Notes on El Capitan - mrklein/openfoam-os-x GitHub Wiki
El Capitan introduces System Integrity Protection and it breaks certain things. In particular it clears LD_LIBRARY_PATH and DYLD_LIBRARY_PATH variables. I.e. if I run the following commands by hand
$ echo $DYLD_LIBRARY_PATH; echo; echo $LD_LIBRARY_PATHI get usual output
/usr/local/opt/boost/lib:/usr/local/opt/cgal/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib/openmpi-system:/usr/local/Cellar/open-mpi/1.10.1/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib/dummy
/usr/local/opt/boost/lib:/usr/local/opt/cgal/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib/openmpi-system:/usr/local/Cellar/open-mpi/1.10.1/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib:$WM_PROJECT_DIR/platforms/darwin64ClangDPInt32Opt/lib/dummy
Yet, if I run these commands from shell script, output is empty.
$ cat test.sh
#!/bin/sh
echo $DYLD_LIBRARY_PATH
echo $LD_LIBRARY_PATH
$ ./test.sh
Since OpenFOAM(R) libraries are installed in non-standard locations, solvers and utilities can not function properly with the variables being empty. I have discovered the problem while using lib ("myLovelyLibrary.dylib") construction in controlDict, later it was reported by Jarle Kramer (#15) that parallel execution breaks.
As a solution you can...
- Disable SIP.
- Add
source $WM_PROJECT_DIR/etc/bashrcline to your scripts (somewhere before you run OpenFOAM executables).