[Swarm-Support] more hdf5 problems

[paul box]

Hello Again

I have finally decided to bite the bullet and start learning how to
work with hdf5 files in swarm.  I have tried experimenting with an
example that marcus posted at an earlier date to this group (thanks,
marcus!):
http://www.swarm.org/pipermail/support/2005-May/014651.html

Can anybody please explain what's happening here?

I have imported a data set from the example into R, and saved it as an
hdf5 file, and then used the included swarm code to read and print out
the information.  The relevant code is included in the above message. 
The sample data file looks like this:

val1   val2
  222  32
  111  16

When saved as an hdf5 file, the output from h5dump looks like this:

yanajipa:~/Documents/swarm/marcustest paulbox$ /usr/local/hdf5_1.6.1/bin/h5dump
test.hdf
HDF5 "test.hdf" {
GROUP "/" {
   DATASET "data" {
      DATATYPE  H5T_COMPOUND {
         H5T_STD_I32BE "val1";
         H5T_STD_I32BE "val2";
      }
      DATASPACE  SIMPLE { ( 2 ) / ( 2 ) }
      DATA {
         {
            222,
            32
         },
         {
            111,
            16
         }
      }
      ATTRIBUTE "type" {
         DATATYPE  H5T_STRING {
               STRSIZE 5;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
         DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
         DATA {
            "List"
         }
      }
      ATTRIBUTE "component-type" {
         DATATYPE  H5T_STRING {
               STRSIZE 8;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
         DATASPACE  SIMPLE { ( 1 ) / ( 1 ) }
         DATA {
            "MyClass"
         }
      }
      ATTRIBUTE "row.names" {
         DATATYPE  H5T_STRING {
               STRSIZE 2;
               STRPAD H5T_STR_NULLTERM;
               CSET H5T_CSET_ASCII;
               CTYPE H5T_C_S1;
            }
         DATASPACE  SIMPLE { ( 2 ) / ( 2 ) }
         DATA {
            "1", "2"
         }
      }
   }
}
}

When I run the code above, I determined via gdb that the program
complains about the following lines (I have added a printf in there):

   vp1 = [[[[VarProbe createBegin: globalZone]
              setProbedClass: class]
             setProbedVariable: "val1"]
            createEnd];

    printf ("\t in between setProbes...\n");

    vp2 = [[[[VarProbe createBegin: globalZone]
              setProbedClass: class]
             setProbedVariable: "val2"]
            createEnd];

and crashes at the line where 'probeAsInt' is called.



The output from the program:

yanajipa:~/Documents/swarm/marcustest paulbox$ ./input
*** event raised for warning: WarningMessage
*** function: -[VarProbe setProbedVariable:](), file: ../../../../src/objectbase
/VarProbe.m, line: 52
It is an error to reset the variable
*** execution continuing...
        in between setProbes...
*** event raised for warning: WarningMessage
*** function: -[VarProbe setProbedVariable:](), file: ../../../../src/objectbase
/VarProbe.m, line: 52
It is an error to reset the variable
*** execution continuing...
Bus error


The gdb backtrace, just in case:

yanajipa:~/Documents/swarm/marcustest paulbox$ gdb input
GNU gdb 5.3-20030128 (Apple version gdb-309) (Thu Dec  4 15:41:30 GMT 2003)
Copyright 2003 Free Software Foundation, Inc.
GDB is free software, covered by the GNU General Public License, and you are
welcome to change it and/or distribute copies of it under certain conditions.
Type "show copying" to see the conditions.
There is absolutely no warranty for GDB.  Type "show warranty" for details.
This GDB was configured as "powerpc-apple-darwin".
Reading symbols for shared libraries ......... done
(gdb) r
Starting program: /Users/paulbox/Documents/swarm/marcustest/input
Reading symbols for shared libraries ++.... done
*** event raised for warning: WarningMessage
*** function: -[VarProbe setProbedVariable:](), file:
../../../../src/objectbase/VarProbe.m, line: 52
It is an error to reset the variable
*** execution continuing...
*** event raised for warning: WarningMessage
*** function: -[VarProbe setProbedVariable:](), file:
../../../../src/objectbase/VarProbe.m, line: 52
It is an error to reset the variable
*** execution continuing...

Program received signal EXC_BAD_ACCESS, Could not access memory.
objc_probe_as_int.63 (probedType=0x0, p=0x450c68) at
../../../../src/objectbase/VarProbe.m:487
487     ../../../../src/objectbase/VarProbe.m: No such file or directory.
        in ../../../../src/objectbase/VarProbe.m
(gdb) bt
#0  objc_probe_as_int.63 (probedType=0x0, p=0x450c68) at
../../../../src/objectbase/VarProbe.m:487
#1  0x00002ac4 in main (argc=0, argv=0x450c68) at main.m:38
(gdb)

--
//////////////////////////
// Paul Box
// Alice Springs, NT  Australia
//