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@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@aei.mpg.de wrote:
On 12 Apr 2016, at 20:01, Bernard Kelly physicsbeany@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