QuantumATK Forum

QuantumATK => General Questions and Answers => Topic started by: hieido on July 16, 2012, 09:17

Title: Parallel system: Output file error!
Post by: hieido on July 16, 2012, 09:17
Dear all,
I build the input file on ATK version win64 and then ran the input on parallel system (Linux based) after finish the calculation, I got *nc file
Usually when I build and run the input file in ATK windows based and get the output *nc file I can see the results in ATK window.
But this time, I cannot obtain the results... I got a messengers like this:
------------------
-----------------------
Traceback (most recent call last):
  File ".\zipdir\NL\GUI\Core\Runner.py", line 230, in run
  File ".\zipdir\NL\GUI\Tools\CustomAnalyzer\Analyzers\IVCurve.py", line 27, in analyzer
  File ".\zipdir\NL\IO\NLSaveUtilities.py", line 250, in nlread
  File ".\zipdir\NL\IO\MetaCDFFile.py", line 241, in __init__
  File ".\zipdir\NL\IO\MetaCDFFile.py", line 888, in _read
  File ".\zipdir\NL\IO\MetaCDFFile.py", line 909, in _readDimensions
NL.ComputerScienceUtilities.Exceptions.NLIOError: Error: unexpected header encountered when reading dimensions

So what's happening now? Could somebody helps me .... please!
Title: Re: Parallel system: Output file error!
Post by: Nordland on July 16, 2012, 12:51
Something went wrong with the file and it is corrupted, and hence it can not be read.
Title: Re: Parallel system: Output file error!
Post by: hieido on July 17, 2012, 09:53
Dear all,

so this file went wrong... but how? because log file show that calculation was done...
I guess that maybe it is parallel system problem...
so I made the test.py test:

# ATK parallel test script
import socket
if processIsMaster():
print 'Master node:',
else:
print 'Slave node:',
print socket.gethostname()

and then I got the log file like this ...

  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 12.2.1 [Build fc22a9c]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
      File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationErrorprint 'Master node:',
        ^
IndentationError: expected an indented block
: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line ", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
  File "     /pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line   4
 ^
    print 'Master node:',
    IndentationError: expected an indented block   
 ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
  File "/pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py", line 4
    print 'Master node:',
        ^
IndentationError: expected an indented block
-------------
---------------
 How can I fix this ... please help me!
Title: Re: Parallel system: Output file error!
Post by: Nordland on July 17, 2012, 09:58
Quote from: hieido on July 17, 2012, 09:53
# ATK parallel test script
import socket
if processIsMaster():
print 'Master node:',
else:
print 'Slave node:',
print socket.gethostname()

This script should look exactly like this (as there is a indentation missing in your version on line 4)
Code
import socket
if processIsMaster():
    print 'Master node:',
else:
    print 'Slave node:',
print socket.gethostname()
Title: Re: Parallel system: Output file error!
Post by: hieido on July 18, 2012, 02:35
thanks you so much!
I tried your script and got the output file:

----------
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node:Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
 sinbaram07.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: Slave node: sinbaram06.plsi.or.kr
sinbaram06.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram02.plsi.or.krSlave node: sinbaram02.plsi.or.kr

Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
+------------------------------------------------------------------------------+
|                                                                              |
| Atomistix ToolKit 12.2.1 [Build fc22a9c]                                     |
|                                                                              |
+------------------------------------------------------------------------------+
Slave node: sinbaram02.plsi.or.kr
Master node: sinbaram04.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram06.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram02.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram04.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram07.plsi.or.kr
Slave node: sinbaram14.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node:Slave node: sinbaram11.plsi.or.kr
 sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
Slave node: sinbaram11.plsi.or.kr
---------------
-------------
because I just amateur in ATK so I cannot understand this code
is it ok? parallel system or not?
and how to fix the output nc* file?
Usually I use cmd file to run the input file on Parallel system...
--------------------
-----------
#!/bin/bash
#@ job_type = MPICH
#@ wall_clock_limit = 120:00:00
#@ step_name = atk_test
#@ notification = complete
#@ class = normal
#@ error = $(step_name).$(jobid).$(stepid).err
#@ output = $(step_name).$(jobid).$(stepid).out
#@ resources = ConsumableCpus(1)
##@ total_tasks = 6
##@ blocking = unlimited
#@ node = 6
#@ tasks_per_node = 16
#@ queue

. /home/applic/compilers/intel/2012.0.032/composer_xe_2011_sp1.6.233/bin/compilervars_arch.sh intel64
. /home/applic/compilers/intel/2012.0.032/impi/4.0.3.008/bin64/mpivars.sh intel64
. /home/applic/compilers/intel/2012.0.032/mkl/bin/mklvars.sh intel64

time mpirun -np $LOADL_TOTAL_TASKS -machinefile $LOADL_HOSTFILE /home/applic/Applications/QuantumWise/atk-12.2.1/atkpython/bin/atkpython /pwork01/p037jhd/Pham_Thu_Hien/2012.07.16/test/test.py
 ------------
-----------------
Title: Re: Parallel system: Output file error!
Post by: Nordland on July 18, 2012, 06:26
Now your parallel setup appear to be working.

Depending on your computer, and the systems you are calculating, you could perhaps gain more by choosing a different strategy
regarding the distribution of nodes, but lets save that for later.

If you delete the old netcdf file that is corrupt and try again, you should be able to use it.
Title: Re: Parallel system: Output file error!
Post by: hieido on July 19, 2012, 04:11
Dear Nordland,
I tried to run again but the out put *nc file still cannot open...  :-[  :'(
if the parallel system is working well it means that the problem may be come from the input file....
Due that I will explain clearly all steps I did ... could you please check for me ... ...
My situation is: using VNL on separated machine.
- making input file (*Py file) on PC -windows xp 64 bit from my lab
- then using Cmd file to upload input file on Parallel system -linux based 64 bit in other place.
1- Making input file:
using ATK.12.2.1 to build the py file, and then change the "nlsave" which looks like this:
------
--------------
#----------------------------------------
# Device Calculator
#----------------------------------------
calculator = DeviceLCAOCalculator(
    basis_set=basis_set,
    numerical_accuracy_parameters=device_numerical_accuracy_parameters,
    electrode_calculators=
        [left_electrode_calculator, right_electrode_calculator],
    electrode_voltages=( 0.6*Volt, 0.0*Volt)
    )

device_configuration.setCalculator(calculator)
nlprint(device_configuration)
device_configuration.update()
nlsave('/pwork01/p037jhd/Hien/test02/test.nc', device_configuration)

# -------------------------------------------------------------
# Transmission spectrum
# -------------------------------------------------------------
transmission_spectrum = TransmissionSpectrum(
    configuration=device_configuration,
    energies=numpy.linspace(-3,3,101)*eV,
    kpoints=MonkhorstPackGrid(1,1),
    energy_zero_parameter=AverageFermiLevel,
    infinitesimal=1e-06*eV,
    self_energy_calculator=DirectSelfEnergy(),
    )
nlsave('/pwork01/p037jhd/Hien/test02/test.nc', transmission_spectrum, labels=['TS'])
nlprint(transmission_spectrum)

# -------------------------------------------------------------
# Electron difference density
# -------------------------------------------------------------
electron_difference_density = ElectronDifferenceDensity(device_configuration)
nlsave('/pwork01/p037jhd/Hien/test02/test.nc', electron_difference_density, labels=['EDD'])
---------
-------------
2- upload file on paralell system by Cmd file:
-----
-------
#!/bin/bash
#@ job_type = MPICH
#@ wall_clock_limit = 120:00:00
#@ step_name = test.py
#@ notification = complete
#@ class = normal
#@ error = $(step_name).$(jobid).$(stepid).err
#@ output = $(step_name).$(jobid).$(stepid).out
#@ resources = ConsumableCpus(1)
##@ total_tasks = 6
##@ blocking = unlimited
#@ node = 6
#@ tasks_per_node = 16
#@ queue

. /home/applic/compilers/intel/2012.0.032/composer_xe_2011_sp1.6.233/bin/compilervars_arch.sh intel64
. /home/applic/compilers/intel/2012.0.032/impi/4.0.3.008/bin64/mpivars.sh intel64
. /home/applic/compilers/intel/2012.0.032/mkl/bin/mklvars.sh intel64

time mpirun -np $LOADL_TOTAL_TASKS -machinefile $LOADL_HOSTFILE /home/applic/Applications/QuantumWise/atk-12.2.1/atkpython/bin/atkpython /pwork01/p037jhd/Hien/test02/test.py
--------------
--------
then submit cmd file on parallel system.
3- Calculation:
after calculation I got the *out file looks like the log file, which shows:
----
----
+----------------------------------------------------------+

Timing:                          Total     Per Step        %

--------------------------------------------------------------------------------

Density Matrix          :     458.90 s      14.34 s      33.78% |=============|
Setting Density Matrix  :     199.01 s      49.75 s      14.65% |=====|
Real Space Integral     :     166.66 s       2.11 s      12.27% |====|
Valence Density         :     118.98 s       1.51 s       8.76% |===|
Transmission Spectrum   :      67.90 s      67.90 s       5.00% |=|
Diagonalization         :      60.92 s       1.42 s       4.48% |=|
Difference Density      :      42.31 s       0.92 s       3.11% ||
Core Density            :      37.15 s       0.81 s       2.73% ||
Hartree Potential       :      34.32 s       0.43 s       2.53% ||
Exchange-Correlation    :      21.31 s       0.27 s       1.57% ||
Constant Terms          :      20.31 s      10.15 s       1.49% ||
Mixing                  :      15.54 s       0.21 s       1.14% |
Basis Set Generation    :      12.68 s       3.17 s       0.93% |
Real Space Basis        :       7.71 s       1.93 s       0.57% |
Neutral Atom Potential  :       2.73 s       0.91 s       0.20% |
File IO, nlsave         :       0.20 s       0.07 s       0.01% |
Hubbard Term            :       0.00 s       0.00 s       0.00% |
--------------------------------------------------------------------------------
Total                   :    1358.68 s (22m38.68s)
----------
-------------
so I think the calculation was done!
automatically I obtained the NC file (around 20mb) .... and I downloaded and saved in my PC...
reopen VnL windows and run analysis file and that shows the error.
.....
so what should I do?
can you hepl me?

Title: Re: Parallel system: Output file error!
Post by: hieido on July 20, 2012, 09:50
every body! 
no reply ....
 ??? ??? ??? :P :-[
Title: Re: Parallel system: Output file error!
Post by: Nordland on July 20, 2012, 10:12
It is a bit unclear for me, if this happens every time or just once?
Title: Re: Parallel system: Output file error!
Post by: hieido on July 20, 2012, 16:35
everytime ...
I cannot obtain the data of netCDF file....
just only transmission spectra i can get from the log file ...
.... what should I do?
Title: Re: Parallel system: Output file error!
Post by: Nordland on July 20, 2012, 16:51
Okay.

What version of ATK do you have on your local machine?
Title: Re: Parallel system: Output file error!
Post by: hieido on July 20, 2012, 16:58
local computer means windows based? : ATK12.2.1
and on the linux base also 12.2.1
Title: Re: Parallel system: Output file error!
Post by: Anders Blom on July 20, 2012, 21:06
Pay attention to the fact that the NetCDF file is a binary file. We have seen cases where people use FTP programs to transfer it, and the program automatically selects ASCII mode, but it must be binary mode to preserve the file structure.