Error with NetCDF: Index exceeds bounds when using ypp

[chwolf]

Dear all!

First of all thank you for accepting me on this board.

I am currently starting using YAMBO and I have encountered an error that I cannot understand.

I am here on Ubuntu 16.04, espresso 5.4.0 and yambo-4.0.3-rev.104;

making yambo (and interfaces, ypp, ypp_ph etc) with iotk and p2y (5.0) worked like a charm; p2y works when called in the prefix.save directory as in the tutorial; however running the tutorials on yambopy (http://yambopy.readthedocs.io/en/latest ... raction-si) gives me the following error:

Code: Select all

/si$ python elph_pw_si.py 
nscf calculation found!
creating random list of q-points


 ___ __  _____  __ __  _____   _____
|   Y  ||  _  ||  Y  ||  _  \ |  _  |
|   |  ||. |  ||.    ||. |  / |. |  |
 \_  _/ |. _  ||.\_/ ||. _  \ |. |  |
  |: |  |: |  ||: |  ||: |   \|: |  |
  |::|  |:.|:.||:.|:.||::.   /|::.  |
  `--"  `-- --"`-- --"`-----" `-----"


 <---> [01] CPU structure, Files & I/O Directories
 <---> [02] Y(ambo) P(ost)/(re) P(rocessor)
 <---> [03] Core DB
 <---> :: Electrons             : 8.000000
 <---> :: Temperature       [ev]: 0.000000
 <---> :: Lattice factors [a.u.]: 5.150000  5.150000  5.150000
 <---> :: K points              : 13
 <---> :: Bands                 : 20
 <---> :: Symmetries            : 12
 <---> :: RL vectors            :  5985
 <---> [04] K-point grid

[ERROR] STOP signal received while in :[04] K-point grid
[ERROR][NetCDF] NetCDF: Index exceeds dimension bound
Traceback (most recent call last):
  File "elph_pw_si.py", line 72, in <module>
    qlist = qpoint_generation(nq)
  File "elph_pw_si.py", line 59, in qpoint_generation
    q[:,:-1] = loadtxt('database/o.random_k_pts')
  File "/home/chris/.local/lib/python2.7/site-packages/numpy/lib/npyio.py", line 803, in loadtxt
    fh = iter(open(fname, 'U'))
IOError: [Errno 2] No such file or directory: 'database/o.random_k_pts'
chris@dft:~/Downloads/yambopy-master/tutorial/si$ 

I interpret this that q-points were not generated because some index exceeded its bounds, thereby killing NetCDF. But I am unable to find the actual culprit. Has anyone encountered this before?

any help is greatly appreciated!

Yours,
Chris

[amolina]

Dear Chris,

we have tried to reproduce the error with the same version but we couldn't make it.

Can you delete all the files (sh clean.sh) in the folder and start from the beginning?

python gs_si.py -s -n

python elph_pw_si.py

Cheers,

Alejandro.