Revisión de 09:17 2 nov 2022

Instalando y usando SMOKE en hydra

Página de SMOKE: https://www.cmascenter.org/smoke/

Compilar

Archivo comprimido desde la página web (bajo registro previo)

smoke_v49.Linux2_x86_64ifort.tar.gz

intel

gcc

Directorio de instalación /home/solange.luque/MODELOS/SMOKE

Desplegando código

mv ~/smoke_v49.Linux2_x86_64ifort.tar.gz ./
mkdir gcc/
tar xvfz ../smoke_v49.Linux2_x86_64ifort.tar.gz 
mv subsys/smoke/src ./
mv subsys/smoke/Linux2_x86_64ifort ./
rmdir subsys/smoke/
rmdir subsys
mkdir Linux2_x86_64

Compilando

cd src
cp Makeinclude Makeinclude.old
cp Makeinclude Makeinclude.Linux2_x86_64
diff Makeinclude.Linux2_x86_64 Makeinclude.old
31c31
< BASEDIR = /home/solange.luque/MODELOS/SMOKE/gcc/src
---
> BASEDIR = ${SMK_HOME}/subsys/smoke/src
35c35
< IOBASE  = /home/solange.luque/libraries/ioapi/v3.2-20200828/gnu
---
> IOBASE  = ${SMK_HOME}/subsys/ioapi
40c40
< INSTDIR = /home/solange.luque/MODELOS/SMOKE/gcc/${BIN}
---
> INSTDIR = /somewhere/apps/${BIN}
48,49c48,49
< # IFLAGS = -I${IOINC} -I${INCDIR} -I${IOBIN}                #  Intel, Absoft, Pathscale, UNIX Fortran
<  IFLAGS = -I${IOINC} -I${INCDIR} -I${IOBIN}                #  GNU   Fortran
---
>  IFLAGS = -I${IOINC} -I${INCDIR} -I${IOBIN}                #  Intel, Absoft, Pathscale, UNIX Fortran
> # IFLAGS = -I${IOINC} -I${INCDIR} -I${IOBIN}                #  GNU   Fortran
53,54c53,54
< # EFLAG = -extend-source 132 -zero                       #  Intel Fortran
<  EFLAG = -ffixed-line-length-132  -fno-backslash       #  GNU   Fortran
---
>  EFLAG = -extend-source 132 -zero                       #  Intel Fortran
> # EFLAG = -ffixed-line-length-132  -fno-backslash       #  GNU   Fortran
59c59
< MFLAGS  = -fbacktrace
---
> MFLAGS  = -traceback

Hay un error de sintaxis Fortran en /home/solange.luque/libraries/ioapi/v3.2-20200828/gnu/ioapi/fixed_src/PARMS3.EXT, en la línea #104, queda:

!        INTEGER, PARAMETER :: M3TYPES( NM3TYPES ) =                             &
!     &        (/ M3INT, M3REAL, M3DBLE, M3INT8 /)
        INTEGER, PARAMETER :: M3TYPES( NM3TYPES ) = (/ M3INT, M3REAL, M3DBLE, M3INT8 /)

Copilamos

export BIN=Linux2_x86_64
ln -s Makeinclude.Linux2_x86_64 ./Makeinclude
make >& run_make.log
ls ../Linux2_x86_64 | grep -v .o | grep -v .mod
aggwndw        bluesky2inv        cemscan        cntlmat        extractida        gcntl4carb
grdmat         grwinven           invsplit       libfileset.a   metscan           mrgelev
mrggrid        mrgpt              pktreduc       smk2emis       smkinven          smkmerge
spcmat         tmpbeis3           tmpbeis4       uam2ncf

Usar

Empecemos por el test-case

NOTA: Los shells son todos #!/bin/csh, pero de verdad se utiliza #!/bin/tcsh

test-case

Sacado de la página de SMOKE https://github.com/CEMPD/SMOKE-TestCase/ (previo registro)

Directorio de trabajo: /home/solange.luque/MODELOS/SMOKE/DATA

googleDrive

SMOKE-TestCase-BEIS4-inputs.tar.gz-20221026T133036Z-001.zip       SMOKE-TestCase-inputs.tar.gz-20221026T133039Z-001.zip
SMOKE-TestCase-BEIS4-output.tar.gz-20221026T133038Z-001.zip       SMOKE-TestCase-output.tar.gz-20221026T133041Z-001.zip

unzip SMOKE-TestCase-BEIS4-inputs.tar.gz-20221026T133036Z-001.zip
unzip SMOKE-TestCase-BEIS4-output.tar.gz-20221026T133038Z-001.zip
unzip SMOKE-TestCase-inputs.tar.gz-20221026T133039Z-001.zip
unzip SMOKE-TestCase-output.tar.gz-20221026T133041Z-001.zip
tar xvfz SMOKE-TestCase-BEIS4-inputs.tar.gz  
tar xvfz SMOKE-TestCase-BEIS4-output.tar.gz  
tar xvfz SMOKE-TestCase-inputs.tar.gz  
tar xvfz SMOKE-TestCase-output.tar.gz

Nos queda:

ls
biogenics_output  SMOKE-TestCase-BEIS4-inputs.tar.gz                           
SMOKE-TestCase-inputs.tar.gz-20221026T133039Z-001.zip
ge_dat            SMOKE-TestCase-BEIS4-inputs.tar.gz-20221026T133036Z-001.zip  
SMOKE-TestCase-output.tar.gz
output_forQA      SMOKE-TestCase-BEIS4-output.tar.gz                           
SMOKE-TestCase-output.tar.gz-20221026T133041Z-001.zip
smoke4.7          SMOKE-TestCase-BEIS4-output.tar.gz-20221026T133038Z-001.zip
SMOKE-TestCase    SMOKE-TestCase-inputs.tar.gz

Descargamos archivos para simular en /home/solange.luque/MODELOS/SMOKE/DATA

mkdir scripts
git clone https://github.com/CEMPD/SMOKE-TestCase.git
ls 
SMOKE-TestCase

Preparando directorio para simular /home/solange.luque/estudios/SMOKE-TestCase

cp -R ~/MODELOS/SMOKE/DATA/SMOKE-TestCase/scripts ./
cd scripts 
diff directory_definitions.csh ~/MODELOS/SMOKE/scripts/SMOKE-TestCase/scripts/directory_definitions.csh 
13c13
< setenv INSTALL_DIR "/home/solange.luque/MODELOS/SMOKE/DATA"
---
> setenv INSTALL_DIR "/proj/ie/proj/SMOKE/chef"
19c19
< setenv MET_ROOT "/home/solange.luque/MODELOS/SMOKE/DATA/SMOKE-TestCase/inputs/biogenics"
---
> setenv MET_ROOT "/proj/ie/proj/TRECH/emissions/mcip"
24c24
< setenv MET_ROOT_3D "/home/solange.luque/MODELOS/SMOKE/DATA/SMOKE-TestCase/inputs/biogenics"
---
> setenv MET_ROOT_3D "/proj/ie/proj/TRECH/emissions/mcip"
46c46
< setenv SMOKE_LOCATION "/home/solange.luque/MODELOS/SMOKE/gcc/Linux2_x86_64"
---
> setenv SMOKE_LOCATION "/proj/ie/proj/CMAS/CMAQ/christos/SMOKE_REPO/exec/Linux2_x86_64ifort_medium"
53c53
< setenv IOAPI_LOCATION "/home/solange.luque/libraries/ioapi/v3.2-20200828/gnu/Linux2_x86_64"
---
> setenv IOAPI_LOCATION "/proj/ie/proj/CMAS/CMAQ/christos/SMOKE_test/SMOKE_4.8.1/subsys/ioapi-3.2/Linux2_x86_64ifort_medium"

Ajustando scripts al cluster:

$ cat /home/solange.luque/MODELOS/SMOKE/DATA/smoke4.7/scripts/emf/smk_ar_annual_emf.csh | grep py
set log_analyzer = $SCRIPTS/log_analyzer/log_analyzer.py
set path_parser  = $SCRIPTS/run/path_parser.py

• línea #1 de /home/solange.luque/MODELOS/SMOKE/DATA/smoke4.7/scripts/log_analyzer/log_analyzer.py, /home/solange.luque/MODELOS/SMOKE/DATA/smoke4.7/scripts/run/path_parser.py, /home/solange.luque/MODELOS/SMOKE/DATA/smoke4.7/scripts/annual_report/annual_report_v2.py

#!/usr/bin/env python3

Error de c-shell en el script /home/solange.luque/MODELOS/SMOKE/DATA/smoke4.7/scripts/run/set_months_v4.csh, sintaxis errónea en dar la cantidad de argumentos: está $# y tiene que ser $#argv web, en línea # 30:

if ( $#argv == 3 ) then

Generando

export LD_LIBRARY_PATH=/opt/netcdf/netcdf-4/gnu/10.2.1/lib/
mkdir /home/solange.luque/MODELOS/SMOKE/DATA/SMOKE-TestCase/scripts/logs
cd nonpoint/
./Annual_np_oilgas_12US1_2017gb_17j_TestCase.csh >& run_nonpoint.log