Difference between revisions of "Installation/Mac OS/OpenFOAM 2.2.2"

Revision as of 12:03, 30 November 2013

1 Introduction and Notes

This guide is derived from OpenFOAM 2.1.x Installation with some modifications, thanks to the help provided on this thread at CFD-Online's Forums.

These compiling instructions have only been tested on the following system:

Macbook (version 6,2)
Intel Core i7 2.66Ghz
Mac OS X Mavericks (version 10.9)

These instructions may need to be tailored to fit your specific system if they deviate from the above; you should be able to ask support on this thread if you needed it.

Many thanks go to Bernhard Gschaider (a.k.a. gschaider at CFD-Online's Forums) for maintaining the latest OpenFOAM Mac OS X patches and for the big help he provided me.

2 Prepare your Mac OS X Environment

2.1 Macports

To install Macports you need to install xCode, you can find it on the App Store. After xCode you need to install the Command Line Tools. Installing Command Line Tools for Mavericks is different from what you would do with previous OSX versions, as explained in the following subsections:

Command Line Tools for OSX 10.9 "Mavericks"
Command Line Tools for OSX version < 10.9

2.1.1 Command Line Tools for OSX 10.9 "Mavericks"

To install CLT on OSX 10.9 open a terminal application (for example Terminal.app) and run:

xcode-select --install

a window will be prompted where you can confirm installation.

2.1.2 Command Line Tools for OSX version < 10.9

In previous versions of OSX (and of xCode) you can download CLT directly from xCode Preferences > Downloads > Components.

2.1.3 xCode License

Now you should accept the xCode License so run, always in the Terminal (this could be needed only on OSX 10.9):

sudo xcodebuild -license

and when asked type "agree" to accept the license. Now xCode "things" should work correctly.

2.1.4 MacPorts Installation

Now to install Macports you can download the pre-compiled package from the Official Macports Website.

2.2 Build and Install the necessary software

To install all the tools we'll need run in Terminal:

sudo port selfupdate

Wait for the end of all operations then do:

sudo port install gcc46 openmpi boost cgal ccache flex bison

Now wait (a bit...)

3 OpenFOAM Building

3.1 Creation of Case Sensitive .sparseimage

Note: Images here shown are taken from Installation/Mac_OS/OpenFOAM_2.1.x, you could change the name of the sparse-image from OpenFOAM-v2.1 to OpenFOAM-v2.2.2 (and this will be assumed from here on).

First, we create a disk image with the Apple Disk Utility. Open /Applications/Utilities/Disk Utility. Click New Image:

It is important to set as Format: Mac OS Extended (Case-sensitive,Journaled). The sparse image will grow with the place used inside the image. Create a sparse image with the following settings (examples, you could change the values):

3.2 OpenFOAM sources and patches

Note: Remember that when you're inside the terminal you can auto-complete your commands pressing the TAB button.

Download OpenFOAM 2.2.2 sources from here and patches (OpenFOAM-2.2.2 Patch || SurfaceCGAL Fix || ThirdParty Patch) ^[1] and put everything inside the .sparseimage (you probably saved in ~/Documents).

Open a Terminal, create a symlink to the OF image:

 ln -s /Volumes/OpenFOAM-v2.2.2 OpenFOAM

now we can go to OF directory just doing (from home directory)

cd OpenFOAM

Let's extract the two archives:

tar -xvf OpenFOAM-2.2.2.tgz
tar -xvf ThirdParty-2.2.2.tgz

Now your OF directory should look like this

****@mbp-di-ruben: ~/OpenFOAM$ ls -al
total 182688
drwxr-xr-x   8 ****  staff       612 13 Nov 02:49 .
drwxrwxrwt@  5 root             admin       170 15 Nov 15:40 ..
-rw-r--r--@  1 ****  staff     12292 13 Nov 03:13 .DS_Store
d--x--x--x   6 ****  staff       238 15 Nov 15:40 .DocumentRevisions-V100
drwxrwxrwt@  3 ****  staff       102 12 Nov 23:29 .TemporaryItems
d-wx-wx-wt   2 ****  staff        68 12 Nov 14:43 .Trashes
drwx------   2 ****  staff      2822 15 Nov 12:03 .fseventsd
drwxr-xr-x@ 10 ****  staff       680 13 Nov 02:55 OpenFOAM-2.2.2
-rw-r--r--@  1 ****  staff  32536146 12 Nov 21:09 OpenFOAM-2.2.2.tgz
-rw-r--r--@  1 ****  staff     41620 13 Nov 02:49 OpenFOAM-2.2.x_Mac-20130309.patch
-rw-r--r--@  1 ****  staff       691 13 Nov 02:49 SurfaceCGALFix.patch
drwxr-x---@  7 ****  staff       782 13 Nov 02:54 ThirdParty-2.2.2
-rw-r--r--@  1 ****  staff  58193818 12 Nov 21:09 ThirdParty-2.2.2.tgz
-rw-r--r--@  1 ****  staff      2686 12 Nov 21:12 ThirdParty-2.2_patch

Let's move the patches inside the right folders

# Current Folder: ~/OpenFOAM$ 
mv OpenFOAM-2.2.x_Mac-20130309 OpenFOAM-2.2.2
mv SurfaceCGALFix.patch OpenFOAM-2.2.2
mv ThirdParty-2.2_Mac-20130309.patch Thirdparty-2.2.2

Let's apply them

#Current Folder: ~/OpenFOAM
cd OpenFOAM-2.2.2
#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2
patch -p1<OpenFOAM-2.2.x_Mac-20130309.patch
patch -p1<SurfaCGALFix.patch
cd ..
#Current Folder: ~/OpenFOAM/
cd ThirdParty-2.2.2
#Current Folder: ~/OpenFOAM/ThirdParty-2.2.2
patch -p1<ThirdParty-2.2_patch
cd ..
#Current Folder: ~/OpenFOAM/

OpenFoam patch badly writes compilers symlinks so we have to fix:

#Current Folder: ~/OpenFOAM/
cd OpenFOAM-2.2.2
#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2
rm wmake/rules/darwinIntel64Gcc4*
cd wmake/rules
#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2/wmake/rules
ln -s darwinIntel64Gcc/ darwinIntel64Gcc46
cd ../..
#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2

3.3 Final Steps

Let's give write permission to addr2line4Mac.py

#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2
chmod a+x bin/addr2line4Mac.py

Now we have to edit the bashrc file

sudo nano etc/bashrc

Use CTRL+W to find those lines

export WM_COMPILER=Gcc
export WM_MPLIB=OPENMPI

and change them with

export WM_COMPILER=Gcc46
export WM_MPLIB=SYSTEMOPENMPI

at the end of this file, add

 
export WM_CC='gcc-mp-4.6'
export WM_CXX='g++-mp-4.6'
export WM_NCOMPPROCS=4
ulimit -n 1024

Save (CTRL+O and exit CTRL+X)

A few notes about these two lines^[2]

Apparently it's best that you manually write these two lines instead of copy-pasting, because apparently some weird characters will show up on your file (source).
The first entry is to increase the number of files which one process may open at a time;
The second entry you should set to the number of processes your CPU could manage in parallel, e.g. 4, 8, 16, ...
If you don't know how many your machine can handle, then run:
```
sysctl -n hw.ncpu
```

Now we need a symlink for openmpirun (this can be useful with snappyHexMesh)

#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2
cd OpenFOAM/OpenFOAM-2.2.2/bin
#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2/bin
ln -s /opt/local/bin/openmpirun mpirun
cd .. 
#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2

There's some hardcoding to do on a file

#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2
sudo nano src/renumber/SloanRenumber/Make/options

Change this line:

 -L$(BOOST_ARCH_PATH)/lib -lboost_thread \

into this:

-L$(BOOST_ARCH_PATH)/lib -lboost_thread-mt \

save and exit.

Source the bashrc file:

#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2
. etc/bashrc

Now we're ready to compile. Cross your fingers and do:

#Current Folder: ~/OpenFOAM/OpenFOAM-2.2.2
./Allwmake 2>&1 | tee logName.log

where logName you should be replaced by a name for your log :P. Now take your time, call your mum, cook, take a shower and then come back to see if something went wrong.

4 Diagnosis and Problems^[3]

You can check if there are any errors by opening the file nameLog.log with a text editor and search for lines have the expression "Error " (including the space after the word "Error").
Keep in mind that if your terminal is returning error messages in another language, then you should search for the respective word for "Error".

If you do find errors, the first one is usually the one to blame for all of the other errors.

If you are still unable to figure out what's wrong, then:

Edit the file nameLog.log with a text editor, search and replace any sensitive information, such as user names and folder paths.
Rename the log-file so that it is unique (preferable with data and unsername. For instance: log_20130401_bgschaid.log)
Pack the log file. For instance with GnuZIP if it is only a single file:
```
gzip log_20130401_bgschaid.log
```
Only tarball it if there are additional files required to diagnose the probelm:
```
tar -czf make.log_20130401_bgschaid.tar.gz make_20130401_bgschaid.log wmake/rules/darwinModified
```
Post the log in this forum thread, along with your question(s).

5 Paraview Installation

Download the right package from official Paraview website and install it.

Let's create a symlink to paraview executable in OpenFOAM to the one installed

#Current Folder ~/
#NOTE: OpenFOAM sparseimage must be mounted and the etc/bashrc file sourced

ln -s /Applications/paraview/Contents/MacOS/paraview $WM_PROJECT_DIR/bin/paraview

The following command creates a file .alias where you can store aliases for commands:

#Current Folder ~/
sudo nano .alias

Add the following lines to it,

alias paraFoam="paraFoam -builtin"

To auto-source the .alias at terminal startup,

#Current Folder ~/
sudo nano .profile 
#Or .bash_profile can work too

add at the end of the file

source ~/.alias

then save and exit.

6 Permanent Installation

You can set a terminal command to auto-mount the .sparseimage and auto-source the OF's bashrc this way

#Current Folder ~/
sudo nano .alias

add at the end of it:

 
alias of222="/usr/bin/open ~/Documents/OpenFOAM-v2.2.2.sparseimage; sleep 1; . ~/OpenFOAM/OpenFOAM-2.2.2/etc/bashrc; . ~/.alias";

Now, if your sparseimage is not mounted simply doing

 of222

will mount the OpenFOAM environment.

↑ More updated patches could be possibly found on this CFD Online Thread
↑ From Installation/Mac_OS/OpenFOAM_2.1.x
↑ From Installation/Mac_OS/OpenFOAM_2.1.x

[1] More updated patches could be possibly found on this CFD Online Thread

[2] From Installation/Mac_OS/OpenFOAM_2.1.x

[3] From Installation/Mac_OS/OpenFOAM_2.1.x

[1]

[2]

[3]

@@ Line 2: / Line 2: @@
 == Introduction and Notes ==
-This guide is derived from <span class="plainlinks">[http://openfoamwiki.net/index.php/Installation/Mac_OS/OpenFOAM_2.1.x OpenFOAM 2.1.x Installation]</span> with some modifications derived thanks to the help provided on [http://www.cfd-online.com/Forums/openfoam-installation-windows-mac/114265-patches-compile-openfoam-2-2-mac-os-x-5.html#post461727 this thread] of [http://www.cfd-online.com CFD Online Forum ].
+This guide is derived from [[Installation/Mac_OS/OpenFOAM_2.1.x|OpenFOAM 2.1.x Installation]] with some modifications, thanks to the help provided on [http://www.cfd-online.com/Forums/openfoam-installation-windows-mac/114265-patches-compile-openfoam-2-2-mac-os-x-5.html#post461727 this thread] at [http://www.cfd-online.com/Forums/ CFD-Online's Forums].
@@ Line 9: / Line 9: @@
   Intel Core i7 2.66Ghz
   Mac OS X Mavericks (version 10.9)
-These instructions may need to be tailored as required to fit your specific system if they deviate from the above; you would be able to ask support on [http://www.cfd-online.com/Forums/openfoam-installation-windows-mac/114265-patches-compile-openfoam-2-2-mac-os-x-5.html#post461727 this thread] if you needed it.
+These instructions may need to be tailored to fit your specific system if they deviate from the above; you should be able to ask support on [http://www.cfd-online.com/Forums/openfoam-installation-windows-mac/114265-patches-compile-openfoam-2-2-mac-os-x-5.html#post461727 this thread] if you needed it.
-Many thanks go to Bernhard Gschaider (a.k.a. [http://www.cfd-online.com/Forums/members/gschaider.html gschaider]) of CFD Online for maintaining the latest OpenFOAM Mac OS X patches and for the big help he provided me.
+Many thanks go to Bernhard Gschaider (a.k.a. [http://www.cfd-online.com/Forums/members/gschaider.html gschaider] at CFD-Online's Forums) for maintaining the latest OpenFOAM Mac OS X patches and for the big help he provided [[User:Tidusuper91|me]].
 __TOC__
@@ Line 20: / Line 20: @@
 To install Macports you need to install <b>xCode</b>, you can find it on the App Store.
-After XCode you need to install the <b>Command Line Tools</b>. Installing Command Line Tools for Mavericks is different from what you would do with previous OSX versions.
+After xCode you need to install the <b>Command Line Tools</b>. Installing Command Line Tools for Mavericks is different from what you would do with previous OSX versions, as explained in the following subsections:
+* [[#Command Line Tools for OSX 10.9 "Mavericks"|Command Line Tools for OSX 10.9 "Mavericks"]]
+* [[#Command Line Tools for OSX version < 10.9|Command Line Tools for OSX version < 10.9]]
 ==== Command Line Tools for OSX 10.9 "Mavericks" ====
-To install CLT on OSX 10.9 open a terminal application (for example <i>Terminal.app</i>) and run<pre>
+To install CLT on OSX 10.9 open a terminal application (for example <i>Terminal.app</i>) and run:
-xcode-select --install
+<bash>xcode-select --install</bash>
-</pre>
 a window will be prompted where you can confirm installation.
 ==== Command Line Tools for OSX version < 10.9 ====
-In previous versions of OSX (and of xCode) you can download CLT directly from xCode Preferences > Downloads > Components
+In previous versions of OSX (and of xCode) you can download CLT directly from xCode {{tt|Preferences > Downloads > Components}}.
 ==== xCode License ====
-Now you should accept the xCode License so run, always in the Terminal (this could be needed only on OSX 10.9)<pre>
+Now you should accept the xCode License so run, always in the Terminal (this could be needed only on OSX 10.9):
-sudo xcodebuild -license
+<bash>sudo xcodebuild -license</bash>
-</pre>
 and when asked type "agree" to accept the license. Now xCode "things" should work correctly.
 ==== MacPorts Installation ====
-Now to install Macports you can download the pre-compiled package from the [http://www.macports.org/install.php#pkg Official Website].
+Now to install Macports you can download the pre-compiled package from the [http://www.macports.org/install.php#pkg Official Macports Website].
 === Build and Install the necessary software ===
-To install all the tools we'll need run in Terminal:<pre>sudo port selfupdate</pre>
+To install all the tools we'll need run in Terminal:
-Wait for the end of all operations then do:<pre>sudo port install gcc46 openmpi boost cgal ccache flex bison
+<bash>sudo port selfupdate</bash>
-</pre>
+Wait for the end of all operations then do:
+<bash>sudo port install gcc46 openmpi boost cgal ccache flex bison</bash>
 Now wait (a bit...)
@@ Line 50: / Line 52: @@
 === Creation of Case Sensitive .sparseimage ===
-'''Note:''' Images here shown are taken from [[Installation/Mac_OS/OpenFOAM_2.1.x]], you could change the name of the sparseimage from '''OpenFOAM-v2.1''' to '''OpenFOAM-v2.2.2''' (and this will be assumed from here on)
+'''Note:''' Images here shown are taken from [[Installation/Mac_OS/OpenFOAM_2.1.x]], you could change the name of the sparse-image from '''OpenFOAM-v2.1''' to '''OpenFOAM-v2.2.2''' (and this will be assumed from here on).
@@ Line 61: / Line 63: @@
 === OpenFOAM sources and patches ===
-'''Note:''' Rember that when you're inside the terminal you can auto-complete your commands pressing the '''TAB''' button
+'''Note:''' Remember that when you're inside the terminal you can auto-complete your commands pressing the '''TAB''' button.