Siesta

nc file not created

Asked by Laszlo Oroszlany

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:
No assignee Edit question
Last query:
Last reply:
Revision history for this message
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

Revision history for this message
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

Revision history for this message
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.

Revision history for this message
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...

Can you help with this problem?

Provide an answer of your own, or ask Laszlo Oroszlany for more information if necessary.

To post a message you must log in.