Initial commit for porting to cori

README.md

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+
+We provide detailed notes on running the coupled CLM-PFLOTRAN model
+on NERSC's Edison supercomputer.
+
+
+### Install PETSc
+
+```
+module rm PrgEnv-intel
+module rm PrgEnv-cray 
+module rm PrgEnv-gnu
+module rm cray-hdf5
+module rm cray-hdf5-parallel
+
+module load PrgEnv-intel
+module swap intel intel/16.0.3.210
+module load cray-hdf5-parallel/1.10.0.3
+module load cmake/3.8.2
+
+setenv BASE_DIR <directory-of-choice>
+cd $BASE_DIR
+setenv PETSC_HASH 03c0fad465
+git clone https://bitbucket.org/petsc/petsc petsc_$PETSC_HASH
+cd petsc_$PETSC_HASH
+git checkout $PETSC_HASH
+
+setenv PETSC_DIR $BASE_DIR/petsc_$PETSC_HASH
+setenv PETSC_ARCH cori_intel_O
+
+./config/configure.py         \
+--PETSC_ARCH=$PETSC_ARCH      \
+--with-cc=cc                  \
+--with-cxx=CC                 \
+--with-fc=ftn                 \
+--CFLAGS='-fast -no-ipo'      \
+--CXXFLAGS='-fast -no-ipo'    \
+--FFLAGS='-fast -no-ipo'      \
+--with-shared-libraries=0     \
+--with-debugging=0            \
+--with-clanguage=c            \
+--with-x=0                    \
+--download-parmetis=1         \
+--download-metis=1            \
+--with-hdf5=1                 \
+--with-hdf5-dir=$HDF5_DIR     \
+--with-c2html=0               \
+--with-clib-autodetect=0      \
+--with-fortranlib-autodetect=0 \
+--with-cxxlib-autodetect=0    \
+--LIBS=-lstdc++
+
+
+make PETSC_DIR=$PETSC_DIR PETSC_ARCH=$PETSC_ARCH all
+
+```
+
+
+### Download code repository
+
+
+#### PFLOTRAN code
+```
+cd $BASE_DIR
+git clone https://bitbucket.org/pflotran/pflotran
+setenv PFLOTRAN_SRC_DIR $BASE_DIR/pflotran
+cd $PFLOTRAN_SRC_DIR
+
+```
+
+#### CLM code
+```
+cd $BASE_DIR
+git clone [email protected]:CLM-PFLOTRAN/clm-pflotran.git 
+setenv CLM_SRC_DIR $BASE_DIR/clm-pflotran
+cd $CLM_SRC_DIR
+```
+
+### Download data repository
+```
+cd $BASE_DIR
+mkdir cases
+git clone [email protected]:pnnl_sbr_sfa/notes-for-gmd-2017-35.git
+setenv CASE_DIR $BASE_DIR/cases
+cd $BASE_DIR/notes-for-gmd-2017-35
+setenv INPUTDATA_DIR ${PWD}/datasets
+```
+
+#### Download data from NCAR repo, instruction for registration can be found at http://www.cesm.ucar.edu/models/cesm1.2
+
+```
+svn export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mozart/emis/megan21_emis_factors_c20120313.nc  \
+${INPUTDATA_DIR}/cesm-inputdata/atm/cam/chem/trop_mozart/emis/megan21_emis_factors_c20120313.nc
+
+svn export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_monthly_1850_mean_1.9x2.5_c090421.nc \
+${INPUTDATA_DIR}/cesm-inputdata/atm/cam/chem/trop_mozart_aero/aero/aerosoldep_monthly_1850_mean_1.9x2.5_c090421.nc
+
+svn export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc \
+${INPUTDATA_DIR}/cesm-inputdata/lnd/clm2/lai_streams/MODISPFTLAI_0.5x0.5_c140711.nc
+
+svn export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/paramdata/clm_params.c140423.nc \
+${INPUTDATA_DIR}/cesm-inputdata/lnd/clm2/paramdata/clm_params.c140423.nc
+
+svn export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc \
+${INPUTDATA_DIR}/cesm-inputdata/lnd/clm2/snicardata/snicar_drdt_bst_fit_60_c070416.nc
+
+svn export https://svn-ccsm-inputdata.cgd.ucar.edu/trunk/inputdata/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc \
+${INPUTDATA_DIR}/cesm-inputdata/lnd/clm2/snicardata/snicar_optics_5bnd_c090915.nc
+
+```
+
+### Create a CLM-PFLOTRAN case
+```
+./create_case.sh                       \
+-clm_source_dir      $CLM_SRC_DIR      \
+-pflotran_source_dir $PFLOTRAN_SRC_DIR \
+-inputdata_dir       $INPUTDATA_DIR    \
+-case_dir            $CASE_DIR         \
+-petsc_dir           $PETSC_DIR        \
+-petsc_arch          $PETSC_ARCH       \
+-case_name           10m_case          \
+-resolution          10m
+```
+
+### Reference
+Bisht, G., Huang, M., Zhou, T., Chen, X., Dai, H., Hammond, G., Riley, W., Downs, J., Liu, Y., and Zachara, J.:
+Coupling a three-dimensional subsurface flow and transport model with a land surface model to simulate stream-aquifer-land interactions (CP v1.0), Geosci. Model Dev., 10(12):4539-4562.  doi:10.5194/gmd-10-4539-2017.
+
+### Declaimer
+CLM4.5 is an open-source software released as part of the Community Earth System Model (CESM) version 1.2 (http://www.cesm.ucar.edu/models/cesm1.2). The version of CLM4.5 used in CP v1.0 is a branch from the CLM developer's repository. Its functionality is scientifically consistent with descriptions in Oleson et al. [2013] with source codes refactored for a modular code design. Additional minor code modifications were added by the authors to support coupling with PFLOTRAN.  Permission from the CESM Land Model Working Group has been obtained to release this CLM4.5 development branch but the National Center for Atmospheric Research cannot provide technical support for this version of the code CP v1.0. PFLOTRAN is an open-source software distributed under the terms of the GNU Lesser General Public License as published by the Free Software Foundation either version 2.1 of the License, or any later version. The CP v1.0 has two separate, open-source repositories for CLM4.5 and PFLOTRAN at:
+https://bitbucket.org/CLM-PFLOTRAN/clm-pflotran
+https://bitbucket.org/pflotran/pflotran
+The README guide for the CP v1.0 and dataset used in this study are available from the open-source repository https://github.com/huangmy/clm-pflotran-scripts.git.