Bales Of Amber Mac OS

Bales Of Amber Mac Os 11
Bales Of Amber Mac Os Download
Bales Of Amber Mac Os X

Amber is a suite of biomolecular simulation programs. It began in the late 1970's, and is maintained by an active develpment community. Amber 18 ajor new features include: Free energy calculations on GPUs; GPU support for 12-6-4 ion potentials; Domain decomposition for CPU-parallelism.
Stonestreet and James David Bales, Published on 10/01/47. Stonestreet and James David Bales, Published on 10/01/47. The latest versions of Adobe Reader do not support viewing PDF files within Firefox on Mac OS and if you are using a modern (Intel) Mac, there is no official plugin for viewing PDF files within the browser.
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So after a fair bit of contemplating I made the decision to switch from MacPorts to Homebrew. This has not been a painless process and even if I like Homebrew, there are a number of caveats and I cannot for the life of me understand the motivation for implementing this “features”. Having this said, I am now fully committed to Homebrew and hence instructions for how to compile software will from now on out use Homebrew (or not).

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With the recent update from OS X 13.X High Sierra to OS X 14.X Mojave a lot of things broke, as anticipated. This is something that I have now sadly come to expect from any update of the macOS. This did of course include the ability to compile amber on macOS. It turns out that, among other things, Apple decided that ”libstdc++” is deprecated and you should now use ”libc++” without leaving any backwards compatibility solution. Some other important files have also gone missing that used to reside in /usr/include/ that you now need to manually installed from an PKG installer buried in Xcode, this will however stop working with the next major Xcode release and undoubtedly brake a lot of other things as well. Long story short, this is what you need to do to compile AmberTools18/amber18 on macOS Mojave using Homebrew GCC8 or just using the macOS clang compiler. The journey resulting in this post is long and includes more issues than reported though I will not describe all of them since that would take a looooong time and would potentially not be very interesting for the general public.

Compile AmberTools18/amber18 using Homebrew GCC8

Install Xcode and Command Line Tools
Xcode10 is most appropriately installed from the AppStore
You need to install Command Line Tools manually by executing the following in Terminal.app
sudo xcode-select --install
Install Homebrew and GCC
/usr/bin/ruby -e '$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)'
brew install gcc
Install missing header files
In Terminal.app, run the following command to open the PKG installer and follow the instructions.
open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
Download the AmberTools18/amber18 archives and extract them where you want to install them.
tar xvf AmberTools18.tar.bz2
Configure and install
export AMBERHOME=/[PATH]/[TO]/amber18
export PATH=${AMBERHOME}:$PATH
cd $AMBERHOME
export MACOSX_DEPLOYMENT_TARGET='10.14'
Eliminates an error: 'cannot find <include> file'.
ln -s /usr/local/bin/gcc-8 /usr/local/bin/gcc
ln -s /usr/local/bin/g++-8 /usr/local/bin/g++
ln -s /usr/local/bin/c++-8 /usr/local/bin/c++
./configure -macAccelerate gnu
make install

This will produce a working version of AmberTools18/amber18 using Homebrew GCC8 though there are still issues and there will undoubtedly be more issues that will surface before everything works as intended. How to compress two files into a zip.

Bales Of Amber Mac Os 11

Compile AmberTools18/amber18 using macOS clang

Bales Of Amber Mac Os Download

Install Xcode and Command Line Tools
Xcode10 is most appropriately installed from the AppStore
You need to install Command Line Tools manually by executing the following in Terminal.app
sudo xcode-select --install
Install the missing header files
In Terminal.app, execute the following command to launch the PKG installer and follow the instructions.
open /Library/Developer/CommandLineTools/Packages/macOS_SDK_headers_for_macOS_10.14.pkg
Download AmberTools18/amber18 archives and extract where you want to install.
tar xvf AmberTools18.tar.bz2
Configure and install
export AMBERHOME=/[PATH]/[TO]/amber18
export PATH=${AMBERHOME}:$PATH
cd $AMBERHOME
export MACOSX_DEPLOYMENT_TARGET='10.14'
Eliminates an error: 'cannot find <include> file'.
vi $AMBERHOME/AmberTools/src/configure2
Comment out rows 2237-2241
# if [ '$intelmpi' = 'yes' ]; then # echo 'Intel MPI must be used with the Intel compilers.' # exit 1 # fi #
vi $AMBERHOME/AmberTools/src/pytraj/setup.py
Change libstdc++ to libc++ on row 142
142 extra_compile_args.append('-stdlib=libstdc++’) ---> 142 extra_compile_args.append('-stdlib=libc++’)
Also change the same on rows 2289-2293
2289 # mac/clang 2290 if [ '$skippython' = 'no' ]; then 2291 cpptrajcxxflags='-stdlib=libstdc++ $cpptrajcxxflags' 2292 cpptrajldflags='-stdlib=libstdc++ -L/usr/lib/' 2293 fi ---> 2289 # mac/clang 2290 if [ '$skippython' = 'no' ]; then 2291 cpptrajcxxflags='-stdlib=libc++ $cpptrajcxxflags' 2292 cpptrajldflags='-stdlib=libc++ -L/usr/lib/' 2293 fi
./configure -macAccelerate clang
make install

Bales Of Amber Mac Os X

This produces a working version of AmberTools18/amber18 using macOS clang though there are still issues and there will, without a doubt, be more issues that will surface.