Auto3dem in OS X

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Dani Badia

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Feb 29, 2012, 4:47:05 AM2/29/12
to Auto3DEM
Dear all

I would like to know if it is possible to run Auto3dem in OS X and if
there is any special requirement for the installation (compilers,
libraries, etc...)

Thanks for your help

Dani Badia, PhD
Abrescia's lab
CIC bioGUNE
Bilbao (Spain)

Giovanni Cardone

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Feb 29, 2012, 5:26:45 PM2/29/12
to auto...@googlegroups.com, daniel...@gmail.com
Hi Dani,

at the moment only part of Auto3DEM can be installed on Mac OSx with
minimal effort. Mac architecture is not supported, but this is something
that we would like to do in the future.
We provide only source code, which means that you need to compile it in
order to get the executables. Gcc compiler provided with Apple works
fine, as long as the version is higher than 4.2, which provide fortran90
compiler and openmp libraries. Usually the compilers are not present by
default, you need to have Apple's Developer Tools installed. They are
included on the retail DVD version of OS X and also available as a free
download from Apple's Developer Site.
Now the hard part: in order to access all the functionality of Auto3DEM,
including the graphical software RobEM and the pre-processing tools in
autopp, you need two additional libraries: XMotif (openmotif), for
graphical display, and mpich2 (or other mpi library), for parallel
execution of the programs. Without these libraries, you can install the
package, but you can only run automated alignment and reconstruction,
starting from stacks of particles already preprocessed. These two
libraries are not provided by Apple, therefore you need to install them
by yourself. There is a project, MacPorts, that easily provides them,
but in this case you also need to use the gcc compiler from the same
project. However, we don't have direct experience on this kind of
installation. From hearsay I can only say that installing the mpich2
library is simpler than installing the XMotif one.
Without these libraries, you can compile and install all the programs
required for the automated reconstruction by specifying 'serial' mode
and only 'nogui' programs. From my experience on Mac machines, the
options included for gcc compilers in the installation script usually
work fine, but for some versions of the OS you need to add '-arch i386'
to the compilation flags.
It is our intention to support more, and better, Mac OSX architecture,
but we don't have a timing frame yet. In the meantime, if you need any
help in installing Auto3DEM, you can contact me directly.

Best,
Giovanni


Giovanni Cardone
Baker's Laboratory
University of California, San Diego
Department of Chemistry and Biochemistry
9500 Gilman Drive, NSB 4107, MC-0378
La Jolla, CA, 92093-0378
(858)534-5852

James Conway

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Apr 2, 2012, 12:44:01 AM4/2/12
to Auto3DEM
I have run AUTO3DEM routinely on Mac OSX (currently 10.6.8) for
several years, although not the ROBEM part. For the rest, gfortran and
the XCode install of GCC, plus openMPI, work fine. Packages from here:

XCode from Apple
http://hpc.sourceforge.net/ - gfortran, use the snow leopard/intel
binaries link
http://www.open-mpi.org/ - need to config, make and install

With gfortran and openMPI installed, the latest AUTO3DEM is built
without ROBEM:
make_all parallel nogui

I haven't needed ROBEM so did not work out the Motif stuff (although I
have it anyway for my own particle picking code).

Mac OSX doesn't work well if you distribute across several machines
with the firewall in place (openMPI uses increasing port numbers), so
I run it on one machine (8 cores with hyperthreading, so I specify up
to 16 processes, 32 GBytes RAM - Mac Pro 2010). It beats an older AMD
Linux machine with 32 cores, but not anything better. Still useful for
modest jobs and I prefer to debug on it. Happy to answer questions
about setting this up.

James Conway
Department of Structural Biology
University of Pittsburgh School of Medicine
Biomedical Science Tower 3, Room 2047
3501 5th Ave
Pittsburgh, PA 15260
U.S.A.
Email: jxc100 (at) pitt.edu
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