pyroms installation

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surja
Posts: 12
Joined: Thu Jan 12, 2012 5:19 pm
Location: Jadavpur university,INCOIS

pyroms installation

#1 Post by surja » Sun Aug 25, 2013 7:02 am

Dear all,
While I am trying to install pyroms the error coming as
/usr/local/lib/python2.6/dist-packages/pyroms/Dataset.py:65: UserWarning: netCDF4 not found -- using pupynere.
warnings.warn('netCDF4 not found -- using pupynere.')
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/lib/python2.6/dist-packages/pyroms/__init__.py", line 15, in <module>
from Dataset import Dataset, MFDataset
ImportError: cannot import name MFDataset
cp: missing destination file operand after `libgridgen.so'
Try `cp --help' for more information.
installing scrip...
gfortran -g -fdefault-real-8 -ffixed-form -O2 -fPIC -I/usr/local/lib/netcdf-4.3.0/include -c ./netcdf.f
./netcdf.f:44: Error: Can't open included file 'netcdf.inc'
./netcdf.f:66.27:

if (istat /= NF_NOERR) then
1
Error: Symbol 'nf_noerr' at (1) has no IMPLICIT type
./netcdf.f:67.36:

print *,'Error in netCDF: ',nf_strerror(istat)
1
Error: Function 'nf_strerror' at (1) has no IMPLICIT type
make: *** [netcdf.o] Error 1
gfortran -g -fdefault-real-8 -ffixed-form -O2 -fPIC -I/usr/local/lib/netcdf-4.3.0/include -c ./netcdf.f
./netcdf.f:44: Error: Can't open included file 'netcdf.inc'
./netcdf.f:66.27:

if (istat /= NF_NOERR) then
1
Error: Symbol 'nf_noerr' at (1) has no IMPLICIT type
./netcdf.f:67.36:

print *,'Error in netCDF: ',nf_strerror(istat)
1
Error: Function 'nf_strerror' at (1) has no IMPLICIT type
make: *** [netcdf.o] Error 1
/bin/cp ./scrip /usr/local/bin
/bin/cp: cannot stat `./scrip': No such file or directory
make: *** [install] Error 1
cp: missing destination file operand after `scrip.so'
Try `cp --help' for more information.
I have installed netcdf-4.3.0 in usr/local/lib/ directory.
The ncdump command returns
ncdump [-c|-h] [-v ...] [[-b|-f] [c|f]] [-l len] [-n name] [-p n[,n]] [-k] [-x] [-s] [-t|-i] [-g ...] [-w] file
[-c] Coordinate variable data and header information
[-h] Header information only, no data
[-v var1[,...]] Data for variable(s) <var1>,... only
[-b [c|f]] Brief annotations for C or Fortran indices in data
[-f [c|f]] Full annotations for C or Fortran indices in data
[-l len] Line length maximum in data section (default 80)
[-n name] Name for netCDF (default derived from file name)
[-p n[,n]] Display floating-point values with less precision
[-k] Output kind of netCDF file
[-s] Output special (virtual) attributes
[-t] Output time data as date-time strings
[-i] Output time data as date-time strings with ISO-8601 'T' separator
[-g grp1[,...]] Data and metadata for group(s) <grp1>,... only
[-w] With client-side caching of variables for DAP URLs
[-x] Output XML (NcML) instead of CDL
file Name of netCDF file (or URL if DAP access enabled)
netcdf library version 4.3.0 of Aug 24 2013 21:57:24 $
Please help to install pyroms.
Thanks in advance.
Surja

User avatar
kate
Posts: 3780
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: pyroms installation

#2 Post by kate » Mon Aug 26, 2013 4:46 pm

You want to install two more pieces after the NetCDF library:
* The newer versions of NetCDF come with the C library - you also need to download and install the NetCDF-fortran package.
* There is a NetCDF4 Python package that sits on top of the NetCDF C library. This should be in the list of prerequisites for pyroms.

surja
Posts: 12
Joined: Thu Jan 12, 2012 5:19 pm
Location: Jadavpur university,INCOIS

Re: pyroms installation

#3 Post by surja » Mon Aug 26, 2013 10:00 pm

Thanks Kate for your suggestion.
After netcdf-4.0 fortran package installation the pyroms installations is going with error massage as
gcc -shared -o libgridgen.so broyden.t delaunay.t geom.t gridgen.t hash.t issimplepoly.t istack.t ode.t swcr.t vertlist.t zode.t triangle.t -lgu -lm
installing gridgen
installing gridgen.h
installing libgridgen.a
installing libgridgen.so
/usr/local/lib/python2.6/dist-packages/pyroms/Dataset.py:65: UserWarning: netCDF4 not found -- using pupynere.
warnings.warn('netCDF4 not found -- using pupynere.')
Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/usr/local/lib/python2.6/dist-packages/pyroms/__init__.py", line 15, in <module>
from Dataset import Dataset, MFDataset
ImportError: cannot import name MFDataset
cp: missing destination file operand after `/home/surja/python/lib/libgridgen.so'
Try `cp --help' for more information.
installing scrip...
bash: cd: /home/surja/python/python/pyroms/external/scrip/source: No such file or directory
The detail log file is in attached file.
please help to fix the problem.
Attachments
pyroms_install.log
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User avatar
kate
Posts: 3780
Joined: Wed Jul 02, 2003 5:29 pm
Location: CFOS/UAF, USA

Re: pyroms installation

#4 Post by kate » Mon Aug 26, 2013 10:32 pm

A little google search shows that it's part of the netcdf4 package you haven't yet installed, and means multi-file dataset: http://netcdf4-python.googlecode.com/sv ... class.html

rsignell
Posts: 123
Joined: Fri Apr 25, 2003 9:22 pm
Location: USGS

Re: pyroms installation

#5 Post by rsignell » Tue Aug 27, 2013 10:42 am

Seems like potentially a problem also knowing what the most up-to-date "pyroms" distribution is:

I see that on https://github.com/kshedstrom/pyroms, it says:
"Pyroms is a collection of tools to help with input and output files
from the Regional Ocean Modeling System (ROMS). It was originally
started by Rob Hetland as a googlecode project, then he morphed it
into octant, also at googlecode. Frederic Castruccio then created a
fork and renamed it back to pyroms. This version is still rather
rough around the edges."

Meanwhile Rob Hetland also moved to Github with his ROMS Python tools:
https://github.com/hetland/octant
and I know he updated the vertical coordinate calculations just a few months ago.

Maybe the Python ROMS folks should have a little meeting to discuss coordination?
-Rich

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