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 Post subject: compiling upwelling
PostPosted: Sun Apr 07, 2019 12:35 pm 
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Joined: Sun Mar 31, 2019 2:01 pm
Posts: 5
Location: Nanjing University of Information Science & Techno
hello everyone:
i am encountering a problem when i am compiling the case of upwelling, it shows that:
cp -f /home/kzf/softwares/packman.active/include/netcdf.mod /home/kzf/myroms/projects/upwelling/Build_romsG
cp -f /home/kzf/softwares/packman.active/include/typesizes.mod /home/kzf/myroms/projects/upwelling/Build_romsG
:No such file or directory
make: **** no rule to make target...
i guess it is the problems of netcdf,the version of netcdf is 4.1.2

i edit my build_roms.bash like that:

export USE_NETCDF4=on
export USE_MY_LIBS=yes
export NETCDF_INCDIR=/home/kzf/softwares/packman.active/include
export NETCDF_LIBDIR=/home/kzf/softwares/packman.active/lib
export NC_CONFIG=/home/kzf/softwares/packman.active/bin/nc-config
export NF_CONFIG=/home/kzf/softwares/packman.active/bin/nf-config

could you help fix this problems,thanks very much!
by the way ,the netcdf.mod and typesizes.mod do exist in the file of Build_romsG. but the compiling is unsucessful


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 Post subject: Re: compiling upwelling
PostPosted: Mon Apr 08, 2019 5:49 am 
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Posts: 11
I suppose that you are trying to compile the test case of upwelling, i too had similiar problems while compiling the test case. Please try to rectify it by changing line 52 of Linux-gfortran.mk as follows ( code from unidata):

Before

LIBS := -L$(NETCDF_LIBDIR) -lnetcdf

After

LIBS := -L$(NETCDF_LIBDIR) -lnetcdf -lnetcdff

Keep a copy of the original or keep a changelog session for future use.


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 Post subject: Re: compiling upwelling
PostPosted: Mon Apr 08, 2019 11:32 am 
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Joined: Wed Dec 31, 2003 6:16 pm
Posts: 785
Location: USGS, USA
you might get to a problem with netcdf, and perhaps the -lnetcdff flag is needed, but right now your problem is:

"cp -f /home/kzf/softwares/packman.active/include/netcdf.mod /home/kzf/myroms/projects/upwelling/Build_romsG
cp -f /home/kzf/softwares/packman.active/include/typesizes.mod /home/kzf/myroms/projects/upwelling/Build_romsG
:No such file or directory"

so:
1) does this directory exist: /home/kzf/softwares/packman.active/include/
2) does that directory contain netcdf.mod and typesizes.mod
3) does this directory exist: /home/kzf/myroms/projects/upwelling/Build_romsG

-john


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 Post subject: Re: compiling upwelling
PostPosted: Wed Apr 10, 2019 8:53 am 
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Joined: Sun Mar 31, 2019 2:01 pm
Posts: 5
Location: Nanjing University of Information Science & Techno
MIDHILAVARNAV wrote:
I suppose that you are trying to compile the test case of upwelling, i too had similiar problems while compiling the test case. Please try to rectify it by changing line 52 of Linux-gfortran.mk as follows ( code from unidata):

Before

LIBS := -L$(NETCDF_LIBDIR) -lnetcdf

After

LIBS := -L$(NETCDF_LIBDIR) -lnetcdf -lnetcdff

Keep a copy of the original or keep a changelog session for future use.


hi, MIDHILAVARNAV:
i have rectified Linux-gfortran.mk as your said, but the problem is still here.
could you provide me the vsrsion of roms you use and the changes you have made in your compiling in detail?


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 Post subject: Re: compiling upwelling
PostPosted: Wed Apr 10, 2019 8:57 am 
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Joined: Sun Mar 31, 2019 2:01 pm
Posts: 5
Location: Nanjing University of Information Science & Techno
jcwarner wrote:
you might get to a problem with netcdf, and perhaps the -lnetcdff flag is needed, but right now your problem is:

"cp -f /home/kzf/softwares/packman.active/include/netcdf.mod /home/kzf/myroms/projects/upwelling/Build_romsG
cp -f /home/kzf/softwares/packman.active/include/typesizes.mod /home/kzf/myroms/projects/upwelling/Build_romsG
:No such file or directory"

so:
1) does this directory exist: /home/kzf/softwares/packman.active/include/
2) does that directory contain netcdf.mod and typesizes.mod
3) does this directory exist: /home/kzf/myroms/projects/upwelling/Build_romsG

-john


hi John,
these three directionies all exist, the netcdf.mod and typesizes.mod have been copied to the directory of Build_romsG. but it still indicates that ":No such file or directory", and the compling interrupt


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 Post subject: Re: compiling upwelling
PostPosted: Wed Apr 10, 2019 11:58 am 
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Location: USGS, USA
so when i build i get something like this:

[jwarner@poseidon-l1 breach338]$ ./coawst.bash

rm -f -r core *.ipo ./Build /vortexfs1/usgs/jwarner/make_macros.mk

makefile:248: INCLUDING FILE /vortexfs1/usgs/jwarner/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS

cp -f /vortexfs1/apps/netcdf-intel/include/netcdf.mod ./Build

cp -f /vortexfs1/apps/netcdf-intel/include/typesizes.mod ./Build

./ROMS/Bin/sfmakedepend --cpp --fext=f90 --file=- --objdir=./Build -DROMS_HEADER="sandy_inwave.h" -I ROMS/Include -I /vortexfs1/usgs/jwarner/Projects/breach_run_files/breach338/Sandy_InWave -I ROMS/Nonlinear -I ROMS/Nonlinear/Biology -I ROMS/Nonlinear/Sediment -I ROMS/Nonlinear/Wec -I ROMS/Nonlinear/Vegetation -I ROMS/Utility -I ROMS/Drivers -I ROMS/Functionals -I /vortexfs1/usgs/jwarner/Projects/breach_run_files/breach338/Sandy_InWave -I SWAN/Src -I Master -I Compilers --silent --moddir ./Build ROMS/Nonlinear/lmd_skpp.F ROMS/Nonlinear/uv3.....


can you post the whole entire build output?
thanks
john


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 Post subject: Re: compiling upwelling
PostPosted: Wed Apr 10, 2019 12:50 pm 
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Joined: Sun Mar 31, 2019 2:01 pm
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Location: Nanjing University of Information Science & Techno
jcwarner wrote:
so when i build i get something like this:

[jwarner@poseidon-l1 breach338]$ ./coawst.bash

rm -f -r core *.ipo ./Build /vortexfs1/usgs/jwarner/make_macros.mk

makefile:248: INCLUDING FILE /vortexfs1/usgs/jwarner/make_macros.mk WHICH CONTAINS APPLICATION-DEPENDENT MAKE DEFINITIONS

cp -f /vortexfs1/apps/netcdf-intel/include/netcdf.mod ./Build

cp -f /vortexfs1/apps/netcdf-intel/include/typesizes.mod ./Build

./ROMS/Bin/sfmakedepend --cpp --fext=f90 --file=- --objdir=./Build -DROMS_HEADER="sandy_inwave.h" -I ROMS/Include -I /vortexfs1/usgs/jwarner/Projects/breach_run_files/breach338/Sandy_InWave -I ROMS/Nonlinear -I ROMS/Nonlinear/Biology -I ROMS/Nonlinear/Sediment -I ROMS/Nonlinear/Wec -I ROMS/Nonlinear/Vegetation -I ROMS/Utility -I ROMS/Drivers -I ROMS/Functionals -I /vortexfs1/usgs/jwarner/Projects/breach_run_files/breach338/Sandy_InWave -I SWAN/Src -I Master -I Compilers --silent --moddir ./Build ROMS/Nonlinear/lmd_skpp.F ROMS/Nonlinear/uv3.....


can you post the whole entire build output?
thanks
john


hi,John:
i changed to a older version of ROMS of 514. and now the messages shows like

.


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 Post subject: Re: compiling upwelling
PostPosted: Wed Apr 10, 2019 1:10 pm 
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Location: USGS, USA
well that looks worse.
can you attach the build.bash. want to make sure you set the compiler.


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 Post subject: Re: compiling upwelling
PostPosted: Wed Apr 10, 2019 8:12 pm 
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Joined: Wed Jul 02, 2003 5:29 pm
Posts: 3601
Location: IMS/UAF, USA
It looks like the Perl script sfmakedepend is failing. First you need to check that ./ROMS/Bin/sfmakedepend exists, then look in it to see what the first line is. I expect that you have the sfmakedepend file, but my first line is:
Code:
#!/usr/bin/env perl
so the problem could be either /usr/bin/env or perl.
Code:
chinook01.rcs.alaska.edu 267% ls -l /usr/bin/env
0 lrwxrwxrwx. 1 root root 13 Jul 10  2018 /usr/bin/env -> ../../bin/env*

Code:
chinook01.rcs.alaska.edu 268% which perl
/usr/local/pkg/lang/Perl/5.22.1-foss-2016b/bin/perl


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 Post subject: Re: compiling upwelling
PostPosted: Fri Apr 12, 2019 11:58 am 
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Joined: Sun Mar 31, 2019 2:01 pm
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Location: Nanjing University of Information Science & Techno
thanks everyone, i have saved this problem.
i execute the command sed -i 's/\r$//' to all of the files under Roms
and now i have compiled the case upwelling successfully!
why does this happen? because i download the codes through a svn version of windows?


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 Post subject: Re: compiling upwelling
PostPosted: Fri Apr 12, 2019 5:55 pm 
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Location: IMS/UAF, USA
Oh that old Windows problem. Exactly.


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