[ase-users] atomic symbols in netcdf file get lost

[John Kitchin]

I think now the problem is related to NFS and the dreaded .nfsxxx files. I
discovered these were being formed (it is surprisingly easy to make them!)
and they were corrupted as described below. I think I have solved the
.nfsxxx problem again, and iso far I don't see the corruption problem.

j
-----------------------------------
John Kitchin
Assistant Professor
NETL-IAES Resident Institute Fellow
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
http://kitchingroup.cheme.cmu.edu




On Thu, Jan 22, 2009 at 9:48 AM, John Kitchin <jkitchin at andrew.cmu.edu>wrote:

> ncdump shows this is exactly what the data is in the ncfile
>
>  DynamicAtomSpecies =
>   "",
>   "",
>   "",
>   "\001T",
>   "Cu",
>   "Cu",
>   "Cu",
>   "Cu",
>   "Cu",
>   "Cu",
>   "Cu",
>   "Cu",
>   "Cu",
>   "Cu",
>   "Cu" ;
> }
>
> so, the python code is reading the file correctly, it is just the first few
> symbols have gotten mangled. Everything else in the ncfile looks fine. This
> makes me think it is related to the fortran code somehow. The dacapo code
> looks like it has exited just fine, and the only reason the jobs fail is
> because the DynamicAtomSpecies causes a KeyError in a dictionary in python.
> very strange.
>
> j
>
>
> -----------------------------------
> John Kitchin
> Assistant Professor
> NETL-IAES Resident Institute Fellow
> Doherty Hall A207F
> Department of Chemical Engineering
> Carnegie Mellon University
> Pittsburgh, PA 15213
> 412-268-7803
> http://kitchingroup.cheme.cmu.edu
>
>
>
>
> On Thu, Jan 22, 2009 at 3:43 AM, Jakob Schiotz <schiotz at fysik.dtu.dk>wrote:
>
>> On Thursday 22 January 2009, John Kitchin wrote:
>> > was there ever any resolution to what caused the problem at:
>> >
>> > https://listserv.fysik.dtu.dk/pipermail/campos/2007-June/002261.html
>> >
>> > the issue is related to the final error:
>> >     Z = numbers[symbol]
>> > KeyError: '\x00\x00'
>> > which is caused because in the netcdf file the atomic symbols are
>> replaced
>> > by '\x00\x00'
>> > I have seen this problem intermittently over the years, and am seeing it
>> > again intermittently lately, especially with parallel NEB calculations.
>> >
>> > I am suspicious that somehow this is a problem with the netcdf library
>> > because the text in the key error above looks alot like
>>
>> I cannot really help you, I have not seen the problem myself.  But a few
>> thoughts:  The \x00\x00 characters are two 0-bytes, so it is most likely
>> caused by uninitialized data.  Does ncdump show something useful for the
>> atomic symbols?  Could it be that the writing script crashed before the
>> NetCDF files was properly closed?
>>
>> /Jakob
>>
>>
>> >
>> > NC_CHAR      = '\x00\x00\x00\x02'  (from the pupynere documentation at).
>> I
>> > am not using pupynere here, but the character strings look similar. it
>> > almost looks like the netcdf library is reading from the wrong place in
>> the
>> > file. I can't explain why the rest of the ncfile looks fine though.
>> > I also suspect the timing of when dacapo fortran does something to the
>> > netcdf file and when python does something, but as I mentioned, the
>> problem
>> > is intermittent.
>> >
>> > any ideas? or solutions from the past?
>> >
>> > thanks,
>> >
>> > j
>> >
>> > -----------------------------------
>> > John Kitchin
>> > Assistant Professor
>> > NETL-IAES Resident Institute Fellow
>> > Doherty Hall A207F
>> > Department of Chemical Engineering
>> > Carnegie Mellon University
>> > Pittsburgh, PA 15213
>> > 412-268-7803
>> > http://kitchingroup.cheme.cmu.edu
>>
>>
>>
>> --
>> Jakob Schiotz, Ph.D., Associate professor (lektor)
>> CINF, Department of Physics
>> Technical University of Denmark
>> DK-2800 Kongens Lyngby, Denmark
>> http://www.cinf.dtu.dk/~schiotz/ <http://www.cinf.dtu.dk/%7Eschiotz/>
>>
>
>
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