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Old   February 24, 2010, 21:57
Default Error will loading makeAxialMesh utility in openFOAM-1.6
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Patrick
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Greetings group members

I was trying to compile the makeAxialMesh utility and use it for generating an axi-symmetric mesh. I untarred the .gz file at this location
$HOME/OpenFOAM-1.6/applications/utilities/mesh//manipulation

Then i typed wmake in the command prompt. I am getting the following error

SOURCE=makeAxialMesh.C ; g++ -m32 -Dlinux -DWM_DP -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-40 -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/dynamicMesh/lnInclude -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/cfdTools/lnInclude -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/meshTools/lnInclude -IlnInclude -I. -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/OpenFOAM/lnInclude -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linuxGccDPOpt/makeAxialMesh.o
mkdir: cannot create directory `/home/patrick/OpenFOAM/patrick-1.6/applications': Permission denied
make: *** [/home/patrick/OpenFOAM/patrick-1.6/applications/bin/linuxGccDPOpt/makeAxialMesh] Error 1
++ echo -ne '\033]0;patrick@patrick-laptop: ~/OpenFOAM/OpenFOAM-1.6/applications/utilities/mesh/manipulation/makeAxialMesh\007'

I am pretty sure I am doing something wrong. Your help will be greatly appreciated. Also, is there any other way for creating axi-sym meshes in OpenFOAM or importing them from Gambit ?
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Old   February 25, 2010, 10:09
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Quote:
Originally Posted by will_avoid_comm_solvers View Post
Greetings group members

I was trying to compile the makeAxialMesh utility and use it for generating an axi-symmetric mesh. I untarred the .gz file at this location
$HOME/OpenFOAM-1.6/applications/utilities/mesh//manipulation

Then i typed wmake in the command prompt. I am getting the following error

SOURCE=makeAxialMesh.C ; g++ -m32 -Dlinux -DWM_DP -Wall -Wno-strict-aliasing -Wextra -Wno-unused-parameter -Wold-style-cast -O3 -DNoRepository -ftemplate-depth-40 -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/dynamicMesh/lnInclude -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/cfdTools/lnInclude -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/meshTools/lnInclude -IlnInclude -I. -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/OpenFOAM/lnInclude -I/home/patrick/OpenFOAM/OpenFOAM-1.6/src/OSspecific/POSIX/lnInclude -fPIC -c $SOURCE -o Make/linuxGccDPOpt/makeAxialMesh.o
mkdir: cannot create directory `/home/patrick/OpenFOAM/patrick-1.6/applications': Permission denied
make: *** [/home/patrick/OpenFOAM/patrick-1.6/applications/bin/linuxGccDPOpt/makeAxialMesh] Error 1
++ echo -ne '\033]0;patrick@patrick-laptop: ~/OpenFOAM/OpenFOAM-1.6/applications/utilities/mesh/manipulation/makeAxialMesh\007'

I am pretty sure I am doing something wrong. Your help will be greatly appreciated. Also, is there any other way for creating axi-sym meshes in OpenFOAM or importing them from Gambit ?
You havn't compiled any utilities on that installation, have you (because that problem should occur with all of them). The problem is not with makeAxialMesh but with the permissions on your machine. You're not allowed to create the directory /home/patrick/OpenFOAM/patrick-1.6/applications (where the binary will be stored).
Bernhard
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Old   February 25, 2010, 12:33
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Thanks Bernhard

I tried compiling few of existing utilities in /manipulation folder like attachMesh, subsetMesh etc. It works fine. One thing i noticed is that in the error message
mkdir: cannot create directory `/home/patrick/OpenFOAM/patrick-1.6/applications': Permission denied

All my openFOAM fiels are in /home/patrick/openFOAM/OpenFOAM-1.6/ directory, not in OpenFOAM/patrick-1.6 directory.

I do not know why it is trying to create folders in a different path. Do I have to change any environment variables?
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Old   February 25, 2010, 13:44
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Quote:
Originally Posted by will_avoid_comm_solvers View Post
Thanks Bernhard

I tried compiling few of existing utilities in /manipulation folder like attachMesh, subsetMesh etc. It works fine. One thing i noticed is that in the error message
mkdir: cannot create directory `/home/patrick/OpenFOAM/patrick-1.6/applications': Permission denied

All my openFOAM fiels are in /home/patrick/openFOAM/OpenFOAM-1.6/ directory, not in OpenFOAM/patrick-1.6 directory.

I do not know why it is trying to create folders in a different path. Do I have to change any environment variables?
All the utilities you mentioned got to $FOAM_APPBIN (because they're part of the distro) whilst makeAxialMesh goes to $FOAM_USER_APPBIN. The fact that you can write $FOAM_APPBIN but not $FOAM_USER_APPBIN ist strange (usually it's supposed to be the other way round - only a privileged user should be able to write to $FOAM_APPBIN). Try "mkdir $FOAM_USER_APPBIN" and see why you're not allowed to create this. Probably you're not allowed to create $WM_PROJECT_USER_DIR, try to get that fixed otherwise you won't have much fun with non-distribution stuff
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Old   March 1, 2010, 14:44
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Thanks Bernhard
I was able to compile the makeAxialMesh utility. But I am getting a "floating point exception error" while running it. Here is the geometry i created using blockMesh

vertices
(
(0 0 -0.05)
(1 0 -0.05)
(1 1 -0.05)
(0 1 -0.05)
(0 0 0.05)
(1 0 0.05)
(1 1 0.05)
(0 1 0.05)
);

blocks
(
hex (0 1 2 3 4 5 6 7) (20 20 1) simpleGrading (1 1 1)
);

edges
(
);

patches
(
wall side_wall
(
(3 7 6 2)
)
patch inlet
(
(0 4 7 3)
)
patch outlet
(
(2 6 5 1)
)
empty center_ax
(
(1 5 4 0)
)
empty frontAndBack
(
(0 3 2 1)
(4 5 6 7)
)
);

mergePatchPairs
(
);

Mesh was created succesfully. checkMesh gives no error. Here is the copy of the Boundary file.

5
(
side_wall
{
type wall;
nFaces 20;
startFace 760;
}
inlet
{
type patch;
nFaces 20;
startFace 780;
}
outlet
{
type patch;
nFaces 20;
startFace 800;
}
center_ax
{
type empty;
nFaces 20;
startFace 820;
}
frontAndBack
{
type empty;
nFaces 800;
startFace 840;
}
)

I changed the type for FrontAndBack from "Empty" to "Wedge". Then i ran the makeAxialMesh ("makeAxialMesh center_ax frontAndBack") I get this error

Build : 1.6-f802ff2d6c5a
Exec : makeAxialMesh center_ax frontAndBack
Date : Mar 01 2010
Time : 13:42:18
Host : crop-l.dese-lab.fda.gov
PID : 23132
Case : /home/pyh8/OpenFOAM/pyh8-1.6/cavity
nProcs : 1
SigFpe : Enabling floating point exception trapping (FOAM_SIGFPE).

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

Create mesh for time = 0
#0 Foam::error:rintStack(Foam::Ostream&) in "/home/pyh8/OpenFOAM/OpenFOAM-1.6
/lib/linux64GccDPOpt/libOpenFOAM.so"
#1 Foam::sigFpe::sigFpeHandler(int) in "/home/pyh8/OpenFOAM/OpenFOAM-1.6/lib/li
nux64GccDPOpt/libOpenFOAM.so"
#2 __restore_rt at sigaction.c:0
#3 Foam::wedgePolyPatch::initTransforms() in "/home/pyh8/OpenFOAM/OpenFOAM-1.6/
lib/linux64GccDPOpt/libOpenFOAM.so"
#4 Foam::wedgePolyPatch::wedgePolyPatch(Foam::word const&, Foam::dictionary con
st&, int, Foam:olyBoundaryMesh const&) in "/home/pyh8/OpenFOAM/OpenFOAM-1.6/li
b/linux64GccDPOpt/libOpenFOAM.so"
#5 Foam:olyPatch::adddictionaryConstructorToTable<F oam::wedgePolyPatch>::New(
Foam::word const&, Foam::dictionary const&, int, Foam:olyBoundaryMesh const&)
in "/home/pyh8/OpenFOAM/OpenFOAM-1.6/lib/linux64GccDPOpt/libOpenFOAM.so"
#6 Foam:olyPatch::New(Foam::word const&, Foam::dictionary const&, int, Foam::
polyBoundaryMesh const&) in "/home/pyh8/OpenFOAM/OpenFOAM-1.6/lib/linux64GccDPOp
t/libOpenFOAM.so"
#7 Foam:olyBoundaryMesh:olyBoundaryMesh(Foam::IOo bject const&, Foam:olyMe
sh const&) in "/home/pyh8/OpenFOAM/OpenFOAM-1.6/lib/linux64GccDPOpt/libOpenFOAM.
so"
#8 Foam:olyMesh:olyMesh(Foam::IOobject const&) in "/home/pyh8/OpenFOAM/Open
FOAM-1.6/lib/linux64GccDPOpt/libOpenFOAM.so"
#9 main in "/home/pyh8/OpenFOAM/pyh8-1.6/applications/bin/linux64GccDPOpt/makeA
xialMesh"
#10 __libc_start_main in "/lib64/libc.so.6"
#11 __gxx_personality_v0 in "/home/pyh8/OpenFOAM/pyh8-1.6/applications/bin/linu
x64GccDPOpt/makeAxialMesh"
Floating point exception



I am not sure what this means

Thanks
Patrick

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Old   March 2, 2010, 13:57
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Quote:
Originally Posted by will_avoid_comm_solvers View Post
Thanks Bernhard
I was able to compile the makeAxialMesh utility. But I am getting a &quot;floating point exception error&quot; while running it. Here is the geometry i created using blockMesh

I changed the type for FrontAndBack from &quot;Empty&quot; to &quot;Wedge&quot;. Then i ran the makeAxialMesh (&quot;makeAxialMesh center_ax frontAndBack&quot I get this error
You don't have to change that. The utility does that for you. Try again without changing (haven't got the time to reproduce the error, but I think this might be the problem)
Bernhard
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Old   July 14, 2010, 23:24
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Dear Bernhard,

I untarred the .gz file at this location

/opt/openfoam170/applications/utilities/mesh/manipulation

and when i try wmake i have this message

akeAxialMesh/makeAxialMesh$ wmake
mkdir: ne peut créer le répertoire `linuxGccDPOpt': Permission non accordée
/bin/sh: cannot create linuxGccDPOpt/options: Directory nonexistent
make: *** [linuxGccDPOpt/options] Erreur 2
/opt/openfoam170/wmake/MakefileFiles:39: linuxGccDPOpt/options: Aucun fichier ou dossier de ce type
make: *** Pas de règle pour fabriquer la cible « linuxGccDPOpt/options ». Arrêt.
wmake error: file 'Make/linuxGccDPOpt/objectFiles' could not be created.

Can you help me please!

Thanks!

Abdel
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Old   July 15, 2010, 03:43
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Quote:
Originally Posted by bruxellois4 View Post
Dear Bernhard,

I untarred the .gz file at this location

/opt/openfoam170/applications/utilities/mesh/manipulation

and when i try wmake i have this message

akeAxialMesh/makeAxialMesh$ wmake
mkdir: ne peut créer le répertoire `linuxGccDPOpt': Permission non accordée
/bin/sh: cannot create linuxGccDPOpt/options: Directory nonexistent
make: *** [linuxGccDPOpt/options] Erreur 2
/opt/openfoam170/wmake/MakefileFiles:39: linuxGccDPOpt/options: Aucun fichier ou dossier de ce type
make: *** Pas de règle pour fabriquer la cible « linuxGccDPOpt/options ». Arrêt.
wmake error: file 'Make/linuxGccDPOpt/objectFiles' could not be created.

Can you help me please!

Thanks!

Abdel
This is neither a problem with makeAxialMesh nor with OpenFOAM. You're trying to compile MAM in a place where you don't have write permissions.

I havn't tried MAM on 1.7 yet, but as it works with 1.6 I don't see why it shouldn't work

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Old   July 15, 2010, 10:09
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Quote:
Originally Posted by gschaider View Post
This is neither a problem with makeAxialMesh nor with OpenFOAM. You're trying to compile MAM in a place where you don't have write permissions.

I havn't tried MAM on 1.7 yet, but as it works with 1.6 I don't see why it shouldn't work

Bernhard
If you don!t mind i've uploaded my case here http://www.4shared.com/file/Q3iXd22B/testtar.html
and i did as it is mentioned in openfoamwiki for makeAxialMesh, could you please apply the makeAxialMesh to it i really need that.

thanks

Abdel
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Old   July 15, 2010, 16:26
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Dear Bernhard,

i've tried the same thing with openFoam1.6 but if i usde

./Allwmake

i got this message : ./Allwmake : 1: wmake not found

Any idea please.
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Old   July 16, 2010, 05:13
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Quote:
Originally Posted by bruxellois4 View Post
Dear Bernhard,

i've tried the same thing with openFoam1.6 but if i usde

./Allwmake

i got this message : ./Allwmake : 1: wmake not found

Any idea please.
If wmake is not found, then this is a pure problem with your OF-installation
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Old   February 17, 2011, 10:05
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hi,

what is the FOAM_DEV_OPTION good for?

neewbie
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Old   February 18, 2011, 07:56
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Originally Posted by neewbie View Post
hi,

what is the FOAM_DEV_OPTION good for?

neewbie
A little bit more context would make it easier to answer such a question. Like "that is defined in Make/options" (I was tempted not to answer because if I need more time to UNDERSTAND the question than it took the asker to research/formulate the question, then I usually don't bother)

That option is needed so that the sources work with the OpenCFD-release as well as with the 1.5-dev/1.6-ext because they differ in the way meshes are manipulated.
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Old   February 18, 2011, 08:30
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sorry...
you´re right about the context, i should have added that.
the $(FOAM_DEV_OPTION) is in the the sources/Make/options-file of makeAxialMesh

what i did:
-tried to compile it against 1.6-ext
-->fatal error: repatch.H is missing
-against 1.6-ext without the FOAM_DEV_OPTION
--> fatal error: repatchPolyTopoChanger is missing
-give the absolute path to repatchPolyTopoChanger without the FOAM_DEV_OPTION
-->compiled and working without errors.

Since i know now that the FOAM_DEV_OPTION is for making the tool working with the different OF-distr. and i changed paths concerning that exact matter i know that there is smth. wrong on my side ... even if the tool is working now.

btw. echo $FOAM_DEV is giving 1 .... ???? that means smth. is wrong with my system/OF-variables ??!!

Thanks for the advice and the explanation of the FOAM_DEV option.

neewbie
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Old   February 18, 2011, 10:25
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Quote:
Originally Posted by neewbie View Post
sorry...
you´re right about the context, i should have added that.
the $(FOAM_DEV_OPTION) is in the the sources/Make/options-file of makeAxialMesh

what i did:
-tried to compile it against 1.6-ext
-->fatal error: repatch.H is missing
-against 1.6-ext without the FOAM_DEV_OPTION
--> fatal error: repatchPolyTopoChanger is missing
-give the absolute path to repatchPolyTopoChanger without the FOAM_DEV_OPTION
-->compiled and working without errors.

Since i know now that the FOAM_DEV_OPTION is for making the tool working with the different OF-distr. and i changed paths concerning that exact matter i know that there is smth. wrong on my side ... even if the tool is working now.

btw. echo $FOAM_DEV is giving 1 .... ???? that means smth. is wrong with my system/OF-variables ??!!

Thanks for the advice and the explanation of the FOAM_DEV option.

neewbie
I THINK (can't verify that right now) the problem is that I havn't compiled it with 1.6-ext yet and in 1.6-ext some stuff concerning mesh-motion was moved to a different directory

Bernhard
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Old   November 8, 2011, 11:19
Default changes compilation with OF1.6-ext
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All:

I haven't looked at the source code for makeAxialMesh in a long time, but it looks like the issue is with the names (not just locations) of the header files changing. I just did a git pull this morning (Nov. 8th) of 1.6-ext and there is no repatch.H anywhere that I can see.

Here are the changes to makeAxialMesh/ that allow compilation (as generated by svn diff). Note that I turned off the FOAM_DEV option.

Index: makeAxialMesh.C
================================================== =================
--- makeAxialMesh.C (revision 1921)
+++ makeAxialMesh.C (working copy)
@@ -51,7 +51,7 @@
#include "argList.H"
#include "Time.H"
#ifdef FOAM_DEV
-#include "repatch.H"
+#include "repatchPolyTopoChanger.H"
#else
#include "repatchPolyTopoChanger.H"
#endif
Index: Make/options
================================================== =================
--- Make/options (revision 1921)
+++ Make/options (working copy)
@@ -1,12 +1,13 @@
-ifdef FOAM_DEV
-FOAM_DEV_OPTION = -DFOAM_DEV
-endif
+//ifdef FOAM_DEV
+//FOAM_DEV_OPTION = -DFOAM_DEV
+//endif

EXE_INC = \
$(FOAM_DEV_OPTION) \
-I$(LIB_SRC)/dynamicMesh/lnInclude \
-I$(LIB_SRC)/cfdTools/lnInclude\
- -I$(LIB_SRC)/meshTools/lnInclude
+ -I$(LIB_SRC)/meshTools/lnInclude\
+ -I$(LIB_SRC)/dynamicMesh/dynamicMesh/lnInclude

EXE_LIBS = \
-ldynamicMesh \

With those changes, it worked for me.
-David
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Old   October 20, 2014, 11:20
Default Problem with installation of makeAxialMesh on OF 1.6 ext
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Dear foamers,

I tried to install makeAxialMesh on OF-1.6-ext to have axisymmetric mesh, but there is an error in the process of making "makeAxialMesh":

user-1.6-ext//applications/bin/linux64GccDPOpt/makeAxialMesh/usr/bin/ld: cannot find -liberty

Could you please guide me if you have any experience with such an error?

Thanks and Best,
Mahdi
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Old   October 20, 2014, 13:10
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Quote:
Originally Posted by Masgar View Post
Dear foamers,

I tried to install makeAxialMesh on OF-1.6-ext to have axisymmetric mesh, but there is an error in the process of making "makeAxialMesh":

user-1.6-ext//applications/bin/linux64GccDPOpt/makeAxialMesh/usr/bin/ld: cannot find -liberty

Could you please guide me if you have any experience with such an error?

Thanks and Best,
Mahdi
Your system is missing a library called libiberty.so
Don't know which package installs that. Google for it and then install that package
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Old   October 20, 2014, 17:49
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Quote:
Originally Posted by gschaider View Post
Your system is missing a library called libiberty.so
Don't know which package installs that. Google for it and then install that package

Thanks a lot Bernhard for the reply.
I checked for the package, it is mentioned to be "benutlis-dev" or "gcc", but when I tried to install them, it turned out they are both already installed!

I am using Ubuntu 14.04, if it affects the installation procedure.

I would be grateful to have your opinion in this regard,
Best,
Mahdi
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Old   October 21, 2014, 04:40
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Quote:
Originally Posted by Masgar View Post
Thanks a lot Bernhard for the reply.
I checked for the package, it is mentioned to be "benutlis-dev" or "gcc", but when I tried to install them, it turned out they are both already installed!

I am using Ubuntu 14.04, if it affects the installation procedure.

I would be grateful to have your opinion in this regard,
Best,
Mahdi
I HAVE an opinion concerning Ubuntu but you won't be grateful to hear it

Seriously: I have no Ubuntu so I can't help you there. Wonder how anything got compiled on your machine without that library
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