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-   -   Help compiling code (newbie) (http://www.cfd-online.com/Forums/openfoam-programming-development/132562-help-compiling-code-newbie.html)

thsb20 April 2, 2014 16:22

Help compiling code (newbie)
 
Hi everyone,

Im currently doing my dissertation at University of Bath, UK on cyclocopter rotors and found the following blog post:

http://lordvon64.blogspot.co.uk/2014...87540156025031

The model he has made closely follows the experimental data from other cyclocopters and I would love to be able to run/edit his code, listed on github here:

https://github.com/lordvon/OpenFOAM_...ster/cycloRamp

Now, bear with me at this point, I am totally new to OpenFOAM, and I dont know how to run this code. I have installed OpenFOAM correctly (done a few of the tutorials to confirm) and downloaded the repository from Github.

What is the next step? In the files on Github he has the 'compiling new OpenFOAM source' file, which lists how to compile. All the steps until the last line seem to have been done in the downloaded repository, if I am correct? The files in /Make have been made. The last line details adding the line to controlDict, does this mean I go into controlDict in the system files and add the line? then run the file remake?

If anyone could give me an idiots guide to doing this I would be very much appreciated, starting from the begining. The author of the blog is helpful but being in different time zones the reply's are quite delayed.

Thanks,

Tom

kmooney April 2, 2014 18:48

Hi Tom,

It looks like you're pretty close. If you have already compiled that library you should be pretty close.

The last step is to add a line to the controlDict of whatever case you're running this on but there is a typo in his instructions. There should be a semicolon closing the parentheses ; like this:

libs ( "libCycloRamp.so" );

Do you already have an example case that will engage the functionality of this new library?

Cheer!
Kyle


Quote:

Originally Posted by thsb20 (Post 483518)
Hi everyone,

Im currently doing my dissertation at University of Bath, UK on cyclocopter rotors and found the following blog post:

http://lordvon64.blogspot.co.uk/2014...87540156025031

The model he has made closely follows the experimental data from other cyclocopters and I would love to be able to run/edit his code, listed on github here:

https://github.com/lordvon/OpenFOAM_...ster/cycloRamp

Now, bear with me at this point, I am totally new to OpenFOAM, and I dont know how to run this code. I have installed OpenFOAM correctly (done a few of the tutorials to confirm) and downloaded the repository from Github.

What is the next step? In the files on Github he has the 'compiling new OpenFOAM source' file, which lists how to compile. All the steps until the last line seem to have been done in the downloaded repository, if I am correct? The files in /Make have been made. The last line details adding the line to controlDict, does this mean I go into controlDict in the system files and add the line? then run the file remake?

If anyone could give me an idiots guide to doing this I would be very much appreciated, starting from the begining. The author of the blog is helpful but being in different time zones the reply's are quite delayed.

Thanks,

Tom


thsb20 April 2, 2014 19:09

Ah OK, I think I get hwo it works now.

I was thinking of the code uplaoded to Github as the code to run on its own. But its actually just the library which other code uses to run.

So I need to find out the example that will use this library, then add the line you said to the controlDict file of that example, then run that example as normal? It doesnt mention anythign about that in his blog post does it? The only sentance that soudns like it points to the right example is 'I used the pimpleDyMFoam solver in PISO mode (no SIMPLE iterations)'. Does that mean anything?

Thanks for your help

Tom

kmooney April 2, 2014 19:24

Without an example case you're going to have to effectively reverse engineer the case configuration. Also, it looks like the mesh he's using its awfully complicated in terms of multiple embedded rotational sliding boundary interfaces.

After having a quick look at his code its going to be really difficult to put a case together from scratch, even with a ton of OpenFOAM experience. I think your best bet is to get in touch with the original developer and ask for an example case.

Cheers,
Kyle

thsb20 April 2, 2014 19:44

Hi Kyle,

Thanks for the info. Ive contacted the author and he is going to post a case file to this thread, which should help me get the simulation up and running.

Thanks for the help, im sure I may have a couple more questions lol, using OpenFOAM is on a whole different level to what im used to

Tom

lordvon April 2, 2014 19:52

1 Attachment(s)
You will not have to reverse-engineer anything!!! I am the author of the post mentioned above. Here I have attached the case and mesh files for the cyclorotor simulation. Here is how I use it:

-I view the mesh by 'gmsh main.geo' inside the mesh folder. I change whatever I need in mesh/inputs.geo.

-run './parallel runname' in the main directory (where case and mesh reside)

-That's it!

That is after of course you have compiled the custom solidBodyMotionFunctions that were referenced above, and installed gmsh. Also, you might have to chmod +x a few files to make them executable.

Please let me know of any questions!

thsb20 April 3, 2014 03:04

I think my problem is with compiling the solver at the moment. when I run the make command I get the following :

wmakeLnInclude: linking include files to ./lnInclude
Making dependency list for source file cycloRamp.C
SOURCE=cycloRamp.C ; g++ -m64 -Dlinux64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O3 -DNoRepository -ftemplate-depth-100 -I/opt/openfoam230/src/dynamicFvMesh/lnInclude -I/opt/openfoam230/src/dynamicFvMesh/solidBodyMotionFvMesh/lnInclude -IlnInclude -I. -I/opt/openfoam230/src/OpenFOAM/lnInclude -I/opt/openfoam230/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linux64GccDPOpt/cycloRamp.o
In file included from cycloRamp.H:38:0,
from cycloRamp.C:26:
/opt/openfoam230/src/dynamicFvMesh/lnInclude/solidBodyMotionFunction.H: In static member function ‘static Foam::autoPtr<Foam::solidBodyMotionFunction> Foam::solidBodyMotionFunction::adddictionaryConstr uctorToTable<solidBodyMotionFunctionType>::New(con st Foam::dictionary&, const Foam::Time&) [with solidBodyMotionFunctionType = Foam::solidBodyMotionFunctions::cycloRamp]’:
/opt/openfoam230/src/dynamicFvMesh/lnInclude/solidBodyMotionFunction.H:90:9: instantiated from ‘Foam::solidBodyMotionFunction::adddictionaryConst ructorToTable<solidBodyMotionFunctionType>::adddic tionaryConstructorToTable(const Foam::word&) [with solidBodyMotionFunctionType = Foam::solidBodyMotionFunctions::cycloRamp]’
cycloRamp.C:46:1: instantiated from here
/opt/openfoam230/src/dynamicFvMesh/lnInclude/solidBodyMotionFunction.H:90:9: error: cannot allocate an object of abstract type ‘Foam::solidBodyMotionFunctions::cycloRamp’
cycloRamp.H:53:7: note: because the following virtual functions are pure within ‘Foam::solidBodyMotionFunctions::cycloRamp’:
/opt/openfoam230/src/dynamicFvMesh/lnInclude/solidBodyMotionFunction.H:110:50: note: virtual Foam::autoPtr<Foam::solidBodyMotionFunction> Foam::solidBodyMotionFunction::clone() const
/opt/openfoam230/src/dynamicFvMesh/lnInclude/solidBodyMotionFunction.H:90:9: warning: control reaches end of non-void function [-Wreturn-type]
make: *** [Make/linux64GccDPOpt/cycloRamp.o] Error 1

It looks like its throwing up a few errors, do you have any idea what it means?

lordvon April 3, 2014 09:12

Hi Thomas,
I made sure it worked before I uploaded it to Github, though the instructions could be better, which I have updated based on feedback from this thread.

Please delete the cycloRamp library files and redownload them and try again. This time, only doing these few things:

-type 'sudo' and then login
-Go inside the main directory of the downloaded files (where Make, cycloRamp.C,cycloRamp.h,etc. reside)
-Make the freshly downloaded file executable by 'chmod +x remake'
-Run './remake'

If you do not get errors, great! Compiling always seems to be the biggest obstacle in running custom OpenFOAM stuff. You then can run a simulation with './parallel yourRunName' in the main directory of the case files I uploaded to this thread. Even if you get errors then, they will be very easy to debug. Since you and I have spent a bit of time on this, I am determined to get it working for you :)

Which version of OpenFOAM are you using?

thsb20 April 3, 2014 09:46

Iv followed the instructions but still get a couple of error messages,a lthough it is far fewer than before.

I get:

linux64GccDPOpt/options:7: *** commands commence before first target. Stop.
wmake error: file 'Make/linux64GccDPOpt/objectFiles' could not be created in /home/tom/OpenFOAM/tom-2.3.0/applications/solvers/cycloRamp
cp: cannot stat `/home/tom/OpenFOAM/root-2.3.0/platforms/linux64GccDPOpt/lib/libCycloRamp.so': No such file or directory

In your 'compiling new OpenFOAM source' file you have the text to put in the options file as different to the file you uploaded. Ive tried both and get the same error though.

It feels like its so close. Im using OpenFOAM 2.3.0 :)

lordvon April 3, 2014 11:08

Oops, I guess they are different but they both should work. After a little Google searching, it might be the format of the text in the Make/options file. I updated the file on Github, and all I did was remove the tabs. Try and see if anything is different.

I wish I could test it, but it works as is on my computer unfortunately.

thsb20 April 3, 2014 15:51

Im getting further and further each time I go through. At the moment its making the /Make/linux64GccDPOpt files and a /lnInclude folder with links to the .C and .H files.

However there is still an error:

cycloRamp.C:46:1: instantiated from here
/opt/openfoam230/src/dynamicFvMesh/lnInclude/solidBodyMotionFunction.H:90:9: error: cannot allocate an object of abstract type ‘Foam::solidBodyMotionFunctions::cycloRamp’
cycloRamp.H:53:7: note: because the following virtual functions are pure within ‘Foam::solidBodyMotionFunctions::cycloRamp’:
/opt/openfoam230/src/dynamicFvMesh/lnInclude/solidBodyMotionFunction.H:110:50: note: virtual Foam::autoPtr<Foam::solidBodyMotionFunction> Foam::solidBodyMotionFunction::clone() const
/opt/openfoam230/src/dynamicFvMesh/lnInclude/solidBodyMotionFunction.H:90:9: warning: control reaches end of non-void function [-Wreturn-type]
make: *** [Make/linux64GccDPOpt/cycloRamp.o] Error 1
cp: cannot stat `/home/tom/OpenFOAM/root-2.3.0/platforms/linux64GccDPOpt/lib/libCycloRamp.so': No such file or directory

Looks like its on line 46 of cycloRamp.C, running this bit of code:

namespace Foam
{
namespace solidBodyMotionFunctions
{
defineTypeNameAndDebug(cycloRamp, 0);
addToRunTimeSelectionTable
(
solidBodyMotionFunction,
cycloRamp,
dictionary
);
}
}

Any ideas?

Tom

lordvon April 4, 2014 21:27

Could be the version. Ill try out 230, as I used 222. Or, you could try out 222. I will try to let you know tomorrow.

thsb20 April 6, 2014 16:39

Hi,

Success on the compiling front, I installed 222 and it compiled perfectly. Now just got to figure out how to run the other code.

When the code runs I get a warning that it could not load libCycloBucket.so. Is there another library called this? The github code only has cycloRamp.so. I also get one for libRampedAxisRotationMotion.so, this is on Github so I will compile it and that error should go away

Tom

lordvon April 6, 2014 17:16

1 Attachment(s)
Great!

libCycloBucket and libRampedAxisRotationMotion were other custom codes of mine I made for different pitching schedule and ramping up the rotor speed for (supposedly) faster transient simulation, respectively. They are utilized in 'system/controlDict' and 'constant/dynamicMeshDict'.

In dynamicMeshDict you specify rotation speed and for my custom code the cyclorotor parameters. It is an error on my part that those case files use cycloBucket instead of cycloRamp in the dynamicMeshDict. So, I have attached the case files that work the same way as the earlier one, except that it has the correct dynamicMeshDict (no need to recompile, etc.). But you should compile rampedAxisRotationMotion if its no problem, otherwise you will need to change the dynamicMeshDict to not use it, and instead use the standard OpenFOAM mesh rotation function, which does a hard start.

The mesh in the new attached case files is different. If you prefer the old mesh, simply copy over your old 'mesh' to replace the one in the new attachment. (I also changed the cyclorotor.zip posted earlier to avoid confusion)

Just as a side note, in libCycloRamp the pitching motion is sinusoidal with respect to azimuthal position (of the blade w.r.t. rotor center). In libCycloBucket the pitching schedule looks more like a clipped sine wave. So if you are interested in implementing this or other more interesting pitching schedules as a function of azimuthal position, let me know and I can upload it. Pretty much any arbitrary sufficiently-smooth pitching schedule is possible with the method described in "Design, Development, and Flight Test of a Small-Scale Cyclogyro UAV Utilizing a Novel Cam-Based Passive Blade Pitching Mechanism" by Zachary Adams, et al. I do not know where to get the PDF for free for everyone, but since you are a University undergrad you should be able to access it for free somehow.

thsb20 April 7, 2014 04:52

Excellent, closer than ever.

I make it through the set up; till the run case question its all fine with no errors. However when I run the case I get the followign error:

Selecting dynamicFvMesh multiSolidBodyMotionFvMesh
Selecting solid-body motion function rampedAxisRotationMotion
[0]
[0]
[0] --> FOAM FATAL IO ERROR:
[0] keyword CofG is undefined in dictionary "/home/tom/OpenFOAM/OpenFOAM-2.2.2/cyclorotor/runname/processor0/../constant/dynamicMeshDict.multiSolidBodyMotionFvMeshCoeffs.r otorVolume.rampedAxisRotationMotionCoeffs"
[0]
[0] file: /home/tom/OpenFOAM/OpenFOAM-2.2.2/cyclorotor/runname/processor0/../constant/dynamicMeshDict.multiSolidBodyMotionFvMeshCoeffs.r otorVolume.rampedAxisRotationMotionCoeffs from line 26 to line 26.
[0]
[0] From function dictionary::lookupEntry(const word&, bool, bool) const
[0] in file db/dictionary/dictionary.C at line 402.
[0]
FOAM parallel run exiting
[0]

rampedAxisRotationMotion compiled correctly with no errors but it looks like this is an error in that library

Tom

lordvon April 7, 2014 14:14

Alright I think we are out of the woods. These are just typos (i had different versions of rampedAxisRotationMotion). I uploaded the corrected cases once again to the links above. The only thing that is different is 'constant/dynamicMeshDict'.

thsb20 April 8, 2014 04:22

Almost there,

I get the error when I run the case:

[0] file: /home/tom/Desktop/cyclorotor/2/processor0/0/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]

There is the folder '0' in the /runname folder, with the p file in, but not within the individual processor folders. It says this for all 4 processors (0, 1, 2, 3)

The newly updated zip files also have 1 error in the mesh but I copied over the old mesh and its working perfectly so no worries there.

Thanks for all the help. I really appreciate it

Tom

lordvon April 8, 2014 08:51

I think an error is occurring earlier. Please put all output into a text file and upload it.

thsb20 April 8, 2014 13:48

When I run ./parallel I get the following:

Code:

root@tom-770Z5E-780Z5E:~/Desktop/cyclorotor# ./parallel 1
./setup: line 18: ./fixBoundary: Permission denied
/*---------------------------------------------------------------------------*\
| =========                |                                                |
| \\      /  F ield        | OpenFOAM: The Open Source CFD Toolbox          |
|  \\    /  O peration    | Version:  2.2.2                                |
|  \\  /    A nd          | Web:      www.OpenFOAM.org                      |
|    \\/    M anipulation  |                                                |
\*---------------------------------------------------------------------------*/
Build  : 2.2.2-9739c53ec43f
Exec  : renumberMesh -constant -overwrite
Date  : Apr 08 2014
Time  : 18:42:53
Host  : "tom-770Z5E-780Z5E"
PID    : 4450
Case  : /home/tom/Desktop/cyclorotor/1
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 = constant

Mesh size: 28575
Before renumbering :
    band          : 4669
    profile        : 1.58332e+07

Using default renumberMethod.

Selecting renumberMethod CuthillMcKee


After renumbering :
    band          : 150
    profile        : 2.11817e+06

Writing mesh to "constant"

End.

/*---------------------------------------------------------------------------*\
| =========                |                                                |
| \\      /  F ield        | OpenFOAM: The Open Source CFD Toolbox          |
|  \\    /  O peration    | Version:  2.2.2                                |
|  \\  /    A nd          | Web:      www.OpenFOAM.org                      |
|    \\/    M anipulation  |                                                |
\*---------------------------------------------------------------------------*/
Build  : 2.2.2-9739c53ec43f
Exec  : decomposePar
Date  : Apr 08 2014
Time  : 18:42:54
Host  : "tom-770Z5E-780Z5E"
PID    : 4455
Case  : /home/tom/Desktop/cyclorotor/1
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 scotch

Finished decomposition in 0.06 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 = 7195
    Number of faces shared with processor 1 = 11
    Number of faces shared with processor 2 = 8
    Number of processor patches = 2
    Number of processor faces = 19
    Number of boundary faces = 14835

Processor 1
    Number of cells = 7185
    Number of faces shared with processor 0 = 11
    Number of faces shared with processor 3 = 12
    Number of processor patches = 2
    Number of processor faces = 23
    Number of boundary faces = 15067

Processor 2
    Number of cells = 7099
    Number of faces shared with processor 0 = 8
    Number of faces shared with processor 3 = 11
    Number of processor patches = 2
    Number of processor faces = 19
    Number of boundary faces = 14803

Processor 3
    Number of cells = 7096
    Number of faces shared with processor 1 = 12
    Number of faces shared with processor 2 = 11
    Number of processor patches = 2
    Number of processor faces = 23
    Number of boundary faces = 14613

Number of processor faces = 42
Max number of cells = 7195 (0.71741% above average 7143.75)
Max number of processor patches = 2 (0% above average 2)
Max number of faces between processors = 23 (9.52381% above average 21)

Time = 0


--> FOAM FATAL IO ERROR:

    patch type 'patch' not constraint type 'empty'
    for patch defaultFaces of field p in file "/home/tom/Desktop/cyclorotor/1/0/p"

file: /home/tom/Desktop/cyclorotor/1/0/p.boundaryField.defaultFaces from line 3 to line 3.

    From function emptyFvPatchField<Type>::emptyFvPatchField
(
    const fvPatch& p,
    const Field<Type>& field,
    const dictionary& dict
)

    in file fields/fvPatchFields/constraint/empty/emptyFvPatchField.C at line 100.

FOAM exiting

/*---------------------------------------------------------------------------*\
| =========                |                                                |
| \\      /  F ield        | OpenFOAM: The Open Source CFD Toolbox          |
|  \\    /  O peration    | Version:  2.2.2                                |
|  \\  /    A nd          | Web:      www.OpenFOAM.org                      |
|    \\/    M anipulation  |                                                |
\*---------------------------------------------------------------------------*/
Build  : 2.2.2-9739c53ec43f
Exec  : renumberMesh -overwrite -parallel
Date  : Apr 08 2014
Time  : 18:42:55
Host  : "tom-770Z5E-780Z5E"
PID    : 4457
Case  : /home/tom/Desktop/cyclorotor/1
nProcs : 4
Slaves :
3
(
"tom-770Z5E-780Z5E.4458"
"tom-770Z5E-780Z5E.4459"
"tom-770Z5E-780Z5E.4460"
)

Pstream initialized with:
    floatTransfer      : 0
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
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 = constant

Mesh size: 28575
Before renumbering :
    band          : 150
    profile        : 2.0311e+06

Using default renumberMethod.

Selecting renumberMethod CuthillMcKee


Renumbering processor cell decomposition map cellProcAddressing
Renumbering processor face decomposition map faceProcAddressing
Renumbering processor point decomposition map pointProcAddressing
After renumbering :
    band          : 150
    profile        : 2.03135e+06

Writing mesh to "constant"

End.

Finalising parallel run
/*---------------------------------------------------------------------------*\
| =========                |                                                |
| \\      /  F ield        | OpenFOAM: The Open Source CFD Toolbox          |
|  \\    /  O peration    | Version:  2.2.2                                |
|  \\  /    A nd          | Web:      www.OpenFOAM.org                      |
|    \\/    M anipulation  |                                                |
\*---------------------------------------------------------------------------*/
Build  : 2.2.2-9739c53ec43f
Exec  : potentialFoam -parallel
Date  : Apr 08 2014
Time  : 18:42:56
Host  : "tom-770Z5E-780Z5E"
PID    : 4465
Case  : /home/tom/Desktop/cyclorotor/1
nProcs : 4
Slaves :
3
(
"tom-770Z5E-780Z5E.4466"
"tom-770Z5E-780Z5E.4467"
"tom-770Z5E-780Z5E.4468"
)

Pstream initialized with:
    floatTransfer      : 0
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
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

Reading field p

[0]
[0]
[0] --> FOAM FATAL IO ERROR:
[0] cannot find file
[0]
[0] file: /home/tom/Desktop/cyclorotor/1/processor0/0/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]
[1]
[1]
[1] --> FOAM FATAL IO ERROR:
[1] cannot find file
[1]
[1] file: /home/tom/Desktop/cyclorotor/1/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]
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 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.
--------------------------------------------------------------------------
[2]
[2]
[2] --> FOAM FATAL IO ERROR:
[2] cannot find file
[2]
[2] file: /home/tom/Desktop/cyclorotor/1/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]
[3]
[3]
[3] --> FOAM FATAL IO ERROR:
[3] cannot find file
[3]
[3] file: /home/tom/Desktop/cyclorotor/1/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]
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 4465 on
node tom-770Z5E-780Z5E exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[tom-770Z5E-780Z5E:04464] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[tom-770Z5E-780Z5E:04464] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
/*---------------------------------------------------------------------------*\
| =========                |                                                |
| \\      /  F ield        | OpenFOAM: The Open Source CFD Toolbox          |
|  \\    /  O peration    | Version:  2.2.2                                |
|  \\  /    A nd          | Web:      www.OpenFOAM.org                      |
|    \\/    M anipulation  |                                                |
\*---------------------------------------------------------------------------*/
Build  : 2.2.2-9739c53ec43f
Exec  : checkMesh -constant -allGeometry -allTopology
Date  : Apr 08 2014
Time  : 18:42:57
Host  : "tom-770Z5E-780Z5E"
PID    : 4472
Case  : /home/tom/Desktop/cyclorotor/1
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 polyMesh for time = constant

Enabling all (cell, face, edge, point) topology checks.

Enabling all geometry checks.

Time = constant

Mesh stats
    points:          59306
    internal points:  0
    edges:            146121
    internal edges:  27485
    internal edges using one boundary point:  0
    internal edges using two boundary points:  27485
    faces:            115384
    internal faces:  56066
    cells:            28575
    faces per cell:  6
    boundary patches: 25
    point zones:      0
    face zones:      0
    cell zones:      8

Overall number of cells of each type:
    hexahedra:    28575
    prisms:        0
    wedges:        0
    pyramids:      0
    tet wedges:    0
    tetrahedra:    0
    polyhedra:    0

Checking topology...
    Boundary definition OK.
    Cell to face addressing OK.
    Point usage OK.
    Upper triangular ordering OK.
    Face vertices OK.
    Topological cell zip-up check OK.
    Face-face connectivity OK.
  <<Writing 2 cells with two non-boundary faces to set twoInternalFacesCells
  *Number of regions: 8
    The mesh has multiple regions which are not connected by any face.
  <<Writing region information to "constant/cellToRegion"

Checking patch topology for multiply connected surfaces...
    Patch              Faces    Points  Surface topology                  Bounding box
    bladeAmi01          64      128      ok (non-closed singly connected)  (-0.149909 0.250091 0) (0.149909 0.549909 0.01)
    blade0              112      224      ok (non-closed singly connected)  (-0.0708681 0.369422 0) (0.070921 0.430525 0.01)
    bladeAmi11          64      128      ok (non-closed singly connected)  (-0.496319 0.0500914 0) (-0.196502 0.349909 0.01)
    blade1              112      224      ok (non-closed singly connected)  (-0.39729 0.1408 0) (-0.295583 0.259147 0.01)
    bladeAmi21          64      128      ok (non-closed singly connected)  (-0.496319 -0.349909 0) (-0.196502 -0.0500914 0.01)
    blade2              112      224      ok (non-closed singly connected)  (-0.39729 -0.259147 0) (-0.295583 -0.1408 0.01)
    bladeAmi31          64      128      ok (non-closed singly connected)  (-0.149909 -0.549909 0) (0.149909 -0.250091 0.01)
    blade3              112      224      ok (non-closed singly connected)  (-0.0708681 -0.430525 0) (0.070921 -0.369422 0.01)
    bladeAmi41          64      128      ok (non-closed singly connected)  (0.196502 -0.349909 0) (0.496319 -0.0500914 0.01)
    blade4              112      224      ok (non-closed singly connected)  (0.315832 -0.270921 0) (0.376935 -0.129132 0.01)
    bladeAmi51          64      128      ok (non-closed singly connected)  (0.196502 0.0500914 0) (0.496319 0.349909 0.01)
    blade5              112      224      ok (non-closed singly connected)  (0.315832 0.129132 0) (0.376935 0.270921 0.01)
    ami1                312      624      ok (non-closed singly connected)  (-0.599998 -0.599998 0) (0.599998 0.599998 0.01)
    bladeAmi00          64      128      ok (non-closed singly connected)  (-0.15 0.25 0) (0.15 0.55 0.01)
    bladeAmi10          64      128      ok (non-closed singly connected)  (-0.49641 0.05 0) (-0.19641 0.35 0.01)
    bladeAmi20          64      128      ok (non-closed singly connected)  (-0.49641 -0.35 0) (-0.19641 -0.05 0.01)
    bladeAmi30          64      128      ok (non-closed singly connected)  (-0.15 -0.55 0) (0.15 -0.25 0.01)
    bladeAmi40          64      128      ok (non-closed singly connected)  (0.19641 -0.35 0) (0.49641 -0.05 0.01)
    bladeAmi50          64      128      ok (non-closed singly connected)  (0.19641 0.05 0) (0.49641 0.35 0.01)
    shaft              24      48      ok (non-closed singly connected)  (-0.025 -0.025 0) (0.025 0.025 0.01)
    tunnel              40      84      ok (non-closed singly connected)  (-24 -24 0) (24 24 0.01)
    outlet              20      42      ok (non-closed singly connected)  (24 -24 0) (24 24 0.01)
    inlet              20      42      ok (non-closed singly connected)  (-24 -24 0) (-24 24 0.01)
    ami0                312      624      ok (non-closed singly connected)  (-0.6 -0.6 0) (0.6 0.6 0.01)
    defaultFaces        57150    59306    ok (non-closed singly connected)  (-24 -24 0) (24 24 0.01)

Checking geometry...
    Overall domain bounding box (-24 -24 0) (24 24 0.01)
    Mesh (non-empty, non-wedge) directions (1 1 1)
    Mesh (non-empty) directions (1 1 1)
    Boundary openness (-1.16238e-20 2.3518e-23 -1.52923e-18) OK.
    Max cell openness = 1.78734e-15 OK.
    Max aspect ratio = 291.433 OK.
    Minimum face area = 1.41039e-07. Maximum face area = 8.4606.  Face area magnitudes OK.
    Min volume = 1.41039e-09. Max volume = 0.084606.  Total volume = 23.0398.  Cell volumes OK.
    Mesh non-orthogonality Max: 30.2646 average: 4.67601
    Non-orthogonality check OK.
    Face pyramids OK.
    Max skewness = 0.608728 OK.
    Coupled point location match (average 0) OK.
    Face tets OK.
    Min/max edge length = 7.15891e-05 3.46237 OK.
    All angles in faces OK.
    Face flatness (1 = flat, 0 = butterfly) : average = 1  min = 1
    All face flatness OK.
    Cell determinant (wellposedness) : minimum: 0 average: 4.08785e-31
 ***Cells with small determinant (< 0.001) found, number of cells: 28575
  <<Writing 28575 under-determined cells to set underdeterminedCells
    Concave cell check OK.

Failed 1 mesh checks.

End


thsb20 April 8, 2014 13:49

and after I run case:

Code:

/*---------------------------------------------------------------------------*\
| =========                |                                                |
| \\      /  F ield        | OpenFOAM: The Open Source CFD Toolbox          |
|  \\    /  O peration    | Version:  2.2.2                                |
|  \\  /    A nd          | Web:      www.OpenFOAM.org                      |
|    \\/    M anipulation  |                                                |
\*---------------------------------------------------------------------------*/
Build  : 2.2.2-9739c53ec43f
Exec  : pimpleDyMFoam -parallel
Date  : Apr 08 2014
Time  : 18:44:59
Host  : "tom-770Z5E-780Z5E"
PID    : 4487
Case  : /home/tom/Desktop/cyclorotor/1
nProcs : 4
Slaves :
3
(
"tom-770Z5E-780Z5E.4488"
"tom-770Z5E-780Z5E.4489"
"tom-770Z5E-780Z5E.4490"
)

Pstream initialized with:
    floatTransfer      : 0
    nProcsSimpleSum    : 0
    commsType          : nonBlocking
    polling iterations : 0
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

Selecting dynamicFvMesh multiSolidBodyMotionFvMesh
Selecting solid-body motion function rampedAxisRotationMotion
Applying solid body motion rampedAxisRotationMotion to 1070 points of cellZone rotorVolume
Selecting solid-body motion function cycloRamp
Applying solid body motion cycloRamp to 0 points of cellZone bladeVolume0
Selecting solid-body motion function cycloRamp
Applying solid body motion cycloRamp to 0 points of cellZone bladeVolume1
Selecting solid-body motion function cycloRamp
Applying solid body motion cycloRamp to 0 points of cellZone bladeVolume2
Selecting solid-body motion function cycloRamp
Applying solid body motion cycloRamp to 6896 points of cellZone bladeVolume3
Selecting solid-body motion function cycloRamp
Applying solid body motion cycloRamp to 6890 points of cellZone bladeVolume4
Selecting solid-body motion function cycloRamp
Applying solid body motion cycloRamp to 0 points of cellZone bladeVolume5
Reading field p

[2] [3]
[3]
[3]
[2]
[2] --> FOAM FATAL IO ERROR:
[2] cannot find file
[2]
[2] file: /home/tom/Desktop/cyclorotor/1/processor2/0/p at line 0.
[2]
--> FOAM FATAL IO ERROR:
[3] cannot find file
[3]
[3] file: /home/tom/Desktop/cyclorotor/1/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]
[1]
[2]    From function regIOobject::readStream()
[2]    in file db/regIOobject/regIOobjectRead.C at line 73.
[2]
FOAM parallel run exiting
[2]
[0]
[0]
[0] --> FOAM FATAL IO ERROR:
[0] cannot find file
[0]
[0] file: /home/tom/Desktop/cyclorotor/1/processor0/0/p at line [1]
[1] --> FOAM FATAL IO ERROR:
[1] cannot find file
[1]
[1] file: /home/tom/Desktop/cyclorotor/1/processor1/0/p at line 0.
[1]
[1]    From function regIOobject::readStream()
[1]    in file db/regIOobject/regIOobjectRead.C0.
[0]
[0]    From function regIOobject::readStream()
[0]  at line 73.
[1]
FOAM parallel run exiting
[1]
    in file db/regIOobject/regIOobjectRead.C at line 73.
[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 2 with PID 4489 on
node tom-770Z5E-780Z5E exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
[tom-770Z5E-780Z5E:04486] 3 more processes have sent help message help-mpi-api.txt / mpi-abort
[tom-770Z5E-780Z5E:04486] Set MCA parameter "orte_base_help_aggregate" to 0 to see all help / error messages
./parallel: line 23: break: only meaningful in a `for', `while', or `until' loop

I have done chmod +x on both parallel and setup, and running with root permissions. After pasting this in I noticed the error on the very first line. I hadnt seen it before because my terminal was limited to 512 lines showing. Having already given permission to setup by chmod I dont know why it is restricting access


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