nc file not created

Asked by Laszlo Oroszlany on 2017-06-13

Running the Fe example provided with the code adding
CDF.Save true
does not create Fe.nc as I expect from the documentation, other nc files on the other hand appear, for example
WriteDMHS.NetCDF true
does create DMHS.nc
Is this a bug or CDF.Save needs some extra flags ?

Question information

Language:
English Edit question
Status:
Answered
For:
Siesta Edit question
Assignee:
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Last query:
2017-06-17
Last reply:
2017-06-17
David Guzman (guzmand) said : #1

Hello,
My best guess is that you failed to compile the code with netCDF support.
Here is a link to my makefile, but be aware that this is for the specific computer clusters at my institution.
https://www.dropbox.com/s/p2kv6qxqzxc4wnv/arch.make?dl=0

Regards,
David
Purdue University

Laszlo Oroszlany (oroszl) said : #2

I did compile my code with netCDF support
WriteDMHS.NetCDF true
does generate a DMHS.nc file which I could read and process with netCDF4-python

I generated a Dockerfile with my arch.make at
https://github.com/oroszl/siesta_in_docker
using docker and this repository my setup can be exactly reproduced
eg by building the docker image and running the container as described in readme.md

Nick Papior (nickpapior) said : #3

As is stated in the documentation, the CDF.* options rely on the internal library (ncdf) to be enabled. To do this, you are required these steps:

1. Compile NetCDF with NetCDF4 support
2. Compile siesta with these additional flags:
-DNCDF -DNCDF_4

Then the *.nc file will be created.

Nick Papior (nickpapior) said : #4

Oh, and sorry, you should also add:

COMP_LIBS += libncdf.a libfdict.a

I hope I remembered everything, it is getting quite late here...

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