E3SM-Project · forsyth2 · Nov 14, 2024 · Oct 10, 2024 · Oct 15, 2024 · Oct 15, 2024
diff --git a/docs/source/SCREAMv0/DYAMOND2/index.rst b/docs/source/SCREAMv0/DYAMOND2/index.rst
@@ -0,0 +1,15 @@
+SCREAMv0 DYAMOND2
+====================
+
+The DYAMOND2 simulation campaign using SCREAMv0 that was submitted to the `DYAMOND2 intercomparison <https://www.esiwace.eu/the-project/past-phases/dyamond-initiative/services-dyamond-winter>`_. 
+
+If you use data from this simulation campaign, please cite the following overview
+manuscript:
+
+* `Caldwell et al. 2021 (JAMES) <https://doi.org/10.1029/2021MS002544>`_ 
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   simulation_data/index
diff --git a/docs/source/SCREAMv0/DYAMOND2/simulation_data/index.rst b/docs/source/SCREAMv0/DYAMOND2/simulation_data/index.rst
@@ -0,0 +1,21 @@
+***************
+Simulation Data 
+***************
+
+The SCREAMv0 simulation data is available on **NERSC HPSS**.
+
+**If you have an account on NERSC**, you can retrieve the data locally or remotely using Globus.
+
+To download simulation data locally on a NERSC machine, refer to NERSC's documentation `here <https://docs.nersc.gov/filesystems/archive/#hsi-commands>`_.
+
+**If you do not have access to NERSC**, you can download simulation data directly through the  NERSC HPSS
+`web interface <https://portal.nersc.gov/archive/home/t/terai/www/SCREAM/SCREAMv0.SCREAM-DY2.ne1024pg2.20201127>`_.
+Note that this will be slow given the large file sizes.
+
+Scripts originally used to run SCREAMv0 DYAMOND2 simulations are available `here <https://github.com/E3SM-Project/e3sm_data_docs/tree/main/run_scripts/SCREAMv0/original/>`_.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   simulation_table
diff --git a/docs/source/SCREAMv0/DYAMOND2/simulation_data/simulation_table.rst b/docs/source/SCREAMv0/DYAMOND2/simulation_data/simulation_table.rst
@@ -0,0 +1,11 @@
+**********************************
+SCREAMv0 DYAMOND2 (2021) simulation table
+**********************************
+
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| Simulation                                                        | Data Size (TB)  | NERSC HPSS Path                                                           |
++===================================================================+=================+===========================================================================+
+| **Main Simulation (40 days)**                                                                                                                                   |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| January 2020 (DYAMOND2 Configuration)                             |  46.6           |  /home/t/terai/www/SCREAM/SCREAMv0.SCREAM-DY2.ne1024pg2.20201127          |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
diff --git a/docs/source/SCREAMv0/index.rst b/docs/source/SCREAMv0/index.rst
@@ -0,0 +1,8 @@
+SCREAMv0
+==========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   DYAMOND2/index
diff --git a/docs/source/SCREAMv1/FourSeasons/index.rst b/docs/source/SCREAMv1/FourSeasons/index.rst
@@ -0,0 +1,17 @@
+SCREAMv1 Four Seasons
+====================
+
+The simulation compaign for the SCREAMv1 Four-Seasons runs.  For more information
+about this simulation campaign see the citation below.
+
+If you use data from this simulation campaign, please cite the relevant overview
+manuscript.
+
+* `Donahue et al. 2024 (JAMES) <https://doi.org/10.1029/2024MS004314>`_ 
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   simulation_data/index
+   reproducing_simulations/index
diff --git a/docs/source/SCREAMv1/FourSeasons/simulation_data/index.rst b/docs/source/SCREAMv1/FourSeasons/simulation_data/index.rst
@@ -0,0 +1,35 @@
+***************
+Simulation Data 
+***************
+
+The SCREAMv1 FourSeasons simulation data is available on **NERSC HPSS**.
+
+**If you have an account on NERSC**, you can retrieve the data locally or remotely using Globus.
+
+To download simulation data locally on a NERSC machine: ::
+
+   zstash extract --hpss=<HPSS path below>
+
+To download simulation data remotely using the zstash Globus interface: ::
+
+   zstash extract --hpss=globus://nersc/<HPSS path below>
+
+or ::
+
+   zstash extract --hpss=globus://9cd89cfd-6d04-11e5-ba46-22000b92c6ec/<HPSS path below>
+
+Note that the data management tool `zstash <https://github.com/E3SM-Project/zstash>`_ is available from the `E3SM-Unified <https://github.com/E3SM-Project/e3sm-unified>`_ conda environment. 
+
+For more information, refer to `zstash usage <https://e3sm-project.github.io/zstash/_build/html/master/usage.html#extract>`_. 
+
+**If you do not have access to NERSC**, you can download simulation data directly through the  NERSC HPSS
+`web interface <https://portal.nersc.gov/archive/home/a/adonahue/www/>`_.
+Note that this will be slow and inefficient since you'll have to download the individual files.
+
+Scripts originally used to run SCREAMv1 FourSeasons simulations are available `here <https://github.com/E3SM-Project/e3sm_data_docs/tree/main/run_scripts/SCREAMv1/original/>`_.
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   simulation_table
diff --git a/docs/source/SCREAMv1/FourSeasons/simulation_data/simulation_table.rst b/docs/source/SCREAMv1/FourSeasons/simulation_data/simulation_table.rst
@@ -0,0 +1,47 @@
+**********************************
+SCREAMv1 Four-Seasons (2024) simulation table
+**********************************
+
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| Simulation                                                        | Data Size (GB)  | NERSC HPSS Path                                                           |
++===================================================================+=================+===========================================================================+
+| **Main Simulation (40 days)**                                                                                                                                   |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| January 2020 (DYAMOND2 Configuration)                             |  129.3          |  /home/a/adonahue/www/DYAMOND2_SCREAMv1                                   |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+|   April 2013                                                      |  130.5          |  /home/a/adonahue/www/Apr1_2013_SCREAMv1                                  |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+|  August 2016 (DYAMOND1 Configuration)                             |  130.4          |  /home/a/adonahue/www/DYAMOND1_SCREAMv1                                   |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| October 2013                                                      |  119.0          |  /home/a/adonahue/www/Oct1_2013_SCREAMv1                                  |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| **Process Impact - Turbulent Mountain Stress (6 days)**                                                                                                         |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| January 2020 (DYAMOND2 Configuration)                             |   38.3          |  /home/a/adonahue/www/Process_Impacts_tests/Wind_Speed/January_DYAMOND2   |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+|   April 2013                                                      |   19.1          |  /home/a/adonahue/www/Process_Impacts_tests/Wind_Speed/April              |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+|  August 2016 (DYAMOND1 Configuration)                             |   19.1          |  /home/a/adonahue/www/Process_Impacts_tests/Wind_Speed/August_DYAMOND1    |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| October 2013                                                      |   19.1          |  /home/a/adonahue/www/Process_Impacts_tests/Wind_Speed/October            |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| **Process Impact - *Improved Cloud Tuning (6 days)**                                                                                                            |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| January 2020 (DYAMOND2 Configuration)                             |   19.1          |  /home/a/adonahue/www/Process_Impacts_tests/Cloud_Tuning/January_DYAMOND2 |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+|   April 2013                                                      |   19.1          |  /home/a/adonahue/www/Process_Impacts_tests/Cloud_Tuning/April            |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+|  August 2016 (DYAMOND1 Configuration)                             |   19.1          |  /home/a/adonahue/www/Process_Impacts_tests/Cloud_Tuning/August_DYAMOND1  |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| October 2013                                                      |   19.1          |  /home/a/adonahue/www/Process_Impacts_tests/Cloud_Tuning/October          |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| **Process Impact - Improved SHOC Tuning (6 days)**                                                                                                              |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| January 2020 (DYAMOND2 Configuration)                             |   15.9          |  /home/a/adonahue/www/Process_Impacts_tests/Warm_T/January_DYAMOND2       |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+|   April 2013                                                      |   15.9          |  /home/a/adonahue/www/Process_Impacts_tests/Warm_T/April                  |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+|  August 2016 (DYAMOND1 Configuration)                             |   15.9          |  /home/a/adonahue/www/Process_Impacts_tests/Warm_T/August_DYAMOND1        |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
+| October 2013                                                      |   15.9          |  /home/a/adonahue/www/Process_Impacts_tests/Warm_T/October                |
++-------------------------------------------------------------------+-----------------+---------------------------------------------------------------------------+
diff --git a/docs/source/SCREAMv1/index.rst b/docs/source/SCREAMv1/index.rst
@@ -0,0 +1,8 @@
+SCREAMv1
+==========================================
+
+.. toctree::
+   :maxdepth: 2
+   :caption: Contents:
+
+   FourSeasons/index
diff --git a/docs/source/index.rst b/docs/source/index.rst
@@ -16,6 +16,8 @@ simulations.
    :caption: Contents:
 
    v2/index
+   SCREAMv0/index
+   SCREAMv1/index
 
 
 .. Indices and tables

diff --git a/run_scripts/SCREAMv0/original/run.production.ne1024pg2_scream.dyamond2.sh b/run_scripts/SCREAMv0/original/run.production.ne1024pg2_scream.dyamond2.sh
@@ -0,0 +1,199 @@
+#!/bin/bash
+
+# Set run options
+#=============================================
+resolution=ne1024pg2_r0125_oRRS18to6v3
+compset=F2010-SCREAM-HR-DYAMOND2
+checkout_date=20201127  #the date you *checked out* the code
+branch=ad0e203          #actual git hash of branch to check out
+run_descriptor=SCREAMv0 #will be SCREAMv0 for production run
+repo=scream
+machine=cori-knl
+compiler=intel
+stop_option="ndays"
+stop_n="4"
+rest_n="1"
+walltime="29:00:00"
+queue="regular"
+debug_compile='FALSE'
+date_string=`date`
+
+# Setup processor layout
+nnodes_atm=1536
+nnodes_ocn=1536
+nthreads=16
+mpi_tasks_per_node=8
+ntasks_atm=$(expr ${nnodes_atm} \* ${mpi_tasks_per_node})
+ntasks_ocn=$(expr ${nnodes_ocn} \* ${mpi_tasks_per_node})
+total_tasks_per_node=$(expr ${mpi_tasks_per_node} \* ${nthreads})
+if [ ${ntasks_ocn} -ne ${ntasks_atm} ]; then
+    nnodes=$(expr ${nnodes_atm} + ${nnodes_ocn})
+else
+    nnodes=${nnodes_atm}
+fi
+pelayout=${nnodes}x${mpi_tasks_per_node}x${nthreads}
+
+# Who to send email updates on run status to
+email_address="[email protected]"
+
+# Set flags specific to running this script
+do_download=true
+do_newcase=true
+do_setup=true
+do_build=true
+do_submit=true
+
+case_name=SCREAMv0.SCREAM-DY2.ne1024pg2.${date_string}
+
+# Set paths
+#code_root=${HOME}/gitwork/scream/
+code_root=${CSCRATCH}/E3SM_code/screamv0_20201127/
+case_root=${CSCRATCH}/e3sm_scratch/cori-knl/${case_name}
+
+######################################################################################
+### USERS PROBABLY DON'T NEED TO CHANGE ANYTHING BELOW HERE EXCEPT user_nl_* FILES ###
+######################################################################################
+
+# Make directories created by this script world-readable:
+#=============================================
+umask 022
+
+# Download code
+#=============================================
+if [ "${do_download}" == "true" ]; then
+
+    echo "Cloning repository repo = $repo into branch = $branch under code_root = $code_root"
+    cdir=`pwd`
+    mkdir -p $code_root/
+
+    # This will put repository, with all code, in directory $tag_name
+    git clone [email protected]:E3SM-Project/${repo}.git $code_root
+
+    # Setup git hooks
+    rm -rf $code_root/.git/hooks
+    git clone [email protected]:E3SM-Project/E3SM-Hooks.git $code_root/.git/hooks
+    cd $code_root
+    git config commit.template $code_root/.git/hooks/commit.template
+
+    # Bring in all submodule components
+    git submodule update --init --recursive
+
+    # Check out desired branch
+    git checkout ${branch}
+    cd ${cdir}
+
+fi
+
+# Create case
+#=============================================
+if [ "${do_newcase}" == "true" ]; then
+    ${code_root}/cime/scripts/create_newcase \
+        --case ${case_root} \
+        --compset ${compset} --res ${resolution} \
+        --machine ${machine} --compiler ${compiler} \
+        --queue ${queue} \
+        --walltime ${walltime} 
+fi
+
+# Copy this script to case directory
+#=============================================
+cp -v `basename $0` ${case_root}/
+
+# Setup
+#=============================================
+if [ "${do_setup}" == "true" ]; then
+    cd ${case_root}
+
+    # Set run length
+    ./xmlchange STOP_OPTION=${stop_option},STOP_N=${stop_n}
+    ./xmlchange REST_N=${rest_n}
+
+    # Set processor layout
+    if [ ${ntasks_ocn} -ne ${ntasks_atm} ]; then
+        ./xmlchange NTASKS=${ntasks_ocn}
+        ./xmlchange NTASKS_ATM=${ntasks_atm}
+        ./xmlchange ROOTPE_ATM=${ntasks_ocn}
+    else
+        ./xmlchange NTASKS=${ntasks_atm}
+    fi
+    ./xmlchange NTHRDS_ATM=${nthreads}
+    ./xmlchange MAX_MPITASKS_PER_NODE=${mpi_tasks_per_node}
+    ./xmlchange MAX_TASKS_PER_NODE=${total_tasks_per_node}
+
+    # Flag for debug compile
+    ./xmlchange --id DEBUG --val ${debug_compile}
+
+    # Set PIO format, use PIO version 2, and increase PIO buffer size 
+    ./xmlchange PIO_NETCDF_FORMAT="64bit_data"
+    ./xmlchange PIO_VERSION="2"
+    ./xmlchange PIO_BUFFER_SIZE_LIMIT=134217728
+
+    # Edit CAM namelist to set dycore options for new grid
+    cat <<EOF >> user_nl_eam
+
+    !*** By default the model dumps hundreds of vars in h0. Don't do that. ***
+    empty_htapes=.true.
+    !*** Outputs for DYAMOND (note fincl can only go to 10) ***
+    nhtfrq = 12,12,12,12,-3,-3,-3,-3,-3,-3 !output freq: 12 steps=15 mi, -3=3hrs
+    mfilt = 96,96,96,96,8,8,8,8,8,8 !new file freq: daily in all cases
+    fincl1 = 'CLDLOW:I', 'CLDMED:I', 'CLDHGH:I', 'CLDTOT:I', 'TMCLDLIQ:I', 
+             'TMCLDICE:I', 'TMRAINQM:I', 'TMCLDRIM:I', 'TMQ:I', 'CAPE:I', 'CIN:I'
+    fincl2 = 'PS:I', 'TS:I', 'TREFHT:I', 'QREFHT:I', 'PRECT:I','PRECSL:I',
+    	     'WINDSPD_10M:I', 'TAUX:I', 'TAUY:I', 'SHFLX:I', 'LHFLX:I'
+    fincl3 = 'FSNTOA:I', 'FLNT:I','FLNTC:I','FSNTOAC:I', 'FSNS:I', 'FSDS:I', 
+    	     'FLNS:I', 'FLDS:I'
+    fincl4 = 'RH200:I',    'RH500:I',    'RH700:I',    'RH850:I',
+	     'OMEGA200:I', 'OMEGA500:I', 'OMEGA700:I', 'OMEGA850:I', 
+             'Z200:I',     'Z500:I',     'Z700:I',     'Z850:I'
+    !*** 3 hrly (mostly 3d) variables below here ***
+    fincl5 = 'PS:I', 'PSL:I', 'TMNUMLIQ:I', 'TMNUMICE:I', 'TMNUMRAI:I'
+    fincl6 = 'U:I', 'V:I'
+    fincl7 = 'T:I', 'Q:I', 
+    fincl8 = 'CLDLIQ:I', 'CLDICE:I'
+    fincl9 = 'CLOUD:I','OMEGA:I'
+    fincl10= 'EMIS:I', 'TOT_ICLD_VISTAU:I'
+    !*** Rad Freq: 4x75sec=5 min which divides 15 min output freq ***
+    iradsw = 4
+    iradlw = 4
+
+EOF
+
+    cat <<EOF >> user_nl_elm
+
+
+EOF
+
+    # Finally, run setup
+    ./case.setup
+
+    # The run location is determined in the bowels of CIME
+    # Symlink to that location from user-chosen $case_root (=current dir)
+    ln -s `./xmlquery -value RUNDIR` run
+
+
+    # This disables the logic that sets tprof_n and tprof_options internally.
+    #./xmlchange --file env_run.xml TPROF_TOTAL=-1
+    #echo "tprof_n = 1" >> user_nl_cpl
+    #echo "tprof_option = 'nsteps'" >> user_nl_cpl
+fi
+
+# Build
+#=============================================
+if [ "${do_build}" == "true" ]; then
+    cd ${case_root}
+    ./case.build
+
+    # Set file striping on run dir for writing large files
+    ls -l run > /dev/null #just using this command as a check that run dir exists
+    lfs setstripe -S 1m -c 64 run
+    lfs getstripe run >& lfs_run.txt
+fi
+
+# Run
+#=============================================
+if [ "${do_submit}" == "true" ]; then
+    cd ${case_root}
+    ./case.submit --batch-args="--mail-type=ALL --mail-user=${email_address}"
+fi
+
+echo "Done working in ${case_root}"