES_PER_NODE="8" /> + +
<machine MACH="bluefire"
DESC="NCAR IBM p6, os is AIX, 32 pes/node, batch system is LSF"
EXEROOT="/ptmp/$CCSMUSER/$CASE"
]]