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Compile hycom oasis intel #219

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Compile hycom oasis intel #219

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500ebb8
Update Linux.fram.ifort_hycom
lilleannette Nov 24, 2023
7c9f9d5
Update nextsim_configuration.src
lilleannette Nov 24, 2023
dbba2e7
Update srjob.sh
lilleannette Nov 24, 2023
265350a
Update blkdat.input
lilleannette Nov 24, 2023
a9036c1
Update blkdat.input
lilleannette Nov 24, 2023
c7869c0
Update Linux.fram.ifort_hycom
caglartac Nov 27, 2023
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1 change: 0 additions & 1 deletion TP2a0.10/expt_01.0/blkdat.input
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Expand Up @@ -211,7 +211,6 @@ S-Z(15-11): dp00/f/x/i=3m/1.125/12m/1m; ds=1m/1.125/4m; src_2.2.12;
0 'flxoff' = net flux offset flag (0=F,1=T)
0 'flxsmo' = smooth surface fluxes (0=F,1=T)
1 'relax ' = activate lateral boundary nudging (0=F,1=T)
0 'trcrlx' = activate lat. bound. tracer nudging (0=F,1=T)
1 'priver' = rivers as a precipitation bogas (0=F,1=T)
0 'triver' = total river including Greenland (0=F,1=T)
0 'epmass' = treat evap-precip as a mass exchange (0=F,1=T)
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10 changes: 6 additions & 4 deletions TP2a0.10/expt_01.0/srjob.sh
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Expand Up @@ -34,10 +34,12 @@
##(( ncores = SLURM_NNODES * 24 ))
##(( ncores = SLURM_NNODES * 32 )) #on Fram

module load NCL/6.6.2-intel-2018b
module load FFTW/3.3.8-intel-2018b
module load Python/2.7.15-intel-2018b

module restore system
module load FFTW/3.3.10-GCC-11.3.0
module load ESMF/8.3.0-intel-2022a
module load Python/3.10.4-GCCcore-11.3.0
module load UDUNITS/2.2.28-GCCcore-11.3.0
module load intel/2022a

export NMPI=220
export SLURM_SUBMIT_DIR=$(pwd)
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1 change: 0 additions & 1 deletion TP5a0.06/expt_01.0/blkdat.input
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Expand Up @@ -213,7 +213,6 @@ S-Z(15-11): dp00/f/x/i=3m/1.125/12m/1m; ds=1m/1.125/4m; src_2.2.12;
1 'relax ' = activate lateral boundary nudging (0=F,1=T)
0 'trcrlx' = activate lat. bound. tracer nudging (0=F,1=T)
0 'priver' = rivers as a precipitation bogas (0=F,1=T)
0 'triver' = total river including Greenland (0=F,1=T)
0 'epmass' = treat evap-precip as a mass exchange (0=F,1=T)
0 'nmrsti' = 'restart' Restart filename. Dot and date appended. Empty: use old hycom name.
0 'nmrsto' = 'restart' Restart filename. Dot and date appended. Empty: use old hycom name.
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48 changes: 22 additions & 26 deletions hycom/RELO/config/Linux.fram.ifort_hycom
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Expand Up @@ -15,25 +15,23 @@
# LDFLAGS: Loader flags.
# EXTRALIBS: Extra local libraries (if any).
#
#INCLUDES = -I/cluster/software/netCDF-Fortran/4.4.4-intel-2017a-HDF5-1.8.18/include -I${ESMF_MOD_DIR} -I${ESMF_DIR}include -I./CICE/rundir/compile

# --- Mostafa: flags required for standalone HYCOM
INCLUDES = -I${ESMF_MOD_DIR} -I${ESMF_DIR}include -I./CICE/rundir/compile
OASIS_DIR = /cluster/projects/nn9878k/guibou/NANUK/oa3-mct_iimpi2022a/
LIBPSMILE = $(OASIS_DIR)/lib/libpsmile.MPI1.a $(OASIS_DIR)/lib/libmct.a $(OASIS_DIR)/lib/libmpeu.a $(OASIS_DIR)/lib/libscrip.
a
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The code seems to compile of with the extension "a" of "libscrip" on the next line (line 20) rather than at the end of $(OASIS_DIR)/lib/libscrip. , but it would be best to delete the newline command for clarity

LIBBUILD = $(OASIS_DIR)/build/lib
INCLUDES = -I$(NETCFD_DIR)/include/

FC = mpiifort
#FCFFLAGS = -traceback -g -O2 -fp-model source -warn nogeneral -convert big_endian -assume byterecl -real-size 64 -integer-size 32
FCFFLAGS = -g -convert big_endian -assume byterecl -cm -vec_report0 -w -O3 -tpp7 -xW -r8
#FCFFLAGS = -traceback -g -O2 -check all -fp-stack-check -fp-model source -warn nogeneral -convert big_endian -assume byterecl -real-size 64 -integer-size 32
#FCFFLAGS = -O2 -fconvert=big-endian -fdefault-real-8 -fdefault-double-8

FCFFLAGS := $(FCFFLAGS) $(INCLUDES)

FCFFLAGS = -g -convert big_endian -assume byterecl -cm -vec_report0 -w -O3 -tpp7 -xW -r8
FCFFLAGS := $(FCFFLAGS) $(INCLUDES) # -I$(LIBBUILD)
FCFFLAGS_OASIS = $(FCFFLAGS) -I$(LIBBUILD) -I$(OASIS_DIR)/build/lib/psmile.MPI1
CC = mpicc
CCFLAGS = -O
CCFLAGS = -O2
CCFLAGS_OASIS = -O2 -I. -cpp -Duse_comm_MPI1 -D__VERBOSE -DTREAT_OVERLAY -DDECOMP_APPLE -DUSE_DOUBLE_PRECISION


CPP = cpp -P
LD = $(FC)
#LDFLAGS = -V $(FCFFLAGS) -shared-intel -mcmodel=medium
LDFLAGS = $(FCFFLAGS) -mcmodel=medium

# ENDIAN_IO not needed due to byteswap compiler flag
Expand All @@ -42,20 +40,15 @@ LDFLAGS = $(FCFFLAGS) -mcmodel=medium
#
# if no STOKES:
# --- Mostafa: flags required for standalone HYCOM
CPPFLAGS = -DIA32 -DREAL8 -DMPI -DSERIAL_IO -DNAN2003 -DTIMER -DRELO -DNERSC_HYCOM_CICE

#CPPFLAGS = -DIA32 -DREAL8 -DMPI -DSERIAL_IO -DNAN2003 -DTIMER -DRELO -DUSE_ESMF -DUSE_ESMF_5 -DNERSC_HYCOM_CICE
CPPFLAGS = -DIA32 -DREAL8 -DMPI -DSERIAL_IO -DNAN2003 -DTIMER -DRELO -DNERSC_HYCOM_CICE -DCPL_OASIS_HYCOM -DOFFICEField
# for STOKES flag use
#CPPFLAGS = -DIA32 -DREAL8 -DMPI -DSERIAL_IO -DNAN2003 -DTIMER -DRELO -DUSE_ESMF -DUSE_ESMF_5 -DNERSC_HYCOM_CICE -DSTOKES
#EXTRALIBS = -L${ESMF_LIB_DIR}/ -lesmf -pgcpplibs
#EXTRALIBS = -L${ESMF_LIB_DIR}/ -lesmf -lfftw3 -lmkl -lnetcdff -lnetcdf -lmpi -lmpifort
# --- Mostafa: flags required for standalone HYCOM
EXTRALIBS = -lfftw3 -lmkl -lnetcdff -lnetcdf -lmpi -lmpifort


# from fabm
#CPPFLAGS += -D_FABM_ -I${HOME}/local/fabm/hycom/include
#EXTRALIBS += -L${HOME}/local/fabm/hycom/lib -lfabm
EXTRALIBS = $(LIBPSMILE) -lfftw3 -lnetcdf -lnetcdff
# from fabm
CPPFLAGS += -D_FABM_ -I${HOME}/local/fabm/hycom/include
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Line 50 should be commented out, so that the default does not require fabm

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added the fix, was tested on an different setup, it works but please have a look

EXTRALIBS += -L${HOME}/local/fabm/hycom/lib -lfabm
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Line 51 should be commented out, so that the default does not require fabm

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added the fix, was tested on an different setup, it works but please have a look


#
# --- generic make definitions
Expand All @@ -67,19 +60,22 @@ RM = \rm -f
# rules.
#

#mod_cpl_oasis:

.c.o:
$(CC) $(CPPFLAGS) $(CCFLAGS) -c $*.c

.f.o:
$(FC) $(FCFFLAGS) -c $*.f

.F.o:
$(FC) $(CPPFLAGS) $(FCFFLAGS) -c $*.F
.F.o:
$(FC) $(CPPFLAGS) $(FCFFLAGS) -c $*.F


#======= for Fabm use these

.f90.o:
$(FC) $(FCFFLAGS) -c $*.f90
$(FC) $(CCFLAGS_OASIS) $(FCFFLAGS_OASIS) -c $*.f90

.F90.o:
$(FC) $(CPPFLAGS) $(FCFFLAGS) -c $*.F90
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25 changes: 5 additions & 20 deletions hycom/RELO/config/nextsim_configuration.src
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Expand Up @@ -2,33 +2,18 @@
# must be sourced before compiling and running
export MACHINE_FRAM=1 # compile of core is slightly different on fram

# Load the right modules
module restore system
module load GCC/6.3.0-2.27
module load Boost/1.63.0-foss-2017a-Python-2.7.13
module load netCDF-C++4/4.3.0-foss-2017a-HDF5-1.8.18
module load CMake/3.9.1
module load netCDF-Fortran/4.4.4-foss-2017a-HDF5-1.8.18
#AS
module load PETSc/3.8.0-foss-2017a-Python-2.7.13
#AS


# Linking module and neXtSIM envinronment variables
CLUSTER_ROOT_DIR=/cluster/projects/nn2993k/sim
export PETSC_DIR=$EBROOTPETSC #AS#$CLUSTER_ROOT_DIR/packages/petsc/
export EBROOTBOOST=/opt/nextsim_intel/boost-1.67/
export BOOST_INCDIR=$EBROOTBOOST/include
export BOOST_LIBDIR=$EBROOTBOOST/lib
export NETCDF_DIR=$EBROOTNETCDFMINCPLUSPLUS4
export NETCDF_FOR_DIR=$EBROOTNETCDF
export OPENMPI_DIR=$EBROOTOPENMPI
export NETCDF_DIR=/cluster/software/netCDF/4.9.0-iimpi-2022a

# User or use-case specific directories
export NEXTSIMDIR=$HOME/Progs/NeXtSIM/nextsim
export NEXTSIMTOOLS_ROOT_DIR=$HOME/Progs/NeXtSIM/nextsim-tools
export NEXTSIMF_ROOT_DIR=$HOME/Progs/NeXtSIM/nextsimf
export NEXTSIM_ENV_ROOT_DIR=$HOME/Progs/NeXtSIM/nextsim-env
export SWARP_ROUTINES=$HOME/Progs/NeXtSIM/SWARP-routines
export INPUT_DATA_DIR=$CLUSTER_ROOT_DIR/data
export XSIM_COMP_VERBOSE=no

Expand All @@ -38,7 +23,7 @@ export NEXTSIM_MESH_DIR=$CLUSTER_ROOT_DIR/mesh
export NEXTSIM_DATA_DIR=$CLUSTER_ROOT_DIR/data_links

# GMSH related variables
export GMSH_DIR=$CLUSTER_ROOT_DIR/packages/gmsh/
export GMSH_DIR=/opt/nextsim_intel/gmsh-3.0.6/
export PATH=$PATH:$GMSH_DIR/bin
export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:$GMSH_DIR/lib

Expand All @@ -48,7 +33,7 @@ export AEROBULK_DIR=$CLUSTER_ROOT_DIR/packages/aerobulk/

# Oasis related variables
export USE_OASIS=true
export OASIS_DIR=/cluster/projects/nn9481k/oasis3-mct/oa3-mct_gfortran/
export OASIS_DIR=/cluster/projects/nn9878k/guibou/NANUK/oa3-mct_iimpi2022a/

# email for slurm jobs
export MY_EMAIL="[email protected]"
export MY_EMAIL=""