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Merge pull request #3 from immerse-project/fix_ssh
Fix ssh issues at the boudary
2 parents cb6b59b + bbafaed commit 36e9d33

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‎README.md‎

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@@ -9,8 +9,8 @@ cd wp6.2-demonstrator
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1010
Slurm examples:
1111
```shell
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./scripts/python/mkslurm_immerse -S 24 -s 16 -m 1 -C 9006 -g 0 -a n01-CLASS -j WP6.2 --gnu > scripts/run_nemo.slurm
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./scripts/python/mkslurm_immerse -S 24 -s 16 -m 1 -C 3668 -g 0 -a n01-CLASS -q short --gnu > scripts/run_nemo-short.slurm
12+
./scripts/python/mkslurm_immerse -S 24 -s 16 -m 1 -C 5504 -g 0 -a n01-CLASS -j WP6.2 -t 1-00:00:00 --gnu > scripts/run_nemo.slurm
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./scripts/python/mkslurm_immerse -S 24 -s 16 -m 1 -C 3712 -g 0 -a n01-CLASS -q short -t 0-00:20:00 --gnu > scripts/run_nemo-short.slurm
1414
```
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## Setup

‎arch/NOC/arch-X86_ARCHER2-Cray.fcm‎

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# compiler options for Archer CRAY XC-30 (using crayftn compiler)
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#
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# NCDF_HOME root directory containing lib and include subdirectories for netcdf4
4+
# HDF5_HOME root directory containing lib and include subdirectories for HDF5
5+
# XIOS_HOME root directory containing lib for XIOS
6+
# OASIS_HOME root directory containing lib for OASIS
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#
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# NCDF_INC netcdf4 include file
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# NCDF_LIB netcdf4 library
10+
# XIOS_INC xios include file (taken into accound only if key_iomput is activated)
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# XIOS_LIB xios library (taken into accound only if key_iomput is activated)
12+
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
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# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
14+
#
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# FC Fortran compiler command
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# FCFLAGS Fortran compiler flags
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# FFLAGS Fortran 77 compiler flags
18+
# LD linker
19+
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
20+
# FPPFLAGS pre-processing flags
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# AR assembler
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# ARFLAGS assembler flags
23+
# MK make
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# USER_INC complete list of include files
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# USER_LIB complete list of libraries to pass to the linker
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# CC C compiler used to compile conv for AGRIF
27+
# CFLAGS compiler flags used with CC
28+
#
29+
# Note that:
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# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
31+
# - fcm variables are starting with a % (and not a $)
32+
#
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%NCDF_HOME $NETCDF_DIR
34+
%HDF5_HOME $HDF5_DIR
35+
%XIOS_HOME /work/n01/shared/nemo/xios-2.5
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#OASIS_HOME
37+
38+
%NCDF_INC -I%NCDF_HOME/include -I%HDF5_HOME/include
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%NCDF_LIB -L%HDF5_HOME/lib -L%NCDF_HOME/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
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%XIOS_INC -I%XIOS_HOME/inc
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%XIOS_LIB -L%XIOS_HOME/lib -lxios
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#OASIS_INC -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
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#OASIS_LIB -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
44+
45+
%CPP cpp -Dkey_nosignedzero
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%FC ftn
47+
%FCFLAGS -em -s integer32 -s real64 -O2 -hflex_mp=intolerant
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%FFLAGS -em -s integer32 -s real64 -O2 -hflex_mp=intolerant
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%LD CC -Wl,"--allow-multiple-definition"
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%FPPFLAGS -P -traditional
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%LDFLAGS -lmpifort_cray
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%AR ar
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%ARFLAGS -r
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%MK gmake
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%USER_INC %XIOS_INC %NCDF_INC
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%USER_LIB %XIOS_LIB %NCDF_LIB
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#USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
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#USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
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60+
%CC cc
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%CFLAGS -O0
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bld::tool::fc_modsearch -J

‎arch/NOC/arch-X86_ARCHER2-Cray_4.2.fcm‎

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1+
# compiler options for Archer CRAY XC-30 (using crayftn compiler)
2+
#
3+
# NCDF_HOME root directory containing lib and include subdirectories for netcdf4
4+
# HDF5_HOME root directory containing lib and include subdirectories for HDF5
5+
# XIOS_HOME root directory containing lib for XIOS
6+
# OASIS_HOME root directory containing lib for OASIS
7+
#
8+
# NCDF_INC netcdf4 include file
9+
# NCDF_LIB netcdf4 library
10+
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
11+
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
12+
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
13+
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
14+
#
15+
# FC Fortran compiler command
16+
# FCFLAGS Fortran compiler flags
17+
# FFLAGS Fortran 77 compiler flags
18+
# LD linker
19+
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
20+
# FPPFLAGS pre-processing flags
21+
# AR assembler
22+
# ARFLAGS assembler flags
23+
# MK make
24+
# USER_INC complete list of include files
25+
# USER_LIB complete list of libraries to pass to the linker
26+
# CC C compiler used to compile conv for AGRIF
27+
# CFLAGS compiler flags used with CC
28+
#
29+
# Note that:
30+
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
31+
# - fcm variables are starting with a % (and not a $)
32+
#
33+
%NCDF_HOME $NETCDF_DIR
34+
%HDF5_HOME $HDF5_DIR
35+
%XIOS_HOME /work/n01/shared/nemo/xios-trunk
36+
#OASIS_HOME
37+
38+
%NCDF_INC -I%NCDF_HOME/include -I%HDF5_HOME/include
39+
%NCDF_LIB -L%HDF5_HOME/lib -L%NCDF_HOME/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
40+
%XIOS_INC -I%XIOS_HOME/inc
41+
%XIOS_LIB -L%XIOS_HOME/lib -lxios
42+
#OASIS_INC -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
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#OASIS_LIB -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
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45+
%CPP cpp -Dkey_nosignedzero
46+
%FC ftn
47+
%FCFLAGS -em -s integer32 -s real64 -O0 -hflex_mp=intolerant -N1023
48+
%FFLAGS -em -s integer32 -s real64 -O0 -hflex_mp=intolerant -N1023
49+
%LD CC
50+
%FPPFLAGS -P -traditional
51+
%LDFLAGS -lmpifort_cray
52+
%AR ar
53+
%ARFLAGS -r
54+
%MK gmake
55+
%USER_INC %XIOS_INC %NCDF_INC
56+
%USER_LIB %XIOS_LIB %NCDF_LIB
57+
#USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
58+
#USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
59+
60+
%CC cc -Wl,"--allow-multiple-definition"
61+
%CFLAGS -O1 -Wl,"--allow-multiple-definition"
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bld::tool::fc_modsearch -J

‎arch/NOC/arch-X86_ARCHER2-Gnu.fcm‎

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1+
# compiler options for Archer CRAY XC-30 (using crayftn compiler)
2+
#
3+
# NCDF_HOME root directory containing lib and include subdirectories for netcdf4
4+
# HDF5_HOME root directory containing lib and include subdirectories for HDF5
5+
# XIOS_HOME root directory containing lib for XIOS
6+
# OASIS_HOME root directory containing lib for OASIS
7+
#
8+
# NCDF_INC netcdf4 include file
9+
# NCDF_LIB netcdf4 library
10+
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
11+
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
12+
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
13+
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
14+
#
15+
# FC Fortran compiler command
16+
# FCFLAGS Fortran compiler flags
17+
# FFLAGS Fortran 77 compiler flags
18+
# LD linker
19+
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
20+
# FPPFLAGS pre-processing flags
21+
# AR assembler
22+
# ARFLAGS assembler flags
23+
# MK make
24+
# USER_INC complete list of include files
25+
# USER_LIB complete list of libraries to pass to the linker
26+
# CC C compiler used to compile conv for AGRIF
27+
# CFLAGS compiler flags used with CC
28+
#
29+
# Note that:
30+
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
31+
# - fcm variables are starting with a % (and not a $)
32+
#
33+
%NCDF_HOME ${NETCDF_DIR}
34+
%HDF5_HOME ${HDF5_DIR}
35+
%XIOS_HOME /work/n01/shared/nemo/xios-2.5-gnu
36+
#OASIS_HOME
37+
38+
%NCDF_INC -I%NCDF_HOME/include -I%HDF5_HOME/include
39+
%NCDF_LIB -L%HDF5_HOME/lib -L%NCDF_HOME/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
40+
%XIOS_INC -I%XIOS_HOME/inc
41+
%XIOS_LIB -L%XIOS_HOME/lib -lxios
42+
#OASIS_INC -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
43+
#OASIS_LIB -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
44+
45+
%CPP cpp -Dkey_nosignedzero
46+
%FC ftn
47+
%FCFLAGS -O2 -cpp -fallow-argument-mismatch -fdefault-real-8 -fcray-pointer -ffree-line-length-none
48+
%FFLAGS -O2 -cpp -fallow-argument-mismatch -fdefault-real-8 -fcray-pointer -ffree-line-length-none
49+
%LD CC
50+
%FPPFLAGS -P -traditional
51+
%LDFLAGS -lmpichf90
52+
%AR ar
53+
%ARFLAGS -r
54+
%MK gmake
55+
%USER_INC %XIOS_INC %NCDF_INC
56+
%USER_LIB %XIOS_LIB %NCDF_LIB
57+
#USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
58+
#USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
59+
60+
%CC cc -Wl,"--allow-multiple-definition"
61+
%CFLAGS -O2 -Wl,"--allow-multiple-definition"
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bld::tool::fc_modsearch -J

‎arch/NOC/arch-X86_ARCHER2-Gnu_4.2.fcm‎

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1+
# compiler options for Archer CRAY XC-30 (using crayftn compiler)
2+
#
3+
# NCDF_HOME root directory containing lib and include subdirectories for netcdf4
4+
# HDF5_HOME root directory containing lib and include subdirectories for HDF5
5+
# XIOS_HOME root directory containing lib for XIOS
6+
# OASIS_HOME root directory containing lib for OASIS
7+
#
8+
# NCDF_INC netcdf4 include file
9+
# NCDF_LIB netcdf4 library
10+
# XIOS_INC xios include file (taken into accound only if key_xios is activated)
11+
# XIOS_LIB xios library (taken into accound only if key_xios is activated)
12+
# OASIS_INC oasis include file (taken into accound only if key_oasis3 is activated)
13+
# OASIS_LIB oasis library (taken into accound only if key_oasis3 is activated)
14+
#
15+
# FC Fortran compiler command
16+
# FCFLAGS Fortran compiler flags
17+
# FFLAGS Fortran 77 compiler flags
18+
# LD linker
19+
# LDFLAGS linker flags, e.g. -L<lib dir> if you have libraries
20+
# FPPFLAGS pre-processing flags
21+
# AR assembler
22+
# ARFLAGS assembler flags
23+
# MK make
24+
# USER_INC complete list of include files
25+
# USER_LIB complete list of libraries to pass to the linker
26+
# CC C compiler used to compile conv for AGRIF
27+
# CFLAGS compiler flags used with CC
28+
#
29+
# Note that:
30+
# - unix variables "$..." are accpeted and will be evaluated before calling fcm.
31+
# - fcm variables are starting with a % (and not a $)
32+
#
33+
%NCDF_HOME ${NETCDF_DIR}
34+
%HDF5_HOME ${HDF5_DIR}
35+
%XIOS_HOME /work/n01/shared/nemo/xios-trunk-gnu
36+
#OASIS_HOME
37+
38+
%NCDF_INC -I%NCDF_HOME/include -I%HDF5_HOME/include
39+
%NCDF_LIB -L%HDF5_HOME/lib -L%NCDF_HOME/lib -lnetcdff -lnetcdf -lhdf5_hl -lhdf5 -lz
40+
%XIOS_INC -I%XIOS_HOME/inc
41+
%XIOS_LIB -L%XIOS_HOME/lib -lxios
42+
#OASIS_INC -I%OASIS_HOME/build/lib/mct -I%OASIS_HOME/build/lib/psmile.MPI1
43+
#OASIS_LIB -L%OASIS_HOME/lib -lpsmile.MPI1 -lmct -lmpeu -lscrip
44+
45+
%CPP cpp -Dkey_nosignedzero
46+
%FC ftn
47+
%FCFLAGS -O2 -cpp -fallow-argument-mismatch -fdefault-real-8 -fcray-pointer -ffree-line-length-none
48+
%FFLAGS -O2 -cpp -fallow-argument-mismatch -fdefault-real-8 -fcray-pointer -ffree-line-length-none
49+
%LD CC
50+
%FPPFLAGS -P -traditional
51+
%LDFLAGS -lmpichf90
52+
%AR ar
53+
%ARFLAGS -r
54+
%MK gmake
55+
%USER_INC %XIOS_INC %NCDF_INC
56+
%USER_LIB %XIOS_LIB %NCDF_LIB
57+
#USER_INC %XIOS_INC %OASIS_INC %NCDF_INC
58+
#USER_LIB %XIOS_LIB %OASIS_LIB %NCDF_LIB
59+
60+
%CC cc -Wl,"--allow-multiple-definition"
61+
%CFLAGS -O2 -Wl,"--allow-multiple-definition"
62+
bld::tool::fc_modsearch -J

‎cfgs/AGRIF_LINSSH/GSRIDGE36Z-GIBSTRA36Z/1_INPUT‎

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‎cfgs/AGRIF_LINSSH/GSRIDGE36Z-GIBSTRA36Z/1_context_nemo.xml‎

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‎cfgs/AGRIF_LINSSH/GSRIDGE36Z-GIBSTRA36Z/1_domain_cfg.nc‎

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