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Instalando y usando CMAQ en hydra

Contenido

Instalando librerias

Instalación en /home/solange.luque/MODELOS/CMAQ/[comp].

Existe un foro: https://forum.cmascenter.org/t/ioapi-installtion-unable/805

ioapi

Agarrar librerías ioapi

Instalándolas en /home/solange.luque/libraries/

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/

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

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/

CMAQ

NOTA: Asegurarse que no hay ningún entorno de compiladores activado automáticamente en el .bashrc

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
$ ./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/openmpi/openmpi-4.1.2/intel/2021.4.0/include/* BLD_CCTM_v54_intel/
$ ./bldit_cctm.csh intel >& run_bldit_cctm.log
$ ls BLD_CCTM_v54_intel/*exe

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/*

Usando

Obtenido de «https://wiki.cima.fcen.uba.ar/mediawiki/index.php?title=CMAQ&oldid=2066»
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