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  • 00:56
    pfebrer edited #388
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    pfebrer opened #388
  • Oct 19 20:51
    zerothi commented #147
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    mnt: removed unnecessary copy s… (compare)

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    zerothi commented #147
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    zerothi commented #147
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  • Oct 14 19:33
    zerothi closed #387
  • Oct 14 19:33
    zerothi commented #387
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  • Oct 13 19:20
    zerothi closed #261
Nick Papior
@zerothi
@HemanthHari also, I would not recommend you to use CDF.Compress 9. It takes forever, and probably 3 is sufficient for most uses. Additionally it is better to compress after the Siesta run. So the most efficient would be CDF.Compress 0 and then subsequent use nccopy in.nc -d 9 out.nc
HemanthHari
@HemanthHari
Sure. Will do that :)
HemanthHari
@HemanthHari
Siesta Version : v4.1-b4
Architecture : unknown
Compiler version: GNU Fortran (Ubuntu 5.4.0-6ubuntu1~16.04.12) 5.4.0 20160609
Compiler flags : f77 -O2 -fPIC -ftree-vectorize -march=native
PP flags : -DFC_HAVE_ABORT
Libraries : /usr/lib/libblas.so /usr/lib/liblapack.so libncdf.a libfdict.a /usr/lib/llibblas.so /usr/lib/liblapack.so libncdf.a libfdict.a
SERIAL version
@zerothi Just a check, is netcdf installed now?
Nick Papior
@zerothi
no, you need to add -DCDF -DNCDF_4 I can't recall flags, see manual :)
HemanthHari
@HemanthHari
FPPFLAGS += -DCDF -DNCDF -DNCDF_4 this flag was enabled in the make file
Nick Papior
@zerothi
If you had enabled it, then it should also have been present in the PP flags line, so check you did it correctly.
HemanthHari
@HemanthHari
i used install_netcdf.sh script that came with siesta
Nick Papior
@zerothi
yes, I am talking about your arch.make. If PP flags line in the output does not specify your FPPFLAGS then you are doing something wrong.
HemanthHari
@HemanthHari
PP flags : -DFC_HAVE_ABORT -DCDF -DNCDF -DNCDF_4 is it fixed now?
Nick Papior
@zerothi
if that is the output of Siesta, then yes.
HemanthHari
@HemanthHari
Thank you for your patience and time.
I'm grateful to you
Thanks again
Nick Papior
@zerothi
You are welcome.
HemanthHari
@HemanthHari
Sorry to bother you again, but the error stays
Nick Papior
@zerothi
I can't guess what is happening, I need output, and list of files.
HemanthHari
@HemanthHari
how can I send you files?
Nick Papior
@zerothi
use gist (on github) is probably the easiest
HemanthHari
@HemanthHari
<script src="https://gist.github.com/HemanthHari/4bab472f36bf4fb7345cd864ff4c0dc6.js"></script>
If you need any more files, kindly let me know
Nick Papior
@zerothi
did you do a complete make clean before building after editing your arch.make file?
HemanthHari
@HemanthHari
yes
I will start afresh again
Nick Papior
@zerothi
could you also list the files in the directory you ran?
and the python script you are using
HemanthHari
@HemanthHari
have sent you the python script
Nick Papior
@zerothi
and list of files?
HemanthHari
@HemanthHari
The files that were generated?
Nick Papior
@zerothi
yes
not all files, just ls -l output?
HemanthHari
@HemanthHari
have sent the list
Nick Papior
@zerothi
could you provide the output of ncdump -h siesta_2.nc
HemanthHari
@HemanthHari
have updated it
Nick Papior
@zerothi
and you get the same error?
I don't see why, it should be able to read from the nc file...

Try this

import sisl as si
si.io.siesta.ncSileSiesta('siesta_2.nc').read_hamiltonian()

and give me the output

Nick Papior
@zerothi
I just tried your input etc. and found no issues... I'll try again...
Nick Papior
@zerothi
@HemanthHari I can't see anything wrong, try from scratch. I have now repeated your calculation with a correctly build Siesta 2 times and I can read the Hamiltonian without any issues.
Another thing would be your sisl version, could you give me the output: sdata --version
HemanthHari
@HemanthHari
I am rebuilding the Siesta installation again. I would update you as soon as it is over.
HemanthHari
@HemanthHari
It worked fine when I completely rebuilt the Siesta including the netcdf installation.
Thanks for the inputs
Nick Papior
@zerothi
great
HemanthHari
@HemanthHari
@zerothi Sorry to bug you again. I had to redeploy siesta-4.1-266 on a new workstation in our lab. I tried to compile the code to run in parallel, but for some reason, it still gets compiled to the serial version.
https://gist.github.com/HemanthHari/87a0e8aa315d394ba9487b6f5172cf75 is the link to the arch.make file that was used for building siesta
Nick Papior
@zerothi
If you want to compile siesta with mpi, then you have to use scalapack as well. I would suggest you to discuss this with some of your local IT personel. :)
yuefei-huang
@yuefei-huang
Hello Nick
Nick Papior
@zerothi
Hi!