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noresm:noresm1-m_for_external_users [2017-08-23 14:41:49]
ingo.bethke@gmail.com [Porting] 		noresm:noresm1-m_for_external_users [2022-05-31 09:29:32] (current)
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 +====== NorESM1-M for external users ======
 +
 +----
 ===== Access ===== ===== 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. 
  
  
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 ===== Installing ===== ===== 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 ===== ===== Porting =====
  
-==== config_machines.xml ====+==== Machine name and characteristics ====
  
-Define the characteristics of your HPC system in **NorESM1-M/scripts/ccsm_utils/Machines/config_machines.xml**.+Define the characteristics of your HPC system in //NorESM1-M/scripts/ccsm_utils/Machines/config_machines.xml//.
  
 Edit following section:  Edit following section: 
 <code> <code>
-<machine MACH="hexagon_intel" +<machine MACH="vilje" 
-         DESC="Parallab XE6m (intel), os is CNL, 32 pes/node, batch system is PBS"+         DESC="NTNU, Trondheim, 16 pes/node, batch system is PBS"
          EXEROOT="/work/$CCSMUSER/noresm/$CASE"          EXEROOT="/work/$CCSMUSER/noresm/$CASE"
          OBJROOT="$EXEROOT"          OBJROOT="$EXEROOT"
          INCROOT="$EXEROOT/lib/include"           INCROOT="$EXEROOT/lib/include" 
-         DIN_LOC_ROOT_CSMDATA="/work/$CCSMUSER/inputdata"+         DIN_LOC_ROOT_CSMDATA="/work/shared/noresm/inputdata"
          DIN_LOC_ROOT_CLMQIAN="UNSET"          DIN_LOC_ROOT_CLMQIAN="UNSET"
          DOUT_S_ROOT="/work/$CCSMUSER/archive/$CASE"          DOUT_S_ROOT="/work/$CCSMUSER/archive/$CASE"
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          CCSM_BASELINE="UNSET"          CCSM_BASELINE="UNSET"
          CCSM_CPRNC="UNSET"          CCSM_CPRNC="UNSET"
-         OS="Linux"+         OS="CNL"
          BATCHQUERY="qstat -f"          BATCHQUERY="qstat -f"
          BATCHSUBMIT="qsub"           BATCHSUBMIT="qsub" 
          GMAKE_J="4"           GMAKE_J="4" 
-         MAX_TASKS_PER_NODE="32"+         MAX_TASKS_PER_NODE="16"
          MPISERIAL_SUPPORT="FALSE" />          MPISERIAL_SUPPORT="FALSE" />
 </code> </code>
  
-Set **MACH** to an acronym of your choice of your HPC system. Update **DESC** correspondingly.+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 //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 //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). +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 =====
  
-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). +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). 
  
-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 +Change directory to //$HOME/NorESM1-M/scripts//. 
  
-Set **BATCHSUBMIT** to the submit command on your HPC system.+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. 
  
-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. +Change directory to //../cases/NorESM1-M_PI_spinup// 
  
-Set **MAX_TASKS_PER_NODE** to the maximum number of MPI tasks that can run on a single node your HPC system (usually the same as the number of cores per node). +Run ''.configure -case'' to set up simulation.  
 +  
 +Run ''./NorESM1-M_PI_spinup.$MACH.build'' to stage namelists in run directory and build model code.   
  
 +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 =====
  
-==== NorESM1-M/scripts/ccsm_utils/Machines/config_pes.xml ====+  * [[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)]]
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