From 9d52abeace3aa3d07141f4e6f42d2306236af7da Mon Sep 17 00:00:00 2001 From: Liz Adams Date: Tue, 8 Jun 2021 15:08:12 -0400 Subject: [PATCH 1/8] Update CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md --- .../Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md | 9 ++++++++- 1 file changed, 8 insertions(+), 1 deletion(-) diff --git a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md index caefe10dec..af98d2a953 100644 --- a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md +++ b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md @@ -173,12 +173,19 @@ BASEDIR = ${INSTALL}/ioapi-3.2-20200828 #OMPLIBS = -fopenmp ``` + ### Create the Makefile in the m3tools directory + + ``` + cd ../m3tools + cp Makefile.nocpl Makefile + ``` + ### Build ioapi using the following command ### (Not clear where to run the make command. Do you run it under ioapi-3.2 or ioapi-3.2/ioapi directory? - ``` + cd .. make |& tee make.log ``` From b5b2d4e88b8b98ea4ab0ccb4b9f45100965864ca Mon Sep 17 00:00:00 2001 From: Liz Adams Date: Tue, 8 Jun 2021 16:35:37 -0400 Subject: [PATCH 2/8] Update CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md --- .../Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md | 5 +++++ 1 file changed, 5 insertions(+) diff --git a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md index af98d2a953..9c18c87660 100644 --- a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md +++ b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md @@ -128,6 +128,11 @@ BASEDIR = ${INSTALL}/ioapi-3.2-20200828 setenv INSTALL [your_install_path]/LIBRARIES/openmpi_4.0.1_gcc_9.1.0 setenv BIN Linux2_x86_64gfort_openmpi_4.0.1_gcc_9.1.0 + + ### set the CPLMODE environment variable + + setenv CPLMODE nocpl + #### Make the installation directory From d1fc461b60a7580f5dc7044c0191f0559ed42772 Mon Sep 17 00:00:00 2001 From: Liz Adams Date: Tue, 8 Jun 2021 16:51:39 -0400 Subject: [PATCH 3/8] Update CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md --- .../Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md | 12 ++++++++++++ 1 file changed, 12 insertions(+) diff --git a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md index 9c18c87660..e97e305e0b 100644 --- a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md +++ b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md @@ -243,6 +243,18 @@ Change directories to the CMAQ_HOME directory setenv NETCDF netcdf_root_gcc # Note please combine netCDF-C & Fortran Libraries (e.g. /usr/local/netcdf-4.7.0) setenv IOAPI ioapi_root_gcc (e.g. /usr/local/ioapi-3.2) setenv WRF_ARCH 34 # [1-75] 64 Bit Linux_x86 Compiler/Architecture options + + #> I/O API, netCDF, and MPI include and library locations + setenv IOAPI_INCL_DIR $IOAPI/ioapi/fixed_src #> I/O API include header files + setenv IOAPI_LIB_DIR $IOAPI/Linux2_x86_64gfort_openmpi_4.0.1_gcc_9.1.0 #> I/O API libraries + setenv NETCDF_LIB_DIR $NETCDF/lib #> netCDF C directory path + setenv NETCDF_INCL_DIR $NETCDF/include #> netCDF C directory path + setenv NETCDFF_LIB_DIR $NETCDF/lib #> netCDF Fortran directory path + setenv NETCDFF_INCL_DIR $NETCDF/include #> netCDF Fortran directory path + setenv MPI_LIB_DIR mpi_lib_gcc + +#> MPI directory path + ``` *Note: WRF_ARCH environment variable is based on the following options:* From b8b268c6a8e29043b787853ca61c0200be1571b7 Mon Sep 17 00:00:00 2001 From: Liz Adams Date: Wed, 9 Jun 2021 09:54:45 -0400 Subject: [PATCH 4/8] Update CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md --- .../CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md | 26 ++++++++++++++++++- 1 file changed, 25 insertions(+), 1 deletion(-) diff --git a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md index e97e305e0b..71dd1926ee 100644 --- a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md +++ b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md @@ -1,6 +1,30 @@ ## WRF-CMAQ Tutorial ## -### Procedure to build and run the WRF-CMAQ model using gnu compiler: ### +## Note, in this new coupled model design, the namelist is used to modify settings for WRF. +Environment variables such as WRF_CMAQ_FREQ are no longer used. +The following commonly modified namelist options for WRF are specified in the run script. + + 1. wrf_cmaq_option (dictates how the coupled model execute) + + 0 = run WRF only + 1 = run WRF only w producing MCIP like GRID and MET files + 2 = run WRF-CMAQ coupled model w/o producing MCIP like GRID and MET files + 3 = run WRF-CMAQ coupled model w producing MCIP like GRID and MET files + + 2. wrf_cmaq_freq (indicate how often WRF and CMAQ interact) + + 3. met_file_tstep (time step size of MCIP like intermediate output files) + + 4. direct_sw_feedback (indicate to turn on aerosol short wave direct effect) + + 5. feedback_restart (indicate aerosol SW direct effect information is + available in the WRF restart file or not) + +* two sample run scripts are provided; run-p.csh (for pure WRF model) and run-cs.csh (for coupled + model with SW feedback on. + + +### Procedure to build the WRF-CMAQ model using gnu compiler: ### ### Step 1: choose your compiler, and load it using the module command if it is available on your system From 93e976ad254a50d118d3353a417802bddf065924 Mon Sep 17 00:00:00 2001 From: Liz Adams Date: Wed, 9 Jun 2021 10:12:18 -0400 Subject: [PATCH 5/8] Update CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md --- .../CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md | 61 ++++++++++--------- 1 file changed, 31 insertions(+), 30 deletions(-) diff --git a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md index 71dd1926ee..f0f2226a0d 100644 --- a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md +++ b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md @@ -1,29 +1,5 @@ ## WRF-CMAQ Tutorial ## -## Note, in this new coupled model design, the namelist is used to modify settings for WRF. -Environment variables such as WRF_CMAQ_FREQ are no longer used. -The following commonly modified namelist options for WRF are specified in the run script. - - 1. wrf_cmaq_option (dictates how the coupled model execute) - - 0 = run WRF only - 1 = run WRF only w producing MCIP like GRID and MET files - 2 = run WRF-CMAQ coupled model w/o producing MCIP like GRID and MET files - 3 = run WRF-CMAQ coupled model w producing MCIP like GRID and MET files - - 2. wrf_cmaq_freq (indicate how often WRF and CMAQ interact) - - 3. met_file_tstep (time step size of MCIP like intermediate output files) - - 4. direct_sw_feedback (indicate to turn on aerosol short wave direct effect) - - 5. feedback_restart (indicate aerosol SW direct effect information is - available in the WRF restart file or not) - -* two sample run scripts are provided; run-p.csh (for pure WRF model) and run-cs.csh (for coupled - model with SW feedback on. - - ### Procedure to build the WRF-CMAQ model using gnu compiler: ### ### Step 1: choose your compiler, and load it using the module command if it is available on your system @@ -446,18 +422,43 @@ setenv WRF_CMAQ 1 ### Step 13: Run the WRF-CMAQ model - - Use the run.twoway_model_411_532_nf_run_script.16pe.csh script and the CMAQv5.3.2 input benchmark dataset to run CMAQ-WRF with no feedback +### Note, in this new coupled model design, the namelist is used to modify settings for WRF. +Environment variables such as WRF_CMAQ_FREQ are no longer used. +The following commonly modified namelist options for WRF are specified in the run script. + + 1. wrf_cmaq_option (dictates how the coupled model execute) + + 0 = run WRF only + 1 = run WRF only w producing MCIP like GRID and MET files + 2 = run WRF-CMAQ coupled model w/o producing MCIP like GRID and MET files + 3 = run WRF-CMAQ coupled model w producing MCIP like GRID and MET files + + 2. wrf_cmaq_freq (indicate how often WRF and CMAQ interact) + + 3. met_file_tstep (time step size of MCIP like intermediate output files) + + 4. direct_sw_feedback (indicate to turn on aerosol short wave direct effect) + + 5. feedback_restart (indicate aerosol SW direct effect information is + available in the WRF restart file or not) + +* two sample run scripts are provided; run-p.csh (for pure WRF model) and run-cs.csh (for coupled + model with SW feedback on, run-c-nswf.csh (for coupled model with SW feedback off). + + + - Start with the run-c-nswf.csh script that specifies direct_sw_feedback = .false. + - and the CMAQv5.3.2 input benchmark dataset to run CMAQ-WRF with no feedback - It is configured to run on 16 processors and for 2 days of model simulation - Edit the script to specify the paths, modify the number of processors and batch queue commands - Verify that the OMIfile definition matches the latest release of CMAQv5.3.2 Modify the following section to specify your local paths ``` -set ROOT_PATH = /proj/ie/proj/CMAS/WRF-CMAQ/openmpi_4.0.1_gcc_9.1.0_debug/ -set WRF_DIR = $ROOT_PATH/WRF-4.1.1 # WRF source code directory +set WORKDIR = /proj/ie/proj/CMAS/WRF-CMAQ/CMAQ_v5.3.2/CCTM/scripts +set WRF_DIR = $WORKDIR/BLD_WRFv4.3_CCTM_v532_gcc # WRF source code directory set INPDIR = /proj/ie/proj/CMAS/WRF-CMAQ/from_EPA/from_gdrive/CMAQv5.3.2_Benchmark_2Day_Input/2016_12SE1 set OMIpath = $WRF_DIR/cmaq # path optics related data files -set OUTPUT_ROOT = $ROOT_PATH/WRF-4.1.1 # output root directory +set OUTPUT_ROOT = $WORKDIR # output root directory set NMLpath = $WRF_DIR/cmaq # path with *.nml file mechanism dependent set NMLpath2 = $WRF_DIR/cmaq # path with Species_Table_TR_0.nml file set EMISSCTRL = $WRF_DIR/cmaq # path of Emissions Control File @@ -471,14 +472,14 @@ set EMISSCTRL = $WRF_DIR/cmaq # path of Emissions - Submit the job using the batch queueing system ``` - sbatch run.twoway_model_411_532_nf_run_script.16pe.csh + sbatch run-c-nswf.csh ``` ### Step 14: Verify that the run was successful - look for the output directory ``` - cd output_12km_nf_rrtmg_20_5_1_v411532_debug + cd output-nswf ``` If the run was successful you will see the following output From 8bacb8948219a64f3ec654e6bff4e7d917c40521 Mon Sep 17 00:00:00 2001 From: Liz Adams Date: Wed, 9 Jun 2021 10:45:53 -0400 Subject: [PATCH 6/8] Update CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md --- .../Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md | 1 + 1 file changed, 1 insertion(+) diff --git a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md index f0f2226a0d..b392a5d1e9 100644 --- a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md +++ b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md @@ -453,6 +453,7 @@ The following commonly modified namelist options for WRF are specified in the ru - Verify that the OMIfile definition matches the latest release of CMAQv5.3.2 Modify the following section to specify your local paths + ``` set WORKDIR = /proj/ie/proj/CMAS/WRF-CMAQ/CMAQ_v5.3.2/CCTM/scripts set WRF_DIR = $WORKDIR/BLD_WRFv4.3_CCTM_v532_gcc # WRF source code directory From bcf6cdc7b7dbec923cedf41a857011ad1d1c680f Mon Sep 17 00:00:00 2001 From: Liz Adams Date: Wed, 9 Jun 2021 10:46:49 -0400 Subject: [PATCH 7/8] Update CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md --- .../CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) diff --git a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md index b392a5d1e9..f5eb6a647e 100644 --- a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md +++ b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md @@ -455,14 +455,14 @@ The following commonly modified namelist options for WRF are specified in the ru Modify the following section to specify your local paths ``` -set WORKDIR = /proj/ie/proj/CMAS/WRF-CMAQ/CMAQ_v5.3.2/CCTM/scripts -set WRF_DIR = $WORKDIR/BLD_WRFv4.3_CCTM_v532_gcc # WRF source code directory -set INPDIR = /proj/ie/proj/CMAS/WRF-CMAQ/from_EPA/from_gdrive/CMAQv5.3.2_Benchmark_2Day_Input/2016_12SE1 -set OMIpath = $WRF_DIR/cmaq # path optics related data files -set OUTPUT_ROOT = $WORKDIR # output root directory -set NMLpath = $WRF_DIR/cmaq # path with *.nml file mechanism dependent -set NMLpath2 = $WRF_DIR/cmaq # path with Species_Table_TR_0.nml file -set EMISSCTRL = $WRF_DIR/cmaq # path of Emissions Control File + set WORKDIR = /proj/ie/proj/CMAS/WRF-CMAQ/CMAQ_v5.3.2/CCTM/scripts + set WRF_DIR = $WORKDIR/BLD_WRFv4.3_CCTM_v532_gcc # WRF source code directory + set INPDIR = /proj/ie/proj/CMAS/WRF-CMAQ/from_EPA/from_gdrive/CMAQv5.3.2_Benchmark_2Day_Input/2016_12SE1 + set OMIpath = $WRF_DIR/cmaq # path optics related data files + set OUTPUT_ROOT = $WORKDIR # output root directory + set NMLpath = $WRF_DIR/cmaq # path with *.nml file mechanism dependent + set NMLpath2 = $WRF_DIR/cmaq # path with Species_Table_TR_0.nml file + set EMISSCTRL = $WRF_DIR/cmaq # path of Emissions Control File ``` - Verify the following settings From e07254750f58a69230e04d6bc34560ae99d77bb2 Mon Sep 17 00:00:00 2001 From: Liz Adams Date: Wed, 9 Jun 2021 10:47:32 -0400 Subject: [PATCH 8/8] Update CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md --- .../Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md index f5eb6a647e..abaa21af5e 100644 --- a/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md +++ b/DOCS/Users_Guide/Tutorials/CMAQ_UG_tutorial_WRF-CMAQ_build_gcc.md @@ -442,8 +442,8 @@ The following commonly modified namelist options for WRF are specified in the ru 5. feedback_restart (indicate aerosol SW direct effect information is available in the WRF restart file or not) -* two sample run scripts are provided; run-p.csh (for pure WRF model) and run-cs.csh (for coupled - model with SW feedback on, run-c-nswf.csh (for coupled model with SW feedback off). +* three sample run scripts are provided; run-p.csh (for pure WRF model), run-cs.csh (for coupled + model with SW feedback on, and run-c-nswf.csh (for coupled model with SW feedback off). - Start with the run-c-nswf.csh script that specifies direct_sw_feedback = .false.