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

[Barry Wardell]

Answering Ian's question: I tested with the release versions of
SimulationTools (1.0.0) and h5mma (1.2.0) using the latest version of OS X
(10.11.4) and Mathematica (10.4.0).

For debugging, you may have more success starting h5mma from the command
line and then connecting to the executable from Mathematica. See
https://bitbucket.org/simulationtools/h5mma/wiki/Debugging for
instructions. As well as being able to use a debugger, this will enable you
to see any standard output that may be printed by the HDF5 library.

On Tue, Apr 12, 2016 at 7:45 PM, Bernard Kelly <physicsbeany at gmail.com>
wrote:

> 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:
>
>
> /Library/Caches/com.apple.xbs/Binaries/Metal/Metal-56.6~1/TempContent/Objects/Metal.build/Framework.build/Objects-normal/x86_64/MTLArgument.o
> [...]
>
> 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
> /usr/lib/system/libsystem_kernel.dylib
> (gdb) continue
> Continuing.
> [Inferior 1 (process 40825) exited normally]
> (gdb) backtrace
> No stack.
> ------------------------------------------------
>
> Presumably that first line might point to something, but I don't know what.
>
> B
>
> 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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