Author Topic: Parallel system: Output file error! (Read 7079 times)

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!

Nordland · « **Reply #1 on:** July 16, 2012, 12:51 »

Something went wrong with the file and it is corrupted, and hence it can not be read.

hieido · « **Reply #2 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!

Nordland · « **Reply #3 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()

hieido · « **Reply #4 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
------------
-----------------

Nordland · « **Reply #5 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.

hieido · « **Reply #6 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?

hieido · « **Reply #7 on:** July 20, 2012, 09:50 »

every body!
no reply ....

Nordland · « **Reply #8 on:** July 20, 2012, 10:12 »

It is a bit unclear for me, if this happens every time or just once?

hieido · « **Reply #9 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?

Nordland · « **Reply #10 on:** July 20, 2012, 16:51 »

Okay.

What version of ATK do you have on your local machine?

hieido · « **Reply #11 on:** July 20, 2012, 16:58 »

local computer means windows based? : ATK12.2.1
and on the linux base also 12.2.1

Anders Blom · « **Reply #12 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.

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Author Topic: Parallel system: Output file error! (Read 7079 times)

hieido

Parallel system: Output file error!

Nordland

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hieido

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Nordland

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hieido

Re: Parallel system: Output file error!

Nordland

Re: Parallel system: Output file error!

hieido

Re: Parallel system: Output file error!

hieido

Re: Parallel system: Output file error!

Nordland

Re: Parallel system: Output file error!

hieido

Re: Parallel system: Output file error!

Nordland

Re: Parallel system: Output file error!

hieido

Re: Parallel system: Output file error!

Anders Blom

Re: Parallel system: Output file error!