[wyldckat]

Well, problem is that there are no instructions that I know about for building on Mac OS X the version of ParaView that comes with OpenFOAM.
This is why the instructions on the wiki, as well as here on the forum, mostly refer to installing the version from the official ParaView website.

[NewVGh01]

Good Morning Bruno,

Yes, but now I am completely lost. I don’t know what to do to overcome the problem without complicating the situation. I spend a lot of time to detail the different posts in the forum and I am now in a muddle. All things seem to be yet in right place but I have not the true understanding of the correct steps chain for Mac 10.6.8 (+OF2.1.1, TP-2.1.1) case :
- Use of the inside ThirdParty parafoam version is it impossible? Should I try to load Paraview from paraview.org ? Then, which version would be correct?
- In which case, stub-files have to be created? What command has to be used to open them?
- Is there any body in the same case as me?

I am sorry to be insistent,
Best regards,
VG

[gschaider]

Originally Posted by NewVGh01

Good Morning Bruno,

Yes, but now I am completely lost. I don’t know what to do to overcome the problem without complicating the situation. I spend a lot of time to detail the different posts in the forum and I am now in a muddle. All things seem to be yet in right place but I have not the true understanding of the correct steps chain for Mac 10.6.8 (+OF2.1.1, TP-2.1.1) case :
- Use of the inside ThirdParty parafoam version is it impossible? Should I try to load Paraview from paraview.org ? Then, which version would be correct?
- In which case, stub-files have to be created? What command has to be used to open them?
- Is there any body in the same case as me?

I am sorry to be insistent,
Best regards,
VG

I usually (this means for the last few years) "only" download the Paraview-binary from Kitware, put it in the Applications folder and define paraview as an alias to /Applications/paraview.app/Contents/MacOS/paraview. That way you CAN'T compile the PV3Reader that comes with OpenFOAM.

Reasons why I do this are:
- the built in OpenFOAM-Reader of Paraview is good enough for me
- I don't want to spend time compiling Paraview myself (and subsequently support people with their problems with compilation)

This doesn't mean that it isn't possible (not even that hard) to compile Paraview and the Plugin and if someone wants to do that and write a recipe I'd even test it

[NewVGh01]

Thanks Bernhard,

I was so focused on possible installation problems than I had totally missed the fact that I can load the paraview binary file. It is done (binary version 3.12.0) and it works well with the alias once installed: /Application/ParaView\ 3.12.0.app/Contents/MacOS/paraview
I apologize and thank you for your patience. It is important: it is people like you who allow people like me to recover freedom-space in their work. I hope to be able to give help back to somebody.
Best regards,
VG

[Naturespirit]

Hello

I have recently tried to compile OpenFoam version 2.1.1 on my iMac version 10.7.5, following closely what website
http://openfoamwiki.net/index.php/Ho...enFOAM_v21_Mac

gave as instructions. I had an mpi version of
mpirun (Open MPI) 1.6.1
installed. I reached as far as creating the make.log file from the compilation and noticed the following errors
configure: error: no vtf3.h found; check path for VTF3 package first...
configure: error: no BPatch.h found; check path for Dyninst package first...

etc
I have attached a smaller version of the compilation log file for closer viewing.
I look forward to any suggestions as why my attempt to compile OpenFoam failed on my iMac.

David Olivieri

[wyldckat]

Greetings David and welcome to the forum!

Originally Posted by Naturespirit

configure: error: no vtf3.h found; check path for VTF3 package first...
configure: error: no BPatch.h found; check path for Dyninst package first...

Don't worry about those error messages. They are only a reflex of Open-MPI's configure mega-script and are not important, at least not for us common mortals

You only have to worry if in the second run of Allwmake, if there are any error messages

Best regards,
Bruno

[Naturespirit]

Hi Bruno

Thank you for your reply. In the website
http://openfoamwiki.net/index.php/Ho...enFOAM_v21_Mac

I do not see where it states that the command ./Allwake is issued twice. I could repeat everything again to ensure I have not done something wrong. Only thing is the compilation log I sent to the forum yesterday there are other errors occurring like


1)
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[3]: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/bin/R] Error 1
make[2]: *** [R] Error 2

2)
OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/bin/Lambda2
Making dependency list for source file wallShearStress.C
g++-mp-4.6 -m64 -fsignaling-nans -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2 -DNoRepository -ftemplate-depth-100 -I/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/src/transportModels -I/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/src/turbulenceModels -I/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/src/turbulenceModels/incompressible/RAS/RASModel -I/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/src/finiteVolume/lnInclude -IlnInclude -I. -I/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/src/OpenFOAM/lnInclude -I/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/src/OSspecific/POSIX/lnInclude -fPIC -Ddarwin -lpthread -L/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-1.5.3 -lPstream Make/darwinIntel64Gcc46DPOpt/createTurbulenceFields.o -L/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib \
-lincompressibleTurbulenceModel -lincompressibleRASModels -lincompressibleTransportModels -lfiniteVolume -lgenericPatchFields -lOpenFOAM -ldl -lpthread -lm -o /Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/bin/createTurbulenceFields
Making dependency list for source file renumberMesh.C
make[2]: Target `application' not remade because of errors.
make[1]: *** [turbulence] Error 2

(See the attached file to see all of them)

Please advise me on the best course of action. Finally, I must make you aware some of the patches did not patch properly.

David Olivieri

[wyldckat]

Hi David,

Sorry about that! I confused the instructions with the ones I wrote for Linux Distributions

I've updated the wiki page, specifically the sections 2.6 and 2.6.1: http://openfoamwiki.net/index.php/Ho...lding_OpenFOAM

• Now it does mention to run Allwmake twice
• It now gives a link to a post that explains what's missing on the instructions:

  The latest summary list of suggested fixes are reported on post #285 at the thread "OF 1.9 (aka OF 2.1) on Mac OS X".

It's a wiki, so feel free to edit the page and correct/add what you feel that is missing or incorrect!

Best regards,
Bruno

[Naturespirit]

Hi Bruno

I have tried what you stated last time and got the following after doing

 ./Allwmake
wcleanAll
wcleanLnIncludeAll
./Allwmake

in terms of errors :--

make: Nothing to be done for `all'.

========================================
Start ThirdParty Allwmake
========================================

========================================
Build MPI libraries if required

========================================
Build Scotch decomposition library scotch_5.1.11
    /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11
+ cd scotch_5.1.11/src
+ prefixDIR=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11
+ libDIR=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib
+ mkdir -p /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11
+ mkdir -p /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib
+ configOpt='prefix=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11 libdir=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib'
+ '[' -f ../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-64 ']'
+ rm -f Makefile.inc
+ ln -s ../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-64 Makefile.inc
+ '[' -f Makefile.inc ']'
+ unset configEnv
+ '[' gcc-mp-4.6 '!=' gcc ']'
+ configEnv='CC=gcc-mp-4.6 CCS=gcc-mp-4.6'
+ make realclean
(cd libscotch ;      make realclean)
rm -f *~ *.o lib*.so parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output dummysizes
(cd scotch ;         make realclean)
rm -f *~ *.o acpl amk_ccc amk_fft2 amk_grf amk_hy amk_m2 amk_p2 atst gbase gcv *ggath *gmap gmk_hy gmk_m2 gmk_m3 gmk_msh gmk_ub2 gmtst *gord gotst gout *gpart *gscat *gtst mcv mmk_m2 mmk_m3 mord mtst
(cd libscotchmetis ; make realclean)
rm -f *~ *.o lib*.so
rm -f ../bin/* ../include/* ../lib/*
+ make -j 1 CC=gcc-mp-4.6 CCS=gcc-mp-4.6 scotch
(cd libscotch ;      make VERSION=5 RELEASE=1 PATCHLEVEL=10 scotch && make install)
rm -f *~ *.o lib*.so parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output dummysizes
make CC="gcc-mp-4.6" CCD="gcc-mp-4.6"    \
                    scotch.h                \
                    scotchf.h                \
                    libscotch.so                \
                    libscotcherr.so            \
                    libscotcherrexit.so
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DSCOTCH_VERSION=5 -DSCOTCH_RELEASE=1 -DSCOTCH_PATCHLEVEL=10 dummysizes.c -o dummysizes -lz -lm -lrt
ld: library not found for -lrt
collect2: ld returned 1 exit status
make[2]: *** [dummysizes] Error 1
make[1]: *** [scotch] Error 2
make: *** [scotch] Error 2
+ make realclean


mpicc -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DSCOTCH_PTSCOTCH -DSCOTCH_VERSION=5 -DSCOTCH_RELEASE=1 -DSCOTCH_PATCHLEVEL=10 dummysizes.c -o dummysizes -lz -lm -lrt
ld: library not found for -lrt
collect2: ld returned 1 exit status
make[2]: *** [dummysizes] Error 1
make[1]: *** [ptscotch] Error 2
make: *** [ptscotch] Error 2
+ make realclean
(cd libscotch ;      make realclean)
rm -f *~ *.o lib*.so parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output dummysizes
(cd scotch ;         make realclean)
rm -f *~ *.o acpl amk_ccc amk_fft2 amk_grf amk_hy amk_m2 amk_p2 atst gbase gcv *ggath *gmap gmk_hy gmk_m2 gmk_m3 gmk_msh gmk_ub2 gmtst *gord gotst gout *gpart *gscat *gtst mcv mmk_m2 mmk_m3 mord mtst
(cd libscotchmetis ; make realclean)
rm -f *~ *.o lib*.so
rm -f ../bin/* ../include/* ../lib/*

    WARNING: required include file 'ptscotch.h' not found!

I also tried to do a installation test with foamInstallationTest and got

Executing /Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/bin/foamInstallationTest:


Checking basic setup...
-------------------------------------------------------------------------------
Shell:              bash
Host:               Davids-iMac
FATAL ERROR: Incompatible operating system "Darwin".
             OpenFOAM  is currently 
             available for Linux and SunOS only.

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


Checking main OpenFOAM env variables...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid      Crit
-------------------------------------------------------------------------------
$WM_PROJECT_INST_DIR /Users/davidolivieri/OpenFOAM            yes       yes
$WM_PROJECT_USER_DIR ...livieri/OpenFOAM/davidolivieri-2.1.1  no        no
$WM_THIRD_PARTY_DIR  ...idolivieri/OpenFOAM/ThirdParty-2.1.1  yes       yes
-------------------------------------------------------------------------------


Checking the OpenFOAM env variables set on the PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$WM_PROJECT_DIR      ...avidolivieri/OpenFOAM/OpenFOAM-2.1.1  yes  yes  yes

$FOAM_APPBIN         ...latforms/darwinIntel64Gcc46DPOpt/bin  yes  yes  yes
$FOAM_SITE_APPBIN    ...latforms/darwinIntel64Gcc46DPOpt/bin  no        no
$FOAM_USER_APPBIN    ...latforms/darwinIntel64Gcc46DPOpt/bin  no        no
$WM_DIR              ...ivieri/OpenFOAM/OpenFOAM-2.1.1/wmake  yes  yes  yes
-------------------------------------------------------------------------------


Checking the OpenFOAM env variables set on the LD_LIBRARY_PATH...
-------------------------------------------------------------------------------
Environment_variable Set_to_file_or_directory                Valid Path Crit
-------------------------------------------------------------------------------
$FOAM_LIBBIN         ...latforms/darwinIntel64Gcc46DPOpt/lib  yes  yes  yes
$FOAM_SITE_LIBBIN    ...latforms/darwinIntel64Gcc46DPOpt/lib  no        no
$FOAM_USER_LIBBIN    ...latforms/darwinIntel64Gcc46DPOpt/lib  no        no
$MPI_ARCH_PATH       /usr/local                               yes  yes  yes
-------------------------------------------------------------------------------


Third party software
-------------------------------------------------------------------------------
Software Version   Location 
-------------------------------------------------------------------------------
flex     2.5.37    /opt/local/bin/flex                                      
gcc      4.6.4     /opt/local/bin/gcc                                       
gzip     1.3.12    /usr/bin/gzip                                            
/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/bin/foamInstallationTest: line 298: --version: command not found
gtar                                                                        
icoFoam  2.1.1     ...AM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/bin/icoFoam
-------------------------------------------------------------------------------


Summary
-------------------------------------------------------------------------------
The system test has evoked 1 fatal error(s).
Critical systems ok.

Review the output for warning messages and consult
the installation guide for troubleshooting.

Done

Davids-iMac:bin davidolivieri$

Finally I tried the alias

 alias of21='hdiutil attach "/PATH/TO/YOUR/DMG/OpenFOAM.dmg" -mountpoint "$HOME/OpenFOAM" > /dev/null ; . $HOME/OpenFOAM/OpenFOAM-2.1.1/etc/bashrc'

which had problems with mounting. I am not sure if the second compilation went wrong. How would a simple test be performed for OpenFoam ? Please help.


David Olivieri

[gschaider]

Originally Posted by Naturespirit

Hi Bruno

I have tried what you stated last time and got the following after doing

./Allwmake
wcleanAll
wcleanLnIncludeAll
./Allwmake

in terms of errors :--


make: Nothing to be done for `all'.

========================================
Start ThirdParty Allwmake
========================================

========================================
Build MPI libraries if required

========================================
Build Scotch decomposition library scotch_5.1.11
/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11
+ cd scotch_5.1.11/src
+ prefixDIR=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11
+ libDIR=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib
+ mkdir -p /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11
+ mkdir -p /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib
+ configOpt='prefix=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11 libdir=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib'
+ '[' -f ../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-64 ']'
+ rm -f Makefile.inc
+ ln -s ../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-64 Makefile.inc
+ '[' -f Makefile.inc ']'
+ unset configEnv
+ '[' gcc-mp-4.6 '!=' gcc ']'
+ configEnv='CC=gcc-mp-4.6 CCS=gcc-mp-4.6'
+ make realclean
(cd libscotch ; make realclean)
rm -f *~ *.o lib*.so parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output dummysizes
(cd scotch ; make realclean)
rm -f *~ *.o acpl amk_ccc amk_fft2 amk_grf amk_hy amk_m2 amk_p2 atst gbase gcv *ggath *gmap gmk_hy gmk_m2 gmk_m3 gmk_msh gmk_ub2 gmtst *gord gotst gout *gpart *gscat *gtst mcv mmk_m2 mmk_m3 mord mtst
(cd libscotchmetis ; make realclean)
rm -f *~ *.o lib*.so
rm -f ../bin/* ../include/* ../lib/*
+ make -j 1 CC=gcc-mp-4.6 CCS=gcc-mp-4.6 scotch
(cd libscotch ; make VERSION=5 RELEASE=1 PATCHLEVEL=10 scotch && make install)
rm -f *~ *.o lib*.so parser_yy.c parser_ly.h parser_ll.c *scotch.h *scotchf.h y.output dummysizes
make CC="gcc-mp-4.6" CCD="gcc-mp-4.6" \
scotch.h \
scotchf.h \
libscotch.so \
libscotcherr.so \
libscotcherrexit.so
gcc-mp-4.6 -O3 -DCOMMON_FILE_COMPRESS_GZ -DCOMMON_RANDOM_FIXED_SEED -DSCOTCH_RENAME -DSCOTCH_RENAME_PARSER -Drestrict=__restrict -DSCOTCH_VERSION=5 -DSCOTCH_RELEASE=1 -DSCOTCH_PATCHLEVEL=10 dummysizes.c -o dummysizes -lz -lm -lrt
ld: library not found for -lrt
collect2: ld returned 1 exit status
make[2]: *** [dummysizes] Error 1
make[1]: *** [scotch] Error 2
make: *** [scotch] Error 2
+ make realclean

<snip>

which had problems with mounting. I am not sure if the second compilation went wrong. How would a simple test be performed for OpenFoam ? Please help.


David Olivieri

Have you applied the ThirdParty-Patch? Because that makes the modifications that are necessary to compile scotch on Darwin

[Naturespirit]

Hi

I did as was stated on
http://openfoamwiki.net/index.php/Ho...enFOAM_v21_Mac

2.3 Apply patches and tweaks

Change into the Third-Party directory and apply the first patch via:
patch -p1 <ThirdParty-2.1.0-Mac.patch

and I got the following error

patching file Allwmake
patching file etc/wmakeFiles/scotch/Makefile.inc.i686_mac_darwin.shlib-OpenFOAM
patching file scotch_5.1.11/src/Makefile.inc
Hunk #1 FAILED at 1.
1 out of 1 hunk FAILED -- saving rejects to file scotch_5.1.11/src/Makefile.inc.rej

remember I am using a patch correction on a version 2.2.1 of OpenFOAM.

I look forward to your reply on this issue.

David Olivieri

[Naturespirit]

Hello Bernhard
I have used the tar file ThirdParty-2.1.1.tar which I installed in the Third-Party directory to patch OpenFOAM build process. Why did I get the error message stated in my previous reply?


It seems the patch failed to patch in the way you intended in the environment I have been working in. Do you have anything to say on this?

The information which was stored in the file Makefile.inc.rej was as follows

***************
*** 1 ****
- ../../etc/wmakeFiles/scotch/Makefile.inc.i686_pc_linux2.shlib-OpenFOAM-64--- 1 ----
+ ../../etc/wmakeFiles/scotch/Makefile.inc.i686_mac_darwin.shlib-OpenFOAM


David Olivieri

[wyldckat]

Greetings David,

This has actually already been asked and answered in the past:

Originally Posted by heba

Hi,
I have that error when applying the patch of ThirdParty

Hunk #1 FAILED at 1.
1 out of 1 hunk FAILED -- saving rejects to file scotch_5.1.11/src/Makefile.inc.rej

Originally Posted by wyldckat

That's just a symbolic link reference. It will be automatically re-generated by Allwmake, so I think that error can be ignored

Best regards,
Bruno

[Naturespirit]

Hello Bruno

Thank you for your reply. Recently I tried to install OpenFOAM again following closely what is given on website

http://openfoamwiki.net/index.php/Ho...enFOAM_v21_Mac

I applied the patches as stated in section 2.3 and also patches SetNanMac.patch and OpenFOAM-2.1.x-Mac_20121009.patch given on website

http://www.cfd-online.com/Forums/ope...tml#post385688

I then applied the following instructions for build

./Allwmake
wcleanAll
wcleanLnIncludeAll
./Allwmake

and got some of the following errors from the build

make[2]: `libptscotchparmetis.dylib' is up to date.
cp parmetis.h ../../include
cp libptscotchparmetis.dylib ../../lib
+ make prefix=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11 libdir=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-1.5.3 includedir=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11/include/openmpi-1.5.3 install
mkdir /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11/include/openmpi-1.5.3
cp -f ../bin/[agm]* /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11/bin
cp: ../bin/[agm]*: No such file or directory
make: [install] Error 1 (ignored)

signals/sigFpe.C: In destructor 'Foam::sigFpe::~sigFpe()':
signals/sigFpe.C:175:12: error: 'system_malloc_' was not declared in this scope

signals/sigFpe.C:392:13: error: 'vm_protect' was not declared in this scope
make: *** [Make/darwinIntel64Gcc46DPOpt/sigFpe.o] Error 1

g++-mp-4.6: error: /Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libOSspecific.o: No such file or directory
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libOpenFOAM.dylib] Error 1

darwinIntel64Gcc46DPOpt/radialActuationDiskSource.o
ld: library not found for -lOpenFOAM
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libfiniteVolume.dylib] Error 1


ld: library not found for -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libgenericPatchFields.dylib] Error 1


ld: library not found for -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libreconstruct.dylib] Error 1


ld: library not found for -ldecompositionMethods
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libdistributed.dylib] Error 1

ld: library not found for -ldynamicMesh
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libdynamicFvMesh.dylib] Error 1

ld: library not found for -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libreactionThermophysicalModels.dylib] Error 1


ld: library not found for -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/liblaminarFlameSpeedModels.dylib] Error 1

ld: library not found for -lbasicThermophysicalModels
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libchemistryModel.dylib] Error 1

and finally at the of the make.log file I got the error


ld: library not found for -lmultiphaseSystem
collect2: ld returned 1 exit status
make[2]: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/bin/multiphaseEulerFoam] Error 1
make[1]: *** [multiphaseEulerFoam] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [multiphase] Error 2
make: Target `application' not remade because of errors.

Bernhard's patches had the usual error message with the first patch for the third party libraries, while last two patches had doubtful use. For example applying the last patch with the command

patch -p1 <SetNanMac-1.patch

gave the message

patching file src/OSspecific/POSIX/signals/sigFpe.C
Reversed (or previously applied) patch detected! Assume -R? [n]

Where is occurred I responded with yes and got

Hunk #1 succeeded at 51 (offset 5 lines).
Hunk #2 FAILED at 101.
Hunk #3 succeeded at 139 (offset -25 lines).
Hunk #4 succeeded at 245 (offset -3 lines).
Hunk #5 succeeded at 275 (offset -3 lines).
1 out of 5 hunks FAILED -- saving rejects to file src/OSspecific/POSIX/signals/sigFpe.C.rej

Anyway, I look forward to any suggestions on how the build could be better done. Maybe the implementation of the patches needs more clarification.



David Olivieri

[gschaider]

Originally Posted by Naturespirit

Hello Bruno

Thank you for your reply. Recently I tried to install OpenFOAM again following closely what is given on website

http://openfoamwiki.net/index.php/Ho...enFOAM_v21_Mac

I applied the patches as stated in section 2.3 and also patches SetNanMac.patch and OpenFOAM-2.1.x-Mac_20121009.patch given on website

http://www.cfd-online.com/Forums/ope...tml#post385688

I then applied the following instructions for build

./Allwmake
wcleanAll
wcleanLnIncludeAll
./Allwmake

and got some of the following errors from the build

make[2]: `libptscotchparmetis.dylib' is up to date.
cp parmetis.h ../../include
cp libptscotchparmetis.dylib ../../lib
+ make prefix=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11 libdir=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/openmpi-1.5.3 includedir=/Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11/include/openmpi-1.5.3 install
mkdir /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11/include/openmpi-1.5.3
cp -f ../bin/[agm]* /Users/davidolivieri/OpenFOAM/ThirdParty-2.1.1/platforms/darwinIntel64Gcc46/scotch_5.1.11/bin
cp: ../bin/[agm]*: No such file or directory
make: [install] Error 1 (ignored)

signals/sigFpe.C: In destructor 'Foam::sigFpe::~sigFpe()':
signals/sigFpe.C:175:12: error: 'system_malloc_' was not declared in this scope

signals/sigFpe.C:392:13: error: 'vm_protect' was not declared in this scope
make: *** [Make/darwinIntel64Gcc46DPOpt/sigFpe.o] Error 1

g++-mp-4.6: error: /Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libOSspecific.o: No such file or directory
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libOpenFOAM.dylib] Error 1

darwinIntel64Gcc46DPOpt/radialActuationDiskSource.o
ld: library not found for -lOpenFOAM
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libfiniteVolume.dylib] Error 1


ld: library not found for -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libgenericPatchFields.dylib] Error 1


ld: library not found for -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libreconstruct.dylib] Error 1


ld: library not found for -ldecompositionMethods
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libdistributed.dylib] Error 1

ld: library not found for -ldynamicMesh
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libdynamicFvMesh.dylib] Error 1

ld: library not found for -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libreactionThermophysicalModels.dylib] Error 1


ld: library not found for -lfiniteVolume
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/liblaminarFlameSpeedModels.dylib] Error 1

ld: library not found for -lbasicThermophysicalModels
collect2: ld returned 1 exit status
make: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/lib/libchemistryModel.dylib] Error 1

and finally at the of the make.log file I got the error


ld: library not found for -lmultiphaseSystem
collect2: ld returned 1 exit status
make[2]: *** [/Users/davidolivieri/OpenFOAM/OpenFOAM-2.1.1/platforms/darwinIntel64Gcc46DPOpt/bin/multiphaseEulerFoam] Error 1
make[1]: *** [multiphaseEulerFoam] Error 2
make[1]: Target `application' not remade because of errors.
make: *** [multiphase] Error 2
make: Target `application' not remade because of errors.

Bernhard's patches had the usual error message with the first patch for the third party libraries, while last two patches had doubtful use. For example applying the last patch with the command

patch -p1 <SetNanMac-1.patch

gave the message

patching file src/OSspecific/POSIX/signals/sigFpe.C
Reversed (or previously applied) patch detected! Assume -R? [n]

Where is occurred I responded with yes and got

Hunk #1 succeeded at 51 (offset 5 lines).
Hunk #2 FAILED at 101.
Hunk #3 succeeded at 139 (offset -25 lines).
Hunk #4 succeeded at 245 (offset -3 lines).
Hunk #5 succeeded at 275 (offset -3 lines).
1 out of 5 hunks FAILED -- saving rejects to file src/OSspecific/POSIX/signals/sigFpe.C.rej

Anyway, I look forward to any suggestions on how the build could be better done. Maybe the implementation of the patches needs more clarification.



David Olivieri

As far as I remember (look it up and tell me if I'm wrong) the order of things was

1. Published first version of the 2.1-patch
2. Developed NaN-fix
3. Published NaN-fix for those who already installed the old version
4. Rolled the NaN-fix into the general patch and published that too (for the new ones)

So the NaN-patch probably doesn't work because you used the patch that already has it included. What is the other patch that doesn't work for you?

[Naturespirit]

Hi

My experience with these patches has been as follows :-
1) ThirdParty-2.1.0-Mac.patch applied and gave
Hunk #1 FAILED at 1. 1 out of 1 hunk FAILED

(Explained earlier by Bruno as non serious.)

2) OpenFOAM-2.1.x-Mac_20121009.patch applied with command
patch -p1 <OpenFOAM-2.1.x-Mac_20121009.patch

gave Reversed or previous applied error.

Therefore, I can concluded I should start again this time not applying the Third Party patch and the other two patches

OpenFOAM-2.1.x-Mac_20121009.patch
SetNanMac-1.patch

If the OpenFOAM completes compilation how could I check quickly to see if the process has completed properly? Another issue where you give advice on using the alias
alias of21='hdiutil attach "/PATH/TO/YOUR/DMG/OpenFOAM.dmg" -mountpoint "$HOME/OpenFOAM" > /dev/null ; . $HOME/OpenFOAM/OpenFOAM-2.1.0/etc/bashrc'

in the user's .profile file, the PATH given above for the hdiutil command I believe should be

alias of21='hdiutil attach "~/OpenFOAM-v2.1.sparseimage" -mountpoint "$HOME/OpenFOAM" > /dev/null ; . $HOME/OpenFOAM/OpenFOAM-2.1.0/etc/bashrc'

The reason why I send this is an error occurs complaining no file called OpenFOAM.dmg exists since a sparse image file has been created not ending with *.dmg ,correct me if I am wrong.

David Olivieri

[gschaider]

Originally Posted by Naturespirit

Hi

My experience with these patches has been as follows :-
1) ThirdParty-2.1.0-Mac.patch applied and gave
Hunk #1 FAILED at 1. 1 out of 1 hunk FAILED

(Explained earlier by Bruno as non serious.)

2) OpenFOAM-2.1.x-Mac_20121009.patch applied with command
patch -p1 <OpenFOAM-2.1.x-Mac_20121009.patch

gave Reversed or previous applied error.

For all hunks or only for some. Anyway. This shouldn't happen IF the source tree is completely clean (==no patch whatsoever has been applied)

Originally Posted by Naturespirit

Therefore, I can concluded I should start again this time not applying the Third Party patch and the other two patches

OpenFOAM-2.1.x-Mac_20121009.patch
SetNanMac-1.patch

If the OpenFOAM completes compilation how could I check quickly to see if the process has completed properly?

Resource etc/bashrc and try to run a tutorial. For instance damBreak. Also rerun ./Allwmake and see if there are any complaints (output should be MUCH shorter)

Originally Posted by Naturespirit

Another issue where you give advice on using the alias
alias of21='hdiutil attach "/PATH/TO/YOUR/DMG/OpenFOAM.dmg" -mountpoint "$HOME/OpenFOAM" > /dev/null ; . $HOME/OpenFOAM/OpenFOAM-2.1.0/etc/bashrc'

in the user's .profile file, the PATH given above for the hdiutil command I believe should be

alias of21='hdiutil attach "~/OpenFOAM-v2.1.sparseimage" -mountpoint "$HOME/OpenFOAM" > /dev/null ; . $HOME/OpenFOAM/OpenFOAM-2.1.0/etc/bashrc'

The reason why I send this is an error occurs complaining no file called OpenFOAM.dmg exists since a sparse image file has been created not ending with *.dmg ,correct me if I am wrong.

David Olivieri

Haven't used disk images for OF for a long time so I can't comment on this. What is wrong with trying the modified command?

[cp703]

Hi,

I have recently decided to make the switch from ANSYS FLUENT to OpenFOAM due to some extensive issues with licensing. I don't currently have access to a Linux machine, but my school computer is a Mac running 10.6.8 (Snow Leopard). I have tried very hard to follow the instructions in the wiki - Installation/Mac OS/OpenFOAM 2.1.x - as carefully as possible. However, I am having a few issues. I'm really sorry for the length of this post. I think maybe I am putting too much information in one post.

Versions I'm using:
Apple Mac OS X 10.6.8
Xcode 3.2.6 (I think this is the same as Apple Developer Tools 3.2.6?)
MacPorts 2.2.1 (For Snow Leopard 10.6)

Patches:
ThirdParty-2.1.0-Mac.patch
OpenFOAM-2.1.x-Mac_20130125.patch
OpenFOAM-2.1.x-Mac-gcc46.patch

Error associated with checking the MacPorts software installation:
After entering "sudo port selfupdate", I got an error stating:

sudo: port: command not found

I fixed this by entering the following commands and then re-entered "sudo port selfupdate":

export PATH=$PATH:/opt/local/bin export 

MANPATH=$MANPATH:/opt/local/share/man export

INFOPATH=$INFOPATH:/opt/local/share/info

Error associated with applying ThirdParty patch:
Applying the ThirdParty-2.1.0-Mac.patch yields the following error (which is not an issue according to post #4 and many subsequent posts by Bruno so I ignored it and kept going):

patching file Allwmake
patching file etc/wmakeFiles/scotch/Makefile.inc.i686_mac_darwin.shlib-OpenFOAM
patching file scotch_5.1.11/src/Makefile.inc
Hunk #1 FAILED at 1.
1 out of 1 hunk FAILED -- saving rejects to file scotch_5.1.11/src/Makefile.inc.rej

Errors associated with applying OpenFOAM-2.1.x-Mac_20130125 patch:
Applying this patch worked partially. The following are the failure notifications that I got.

Hunk #1 FAILED at 19.
1 out of 1 hunk FAILED -- saving rejects to file applications/solvers/multiphase/multiphaseEulerFoam/Make/options.rej
patching file applications/utilities/mesh/generation/blockMesh/Make/options
patching file applications/utilities/postProcessing/miscellaneous/execFlowFunctionObjects/Make/options
patching file applications/utilities/postProcessing/turbulence/R/Make/options
Hunk #1 FAILED at 7.
1 out of 1 hunk FAILED -- saving rejects to file applications/utilities/postProcessing/turbulence/R/Make/options.rej
patching file applications/utilities/postProcessing/turbulence/createTurbulenceFields/Make/options
patching file applications/utilities/postProcessing/velocityField/Pe/Make/options
patching file applications/utilities/postProcessing/wall/wallHeatFlux/Make/options
patching file applications/utilities/postProcessing/wall/wallShearStress/Make/options
Hunk #1 FAILED at 6.
1 out of 1 hunk FAILED -- saving rejects to file applications/utilities/postProcessing/wall/wallShearStress/Make/options.rej
patching file applications/utilities/postProcessing/wall/yPlusLES/Make/options
patching file applications/utilities/postProcessing/wall/yPlusRAS/Make/options
patching file applications/utilities/preProcessing/applyBoundaryLayer/Make/options
Hunk #1 succeeded at 8 with fuzz 2.
patching file bin/addr2line4Mac.py
patching file etc/bashrc
patching file etc/config/settings.sh
Hunk #3 FAILED at 500.
1 out of 3 hunks FAILED -- saving rejects to file etc/config/settings.sh.rej

Errors associated with building OpenFOAM:
So far as I can tell, there are three primary errors that I encounter when trying to build OpenFOAM.

The first is related to ptscotch.h (not sure what to do about this):

Making dependency list for source file ptscotchDecomp.C
could not open file mpi.h for source file ptscotchDecomp.C
could not open file ptscotch.h for source file ptscotchDecomp.C
SOURCE=ptscotchDecomp.C ;  g++-mp-4.6 -m64 -fsignaling-nans  -ftrapping-math -DdarwinIntel64 -DWM_DP -Wall -Wextra -Wno-unused-parameter -Wold-style-cast -Wnon-virtual-dtor -O2  -DNoRepository -ftemplate-depth-100 -DOMPI_SKIP_MPICXX -I/include/openmpi -I/include -I/Users/caj5p/OpenFOAM/ThirdParty-2.1.0/platforms/darwinIntel64Gcc46/scotch_5.1.11/include/dummy -I/usr/include/scotch -I../decompositionMethods/lnInclude -IlnInclude -I. -I/Users/caj5p/OpenFOAM/OpenFOAM-2.1.0/src/OpenFOAM/lnInclude -I/Users/caj5p/OpenFOAM/OpenFOAM-2.1.0/src/OSspecific/POSIX/lnInclude   -fPIC -Ddarwin -c $SOURCE -o Make/darwinIntel64Gcc46DPOptMACPORTOPENMPI/ptscotchDecomp.o
ptscotchDecomp.C:126:22: fatal error: ptscotch.h: No such file or directory
compilation terminated.
make: *** [Make/darwinIntel64Gcc46DPOptMACPORTOPENMPI/ptscotchDecomp.o] Error 1

Next, there are several related to the chemistry model library not being built yet/ found. I don't know how to fix this:

ld: library not found for -lchemistryModel
collect2: ld returned 1 exit status

I think I have actually fixed these next two errors using post 89 from Bruno:

Undefined symbols for architecture x86_64:
  "Foam::incompressible::turbulenceModel::typeName", referenced from:
      _main in R.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[3]: *** [/Users/cp703/OpenFOAM/OpenFOAM-2.1.0/platforms/darwinIntel64Gcc46DPOpt/bin/R] Error 1
make[2]: *** [R] Error 2

Undefined symbols for architecture x86_64:
  "Foam::incompressible::turbulenceModel::typeName", referenced from:
      _main in multiphaseEulerFoam.o
ld: symbol(s) not found for architecture x86_64
collect2: ld returned 1 exit status
make[2]: *** [/Users/cp703/OpenFOAM/OpenFOAM-2.1.0/platforms/darwinIntel64Gcc46DPOpt/bin/multiphaseEulerFoam] Error 1
make[1]: *** [multiphaseEulerFoam] Error 2

I can post my .log file, but I wasn't sure if it was easier to just extracct the errors themselves. Any feedback is very welcome! I'd be thrilled to be able to get this up and running. Thank you!