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Re: [[cellml-dev] ] Mac OS X CellML API 1.12


Chronological Thread 
  • From: Ivo Siekmann <ivo.siekmann AT unimelb.edu.au>
  • To: cellml-tools-developers AT lists.cellml.org
  • Subject: Re: [[cellml-dev] ] Mac OS X CellML API 1.12
  • Date: Wed, 14 May 2014 09:54:26 +1000
Hi David (and others interested in the Mac OS X binaries),

I was able to link to the dynamic libraries provided in the Cell ML SDK package... but it is not very convenient to use them.

I believe that the "install name" in the .dylib files (see, for example, the response to this question)
http://stackoverflow.com/questions/10021428/macos-how-to-link-a-dynamic-library-with-a-relative-path-using-gcc-ld
is set to "./". Therefore linking to the libraries in the Cell ML SDK works but running the executable fails unless all .dylib files are copied to the directory of the executable. I'm not sure if this is the reason that the Cell ML SDK package is shown as "damaged or incomplete" by Mac OS X 10.9. And I don't know enough about building dynamic libraries on Mac OS X that I would have an idea how to fix this. But I'll be happy to enter this in the tracker if you think this is a good idea?!?

Cheers
Ivo

P.S.: I managed to compile the API from source and link to OpenCMISS (which was what I wanted), so thanks for the hint!

On 6/05/14 10:29 am, David Nickerson wrote:
Hi Ivo,

See https://tracker.physiomeproject.org/show_bug.cgi?id=3673,
https://tracker.physiomeproject.org/show_bug.cgi?id=3671, and
https://tracker.physiomeproject.org/show_bug.cgi?id=3670 for some
recent tracker items regarding building the CellML API under OS X
10.9.

The upshot is that you should be able to build the current trunk code
(which has some fixes that are not in the 1.12 release, so I would
recommend using that), but you will not be able to build all the
tests. I have been able to build CellML2C (the code generation test)
but haven't tried the other test codes. I use clang for all
compilation/linking on OS X:
$ clang --version
Apple LLVM version 5.1 (clang-503.0.40) (based on LLVM 3.4svn)
Target: x86_64-apple-darwin13.1.0
Thread model: posix

The 1.12 binaries should work - not sure why you're getting that
error. I know I have linked my own code agains the 1.12 binaries
(using clang), but generally use my own build of the current trunk
code nowadays.

If needed, Alan Garny has the OpenCOR development environment all
nicely set up so you can probably extract the required binaries from
that source.


Cheers,
Andre.

On Mon, May 5, 2014 at 5:12 PM, Ivo Siekmann
<ivo.siekmann AT unimelb.edu.au>
wrote:
Hi CellMLers,

I'm trying to get the CellML API running on Mac and I ran into some
difficulties.

1) Compiling from source code:
a) This fails with clang (Apple LLVM version 5.1 (clang-503.0.40)),
apparently due to a forward declaration of the << operator in TestAssert.h
when attempting to build DOMTEST.cpp.o (I don't know much about this but
from some googling it seems to me that clang is stricter about the standard
than some other compilers. So it may see errors where other compilers
don't).

b) Compiling with gcc 4.8.2 goes through and passes the tests of
'CheckCodeGenerator' and 'CheckVACSS' but fails for 'RunTestBin'. I didn't
find out a lot more about how/why it failed.

2) Binaries:
I've downloaded the binaries and Mac OS X complains that the package can't
be opened "because it may be damaged or incomplete". Well, I can open the
package and look at its contents, so it may be possible to link the
libraries but I haven't tried.

Any help would be greatly appreciated.
Cheers
Ivo


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