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Merge pull request #100 from GEOS-ESM/develop
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develop into main
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@mmanyin
mmanyin authored Aug 17, 2020
2 parents 5522894 + 0bf97c0 commit c4b92c3
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Showing 2 changed files with 80 additions and 79 deletions.
7 changes: 4 additions & 3 deletions .circleci/config.yml
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Original file line number Diff line number Diff line change
@@ -1,8 +1,9 @@
version: 2
version: 2.1
jobs:
build:
docker:
- image: gmao/geos-build-env-gcc-source:6.0.13-openmpi_4.0.3-gcc_9.3.0
- image: gmao/ubuntu20-geos-env-mkl:6.0.13-openmpi_4.0.4-gcc_10.2.0
resource_class: xlarge
working_directory: /root/project
steps:
- run:
Expand Down Expand Up @@ -34,4 +35,4 @@ jobs:
name: "Build"
command: |
cd ${CIRCLE_WORKING_DIRECTORY}/GEOSgcm/build
make -j2 install
make -j"$(nproc)" install
152 changes: 76 additions & 76 deletions GEOSpchem_GridComp/GEOS_PChemGridComp.F90
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Original file line number Diff line number Diff line change
Expand Up @@ -112,12 +112,12 @@ module GEOS_PChemGridCompMod
use ESMF
use MAPL
use Chem_Mod
use netcdf


implicit none
private
#include "mpif.h"
include "netcdf.inc"

! !PUBLIC MEMBER FUNCTIONS:

Expand Down Expand Up @@ -826,53 +826,53 @@ subroutine Initialize ( GC, IMPORT, EXPORT, CLOCK, RC )
VERIFY_(STATUS)

#ifdef NETCDF_NEED_NF_MPIIO
STATUS = NF_OPEN_PAR(trim(PCHEMFILE),IOR(NF_NOWRITE,NF_MPIIO),comm,info,UNIT)
STATUS = NF90_OPEN_PAR(trim(PCHEMFILE),IOR(NF90_NOWRITE,NF90_MPIIO),comm,info,UNIT)
#else
STATUS = NF_OPEN_PAR(trim(PCHEMFILE),NF_NOWRITE,comm,info,UNIT)
STATUS = NF90_OPEN_PAR(trim(PCHEMFILE),NF90_NOWRITE,comm,info,UNIT)
#endif

#else
if ( MAPL_am_I_root() ) then
STATUS = NF_OPEN(trim(PCHEMFILE),NF_NOWRITE,UNIT)
STATUS = NF90_OPEN(trim(PCHEMFILE),NF90_NOWRITE,UNIT)
#endif
if(status /= nf_noerr) then
if(status /= NF90_NOERR) then
print*,'Error opening file ',trim(PCHEMFILE), status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif

! Read various dimension and global information including
! number of levels, and the number of species in the PCHEMFILE.
!--------------------------------------------------------------

STATUS = NF_INQ_DIMID(UNIT, 'lat', dimid)
if(status /= nf_noerr) then
STATUS = NF90_INQ_DIMID(UNIT, 'lat', dimid)
if(status /= NF90_NOERR) then
print*,'Error getting dimid for lat', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_INQ_DIMLEN(UNIT, dimid, PCHEM_STATE%NLATS)
if(status /= nf_noerr) then
STATUS = NF90_INQUIRE_DIMENSION(UNIT, dimid, len=PCHEM_STATE%NLATS)
if(status /= NF90_NOERR) then
print*,'Error getting dimlen for lat', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_INQ_DIMID(UNIT, 'lev', dimid)
if(status /= nf_noerr) then
STATUS = NF90_INQ_DIMID(UNIT, 'lev', dimid)
if(status /= NF90_NOERR) then
print*,'Error getting dimid for lev', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_INQ_DIMLEN(UNIT, dimid, PCHEM_STATE%NLEVS)
if(status /= nf_noerr) then
STATUS = NF90_INQUIRE_DIMENSION(UNIT, dimid, len=PCHEM_STATE%NLEVS)
if(status /= NF90_NOERR) then
print*,'Error getting dimlen for lev', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_GET_ATT_INT(UNIT, NF_GLOBAL, 'NSPECIES', NSPECIES)
if(status /= nf_noerr) then
STATUS = NF90_GET_ATT(UNIT, NF90_GLOBAL, 'NSPECIES', NSPECIES)
if(status /= NF90_NOERR) then
print*,'Error getting NSPECIES', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
_ASSERT(PCHEM_STATE%NSPECIES==NSPECIES,'needs informative message')
Expand All @@ -884,22 +884,22 @@ subroutine Initialize ( GC, IMPORT, EXPORT, CLOCK, RC )
PCHEM_STATE%begClimYear = 1
PCHEM_STATE%endClimYear = 1
ELSE
STATUS = NF_GET_ATT_INT(UNIT, NF_GLOBAL, 'begClimYear', PCHEM_STATE%begClimYear)
if(status /= nf_noerr) then
STATUS = NF90_GET_ATT(UNIT, NF90_GLOBAL, 'begClimYear', PCHEM_STATE%begClimYear)
if(status /= NF90_NOERR) then
print*,'Error getting begClimYear', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_GET_ATT_INT(UNIT, NF_GLOBAL, 'endClimYear', PCHEM_STATE%endClimYear)
if(status /= nf_noerr) then
STATUS = NF90_GET_ATT(UNIT, NF90_GLOBAL, 'endClimYear', PCHEM_STATE%endClimYear)
if(status /= NF90_NOERR) then
print*,'Error getting endClimYear', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_GET_ATT_INT(UNIT, NF_GLOBAL, 'climYears' , climYears)
if(status /= nf_noerr) then
STATUS = NF90_GET_ATT(UNIT, NF90_GLOBAL, 'climYears' , climYears)
if(status /= NF90_NOERR) then
print*,'Error getting climYears', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif

Expand Down Expand Up @@ -937,28 +937,28 @@ subroutine Initialize ( GC, IMPORT, EXPORT, CLOCK, RC )
if ( MAPL_am_I_root() ) then
#endif

STATUS = NF_INQ_VARID(UNIT, 'lat', varid)
if(status /= nf_noerr) then
STATUS = NF90_INQ_VARID(UNIT, 'lat', varid)
if(status /= NF90_NOERR) then
print*,'Error getting varid for lat', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_GET_VAR_REAL(UNIT, varid, PCHEM_STATE%LATS)
if(status /= nf_noerr) then
STATUS = NF90_GET_VAR(UNIT, varid, PCHEM_STATE%LATS)
if(status /= NF90_NOERR) then
print*,'Error getting values for lat', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_INQ_VARID(UNIT, 'lev', varid)
if(status /= nf_noerr) then
STATUS = NF90_INQ_VARID(UNIT, 'lev', varid)
if(status /= NF90_NOERR) then
print*,'Error getting varid for lev', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
STATUS = NF_GET_VAR_REAL(UNIT, varid, PCHEM_STATE%LEVS)
if(status /= nf_noerr) then
STATUS = NF90_GET_VAR(UNIT, varid, PCHEM_STATE%LEVS)
if(status /= NF90_NOERR) then
print*,'Error getting values for lev', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
#ifdef H5_HAVE_PARALLEL
Expand All @@ -973,7 +973,7 @@ subroutine Initialize ( GC, IMPORT, EXPORT, CLOCK, RC )
VERIFY_(STATUS)

#endif
STATUS = NF_CLOSE(UNIT)
STATUS = NF90_CLOSE(UNIT)
call MAPL_TimerOff (MAPL,"-Read Header" )

! Allocate concentration and production rates and loss frequencies.
Expand Down Expand Up @@ -1318,18 +1318,18 @@ subroutine RUN ( GC, IMPORT, EXPORT, CLOCK, RC )
VERIFY_(STATUS)

#ifdef NETCDF_NEED_NF_MPIIO
STATUS = NF_OPEN_PAR(trim(PCHEMFILE),IOR(NF_NOWRITE,NF_MPIIO),comm,info,UNIT)
STATUS = NF90_OPEN_PAR(trim(PCHEMFILE),IOR(NF90_NOWRITE,NF90_MPIIO),comm,info,UNIT)
#else
STATUS = NF_OPEN_PAR(trim(PCHEMFILE),NF_NOWRITE,comm,info,UNIT)
STATUS = NF90_OPEN_PAR(trim(PCHEMFILE),NF90_NOWRITE,comm,info,UNIT)
#endif

#else
if ( MAPL_am_I_root() ) then
STATUS = NF_OPEN(trim(PCHEMFILE),NF_NOWRITE,UNIT)
STATUS = NF90_OPEN(trim(PCHEMFILE),NF90_NOWRITE,UNIT)
#endif
if(status /= nf_noerr) then
if(status /= NF90_NOERR) then
print*,'Error opening file ',trim(PCHEMFILE), status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif

Expand All @@ -1341,26 +1341,26 @@ subroutine RUN ( GC, IMPORT, EXPORT, CLOCK, RC )

DO K = 1,PCHEM_STATE%NSPECIES
FieldName = PCHEM_STATE%ITEMNAMES(K)
STATUS = NF_INQ_VARID(UNIT, trim(FieldName), varid)
if(status /= nf_noerr) then
STATUS = NF90_INQ_VARID(UNIT, trim(FieldName), varid)
if(status /= NF90_NOERR) then
print*,'Error getting varid for variable ',trim(FieldName), status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
! Need two separate reads because INDX2 isn't always sequentially after INDX1, otherwise
! we could combine the reads into one
start(3) = INDX1
STATUS = NF_GET_VARA_REAL(UNIT, varid, start, cnt, PCHEM_STATE%MNCV(:,:,K,1))
if(status /= nf_noerr) then
STATUS = NF90_GET_VAR(UNIT, varid, PCHEM_STATE%MNCV(:,:,K,1), start, cnt)
if(status /= NF90_NOERR) then
print*,'Error reading lower bracket month ',status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
start(3) = INDX2
STATUS = NF_GET_VARA_REAL(UNIT, varid, start, cnt, PCHEM_STATE%MNCV(:,:,K,2))
if(status /= nf_noerr) then
STATUS = NF90_GET_VAR(UNIT, varid, PCHEM_STATE%MNCV(:,:,K,2), start, cnt)
if(status /= NF90_NOERR) then
print*,'Error reading upper bracket month ',status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif

Expand All @@ -1375,55 +1375,55 @@ subroutine RUN ( GC, IMPORT, EXPORT, CLOCK, RC )
! ---------------------------------------------------------------------------------
IF(PCHEM_STATE%climYears == 1) THEN

STATUS = NF_INQ_VARID(UNIT, trim(FieldName)//'_PROD', varid)
if(status /= nf_noerr) then
STATUS = NF90_INQ_VARID(UNIT, trim(FieldName)//'_PROD', varid)
if(status /= NF90_NOERR) then
print*,'Error getting varid for variable ',trim(FieldName)//'_PROD', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
start(3) = INDX1
STATUS = NF_GET_VARA_REAL(UNIT, varid, start, cnt, PCHEM_STATE%MNPL(:,:,K,1,1))
if(status /= nf_noerr) then
STATUS = NF90_GET_VAR(UNIT, varid, PCHEM_STATE%MNPL(:,:,K,1,1), start, cnt)
if(status /= NF90_NOERR) then
print*,'Error reading lower bracket month for production ',status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
start(3) = INDX2
STATUS = NF_GET_VARA_REAL(UNIT, varid, start, cnt, PCHEM_STATE%MNPL(:,:,K,1,2))
if(status /= nf_noerr) then
STATUS = NF90_GET_VAR(UNIT, varid, PCHEM_STATE%MNPL(:,:,K,1,2), start, cnt)
if(status /= NF90_NOERR) then
print*,'Error reading upper bracket month for production ',status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
IF(K == PCHEM_STATE%H2O) PCHEM_STATE%MNPL(:,:,K,1,1) = PCHEM_STATE%MNPL(:,:,K,1,1)*(MAPL_H2OMW/MAPL_AIRMW)
IF(K == PCHEM_STATE%H2O) PCHEM_STATE%MNPL(:,:,K,1,2) = PCHEM_STATE%MNPL(:,:,K,1,2)*(MAPL_H2OMW/MAPL_AIRMW)
! Loss
! ----
STATUS = NF_INQ_VARID(UNIT, trim(FieldName)//'_LOSS', varid)
if(status /= nf_noerr) then
STATUS = NF90_INQ_VARID(UNIT, trim(FieldName)//'_LOSS', varid)
if(status /= NF90_NOERR) then
print*,'Error getting varid for variable ',trim(FieldName)//'_LOSS', status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
start(3) = INDX1
STATUS = NF_GET_VARA_REAL(UNIT, varid, start, cnt, PCHEM_STATE%MNPL(:,:,K,2,1))
if(status /= nf_noerr) then
STATUS = NF90_GET_VAR(UNIT, varid, PCHEM_STATE%MNPL(:,:,K,2,1), start, cnt)
if(status /= NF90_NOERR) then
print*,'Error reading lower bracket month for loss ',status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
start(3) = INDX2
STATUS = NF_GET_VARA_REAL(UNIT, varid, start, cnt, PCHEM_STATE%MNPL(:,:,K,2,2))
if(status /= nf_noerr) then
STATUS = NF90_GET_VAR(UNIT, varid, PCHEM_STATE%MNPL(:,:,K,2,2), start, cnt)
if(status /= NF90_NOERR) then
print*,'Error reading upper bracket month for loss ',status
print*, NF_STRERROR(status)
print*, NF90_STRERROR(status)
stop
endif
ENDIF

ENDDO

STATUS = NF_CLOSE(UNIT)
STATUS = NF90_CLOSE(UNIT)
VERIFY_(STATUS)

#ifdef H5_HAVE_PARALLEL
Expand Down

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