Installing on Mac
We are trying to create a running version of Scipion on OS X. Porting the whole set of libraries, python modules and xmipp is not trivial.
In this page we comment on the progress of this project.
After downloading the software and starting to compile it following the instructions in the installation page, we find that the process stops at some point. We try to find the cause and fix it, and run the installation again.
After running scipion config, we had to change:
JAVA_HOME=/System/Library/Frameworks/JavaVM JAVA_BINDIR=/System/Library/Frameworks/JavaVM/Commands MPI_LIBDIR=/usr/local/lib MPI_BINDIR=/usr/local/bin MPI_INCLUDE=/usr/local/include
The MacPorts Project tries to design an easy-to-use system for compiling, installing, and upgrading open-source software on OS X. We use some of the available "ports" (software packages) as part of our installation.
Common commands:
-
To install packages with macports, you use:
sudo port install <packagename> -
To search for a package:
port search <important_software> -
Update list of ports:
sudo port selfupdate
We had to install at least these packages to let the installation of scipion go further:
From macports:
-
wget -
g++ -
g95 -
cmake -
OpenBLAS-devel(though it is not clear that it helped…)
From dmgs:
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XQuartz (http://xquartz.macosforge.org/landing/)
-
Fix the test for the xft library
-
opencv
-
matplotlib (but maybe we can use the one from enthought with it preinstalled, at https://www.enthought.com/products/epd/)
-
xmipp
-
ldd→otool -L -
/var/log/messages→ Use "Console" (from Applications→Utilities)