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Old 03-02-2014, 11:41 AM   #1
sarasari
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error in compiling +command to find netcdf path


Hi all,
I try to find the path where my netcdf is installed but I can't find it.

find netcdf
No such file or directory

which netcdf
/usr/no netcdf in (/usr/lib64/ccache:/usr/local/bin:/usr/bin:/bin:/usr/local/sbin:/usr/sbin:/sbin:/home/fedora/bin)

locte netcdf
bash: locte: command not found...

whereis netcdf
netcdf:


but when I type:
which ncdump
/usr/bin/ncdump


I need to enter the correct path in gfortran part to compile a testcase and I think as the path is not correct, this error comes up:

make linux-gfort
make coherens "FC=gfortran" "FCOPTS= -O3" "FCDEFS=" "FCDEBUG=" \
"CPP=" "CPPF=cpp" "CPPOPTS=-traditional-cpp" "CPPDEFS=-DALLOC -DCDF"
make[1]: Entering directory `/home/fedora/models/work'
gfortran -I/usr/local/bin/include -O3 -c cf90_routines.f90 -o cf90_routines.o
COHERENS/code/source/cf90_routines.F90:37.13:

USE netcdf
1
Fatal Error: Can't open module file 'netcdf.mod' for reading at (1): No such file or directory
make[1]: *** [cf90_routines.o] Error 1
make[1]: Leaving directory `/home/fedora/models/work'
make: *** [linux-gfort] Error 2

any one knows what causes this error?
thanks group
 
Old 03-02-2014, 01:31 PM   #2
knudfl
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Example Fedora 20 : There are 34 netcdf packages :
http://dl.fedoraproject.org/pub/fedo...os/Packages/n/

Packages required at compile time are the <name>-devel packages :
netcdf-devel netcdf-fortran-devel netcdf-cxx-devel
netcdf-cxx4-devel netcdf-openmpi-devel netcdf-mpich-devel , etc.

* Howto list files from an installed package : $ rpm -ql <package-name>
Like $ rpm -ql netcdf

* Deciding if packages "netcdf" are installed : $ rpm -qa | grep netcdf

-

Last edited by knudfl; 03-02-2014 at 01:34 PM.
 
1 members found this post helpful.
Old 03-02-2014, 03:04 PM   #3
sarasari
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Quote:
Originally Posted by knudfl View Post
Example Fedora 20 : There are 34 netcdf packages :
http://dl.fedoraproject.org/pub/fedo...os/Packages/n/

Packages required at compile time are the <name>-devel packages :
netcdf-devel netcdf-fortran-devel netcdf-cxx-devel
netcdf-cxx4-devel netcdf-openmpi-devel netcdf-mpich-devel , etc.

* Howto list files from an installed package : $ rpm -ql <package-name>
Like $ rpm -ql netcdf

* Deciding if packages "netcdf" are installed : $ rpm -qa | grep netcdf

-
Thank you dear knudfl. but I've changed my fedora to 15.
and I have another question. could you please explain more about the first part? I dont get what you mean by mentioning the packages required at compile....
I'm very beginner..infact I don't know what to type in the path part at this part during compiling: gfortran -I/usr/share/doc/include ??? seems this path which I entered is not correct. how to know where my netcdf is installed?
 
Old 03-02-2014, 03:15 PM   #4
knudfl
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# 3 .
Quote:
I dont get what you mean by mentioning the packages required at compile ..
Compile time / build time :
Is when you compile some source code.
That's what you show in post #1 : The 'make' command calls e.g. gfortran →
.. and gfortran compiles the code.


Quote:
how to know where my netcdf is installed?
Read post #2 : $ rpm -ql netcdf


Quote:
I don't know what to type in the path part at this part during compiling :
gfortran -I/usr/share/doc/include ?
Why type anything, when you have a Makefile / are using make ?
Anyway -I/usr/share/doc/include looks wrong.
Which software is it you are trying to build ?

-
 
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Old 03-02-2014, 03:37 PM   #5
sarasari
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I try to run one of the COHERENS software testcases which is an oceangraphy software.
when I typed rpm -ql netcdf I got:
/usr/bin/nccopy
/usr/bin/ncdump
/usr/bin/ncgen
/usr/bin/ncgen3
/usr/lib64/libnetcdf.so.6
/usr/lib64/libnetcdf.so.6.0.0
/usr/lib64/libnetcdf_c++.so.5
/usr/lib64/libnetcdf_c++.so.5.0.0
/usr/lib64/libnetcdff.so.5
/usr/lib64/libnetcdff.so.5.0.0
/usr/share/doc/netcdf
/usr/share/doc/netcdf-4.1.1
/usr/share/doc/netcdf-4.1.1/COPYRIGHT
/usr/share/doc/netcdf-4.1.1/README
/usr/share/doc/netcdf/ncdump-man-1.html
/usr/share/doc/netcdf/ncgen-man-1.html
/usr/share/doc/netcdf/ncgen3-man-1.html
/usr/share/doc/netcdf/netcdf-c.html
/usr/share/doc/netcdf/netcdf-c.info
/usr/share/doc/netcdf/netcdf-c.pdf
/usr/share/doc/netcdf/netcdf-c.ps
/usr/share/doc/netcdf/netcdf-c.txt
/usr/share/doc/netcdf/netcdf-cxx.html
/usr/share/doc/netcdf/netcdf-cxx.info
/usr/share/doc/netcdf/netcdf-cxx.pdf
/usr/share/doc/netcdf/netcdf-cxx.ps
/usr/share/doc/netcdf/netcdf-cxx.txt
/usr/share/doc/netcdf/netcdf-f77.html
/usr/share/doc/netcdf/netcdf-f77.info
/usr/share/doc/netcdf/netcdf-f77.pdf
/usr/share/doc/netcdf/netcdf-f77.ps
/usr/share/doc/netcdf/netcdf-f77.txt
/usr/share/doc/netcdf/netcdf-f90.html
/usr/share/doc/netcdf/netcdf-f90.info
/usr/share/doc/netcdf/netcdf-f90.pdf
/usr/share/doc/netcdf/netcdf-f90.ps
/usr/share/doc/netcdf/netcdf-f90.txt
/usr/share/doc/netcdf/netcdf-install.html
/usr/share/doc/netcdf/netcdf-install.info
/usr/share/doc/netcdf/netcdf-install.pdf
/usr/share/doc/netcdf/netcdf-install.ps
/usr/share/doc/netcdf/netcdf-install.txt
/usr/share/doc/netcdf/netcdf-man-3.html
/usr/share/doc/netcdf/netcdf-tutorial.html
/usr/share/doc/netcdf/netcdf-tutorial.info
/usr/share/doc/netcdf/netcdf-tutorial.pdf
/usr/share/doc/netcdf/netcdf-tutorial.ps
/usr/share/doc/netcdf/netcdf-tutorial.txt
/usr/share/doc/netcdf/netcdf.html
/usr/share/doc/netcdf/netcdf.info
/usr/share/doc/netcdf/netcdf.pdf
/usr/share/doc/netcdf/netcdf.ps
/usr/share/doc/netcdf/netcdf.txt
/usr/share/doc/netcdf/netcdf_f77-man.html
/usr/share/doc/netcdf/netcdf_f90-man.html
/usr/share/info/netcdf-c.info-1.gz
/usr/share/info/netcdf-c.info-2.gz
/usr/share/info/netcdf-c.info.gz
/usr/share/info/netcdf-cxx.info.gz
/usr/share/info/netcdf-f77.info-1.gz
/usr/share/info/netcdf-f77.info-2.gz
/usr/share/info/netcdf-f77.info.gz
/usr/share/info/netcdf-f90.info.gz
/usr/share/info/netcdf-install.info.gz
/usr/share/info/netcdf-tutorial.info.gz
/usr/share/info/netcdf.info.gz
/usr/share/man/man1/nccopy.1.gz
/usr/share/man/man1/ncdump.1.gz
/usr/share/man/man1/ncgen.1.gz
/usr/share/man/man1/ncgen3.1.gz

and that's what makes me confused. as I don't know which one is the right path to type.
 
Old 03-02-2014, 05:51 PM   #6
knudfl
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# 5 .

Well, you asked "how to know where my netcdf is installed?"
* But : netcdf does not provide the files you want.
* I.e. you want to compile some code : Install the required <packages>-devel.

Please use yum to know what's providing "netcdf.mod" :
$ yum provides */netcdf.mod
... And you should get a list of three packages (It's a Fedora 20 example again) →
netcdf-fortran-devel netcdf-fortran-mpich-devel netcdf-fortran-openmpi-devel
... then choose one and install it with # yum install <package-name>

Then you will discover if setting a path is required at all.

-

Last edited by knudfl; 03-02-2014 at 05:54 PM.
 
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Old 03-02-2014, 06:31 PM   #7
sarasari
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Thanks again I installed what you've said. but please consider this:
this is one part of my coherensflags.cmp file that in this part i'm asked to enter the netcdf path.

# options for compilation with CPP
## -DALLOC :allocates/deallocates local arrays
## -DMPI :includes MPI library
## -DCDF :includes netCDF library
## -DVERIF :enables output for verification procedure
## -DPETSC : includes PETSc library

CPPDFLAGS = -DALLOC -DCDF

# netCDF directory path
NETCDF_PATH = ???????????????????????????????? (this is the part that I have problem)


and when I compile it then the error in the first post comes up.
 
Old 03-03-2014, 07:12 AM   #8
knudfl
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# 7 . Please show some links to the used software.

"COHERENS software testcases which is an oceangraphy (oceanographic?) software":
1) COHERENS software testcases.
2) The `oceanographic software'.
3) PETSc http://www.mcs.anl.gov/petsc/ → ? Which PETSc version ?

And : Which version of Fedora ? Still Fedora 15 ?
Is it i686 or x86_64 ? → $ uname -m <Enter>

-
 
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Old 03-03-2014, 10:41 AM   #9
sarasari
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Here you can find more information: http://www2.mumm.ac.be/coherens/
I use fedora 15 as it was compiling correctly before I switch on netcdf. and the problems come fter switching on netcdf. but I also have fedora 20 on my virtual machine but t couldnt compile correctly even when the netcdf switch was off, so thats why I decided to keep using fedora 15.
also my machine is x86_64. and I don't know how to find my petsc version.
thank you
 
  


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