[Users] SimulationTools/h5mma: Unable to communicate with closed link

Bernard Kelly physicsbeany at gmail.com
Tue Apr 12 13:45:10 CDT 2016

Nice idea.

The first thing I notice when loading h5mma is that gdb (now ggdb BTW,
and I have to "sudo" for this purpose as well) generates an assload of
Warnings of nonexistent files:


In fact, the directory /Library/Caches/com.apple.xbs doesn't exist on
my system. I wonder if this is related to my ultimate problem?

Moving on, the failure when using ImportHDF5 appears to exit
"cleanly", leaving no backtrace:

0x00007fff92f9b07a in select$DARWIN_EXTSN () from
(gdb) continue
[Inferior 1 (process 40825) exited normally]
(gdb) backtrace
No stack.

Presumably that first line might point to something, but I don't know what.


On 12 April 2016 at 14:11, Ian Hinder <ian.hinder at aei.mpg.de> wrote:
> On 12 Apr 2016, at 20:01, Bernard Kelly <physicsbeany at gmail.com> wrote:
> Hi Ian.
> Thanks; I'm trying the compilation now, but am failing with a linking
> error I've encountered lately: "Undefined symbols for architecture
> x86_64". This seems to be an issue with MacPorts gcc compilers. I
> don't know if my MacPorts installation is borked, but I can't compile
> this right now.
> ... so any additional ideas on the precompiled h5mma binary are appreciated.
> Maybe you could try with homebrew?
> The only thing I can think for the precompiled binary is to attach a
> debugger to it.  h5mma should be loaded when you load SimulationTools; it
> will appear as a process in "ps".  You could attach gdb:
> /opt/local/libexec/gnubin/gdb --pid $(pgrep h5mma)
> and then type "continue".  Now, evaluate the ImportHDF5 expression from
> Mathematica. With any luck, you will get a backtrace in gdb when h5mma
> crashes.  I wonder if the problem is related to the executable being
> compiled on an earlier version of OS X.
> --
> Ian Hinder
> http://members.aei.mpg.de/ianhin

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