use debug build of Hdf5 for development

[davidslac]

Getting seg faults when reading, checking Hdf5 invariant conditions should alert me. I've built a debug version of hdf5 1.10, I'm doing

./configure --prefix=$PREFIX \
    --with-szlib=$PREFIX \
    --enable-threadsafe \
    --enable-unsupported \
    --enable-cxx \
    --enable-build-mode=debug \
    --enable-trace \
--enable-parallel 

Now need to change the lc2 conda environment I'm using:

(lc2) pslogin7d: /reg/neh/home4/davidsch/rel/lc2-hdf5-110 $ conda upgrade hdf5
Fetching package metadata .......................
Solving package specifications: .

Package plan for installation in environment /reg/neh/home/davidsch/.conda/envs/lc2:

The following packages will be UPDATED:

    h5py:    2.7.0rc2-py35_hdf5110_1 file:///reg/g/psdm/sw/conda/channels/system-rhel7 --> 2.7.0rc2-py35_hdf5110_4 file:///reg/g/psdm/sw/conda/channels/system-rhel7
    hdf5:    1.10.0-openmpi_1        file:///reg/g/psdm/sw/conda/channels/system-rhel7 --> 1.10.0-openmpi_dbg_4    file:///reg/g/psdm/sw/conda/channels/system-rhel7
    mpi4py:  2.0.0-py35_openmpi_102  file:///reg/g/psdm/sw/conda/channels/system-rhel7 --> 2.0.0-py35_openmpi_104  file:///reg/g/psdm/sw/conda/channels/system-rhel7

The following packages will be DOWNGRADED due to dependency conflicts:

    openmpi: 2.0.1-lsf_verbs_1       file:///reg/g/psdm/sw/conda/channels/system-rhel7 --> 1.10.6-lsf_verbs_1      file:///reg/g/psdm/sw/conda/channels/system-rhel7

Proceed ([y]/n)? y

[davidslac]

I ran into a bug with the invariants, I thought it was only the H5Oappend function, but I think it is any kind of writing, need to undo this

[davidslac]

did this

conda install hdf5=1.10.0=openmpi_1 h5py=2.7.0rc2=py35_hdf5110_1 mpi4py=2.0.0=py35_openmpi_102 openmpi=2.0.1=lsf_verbs_1

no, now the program seg faults again