empty decomposePar

immortality · August 15, 2013, 01:17

decomposePar results processors files only including constant folders without fields.why it behaves so now?

Code:

[0] [2] --> FOAM FATAL IO ERROR:
[2]
[2] --> FOAM FATAL IO ERROR:
[2] cannot find file
[2]
[2] file: /home/ehsan/Desktop/WR_3/processor2/0/p at line 0.
[2]
[2]     From function regIOobject::readStream()
[2]     in file db/regIOobject/regIOobjectRead.C at line 73.
[2]
FOAM parallel run exiting
[2]

[0] cannot find file
[0]
[0] file: /home/ehsan/Desktop/WR_3/processor0/0/p at line 0.
[0]
[0] [3]     From function
[3]
[3] --> FOAM FATAL IO ERROR:
[3] cannot find file
[3]
[3] file: /home/ehsan/Desktop/WR_3/processor3/0/p at line 0.
[3]
[3]     From function regIOobject::readStream()
[3]     in file db/regIOobject/regIOobjectRead.C at line 73.
[3]
FOAM parallel run exiting
[3]
regIOobject::readStream()
[0]     in file db/regIOobject/regIOobjectRead.C at line 73.
[1]
[1]
[1] --> FOAM FATAL IO ERROR:
[1] cannot find file
[1]
[1] file: /home/ehsan/Desktop/WR_3/processor1/0/p at line 0.
[1]
[1]     From function regIOobject::readStream()
[1]     in file db/regIOobject/regIOobjectRead.C at line 73.
[1]
FOAM parallel run exiting
[1]
[0]
FOAM parallel run exiting
[0]
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 2 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun has exited due to process rank 3 with PID 27486 on
node Ehsan-com exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[Ehsan-com:27480] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[Ehsan-com:27480] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Killing PID 27479
 PyFoam WARNING on line 232 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/FoamThread.py : Process 27479 was already dead

immortality · August 15, 2013, 02:01

it even occurs when I use serial run.but p file is in the time folder like other fields and like before.

Code:

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.2.0                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.2.0-b363e8d14789
Exec   : rhoCentralFoamGasCont
Date   : Aug 15 2013
Time   : 10:25:54
Host   : "Ehsan-com"
PID    : 2529
Case   : /home/ehsan/Desktop/WR_3
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time

Create mesh for time = 0.0103469

Reading thermophysical properties

Selecting thermodynamics package 
{
    type            hePsiThermo;
    mixture         pureMixture;
    transport       sutherland;
    thermo          janaf;
    equationOfState perfectGas;
    specie          specie;
    energy          sensibleEnthalpy;
}



--> FOAM FATAL IO ERROR: 
cannot find file

file: /home/ehsan/Desktop/WR_3/0.0103469/p at line 0.

    From function regIOobject::readStream()
    in file db/regIOobject/regIOobjectRead.C at line 73.

FOAM exiting

immortality · August 15, 2013, 02:55

I deleted that time folder and went to a later one and used it:

Code:

decomposePar -time '0.01034593' -force

but an error like before occurred again.

Code:

[0] [1]
[1]
[1] --> FOAM FATAL IO ERROR:
[1] cannot find file
[1]
[1] file: /home/ehsan/Desktop/WR_3/processor1/0.0103459/p at line 0.
[1]
[1]     From function regIOobject::readStream()
[1]     in file db/regIOobject/regIOobjectRead.C at line 73.
[1]
FOAM parallel run exiting
[1]

[0]
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD
with errorcode 1.

NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
[0] --> FOAM FATAL IO ERROR:
[0] cannot find file
[0]
[0] file: /home/ehsan/Desktop/WR_3/processor0/0.0103459/p at line 0.
[0]
[0]     From function regIOobject::readStream()
[0]     in file db/regIOobject/regIOobjectRead.C at line 73.
[0]
FOAM parallel run exiting
[0]
--------------------------------------------------------------------------
mpirun has exited due to process rank 1 with PID 5374 on
node Ehsan-com exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[Ehsan-com:05372] 1 more process has sent help message help-mpi-api.txt / mpi-abort
[Ehsan-com:05372] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Killing PID 5369
 PyFoam WARNING on line 232 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/FoamThread.py : Process 5369 was already dead

why compiler can't read p file in time folder when its over there?

immortality · August 21, 2013, 07:27

it repeated after a while in the new case I established again:

Code:

/*---------------------------------------------------------------------------*\
| =========                 |                                                 |
| \\      /  F ield         | OpenFOAM: The Open Source CFD Toolbox           |
|  \\    /   O peration     | Version:  2.2.0                                 |
|   \\  /    A nd           | Web:      www.OpenFOAM.org                      |
|    \\/     M anipulation  |                                                 |
\*---------------------------------------------------------------------------*/
Build  : 2.2.0-b363e8d14789
Exec   : decomposePar
Date   : Aug 21 2013
Time   : 15:50:11
Host   : "Ehsan-com"
PID    : 28022
Case   : /home/ehsan/Desktop/WR_4
nProcs : 1
sigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).
fileModificationChecking : Monitoring run-time modified files using timeStampMaster
allowSystemOperations : Disallowing user-supplied system call operations

// * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * * //
Create time



Decomposing mesh region0

Create mesh

Calculating distribution of cells
Selecting decompositionMethod simple

Finished decomposition in 0.01 s

Calculating original mesh data

Distributing cells to processors

Distributing faces to processors

Distributing points to processors

Constructing processor meshes

Processor 0
    Number of cells = 9450
    Number of faces shared with processor 1 = 54
    Number of processor patches = 1
    Number of processor faces = 54
    Number of boundary faces = 19304

Processor 1
    Number of cells = 9450
    Number of faces shared with processor 0 = 54
    Number of faces shared with processor 2 = 54
    Number of processor patches = 2
    Number of processor faces = 108
    Number of boundary faces = 19250

Processor 2
    Number of cells = 9450
    Number of faces shared with processor 1 = 54
    Number of faces shared with processor 3 = 54
    Number of processor patches = 2
    Number of processor faces = 108
    Number of boundary faces = 19250

Processor 3
    Number of cells = 9450
    Number of faces shared with processor 2 = 54
    Number of processor patches = 1
    Number of processor faces = 54
    Number of boundary faces = 19304

Number of processor faces = 162
Max number of cells = 9450 (0% above average 9450)
Max number of processor patches = 2 (33.333333333333% above average 1.5)
Max number of faces between processors = 108 (33.333333333333% above average 81)

Time = 0.0111974

Processor 0: field transfer
Processor 1: field transfer
Processor 2: field transfer
Processor 3: field transfer

End.

apparently decomposePar doing well,but when I want to run,this error is shown:

Code:

[1]     From function regIOobject::readStream()
[1]     in file db/regIOobject/regIOobjectRead.C at line 73.
[1]
FOAM parallel run exiting
[1]
[3]
[3]
[3] --> FOAM FATAL IO ERROR:
[3] cannot find file
[3]
[3] file: /home/ehsan/Desktop/WR_4/processor3/0/p at line 0.
[3]
[3]     From function regIOobject::readStream()
[3]     in file db/regIOobject/regIOobjectRead.C at line 73.
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 28183 on
node Ehsan-com exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[Ehsan-com:28181] 2 more processes have sent help message help-mpi-api.txt / mpi-abort
[Ehsan-com:28181] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
Killing PID 28177
 PyFoam WARNING on line 232 of file /usr/local/lib/python2.7/dist-packages/PyFoam/Execution/FoamThread.py : Process 28177 was already dead 
Getting LinuxMem: [Errno 2] No such file or directory: '/proc/28177/status'

what may be the reason of such decomposePar issues and how to solve?

immortality · August 21, 2013, 08:16

it resolved

I don't know why decomposePar command wanted to decompose .0111974 time folder while the correct name of last time folder was 0.01119737
I used:

Code:

decomposePar -latestTime -force

and then decomposePar worked and copied time folders in processors folders.
but when I wanted to run it again said that the field files aren't in folder 0.0111974.
then I changed

Code:

timePrecision   7;

from 6 to 7 in controlDict and it started working!
I'm not sure about the reason of these all!because I hadn't change anything in controlDict and all was like it was before the error!
is it because of digit in time folders names?
I had time folders like:0.004665(4 significant digits),0.00658536(6 significant digits) and the last time folder had 7 significant digits(0.01119737)
then how should assign time precision so that can be sure it won't occur in future?a large number like 10 is better?

August 21, 2013, 08:16		#5
immortality Senior Member Ehsan Join Date: Oct 2012 Location: Iran Posts: 2,208 Rep Power: 26	it resolved I don't know why decomposePar command wanted to decompose .0111974 time folder while the correct name of last time folder was 0.01119737 I used: Code: decomposePar -latestTime -force and then decomposePar worked and copied time folders in processors folders. but when I wanted to run it again said that the field files aren't in folder 0.0111974. then I changed Code: timePrecision 7; from 6 to 7 in controlDict and it started working! I'm not sure about the reason of these all!because I hadn't change anything in controlDict and all was like it was before the error! is it because of digit in time folders names? I had time folders like:0.004665(4 significant digits),0.00658536(6 significant digits) and the last time folder had 7 significant digits(0.01119737) then how should assign time precision so that can be sure it won't occur in future?a large number like 10 is better? sadjad.s, jensi_t, qjh888 and 3 others like this. __________________ Injustice Anywhere is a Threat for Justice Everywhere.Martin Luther King. To Be or Not To Be,Thats the Question! The Only Stupid Question Is the One that Goes Unasked.

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