- How To Install Wget Mac
- Install Wget Mac Catalina Download
- Install Wget Mac Catalina Free
- Install Wget Mac Catalina Update
Third-Party Libraries
What is Homebrew? Homebrew (brew) is a free and open-source package manager that allows installing apps and software in macOS, depending on the user’s desire. It has been recommended for its simplicity and effectiveness in saving time and effort. Its famous description is “The missing package manager for macOS”. Follow the prompts to complete the installation. Run the following command to install the essential packages. Brew install bash cliclick coreutils gawk wget dialog unix2dos grep w3m. Run the following commands to install wine and winetricks. First add the tap: brew tap gcenx/wine. Then install Wine: brew install cask -no-quarantine wine.
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These instructions describe building and installing IBAMR and its requiredthird-party libraries on a macOS system. The instructions below create both adebug build, where the libraries are compiled with additional checking and canbe used with a debugger, and an optimized build, which is generally severaltimes faster than the debug build because most error checking is turned offand debugging information is not available.
All libraries specified below are compiled with the make program. We recommendrunning make in parallel whenever possible: make is smart enough to compilemultiple files at once. One can specify the number of jobs, or concurrent copiesof make to run, with the -j flag: i.e., running make -j4 will compile fourfiles at once. We recommend using the same number of make jobs as physicalprocessors on a machine. The sample instructions here use four jobs.
How To Install Wget Mac
The package manager HomeBrew is used here to install severalpackages IBAMR depends on. After installing HomeBrew, install necessarypackages:
At the present time IBAMR is not compatible with the version of hypre installedthrough homebrew, so hypre (and PETSc) must be installed manually. You may alsoinstall these optional packages:
Note: You do not need to build your own versions of Boost, HDF5, orMPICH. All of these packages are now installed, by default, in /usr/local.
It will be useful to install the wget command through HomeBrew:
Picking good optimization flags
IBAMR’s performance in release mode is very sensitive to the choice ofoptimization flags. For example: switching from -O3 to -march=native -O3roughly doubled the performance of some IBFE-based codes. This is because alarge fraction of the time spent in IBAMR is spent doing structured gridcalculations that can benefit heavily from applying processor-specificoptimizations.
If you want good performance then we recommend adding -march=native to theflags chosen below for optimization purposes (i.e., any place where we write-O3, we recommend you use -O3 -march=native). This is not listed as thedefault compiler flag because it generates processor-specific instructions, whichmay not be valid if you compile on one machine and execute on another (e.g., ifyou compile on a cluster’s login node and then run on a partition that uses adifferent set of hardware). For the most part this is not relevant on a mac(since these are not usually networked) unless you are doing something unusual.
Most of the time spent by IBAMR applications is spent inside IBAMR functions, somost of the benefit of processor-specific compilation flags is achieved bycompiling IBAMR itself (i.e., it is not necessary to recompile dependencies with-march=native, but it can only help).
For more information see The GCC page on compilerflags. The flag-march=native is supported on all major C++ compilers (GCC, Clang, and Intel).
Setup
Boost
Currently, IBAMR requires Boost version greater than or equal to 1.57.
This is available in /usr/local through HomeBrew.
Eigen
Currently, IBAMR requires Eigen version greater than or equal to 3.2.5.
NOTE: Eigen 3.2.5 is bundled with IBAMR and is built automatically by IBAMRconfigure. It is also possible to use an external installation of Eigen withIBAMR. If you will be using libMesh, you must use an external Eigen.
HDF5
any version of HDF5 >= 1.8.7 is likely to work with IBAMR.
This is available in /usr/local through HomeBrew.
Silo
(optional)
We recommend using the latest available version of Silo (currently 4.10), butearlier versions of Silo are also likely to work with IBAMR. We recommendletting PETSc download Silo (via --download-silo=1). If you let PETSc buildSilo then all paths supplied later on to indicate where Silo is must point toPETSc’s installation directory.
NOTE: Silo 4.10 requires an installation of zlib that includes its headersand development files: make sure that your installation includes zlib.h. Ifyou build it from source from http://zlib.net/, specify itslocation with:
--with-zlib='path/to/zlib/1.2.8/include,path/to/zlib/1.2.8/lib' .
Notice that you have to specify its include and lib directories.
If you do not have the GNU readline library installed, you may need--without-readline.
muParser
NOTE: A patched version of muParser 2.2.3 is bundled with IBAMR and installedautomatically by IBAMR configure. It is also possible to use an externalinstallation of muParser with IBAMR.
MPI
IBAMR requires that MPI be available but does not require the use of a specificMPI library. We recommend using a system-provided MPI installation ifavailable. If you will be using your system MPI, wherever you see the path tothe MPICH compilers specified, replace it with the path to your system’s MPIcompilers. If you do not have a system MPI installation available, we recommendusing MPICH. MPICH is available through HomeBrew in /usr/local.
Hypre
IBAMR requires Hypre verion 2.10b or later. We recommend you let PETSc install hypre.
PETSc
IBAMR requires the PETSc (portable toolkit for scientific computing) library.IBAMR is compatible with PETSc versions 3.7 and newer. If you use a new version of PETScthen you will also need to use a new version of libMesh. These instructions arefor PETSc version 3.13.4.
These configure options direct PETSc to download and install hypre.First, unpack PETSc:
Next, configure and compile a debugging build of PETSc:
(Note that if you are using your system MPI, you must modify the following to reflect the correct path to your MPI compilers)
Finally, configure and compile an optimized build of PETSc:
(Note that if you are using your system MPI, you must modify the following to reflect the correct path to your MPI compilers)
NOTE: You may wish to add the lines:
to your ~/.bashrc file.
SAMRAI
IBAMR requires a specific version of SAMRAI. At this time, IBAMR requires the use of SAMRAI 2.4.4.
First, unpack SAMRAI:
Next, patch SAMRAI using the patch fileibamr-samrai-fixes.patch:
Next, configure and compile a debugging build of SAMRAI. It may be necessary, if you are not using your system installation of MPI, to modify the paths to the MPI compiler wrappers:
Finally, configure and compile an optimized build of SAMRAI:
libMesh
libMesh is a finite element library required by the IBFE subsystem. It is not arequired dependency of IBAMR but is strongly recommended.
IBAMR is compatible with libMesh 1.2.0 or newer. The instructions below use thelatest version of libMesh (1.6.1). If you use libMesh with boost, then you MUSTuse an external build of boost for both IBAMR and libMesh since the subset ofboost included with libMesh does not contain everything that IBAMR needs. Werecommend compiling libMesh without boost to avoid this issue.
NOTE: libMesh assumes that PETSc was installed in place, i.e., withoutcalling make install at the end. The instructions on this page assume thatPETSc is installed in place. However, if you choose instead to run makeinstall, then one should provide the full path to the PETSc installation asPETSC_DIR: e.g., in this case, one would providePETSC_DIR=$HOME/sfw/petsc/3.13.4/linux-debug as an argument.
First, a debug build:
(Note that if you are using your system MPI, you must modify the following to reflect the correct path to your MPI compilers)
Then, an optimized build:
(Note that if you are using your system MPI, you must modify the following toreflect the correct path to your MPI compilers)
IBAMR
First, download IBAMR:
IBAMR does not set any compiler flags (with the sole exception of the C++ versionflag): instead, the compiler flags are set to the provided values of CFLAGS,CXXFLAGS, and FCFLAGS. The values given below are good defaults for Clang,GCC, and Intel compilers. While optional, we recommend adding some warningsuppression flags to silence some unnecessarily pedantic warnings that show upin newer versions of GCC and clang:
- If you are using GCC 9.1 or newer, we recommend adding
-Wno-deprecated-copy. - If you are using Clang, we recommend adding
-Wno-unneeded-internal-declarationand (for clang version 8.0 or later,i.e., installations newer than about 2018)-Wno-undefined-var-templatetoCXXFLAGS. (Note that clang versions numbers are different on Mac and Linux.)
Next, configure and compile a debugging build of IBAMR:
(Note that if you are using your system MPI, you must modify the following toreflect the correct path to your MPI compilers)
If you had to install your own copy of zlib for Silo, you will also need to specifythe installation directory of zlib here via --with-zlib=PATH, where PATH is thedirectory where zlib was installed.
IBAMR’s configure script will automatically add the correct flag to enable C++11 support.
You may now compile and run the IBAMR examples, e.g.,
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Next, configure and compile an optimized build of IBAMR. If you are running on acluster you may want to use additional optimization flags: please refer to thenote at the top of the page for more information on how to do this.
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(Note that if you are using your system MPI, you must modify the following to reflect the correct path to your MPI compilers)
Install Wget Mac Catalina Update
You may now compile and run the IBAMR examples with compiler optimizations enabled, e.g.,