CMAQ
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Última revisión de 13:30 18 oct 2023
Instalando y usando CMAQ en hydra
Para inventarios y condiciones de borde e iniciales CMAQInvCbCi
Contenido |
[editar] Instalando librerías
Instalación en /home/solange.luque/MODELOS/CMAQ/[comp].
Existe un foro: https://forum.cmascenter.org/t/ioapi-installtion-unable/805
[editar] ioapi
Agarrar librerías ioapi
Instalándolas en /home/solange.luque/libraries/
Instalación y uso de ioapi desde python con PseudoNetCDF /pyIOAPI
[editar] intel
mkdir -p ioapi/v3.2-20200828/intel cd ioapi/v3.2-20200828/intel tar xvfz ~/ioapi-3.2-20200828.tar.gz mv ioapi-3.2-20200828/* ./ rmdir ioapi-3.2-20200828 export BIN=Linux2_x86_64ifort mkdir Linux2_x86_64ifort ln -s /opt/netcdf/netcdf-4/intel/2021.4.0/lib/*.so Linux2_x86_64ifort/ ln -s /opt/netcdf/netcdf-4/intel/2021.4.0/lib/libnetcdf.a Linux2_x86_64ifort/ ln -s /opt/netcdf/netcdf-4/intel/2021.4.0/lib/libnetcdff.a Linux2_x86_64ifort/ ln -s /opt/hdf5/hdf5-1.10.5/intel/2021.4.0/lib/libhdf5*a Linux2_x86_64ifort/ ln -s /opt/hdf5/hdf5-1.10.5/intel/2021.4.0/lib/libhdf5*so Linux2_x86_64ifort/ ln -s /opt/curl/curl-4.1.2/intel/2021.4.0/lib/libcurl.* ./ cp ioapi/Makefile.nocpl ioapi/Makefile cp m3tools/Makefile.nocpl m3tools/Makefile cp Makefile.template Makefile
Seguimos (https://forum.cmascenter.org/t/ioapi-error-in-m3too/2341)[CMAS forum `Ioapi error in m3too;`]
Editamos los Makefiles (Makefile y ioapi/Makeinclude.Linux2_x86_64ifort)
diff Makefile Makefile.template
138,145c138,145
< BIN = Linux2_x86_64ifort
< BASEDIR = ${PWD}
< INSTALL = /home/solange.luque/MODELOS/CMAQ/intel/LIBRARIES/ioapi
< LIBINST = $(INSTALL)/$(BIN)
< BININST = $(INSTALL)/$(BIN)
< CPLMODE = nocpl
< IOAPIDEFS =
< PVMINCL =
---
> # BIN = Linux2_x86_64
> # BASEDIR = ${PWD}
> # INSTALL = ${HOME}
> # LIBINST = $(INSTALL)/$(BIN)
> # BININST = $(INSTALL)/$(BIN)
> # CPLMODE = nocpl
> # IOAPIDEFS =
> # PVMINCL =
Instalamos librerías
/opt/load-libs.sh 1 make configure >& run_configure.log make all >& run_make.log
Si todo fue bien:
ls -l Linux2_x86_64ifort/ | grep rwx | grep -v lrwxrwxrwx | awk '{print $9}' | tr '\n' ' '
airs2m3 bcwndw camxtom3 datshift dayagg factor findwndw greg2jul gregdate gridprobe insertgrid
jul2greg juldate juldiff julshift kfxtract latlon m3agmask m3agmax m3combo m3cple m3diff m3edhdr
m3fake m3hdr m3interp m3mask m3merge m3pair m3probe m3stat m3totxt m3tproc m3tshift m3wndw
m3xtract mpasdiff mpasstat mpastom3 mtxblend mtxbuild mtxcalc mtxcple presterp presz projtool
randomstat selmrg2d timediff timeshift vertimeproc vertintegral vertot wndwdesc wrfgriddesc wrftom3
Instalando:
mkdir -p ~/MODELOS/CMAQ/intel/LIBRARIES/ioapi make install >& run_install.log ls ~/MODELOS/CMAQ/intel/LIBRARIES/ioapi/Linux2_x86_64ifort/ airs2m3 greg2jul julshift m3cple m3merge m3utilio.mod modpdata.mod mtxcalc timediff wrftom3 bcwndw gregdate kfxtract m3diff m3pair m3wndw modwrfio.mod mtxcple timeshift camxtom3 gridprobe latlon m3edhdr m3probe m3xtract mpasdiff presterp vertimeproc datshift insertgrid libioapi.a m3fake m3stat modatts3.mod mpasstat presz vertintegral dayagg jul2greg m3agmask m3hdr m3totxt modgctp.mod mpastom3 projtool vertot factor juldate m3agmax m3interp m3tproc modmpasfio.mod mtxblend randomstat wndwdesc findwndw juldiff m3combo m3mask m3tshift modncfio.mod mtxbuild selmrg2d wrfgriddesc cp ioapi/fixed_src/* Linux2_x86_64ifort/ cp ioapi/fixed_src/* ~/MODELOS/CMAQ/intel/LIBRARIES/ioapi/Linux2_x86_64ifort/
[editar] gnu
NOTA: Antes de empezar, quitar del .bashrc la carga por defecto del entorno intel
##Para compiladores INTEL #source /opt/intel/oneapi/setvars.sh > /dev/null #export PATH=/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin:$PATH #export LD_LIBRARY_PATH=/opt/jasper/jasper-version-2.0.33/intel/2021.4.0/lib: /opt/netcdf/netcdf-4/intel/2021.4.0/lib:$LD_LIBRARY_PATH /opt/load-libs.sh 3 source /opt/env_scripts/load_gnu-10.2.1_mpich-3.4.2.sh
mkdir -p ioapi/v3.2-20200828/gnu cd ioapi/v3.2-20200828/gnu tar xvfz ~/ioapi-3.2-20200828.tar.gz mv ioapi-3.2-20200828/* ./ rmdir ioapi-3.2-20200828 export BIN=Linux2_x86_64 mkdir Linux2_x86_64 ln -s /opt/netcdf/netcdf-4/gnu/10.2.1/lib/*.so Linux2_x86_64/ ln -s /opt/netcdf/netcdf-4/gnu/10.2.1/lib/libnetcdf.a Linux2_x86_64/ ln -s /opt/netcdf/netcdf-4/gnu/10.2.1/lib/libnetcdff.a Linux2_x86_64/ ln -s /opt/hdf5/hdf5-1.10.5/gnu/10.2.1/lib/libhdf5*a Linux2_x86_64/ ln -s /opt/hdf5/hdf5-1.10.5/gnu/10.2.1/lib/libhdf5*so Linux2_x86_64/ ln -s /usr/lib/x86_64-linux-gnu/*curl*a Linux2_x86_64/ ln -s /usr/lib/x86_64-linux-gnu/*curl*so Linux2_x86_64/ cp ioapi/Makefile.nocpl ioapi/Makefile cp m3tools/Makefile.nocpl m3tools/Makefile cp Makefile.template Makefile
Editamos los Makefiles (Makefile y ioapi/Makeinclude.Linux2_x86_64)
diff Makefile Makefile.template
138,145c138,145
< BIN = Linux2_x86_64
< BASEDIR = ${PWD}
< INSTALL = /home/solange.luque/MODELOS/CMAQ/gnu/LIBRARIES/ioapi
< LIBINST = $(INSTALL)/$(BIN)
< BININST = $(INSTALL)/$(BIN)
< CPLMODE = nocpl
< IOAPIDEFS =
< PVMINCL =
---
> # BIN = Linux2_x86_64
> # BASEDIR = ${PWD}
> # INSTALL = ${HOME}
> # LIBINST = $(INSTALL)/$(BIN)
> # BININST = $(INSTALL)/$(BIN)
> # CPLMODE = nocpl
> # IOAPIDEFS =
> # PVMINCL =
Instalamos librerías
make configure >& run_configure.log make all >& run_make.log
Si no hay problemas
$ ls -l Linux2_x86_64/ | grep rwx | grep -v lrwxrwxrwx | awk '{print $9}' | tr '\n' ' '
airs2m3 bcwndw camxtom3 datshift dayagg factor findwndw greg2jul gregdate gridprobe insertgrid jul2greg juldate juldiff julshift kfxtract
latlon m3agmask m3agmax m3combo m3cple m3diff m3edhdr m3fake m3hdr m3interp m3mask m3merge m3pair m3probe m3stat m3totxt m3tproc m3tshift
m3wndw m3xtract mpasdiff mpasstat mpastom3 mtxblend mtxbuild mtxcalc mtxcple presterp presz projtool randomstat selmrg2d timediff timeshift
vertimeproc vertintegral vertot wndwdesc wrfgriddesc wrftom3
Instalando:
mkdir ~/MODELOS/CMAQ/gnu/LIBRARIES/ioapi make install >& run_install.log ls ~/MODELOS/CMAQ/gnu/LIBRARIES/ioapi/Linux2_x86_64/ airs2m3 greg2jul julshift m3cple m3merge m3utilio.mod modpdata.mod mtxcalc timediff wrftom3 bcwndw gregdate kfxtract m3diff m3pair m3wndw modwrfio.mod mtxcple timeshift camxtom3 gridprobe latlon m3edhdr m3probe m3xtract mpasdiff presterp vertimeproc datshift insertgrid libioapi.a m3fake m3stat modatts3.mod mpasstat presz vertintegral dayagg jul2greg m3agmask m3hdr m3totxt modgctp.mod mpastom3 projtool vertot factor juldate m3agmax m3interp m3tproc modmpasfio.mod mtxblend randomstat wndwdesc findwndw juldiff m3combo m3mask m3tshift modncfio.mod mtxbuild selmrg2d wrfgriddesc cp ioapi/fixed_src/* Linux2_x86_64/ cp ioapi/fixed_src/* /home/solange.luque/MODELOS/CMAQ/gnu/LIBRARIES/ioapi/Linux2_x86_64/
[editar] gnu - debug
NOTA: Antes de empezar, quitar del .bashrc la carga por defecto del entorno intel
##Para compiladores INTEL #source /opt/intel/oneapi/setvars.sh > /dev/null #export PATH=/opt/mpich/mpich-3.4.2/intel/2021.4.0/bin:$PATH #export LD_LIBRARY_PATH=/opt/jasper/jasper-version-2.0.33/intel/2021.4.0/lib: /opt/netcdf/netcdf-4/intel/2021.4.0/lib:$LD_LIBRARY_PATH
mkdir -p ioapi/v3.2-20200828/gnu-dbg cd ioapi/v3.2-20200828/gnu-dbg tar xvfz /home/solange.luque/libraries/ioapi-3.2-20200828.tar.gz mv ioapi-3.2-20200828/* ./ rmdir ioapi-3.2-20200828 export BIN=Linux2_x86_64dbg mkdir Linux2_x86_64dbg ln -s /opt/netcdf/netcdf-4/gnu/10.2.1/lib/*.so Linux2_x86_64dbg/ ln -s /opt/netcdf/netcdf-4/gnu/10.2.1/lib/libnetcdf.a Linux2_x86_64dbg/ ln -s /opt/netcdf/netcdf-4/gnu/10.2.1/lib/libnetcdff.a Linux2_x86_64dbg/ ln -s /opt/hdf5/hdf5-1.10.5/gnu/10.2.1/lib/libhdf5*a Linux2_x86_64dbg/ ln -s /opt/hdf5/hdf5-1.10.5/gnu/10.2.1/lib/libhdf5*so Linux2_x86_64dbg/ ln -s /usr/lib/x86_64-linux-gnu/*curl*a Linux2_x86_64dbg/ ln -s /usr/lib/x86_64-linux-gnu/*curl*so Linux2_x86_64dbg/ cp ioapi/Makefile.nocpl ioapi/Makefile cp m3tools/Makefile.nocpl m3tools/Makefile cp Makefile.template Makefile cp ioapi/Makeinclude.Linux2_x86_64dbg ioapi/Makeinclude.Linux2_x86_64dbg.old
Editamos los Makefiles (Makefile y ioapi/Makeinclude.Linux2_x86_64)
diff Makefile Makefile.template
138,145c138,145
< BIN = Linux2_x86_64dbg
< BASEDIR = ${PWD}
< INSTALL = /home/solange.luque/libs/ioapi/v3.2-20200828/gnu-dbg
< LIBINST = $(INSTALL)/$(BIN)
< BININST = $(INSTALL)/$(BIN)
< CPLMODE = nocpl
< IOAPIDEFS =
< PVMINCL =
---
> # BIN = Linux2_x86_64
> # BASEDIR = ${PWD}
> # INSTALL = ${HOME}
> # LIBINST = $(INSTALL)/$(BIN)
> # BININST = $(INSTALL)/$(BIN)
> # CPLMODE = nocpl
> # IOAPIDEFS =
> # PVMINCL =
diff ioapi/Makeinclude.Linux2_x86_64dbg ioapi/Makeinclude.Linux2_x86_64dbg.old
26,28c26
< DBGFLAGS = -g -Wall -Wextra -Warray-temporaries -Wconversion -fimplicit-none -fbacktrace -ffree-line-length-none -fcheck=all -ffpe-trap=zero,overflow,underflow -finit-real=nan
< DBGFLAGS =
< MFLAGS = -Wsurprising -fbounds-check -finit-real=snan -m64 ${DBGFLAGS} -Wno-tabs
---
> MFLAGS = -Wsurprising -fbounds-check -finit-real=snan -m64
Instalamos librerías
make configure >& run_configure.log make all >& run_make.log
Si no hay problemas
$ ls -l Linux2_x86_64/ | grep rwx | grep -v lrwxrwxrwx | awk '{print $9}' | tr '\n' ' '
airs2m3 bcwndw camxtom3 datshift dayagg factor findwndw greg2jul gregdate gridprobe insertgrid jul2greg juldate juldiff julshift kfxtract
latlon m3agmask m3agmax m3combo m3cple m3diff m3edhdr m3fake m3hdr m3interp m3mask m3merge m3pair m3probe m3stat m3totxt m3tproc m3tshift
m3wndw m3xtract mpasdiff mpasstat mpastom3 mtxblend mtxbuild mtxcalc mtxcple presterp presz projtool randomstat selmrg2d timediff timeshift
vertimeproc vertintegral vertot wndwdesc wrfgriddesc wrftom3
Instalando:
mkdir ~/MODELOS/CMAQ/gnu/LIBRARIES/ioapi make install >& run_install.log ls ~/MODELOS/CMAQ/gnu/LIBRARIES/ioapi/Linux2_x86_64/ airs2m3 greg2jul julshift m3cple m3merge m3utilio.mod modpdata.mod mtxcalc timediff wrftom3 bcwndw gregdate kfxtract m3diff m3pair m3wndw modwrfio.mod mtxcple timeshift camxtom3 gridprobe latlon m3edhdr m3probe m3xtract mpasdiff presterp vertimeproc datshift insertgrid libioapi.a m3fake m3stat modatts3.mod mpasstat presz vertintegral dayagg jul2greg m3agmask m3hdr m3totxt modgctp.mod mpastom3 projtool vertot factor juldate m3agmax m3interp m3tproc modmpasfio.mod mtxblend randomstat wndwdesc findwndw juldiff m3combo m3mask m3tshift modncfio.mod mtxbuild selmrg2d wrfgriddesc cp ioapi/fixed_src/* Linux2_x86_64/ cp ioapi/fixed_src/* /home/solange.luque/MODELOS/CMAQ/gnu/LIBRARIES/ioapi/Linux2_x86_64/
[editar] CMAQ
NOTA: Asegurarse que no hay ningún entorno de compiladores activado automáticamente en el .bashrc
[editar] intel
Yendo al directorio de trabajo
cd /home/solange.luque/MODELOS/CMAQ/intel mkdir src cd src git clone https://github.com/USEPA/CMAQ.git CMAQ-master head -n 1 CMAQ-master/README.md CMAQv5.4 cd CMAQ-master/ ls bldit_project.csh CCTM config_cmaq.csh DOCS license.md POST PREP PYTOOLS README.md UTIL
Preparando configuración de la compilación
cp bldit_project.csh bldit_project.csh.old
diff bldit_project.csh bldit_project.csh.old
19,20c19
< #set CMAQ_HOME = ${PWD}/CMAQ_Project
< set CMAQ_HOME = /home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project
---
> set CMAQ_HOME = /home/username/path
Compilamos!
./bldit_project.csh >& run_bldit.log tail run_bldit.log mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/POST/hr2day' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/POST/hr2day/scripts' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/POST/sitecmp' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/POST/sitecmp/scripts' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/POST/sitecmp_dailyo3' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/POST/sitecmp_dailyo3/scripts' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/POST/writesite' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/POST/writesite/scripts' Configuration and Run Scripts have been Extracted and placed in: /home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project You may now edit these scripts to conform to your system and run options.
Vamos al directorio
cd CMAQ_Project/ cp config_cmaq.csh config_cmaq.csh.old diff config_cmaq.csh config_cmaq.csh.old 88,95c88,95 < setenv IOAPI_INCL_DIR /home/solange.luque/libraries/ioapi/v3.2-20200828/intel/Linux2_x86_64ifort #> I/O API include header files < setenv IOAPI_LIB_DIR /home/solange.luque/libraries/ioapi/v3.2-20200828/intel/Linux2_x86_64ifort #> I/O API libraries < setenv NETCDF_LIB_DIR /opt/netcdf/netcdf-4/intel/2021.4.0/lib #> netCDF C directory path < setenv NETCDF_INCL_DIR /opt/netcdf/netcdf-4/intel/2021.4.0/include #> netCDF C directory path < setenv NETCDFF_LIB_DIR /opt/netcdf/netcdf-4/intel/2021.4.0/lib #> netCDF Fortran directory path < setenv NETCDFF_INCL_DIR /opt/netcdf/netcdf-4/intel/2021.4.0/include #> netCDF Fortran directory path < setenv MPI_INCL_DIR /opt/intel/oneapi/mpi/2021.4.0/include #> MPI Include directory path < setenv MPI_LIB_DIR /opt/intel/oneapi/mpi/2021.4.0/lib #> MPI Lib directory path --- > setenv IOAPI_INCL_DIR ioapi_inc_intel #> I/O API include header files > setenv IOAPI_LIB_DIR ioapi_lib_intel #> I/O API libraries > setenv NETCDF_LIB_DIR netcdf_lib_intel #> netCDF C directory path > setenv NETCDF_INCL_DIR netcdf_inc_intel #> netCDF C directory path > setenv NETCDFF_LIB_DIR netcdff_lib_intel #> netCDF Fortran directory path > setenv NETCDFF_INCL_DIR netcdff_inc_intel #> netCDF Fortran directory path > setenv MPI_INCL_DIR mpi_incl_intel #> MPI Include directory path > setenv MPI_LIB_DIR mpi_lib_intel #> MPI Lib directory path 99c99 < setenv myFC /opt/intel/oneapi/mpi/2021.4.0/bin/mpiifort --- > setenv myFC mpiifort 103c103 < setenv myLINK_FLAG "-qopenmp" --- > setenv myLINK_FLAG #"-qopenmp-simd" openMP not supported w/ CMAQ ./config_cmaq.csh intel >& run_config-cmaq.log cat run_config-cmaq.log Compiler is set to intel
Compilamos!
cd CCTM/scripts/ mkdir BLD_CCTM_v54_intel cp -R /opt/intel/oneapi/mpi/2021.4.0/include/* BLD_CCTM_v54_intel/ ./bldit_cctm.csh intel >& run_bldit_cctm.log ls BLD_CCTM_v54_intel/*exe BLD_CCTM_v54_intel/CCTM_v54.exe
NOTA: Si se está intentando una recompilación, antes vaciar el directorio
rm -rf BLD_CCTM_v54_intel/*
[editar] gnu
Yendo al directorio de trabajo
/home/solange.luque/MODELOS/CMAQ/gnu/ mkdir src cd src git clone https://github.com/USEPA/CMAQ.git CMAQ-master head -n 1 ../../../README.md CMAQv5.4 cd CMAQ-master/ ls bldit_project.csh CCTM config_cmaq.csh DOCS license.md POST PREP PYTOOLS README.md UTIL
Preparando configuración de la compilación
cp bldit_project.csh bldit_project.csh.old
diff bldit_project.csh bldit_project.csh.old
19,20c19
< #set CMAQ_HOME = ${PWD}/CMAQ_Project
< set CMAQ_HOME = /home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project
---
> set CMAQ_HOME = /home/username/path
Compilamos!
./bldit_project.csh >& run_bldit.log tail run_bldit.log mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project/POST/hr2day' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project/POST/hr2day/scripts' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project/POST/sitecmp' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project/POST/sitecmp/scripts' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project/POST/sitecmp_dailyo3' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project/POST/sitecmp_dailyo3/scripts' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project/POST/writesite' mkdir: created directory '/home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project/POST/writesite/scripts' Configuration and Run Scripts have been Extracted and placed in: /home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/CMAQ_Project You may now edit these scripts to conform to your system and run options.
Vamos al directorio
cd CMAQ_Project/ cp config_cmaq.csh config_cmaq.csh.old diff config_cmaq.csh config_cmaq.csh.old 151,158c151,158 < setenv IOAPI_INCL_DIR /home/solange.luque/libraries/ioapi/v3.2-20200828/gnu/Linux2_x86_64 #> I/O API include header files < setenv IOAPI_LIB_DIR /home/solange.luque/libraries/ioapi/v3.2-20200828/gnu/Linux2_x86_64 #> I/O API libraries < setenv NETCDF_LIB_DIR /opt/netcdf/netcdf-4/gnu/10.2.1/lib #> netCDF C directory path < setenv NETCDF_INCL_DIR /opt/netcdf/netcdf-4/gnu/10.2.1/include #> netCDF C directory path < setenv NETCDFF_LIB_DIR /opt/netcdf/netcdf_c-4.8.1_fortran-4.5.3/gnu/10.2.1/lib #> netCDF Fortran directory path < setenv NETCDFF_INCL_DIR /opt/netcdf/netcdf_c-4.8.1_fortran-4.5.3/gnu/10.2.1/include #> netCDF Fortran directory path < setenv MPI_INCL_DIR /opt/openmpi/openmpi-4.1.2/gnu/10.2.1/include #> MPI Include directory path < setenv MPI_LIB_DIR /opt/openmpi/openmpi-4.1.2/gnu/10.2.1/lib #> MPI Lib directory path --- > setenv IOAPI_INCL_DIR iopai_inc_gcc #> I/O API include header files > setenv IOAPI_LIB_DIR ioapi_lib_gcc #> I/O API libraries > setenv NETCDF_LIB_DIR netcdf_lib_gcc #> netCDF C directory path > setenv NETCDF_INCL_DIR netcdf_inc_gcc #> netCDF C directory path > setenv NETCDFF_LIB_DIR netcdff_lib_gcc #> netCDF Fortran directory path > setenv NETCDFF_INCL_DIR netcdff_inc_gcc #> netCDF Fortran directory path > setenv MPI_INCL_DIR mpi_incl_gcc #> MPI Include directory path > setenv MPI_LIB_DIR mpi_lib_gcc #> MPI Lib directory path 162c162 < setenv myFC /opt/openmpi/openmpi-4.1.2/gnu/10.2.1/bin/mpifort --- > setenv myFC mpifort 166,167c166,167 < setenv myFFLAGS "-ffixed-form -ffixed-line-length-132 -funroll-loops -finit-character=32 -fallow-argument-mismatch" < setenv myFRFLAGS "-ffree-form -ffree-line-length-none -funroll-loops -finit-character=32 -frecursive -fallow-argument-mismatch" --- > setenv myFFLAGS "-ffixed-form -ffixed-line-length-132 -funroll-loops -finit-character=32" > setenv myFRFLAGS "-ffree-form -ffree-line-length-none -funroll-loops -finit-character=32" 169c169 < setenv myLINK_FLAG "-fopenmp" # openMP not supported w/ CMAQ --- > setenv myLINK_FLAG # "-fopenmp" openMP not supported w/ CMAQ ./config_cmaq.csh gcc >& run_config-cmaq.log cat run_config-cmaq.log Compiler is set to gcc
NOTA: en caso que aparezca en el run_config-cmaq.log 0: Event not found., editar el config_cmaq.csh e imprimir por pantalla la variable $CMAQ_LIB. Ahí se creean unos directorios que si ha habido algún problema, no se llenan bien. Es recomendable borrarlos y volver a lanzar.
rm -rf /home/solange.luque/MODELOS/CMAQ/gnu/src/CMAQ-master/lib/x86_64/gcc/ioapi
Compilar el Chemistry Transport Model (CCTM)
cd CCTM/scripts/ mkdir BLD_CCTM_v54_gcc cp -R /opt/openmpi/openmpi-4.1.2/gnu/10.2.1/include/* BLD_CCTM_v54_gcc/ ./bldit_cctm.csh gcc >& run_bldit_cctm.log ls BLD_CCTM_v54_gcc/*exe BLD_CCTM_v54_gcc/CCTM_v54.exe
NOTA: Si se está intentando una recompilación, antes vaciar el directorio
rm BLD_CCTM_v54_gcc/*
[editar] Usando
Ejemplos de uso de CMAQ (útiles ya compilados e instalados en hydra)
* Editor emisiones: SMOKE * Editor condiciones atmosféricas iniciales / entorno: MCIP * Editor condiciones iniciales químicas: icon * Editor condiciones borde químicas: bcon
[editar] Compilación MCIP
Preparado de las condiciones con MCIP usando la script: /home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/PREP/mcip/scripts/run_mcip.csh
export CMAQ_HOME=/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/ cd /home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/PREP/mcip/scripts cp run_mcip.csh run_mcip.csh.old diff run_mcip.csh run_mcip.csh.old 125,129c125 < # config_cmaq.csh modifies $CMAQ_HOME < set val = $CMAQ_HOME < source $CMAQ_HOME/config_cmaq.csh intel < set CMAQ_HOME = $val < echo $0": Solange 2 CMAQ_HOME: "$CMAQ_HOME --- > source $CMAQ_HOME/config_cmaq.csh 133c129 < set GridName = AMBA # 16-character maximum --- > set GridName = 2016_12SE1 # 16-character maximum 135,136c131,132 < set DataPath = /home/solange.luque/estudios/CMAQ-ideal/DATA < set InMetDir = $DataPath/wrf --- > set DataPath = $CMAQ_DATA > set InMetDir = $DataPath/wrf 142,143d137 < < echo $0": Solange: "$ProgDir 163,164c157,159 < set InMetFiles = ( $InMetDir/wrfout_d03_2012-11-15_00:00:00 \ < $InMetDir/wrfout_d03_2012-11-15_12:00:00 ) --- > set InMetFiles = ( $InMetDir/subset_wrfout_d01_2016-07-01_00:00:00 \ > $InMetDir/subset_wrfout_d01_2016-07-02_00:00:00 \ > $InMetDir/subset_wrfout_d01_2016-07-03_00:00:00 ) 166,167c161,162 < set IfGeo = "T" < set InGeoFile = $InGeoDir/geo_em.d03.nc --- > set IfGeo = "F" > set InGeoFile = $InGeoDir/geo_em_d01.nc 194,195c189,190 < set MCIP_START = 2012-11-15-00:10:00.0000 # [UTC] < set MCIP_END = 2012-11-15-50:00:00.0000 # [UTC] --- > set MCIP_START = 2016-07-02-00:00:00.0000 # [UTC] > set MCIP_END = 2016-07-03-00:00:00.0000 # [UTC] 197c192 < set INTVL = 10 # [min] --- > set INTVL = 60 # [min] 221c216 < set BTRIM = 5 --- > set BTRIM = 0
Compilando mcip
cd /home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/PREP/mcip/src vim /opt/load-libs.sh source /opt/env_scripts/load_intel-2021.4.0_mpich-3.4.2.sh diff Makefile Makefile.old 50,52c50,52 < FC = /opt/intel/oneapi/compiler/2021.4.0/linux/bin/intel64/ifort < NETCDF = /opt/netcdf/netcdf-4/intel/2021.4.0 < IOAPI_ROOT = /home/solange.luque/MODELOS/CMAQ/intel/LIBRARIES/ioapi --- > FC = ifort > NETCDF = /usr/local/apps/netcdf-4.7.3/intel-19.0 > IOAPI_ROOT = /usr/local/apps/ioapi-3.2_20181011/intel-19.0 56,59c56,57 < #LIBS = -L$(IOAPI_ROOT)/lib -lioapi \ < # -L$(NETCDF)/lib -lnetcdff -lnetcdf < LIBS = -L$(IOAPI_ROOT)/Linux2_x86_64ifort -lioapi \ < -L$(NETCDF)/lib -lnetcdff -lnetcdf -qopenmp --- > LIBS = -L$(IOAPI_ROOT)/lib -lioapi \ > -L$(NETCDF)/lib -lnetcdff -lnetcdf make all >& run_make.log ls *exe mcip.exe
Se copia la script en donde se generaron los datos para asegurar su reproducibilidad
cp run_mcip.csh /home/solange.luque/estudios/CMAQ-ideal/DATA
[editar] Compilación icon
Empezando en
/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/PREP/icon/scripts ./bldit_icon.csh intel >& run_bldit_icon.log ls BLD_ICON_v54_intel/ avprofile_cb6r3m_ae7_kmtbr_hemi2016_v53beta2_m3dry_col051_row068.csv avprofile_racm_ae6_aq_derived_from_cb6r3m_ae7_kmtbr_hemi2016_v53beta2_m3dry_col051_row068.csv avprofile_saprc07tc_ae6_aq_derived_from_cb6r3m_ae7_kmtbr_hemi2016_v53beta2_m3dry_col051_row068.csv avprofile_saprc07tic_ae7i_aq_derived_from_cb6r3m_ae7_kmtbr_hemi2016_v53beta2_m3dry_col051_row068.csv findex.F HGRD_DEFN.F icon.F ICON_v54.cfg IC_PARMS.F lat_lon.F legacy_PM_toxics_profile.csv lr_interp.F m3_ck_ctmmet.F m3_ck_ctms.F m3_ck_icmet.F m3_driver.F m3_icout.F m3_vinterp.F Makefile Makefile.intel opn_ic_file.F prof_driver.F prof_icout.F prof_vinterp.F VGRD_DEFN.F
Compilando:
cd BLD_ICON_v54_intel /opt/load-libs.sh 1 source /opt/env_scripts/load_intel-2021.4.0_mpich-3.4.2.sh make >& run_make.log ls *exe ICON_v54.exe
[editar] Compilación bcon
Empezando desde /home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/PREP/bcon/scripts
./bldit_bcon.csh intel >& run_bldit_bcon.log cd BLD_BCON_v54_intel/ ls BLD_BCON_v54_intel/*exe BLD_BCON_v54_intel/BCON_v54.exe
[editar] Benchmark
Descargando los datos del test-case de acá
Datos en hydra $CMAQ_DATA=/home/solange.luque/MODELOS/CMAQ/DATA/benchmark
tar xvfz CMAQv5.4_2018_12NE3_Benchmark_2Day_Input.tar.gz du -hsc ./CMAQv5.4_2018_12NE3_Benchmark_2Day_Input 56G ./CMAQv5.4_2018_12NE3_Benchmark_2Day_Input
Home CMAQ en hydra $CMAQ_HOME=/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project
Enlazando los datos
cd /home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project mkdir -p data cd data ln -s /home/solange.luque/MODELOS/CMAQ/DATA/benchmark/CMAQv5.4_2018_12NE3_Benchmark_2Day_Input/2018_12NE3 ./
Corriendo benchmark
source /opt/env_scripts/load_intel-2021.4.0_mpich-3.4.2.sh
cd $CMAQ_HOME/CCTM/scripts
cp run_cctm_Bench_2018_12NE3.csh run_cctm_Bench_2018_12NE3.csh.old
diff run_cctm_Bench_2018_12NE3.csh run_cctm_Bench_2018_12NE3.csh.old
716,717c716
< #( time -p mpirun -np $NPROCS $BLD/$EXEC ) |& tee buff_${EXECUTION_ID}.txt
< (mpirun -np $NPROCS $BLD/$EXEC ) |& tee buff_${EXECUTION_ID}.txt
---
> ( /usr/bin/time -p mpirun -np $NPROCS $BLD/$EXEC ) |& tee buff_${EXECUTION_ID}.txt
721c720
< #rm -rf buff_${EXECUTION_ID}.txt
---
> rm -rf buff_${EXECUTION_ID}.txt
732d730
< echo "Have a look into buff_${EXECUTION_ID}.txt"
735d732
< rm -rf buff_${EXECUTION_ID}.txt
qsub launch_cctm_intel.pb
#./run_cctm_Bench_2018_12NE3.csh >& run_Bench_2018-12NE3.log
tail -n 30 run_Bench_2018-12NE3.log
==============================================
|>--- PROGRAM COMPLETED SUCCESSFULLY ---<|
==============================================
Date and time 0:00:00 July 2, 2018 (2018183:000000)
The elapsed time for this simulation was 2206.0 seconds.
CMAQ Processing of Day 20180701 Finished at Wed 16 Nov 2022 04:11:26 PM -03
\\\\\=====\\\\\=====\\\\\=====\\\\\=====/////=====/////=====/////=====/////
==================================
***** CMAQ TIMING REPORT *****
==================================
Start Day: 2018-07-01
End Day: 2018-07-01
Number of Simulation Days: 1
Domain Name: 2018_12NE3
Number of Grid Cells: 367500 (ROW x COL x LAY)
Number of Layers: 35
Number of Processes: 32
All times are in seconds.
Num Day Wall Time
01 2018-07-01 2206.0
Total Time = 2206.00
Avg. Time = 2206.00
[editar] caso ideal
Partimos de una simulación de WRF y creamos los forzantes atmosféricos
Directorio de trabajo: /home/solange.luque/estudios/CMAQ-ideal
[editar] Meteorología
Para generar las condiciones meteorológicas ideales vamos a usar de base condiciones reales de una corridade WRF (wrfout_d03: dominio sobre AMBA a 1 km resolución, wrfour_d01: dominio centro SA a 50 km):
ls /home/solange.luque/estudios/CMAQ-ideal/DATA/wrf geo_em.d03.nc wrfout_d01_2012-08-03_00:00:00 wrfout_d03_2012-11-15_00:00:00 wrfout_d03_2012-11-15_12:00:00
A partir de estos ficheros creamos los ficheros meteorológicos ideales con velocidad constante usando el script getpoint_everywhere. Por ejemplo, para una simulación con solo velocidad de viento en la dirección horizontal y velocidad de 3m/s
python3 getpoint_everywhere.py -i 60 -j 60 -x west_east -y south_north -f 'wrfout_d03_2012-11-15_00:00:00' -v 'U@alloverct@3.:V@alloverct@0.' -s 'Time@0@-9@6' python3 getpoint_everywhere.py -i 60 -j 60 -x west_east -y south_north -f 'wrfout_d03_2012-11-15_12:00:00' -v 'U@alloverct@3.:V@alloverct@0.' -s 'Time@0@-9@6'
Esto genera dos ficheros que renombramos:
wrfout_d03_2012-11-15_00:00:00_3 wrfout_d03_2012-11-15_12:00:00_3
Ahora vamos a correr mcip con estas condiciones. Partiendo del run_mcip.csh</pre> que creamos para el AMBA (caso prueba):
export CMAQ_HOME=/home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/ cd /home/solange.luque/MODELOS/CMAQ/intel/src/CMAQ-master/CMAQ_Project/PREP/mcip/scripts/ cp run_mcip.csh run_mcip_ideal.csh diff run_mcip.csh run_mcip_ideal.csh 131c131 < set APPL = AMBA --- > set APPL = AMBAidealArea 135c135 < set DataPath = /home/solange.luque/estudios/CMAQ-AMBA/prueba/DATA --- > set DataPath = /home/solange.luque/estudios/CMAQ-ideal/DATA 163,165c163,164 < set InMetFiles = ( $InMetDir/wrfout_d03_2012-11-14_12:00:00 \ < $InMetDir/wrfout_d03_2012-11-15_00:00:00 \ < $InMetDir/wrfout_d03_2012-11-15_12:00:00 ) --- > set InMetFiles = ( $InMetDir/wrfout_d03_2012-11-15_00:00:00_3 \ > $InMetDir/wrfout_d03_2012-11-15_12:00:00_3)
Ahora sí, corremos mcip:
./run_mcip_ideal.csh >& run_mcip_ideal.log
[editar] caso prueba AMBA
WORKDIR = /home/solange.luque/estudios/CMAQ-AMBA/prueba
Qué se necesita:
- Tener una salida de WRF y perararla para CMAQ
- Inventarios de emisiones y prepararlos para CMAQ
- Condiciones de contorno e iniciales para la química atmosférica
- Configurar CMAQ
- Simular CMAQ
Todos los pasos se explican con más detalle CMAQ/pruebaAMBA
