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--- noresm:noresm1-m_for_external_users [2017-08-23 14:11:28]
ingo.bethke@gmail.com [Installing]
+++ noresm:noresm1-m_for_external_users [2022-05-31 09:29:32] (current)
@@ Line 1: / Line 1: @@
+====== NorESM1-M for external users ======
+----
 ===== Access =====
-To request model access, please send a request to **noresm-ncc@met.no** with some background information on how you plan to use the model.
+To request model access, please send a request to //noresm-ncc@met.no// with some background information on how you plan to use the model.
@@ Line 7: / Line 10: @@
 ===== Installing =====
-Untar **NorESM1-M_sourceCode_vXXX.tar.zg** in your home directory. This will install the model source code in the folder **$HOME/NorESM1-M**.
+Untar //NorESM1-M_sourceCode_vXXX.tar.zg// in your home directory. This will install the model source code in the folder //$HOME/NorESM1-M//.
-Untar **NorESM1-M_inputdata_vXXX.tar.zg** to a folder that is available during run-time and has at least 70 GB of free space. This will create a sub-folder inputdata and install NorESM's forcing data and other boundary conditions to it.
+Untar //NorESM1-M_inputdata_vXXX.tar.zg// to a folder that is available during run-time and has at least 70 GB of free space. This will create a sub-folder inputdata and install NorESM's forcing data and other boundary conditions to it.
-Untar **NorESM1-M_initialPiHist1_vXXX.tar.zg** to a folder that is available during run-time and has at least 2 GB of free space. This will install restart conditions for the CMIP5 PiControl and first member of historical experiment.
+Untar //NorESM1-M_initialPiHist1_vXXX.tar.zg// to a folder that is available during run-time and has at least 2 GB of free space. This will install restart conditions for the CMIP5 PiControl and first member of historical experiment.
 ----
 ===== Porting =====
-==== NorESM1-M/scripts/ccsm_utils/Machines/config_machines.xml ====
+==== Machine name and characteristics ====
+Define the characteristics of your HPC system in //NorESM1-M/scripts/ccsm_utils/Machines/config_machines.xml//.
+Edit following section:
+<code>
+<machine MACH="vilje"
+         DESC="NTNU, Trondheim, 16 pes/node, batch system is PBS"
+         EXEROOT="/work/$CCSMUSER/noresm/$CASE"
+         OBJROOT="$EXEROOT"
+         INCROOT="$EXEROOT/lib/include"
+         DIN_LOC_ROOT_CSMDATA="/work/shared/noresm/inputdata"
+         DIN_LOC_ROOT_CLMQIAN="UNSET"
+         DOUT_S_ROOT="/work/$CCSMUSER/archive/$CASE"
+         DOUT_L_HTAR="FALSE"
+         DOUT_L_MSROOT="/norstore/project/norclim/noresm/cases/$CASE"
+         DOUT_L_MSHOST="norstore-trd-app0.hpc.ntnu.no"
+         CCSM_BASELINE="UNSET"
+         CCSM_CPRNC="UNSET"
+         OS="CNL"
+         BATCHQUERY="qstat -f"
+         BATCHSUBMIT="qsub"
+         GMAKE_J="4"
+         MAX_TASKS_PER_NODE="16"
+         MPISERIAL_SUPPORT="FALSE" />
+</code>
+Set //MACH// to an acronym/name tag of your choice of your HPC system. Update //DESC// correspondingly.
+Set //EXEROOT// to the root location where the model should create the build and run-directories. The model will replace //$CCSMUSER// with your unix user and //$CASE// with the specific case name (=simulation/experiment name).
+Set //DIN_LOC_ROOT_CSMDATA// to the location where you installed the forcing and boundary condition data (this path should end with "/inputdata").
+Set //DOUT_S_ROOT// to the root location for the short-term archiving (normally on the work disk area of the HPC system).
+Optionally, set //DOUT_L_MSROOT// to the root location for the long-term archiving (normally a location that is not subject to automatic deletion). Leave unchanged if you don't plan to use automatic long-term archiving (e.g., if you want to move the data manually).
+Optionally, set //DOUT_L_MSHOST// to the name of the (remote)-server for long-term archiving. Leave unchanged if you don't plan to use automatic long-term archiving
+Set //BATCHSUBMIT// to the submit command on your HPC system.
+Set //GMAKE_J// to the number of make instances run in parallel when building the system. Set to 1 if licence or memory issues occur.
+Set //MAX_TASKS_PER_NODE// to the maximum number of MPI tasks that can run on a single node on your HPC system (usually the same as the number of cores per node).
+==== CPU configurations ====
+Define NorESM1-M CPU-configurations for your HPC system in //NorESM1-M/scripts/ccsm_utils/Machines/config_pes.xml//.
+As a start, we recommend to simply replace all instances of //vilje// with your choice for //MACH// (i.e. the name tag of your machine).
+==== Building and runtime options ====
+Copy //env_machopts.vilje// to //env_machopts.$MACH// where //$MACH// has to be replaced with the name of your machine.
+Edit settings as necessary. The settings should make compilers, libraries, queuing system commands ect. available during building and model execution. You will likely have to remove/replace all module specifications, while the runtime environment settings should work for most systems.
+==== Compiler and linker options ====
+Copy //Macros.vilje// to //Macros.$MACH// if your compiler is intel. If your compiler is pgi, then instead use //Macros.hexagon// as template.
+Following lines need to be customised:
+<code>
+FC            := FORTRAN COMPILER COMMAND
+CC            := FORTRAN COMPILER COMMAND
+NETCDF_PATH   := ROOT PATH FOR NETCDF LIBRARY
+MPI_ROOT      := ROOT PATH FOR MPI LIBRARY
+INC_NETCDF    := $(NETCDF_PATH)/include
+LIB_NETCDF    := $(NETCDF_PATH)/lib
+MOD_NETCDF    := $(NETCDF_PATH)/include
+INC_MPI       := $(MPI_ROOT)/include
+LIB_MPI       := $(MPI_ROOT)/lib
+</code>
+==== Batch/queuing system rules ====
+Copy //mkbatch.vilje// to //mkbatch.$MACH//.
+Change as necessary the settings for //mach//, //group_id//, //mppsize//, //mppnodes//, etc.
+Replace the line ''mpiexec_mpt -stats -n $mpptotal omplace -nt ${maxthrds} ./ccsm.exe >&! ccsm.log.\$LID'' with the submit command and appropriate options for your HPC system.
+----
+===== Testing =====
+We suggest to test the installation by running a pre-industrial spin-up experiment that is configured as 'start-up' simulation (i.e. uses idealised conditions and observational climatologies as initial conditions).
+Change directory to //$HOME/NorESM1-M/scripts//.
+Set up pre-industrial spin-up simulation with
+''./create_newcase -case ../cases/NorESM1-M_PI_spinup -compset NAER1850CN -res f19_g16 -mach $MACH -pecount S''
+where //$MACH// is the name tag of your machine.
+Change directory to //../cases/NorESM1-M_PI_spinup//
+Run ''.configure -case'' to set up simulation.
+Run ''./NorESM1-M_PI_spinup.$MACH.build'' to stage namelists in run directory and build model code.
-==== NorESM1-M/scripts/ccsm_utils/Machines/config_pes.xml ====
+Submit run-script //./NorESM1-M_PI_spinup.$MACH.run// (use appropriate submit command for your HPC system, e.g. qsub).
+If the test was successful then the model should run for 5 days and write our restart conditions at the beginning of the 6th day. The location of the run directory is specified via EXEROOT in config_machines.xml (see section Porting).
+===== Resources =====
+  * [[noresm:runmodel:newbie|Quickstart for running NorESM1]]
+  * [[noresm:runmodel:advanced|Advanced options for running NorESM1]]
+  * [[http://www.teriin.org/projects/nfa/pdf/Working_paper7.pdf|Porting of NorESM1 to TERI (India)]]