CFD Online Discussion Forums - [OpenFOAM.org] OpenFOAM 2.3.x on Mac OS X Yosemite 10.10.5 Installation Errors

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OpenFOAM 2.3.x on Mac OS X Yosemite 10.10.5 Installation Errors

Dear All,

First time I try to install OpenFOAM 2.3.x on MAC OS X Yosemite 10.10.5 using the instructionhttp://openfoamwiki.net/index.php/Installation/Mac_OS/OpenFOAM_2.3.x.

Although I am struggling since several days to set the port selection similar to tutorial, I have following errors during setting db:

First one:

Code:

sudo port select --set db db48

Selecting 'db48' for 'db' failed: The configuration file '/opt/local/etc/select/db/base' could not be opened

Second one:

Code:

sudo port select --set llvm mp-llvm-3.5

Selecting 'mp-llvm-3.5' for 'llvm' failed: The specified version 'mp-llvm-3.5' is not valid.

How can I fix these problems. Your help will be appreciated.

By the way my selection looks $port sure select --summary

Code:

Name     Selected               Options

====     ========               =======

db       none                   db46 db48 none

gcc      mp-gcc48               mp-gcc46 mp-gcc47 mp-gcc48 mp-gcc49 none

llvm     mp-llvm-3.4            mp-llvm-3.4 none

mpi      openmpi-gcc48-fortran  mpich-mp-fortran openmpi-gcc48-fortran openmpi-mp-fortran none

python   python27               python26-apple python27 python27-apple none

python2  none                   python26-apple python27 python27-apple none

Thank you.

Baris

Quote:

Originally Posted by wyldckat (Post 567445)

Quick answer: http://www.cfd-online.com/Forums/ope...lems-db48.html

Dear Bruno,

Thank you very much for your kind reply. I have installed finally openfoam into this version of mac. It can be run both manual and parallel as well. However, I have 2 other problems, If you can help be I will be really appraciated.

First one is when I open new terminal and write icoFoam -help it shows following error:

Code:

-bash: icoFoam: command not found

to get rid of this error I should always go into OpenFOAM-2.3.x/ and then should run source etc/bashrc then it works: you can find my .bashrc as follows. How can I set it to work at every opening of terminal?

Code:

export WM_PROJECT=OpenFOAM

export WM_PROJECT_VERSION=2.3.x



################################################################################

# USER EDITABLE PART: Changes made here may be lost with the next upgrade

#

# either set $FOAM_INST_DIR before sourcing this file or set

# 'foamInstall' below to where OpenFOAM is installed

#

# Location of the OpenFOAM installation

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

foamInstall=$HOME/$WM_PROJECT

# foamInstall=~$WM_PROJECT

# foamInstall=/opt/$WM_PROJECT

# foamInstall=/usr/local/$WM_PROJECT

#

# END OF (NORMAL) USER EDITABLE PART

################################################################################



#

# These are the defaults for this version which should generally be

# overridden from the prefs.sh file or from command-line specification

#

#- note the location for later use (eg, in job scripts)

: ${FOAM_INST_DIR:=$foamInstall}; export FOAM_INST_DIR



#- Compiler location:

#    foamCompiler= system | ThirdParty (OpenFOAM)

foamCompiler=system



#- Compiler:

#    WM_COMPILER = Gcc | Gcc45 | Gcc46 | Gcc47 | Clang | Icc (Intel icc)

export WM_COMPILER=Gcc

unset WM_COMPILER_ARCH WM_COMPILER_LIB_ARCH



#- Architecture:

#    WM_ARCH_OPTION = 32 | 64

export WM_ARCH_OPTION=64



#- Precision:

#    WM_PRECISION_OPTION = DP | SP

export WM_PRECISION_OPTION=DP



#- Optimised, debug, profiling:

#    WM_COMPILE_OPTION = Opt | Debug | Prof

export WM_COMPILE_OPTION=Opt



#- MPI implementation:

#    WM_MPLIB = SYSTEMOPENMPI | OPENMPI | SYSTEMMPI | MPICH | MPICH-GM | HPMPI

#               | MPI | QSMPI | SGIMPI

export WM_MPLIB=SYSTEMOPENMPI



#- Operating System:

#    WM_OSTYPE = POSIX | ???

export WM_OSTYPE=POSIX



#- Floating-point signal handling:

#    set or unset

export FOAM_SIGFPE=



#- memory initialisation:

#    set or unset

#export FOAM_SETNAN=





################################################################################



# The old dirs to be cleaned from the various environment variables

# - remove anything under top-level directory.

# NB: the WM_PROJECT_INST_DIR might not be identical between versions

foamOldDirs="$FOAM_INST_DIR $WM_PROJECT_SITE $HOME/$WM_PROJECT/$USER"

if [ "$WM_PROJECT_INST_DIR" != "$FOAM_INST_DIR" ]

then

    foamOldDirs="$WM_PROJECT_INST_DIR $foamOldDirs"

fi





# Location of installation

# ~~~~~~~~~~~~~~~~~~~~~~~~

export WM_PROJECT_INST_DIR=$FOAM_INST_DIR

export WM_PROJECT_DIR=$WM_PROJECT_INST_DIR/$WM_PROJECT-$WM_PROJECT_VERSION



# Location of third-party software

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

export WM_THIRD_PARTY_DIR=$WM_PROJECT_INST_DIR/ThirdParty-$WM_PROJECT_VERSION



# Location of site-specific templates etc

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

# unset is equivalent to $WM_PROJECT_INST_DIR/site

if [ -d "$WM_PROJECT_SITE" ]

then

    export WM_PROJECT_SITE

else

    unset WM_PROJECT_SITE

fi



# Location of user files

# ~~~~~~~~~~~~~~~~~~~~~~

export WM_PROJECT_USER_DIR=$HOME/$WM_PROJECT/$USER-$WM_PROJECT_VERSION





# Source files, possibly with some verbosity

_foamSource()

{

    while [ $# -ge 1 ]

    do

        [ "$FOAM_VERBOSE" -a "$PS1" ] && echo "Sourcing: $1" 1>&2

        . $1

       shift

    done

}



# Evaluate command-line parameters

_foamEval()

{

    while [ $# -gt 0 ]

    do

        case "$1" in

        -*)

            # stray option (not meant for us here) -> get out

            break

            ;;

        *=)

            # name=       -> unset name

            [ "$FOAM_VERBOSE" -a "$PS1" ] && echo "unset ${1%=}" 1>&2

            eval "unset ${1%=}"

            ;;

        *=*)

            # name=value  -> export name=value

            [ "$FOAM_VERBOSE" -a "$PS1" ] && echo "export $1" 1>&2

            eval "export $1"

            ;;

        *)

            # filename: source it

            if [ -f "$1" ]

            then

                _foamSource "$1"

            else

                _foamSource `$WM_PROJECT_DIR/bin/foamEtcFile -silent "$1"`

            fi

            ;;

        esac

        shift

    done

}





# Add in preset user or site preferences:

_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile prefs.sh`



# Evaluate command-line parameters and record settings for later

# these can be used to set/unset values, or specify alternative pref files

export FOAM_SETTINGS="$@"

_foamEval $@



# Clean standard environment variables (PATH, LD_LIBRARY_PATH, MANPATH)

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

foamClean=$WM_PROJECT_DIR/bin/foamCleanPath



#- Clean PATH

cleaned=`$foamClean "$PATH" "$foamOldDirs"` && PATH="$cleaned"



#- Clean LD_LIBRARY_PATH

cleaned=`$foamClean "$LD_LIBRARY_PATH" "$foamOldDirs"` \

    && LD_LIBRARY_PATH="$cleaned"



#- Clean MANPATH

cleaned=`$foamClean "$MANPATH" "$foamOldDirs"` && MANPATH="$cleaned"

if [[ `uname -s` == "Darwin" ]]

then

    cleaned=`$foamClean "$DYLD_LIBRARY_PATH" "$foamOldDirs"` && DYLD_LIBRARY_PATH="$cleaned"

fi



export PATH LD_LIBRARY_PATH MANPATH





# Source project setup files

# ~~~~~~~~~~~~~~~~~~~~~~~~~~

_foamSource $WM_PROJECT_DIR/etc/config/settings.sh

_foamSource $WM_PROJECT_DIR/etc/config/aliases.sh





# Source user setup files for optional packages

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config/paraview.sh`

_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config/ensight.sh`

_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config/gperftools.sh`

_foamSource `$WM_PROJECT_DIR/bin/foamEtcFile config/CGAL.sh`





# Clean environment paths again. Only remove duplicates

# ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

#- Clean PATH

cleaned=`$foamClean "$PATH"` && PATH="$cleaned"



#- Clean LD_LIBRARY_PATH

cleaned=`$foamClean "$LD_LIBRARY_PATH"` && LD_LIBRARY_PATH="$cleaned"



#- Clean MANPATH (trailing ':' to find system pages)

cleaned=`$foamClean "$MANPATH"`: && MANPATH="$cleaned"



export PATH LD_LIBRARY_PATH MANPATH



#- Clean LD_PRELOAD

if [ -n "$LD_PRELOAD" ]

then

    cleaned=`$foamClean "$LD_PRELOAD"` && LD_PRELOAD="$cleaned"

    export LD_PRELOAD

fi



if [[ `uname -s` == "Darwin" ]]

then

    if [[ `ulimit -n` == "unlimited" || `ulimit -n` < 8192 ]]

    then

        # higher limit needed for wmkdeps

        ulimit -n 8192

    fi

fi



if [ -f $/Users/wuguanghao/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc ]; then

  . $/Users/wuguanghao/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc

fi



# cleanup environment:

# ~~~~~~~~~~~~~~~~~~~~

unset cleaned foamClean foamInstall foamOldDirs

unset _foamSource _foamEval









# ----------------------------------------------------------------- end-of-file



echo "WM_CC=mpicc" >> /Users/wuguanghao/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc

echo "WM_CXX=mpicxx" >> /Users/wuguanghao/OpenFOAM/OpenFOAM-2.3.x/etc/bashrcWM_CC=mpicc

WM_CXX=mpicxx

WM_CC=mpicc

WM_CC=mpicc

WM_CC=mpicc

WM_CC=mpicc

Another problem is that after running simply a case I can't open paraview. It gives following error:

Code:

ERROR: ParaView not found in /Users/wuguanghao/OpenFOAM/ThirdParty-2.3.x/platforms/darwinIntel64Gcc/ParaView-4.1.0/



FATAL ERROR: ParaView reader module libraries do not exist



Please build the reader module before continuing:

cd $FOAM_UTILITIES/postProcessing/graphics/PV4Readers

./Allwclean

./Allwmake

To install the preview into mac i followed following link: https://openfoamwiki.net/index.php/I...OpenFOAM_2.2.2

Thank you in advance.

Baris

Hi Baris,

In the file "~/.bashrc" you should not have all of that content. The idea is to only have the content that you originally had and then to add the line related to sourcing the OpenFOAM environment, for example:

Code:

source /Users/wuguanghao/OpenFOAM/OpenFOAM-2.3.x/etc/bashrc

I don't have access to a Mac, so I don't know what is the default content of the file "~/.bashrc".

As for using paraFoam, the instructions are given here: https://openfoamwiki.net/index.php/I...w_Installation

Best regards,
Bruno

Hi Bruno,

Thank you very much for your help. You are great man :) Finally successfully I have installed OF into my mac. After that a friend asked me to install OF into same version of his MAC. I have tried several times same way, however I am getting following error when I am installing mpirun-gcc48 or mpirun-gcc49. By the way I can't not install gcc48 but I was able to install gcc49. I don't know the reason. Could you tell me that How can I fix following problem and install mpirun:

Quote:

Error: org.macports.build for port openmpi-gcc49 returned: command execution failed

/opt/local/var/macports/build/_opt_local_var_macports_sources_rsync.macports.org _release_tarballs_ports_sc ience_openmpi/openmpi-gcc49/work/openmpi-1.10.0/opal/mca/hwloc/base/hwloc_base_util.c:1482:13: error: 'HWLOC_OBJ_OSDEV_COPROC' undeclared (first use in this function)

Your help will make me so appreacited.

Thanks in advance.

Baris

Quick answer: I have no specific idea about this, because I don't have access to a Mac.
Nonetheless, I suspect that it has something to do with using OpenMPI 1.10, which is very recent and is possibly the reason for the problems you're having.

I'm currently advising people to follow the instructions given by Alexei, which relies in Homebrew instead of Macports: https://github.com/mrklein/openfoam-...ion-&-Homebrew

Hi,

I have the same problem when I want to install Openfoam on my macbook OS X 10.9.4

sudo port select --set llvm mp-llvm-3.5
Selecting 'mp-llvm-3.5' for 'llvm' failed: The specified version 'mp-llvm-3.5' is not valid.

Any help is highly appreciated

Quote:

Originally Posted by AliVali (Post 600181)

What is output of port select --summary? Presumably a version after 3.5 should work. (Myself, I have only 3.7 since installing 10.11)

Hi to all,

This is the tutorial which I have prepared how to install openfoam into MAC.

Hope it helps you.

https://www.researchgate.net/publica...nFOAM_into_MAC

Hi Windscin,
port select --summary
Name Selected Options
==== ======== =======
db none db48 none
gcc mp-gcc48 mp-gcc48 mp-gcc5 none
llvm none mp-llvm-3.7 none
mpi openmpi-gcc48-fortran openmpi-gcc48-fortran openmpi-mp-fortran none
python python27 python25-apple python26-apple python27 python27-apple none
python2 none python25-apple python26-apple python27 python27-apple none

I'll try to install a newer version next week.

Quote:

Originally Posted by shipman (Post 600273)

Hi to all,

This is the tutorial which I have prepared how to install openfoam into MAC.

Hope it helps you.

https://www.researchgate.net/publica...nFOAM_into_MAC

Thanks Shipman,
your tutorial looks very useful, I'll try it soon.

Regards

Ali: Looks okay so far, except that you don't have mp-llvm-3.7 selected, which I am guessing is irrelevant since the only alternative is none.

I used this setup:
Name Selected Options
==== ======== =======
cython none cython26 none
gcc mp-gcc49 mp-gcc49 mp-gcc5 none
llvm mp-llvm-3.7 mp-llvm-3.7 none
mpi openmpi-gcc49-fortran mpich-gcc49-fortran openmpi-gcc49-fortran openmpi-mp-fortran none
nosetests none nosetests26 none
python python27 python26 python26-apple python27 python27-apple none
python2 none python26 python27 none
wxWidgets none wxWidgets-3.0 none

I managed to get 2.3.x working with gcc49 and mp-llvm-3.7, but I also added WM_CC=/opt/local/bin/mpicc and WM_CXX=/opt/local/bin/mpicxx at the end of $HOME/OpenFoam/OpenFoam-2.3.x/etc/bashrc. (After verifying that the chain of symbolic links ended successfully. No kidding, at one point the chain broke and `which mpicc` said one thing, but mpicc -v said another.)

Then I used this hack to allow macport's flex (2.6.0) to work with the package:

% find . -name '*.L' -print

then for each file found above, change
#if YY_FLEX_SUBMINOR_VERSION < 34
to
#if YY_FLEX_SUBMINOR_VERSION < 34 && YY_FLEX_MINOR_VERSION < 6
and then the code will work properly with flex 2.6

I used gcc49 mostly because it saved me adding another compiler version, but also because it has memory safeguards not found in gcc48.

I trust you are installing on a case-sensitive filesystem? I.e., not the root filesystem -- which must be case insensitive or OS X breaks.