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Make HDF5.jl compatible with profilers that use LD_PRELOAD #791

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Make HDF5.jl compatible with profilers that use LD_PRELOAD #791

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e65a476
libversion uses Ref
lyon-fnal Dec 31, 2020
0e1b1e7
Remove explicit library name in ccall
lyon-fnal Dec 31, 2020
6332a0b
Don't give explicit library in ccall
lyon-fnal Dec 31, 2020
dd1d33e
hdf5 libraries are loaded in __init__
lyon-fnal Dec 31, 2020
cd71097
Don't use the libversion constant; call fcn
lyon-fnal Dec 31, 2020
3a01b02
Use handle to hdf5 shared object
lyon-fnal Dec 31, 2020
08ff5be
Merge branch 'master' of https://github.com/JuliaIO/HDF5.jl
lyon-fnal Jan 21, 2021
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2 changes: 1 addition & 1 deletion deps/build.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ else
if libhdf5_size != filesize(Libdl.dlpath(libhdf5))
error("HDF5 library has changed, re-run Pkg.build(\\\"HDF5\\\")")
end
if libversion < v"1.10.4"
if libversion[] < v"1.10.4"
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libversion is now set in HDF5.__init__ so it needs to be a Ref.

error("HDF5.jl requires ≥ v1.10.4 of the HDF5 library.")
end
end
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2 changes: 1 addition & 1 deletion gen/bind_generator.jl
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Expand Up @@ -159,7 +159,7 @@ function _bind(__module__, __source__, sig::Expr, err::Union{String,Expr,Nothing
statsym = Symbol("#status#") # not using gensym() to have stable naming

# The ccall(...) itself
cfunclib = Expr(:tuple, quot(cfuncname), lib)
cfunclib = Expr(:quote, cfuncname)
ccallexpr = :(ccall($cfunclib, $rettype, ($(argt...),), $(args...)))

# The error condition expression
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11 changes: 10 additions & 1 deletion src/HDF5.jl
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Expand Up @@ -38,6 +38,9 @@ dataspace, datatype
# H5DataStore, Attribute, File, Group, Dataset, Datatype, Opaque,
# Dataspace, Object, Properties, VLen, ChunkStorage, Reference

# Define the handles to the shared objects (these will be set in __init__)
const dlhdf5 = Ref{Ptr{Nothing}}(0)
const dlhdf5_hl = Ref{Ptr{Nothing}}(0)

const depsfile = joinpath(dirname(@__DIR__), "deps", "deps.jl")
if isfile(depsfile)
Expand Down Expand Up @@ -1899,7 +1902,7 @@ h5t_get_native_type(type_id) = h5t_get_native_type(type_id, H5T_DIR_ASCEND)

# Functions that require special handling

const libversion = h5_get_libversion()
const libversion = Ref{VersionNumber}(v"0.0.0")

vlen_get_buf_size(dset::Dataset, dtype::Datatype, dspace::Dataspace) = h5d_vlen_get_buf_size(dset, dtype, dspace)

Expand Down Expand Up @@ -1990,8 +1993,14 @@ For the second condition to be true, MPI.jl must be imported before HDF5.jl.
has_parallel() = HAS_PARALLEL[]

function __init__()
# Load the shared objects (dlhdf5 Ref declared way above)
dlhdf5[] = Libdl.dlopen(libhdf5, Libdl.RTLD_GLOBAL | Libdl.RTLD_LAZY)
dlhdf5_hl[] = Libdl.dlopen(libhdf5_hl, Libdl.RTLD_GLOBAL | Libdl.RTLD_LAZY)

libversion[] = h5_get_libversion()
check_deps()


# disable file locking as that can cause problems with mmap'ing
if !haskey(ENV, "HDF5_USE_FILE_LOCKING")
ENV["HDF5_USE_FILE_LOCKING"] = "FALSE"
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396 changes: 198 additions & 198 deletions src/api.jl
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6 changes: 3 additions & 3 deletions src/api_helpers.jl
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Expand Up @@ -239,7 +239,7 @@ end
See `libhdf5` documentation for [`H5Oopen`](https://portal.hdfgroup.org/display/HDF5/H5P_GET_CLASS_NAME).
"""
function h5p_get_class_name(pcid)
pc = ccall((:H5Pget_class_name, libhdf5), Ptr{UInt8}, (hid_t,), pcid)
pc = ccall(:H5Pget_class_name, Ptr{UInt8}, (hid_t,), pcid)
if pc == C_NULL
error("Error getting class name")
end
Expand Down Expand Up @@ -310,7 +310,7 @@ end
See `libhdf5` documentation for [`H5Oopen`](https://portal.hdfgroup.org/display/HDF5/H5T_GET_MEMBER_NAME).
"""
function h5t_get_member_name(type_id, index)
pn = ccall((:H5Tget_member_name, libhdf5), Ptr{UInt8}, (hid_t, Cuint), type_id, index)
pn = ccall(:H5Tget_member_name, Ptr{UInt8}, (hid_t, Cuint), type_id, index)
if pn == C_NULL
error("Error getting name of compound datatype member #", index)
end
Expand All @@ -325,7 +325,7 @@ end
See `libhdf5` documentation for [`H5Oopen`](https://portal.hdfgroup.org/display/HDF5/H5T_GET_TAG).
"""
function h5t_get_tag(type_id)
pc = ccall((:H5Tget_tag, libhdf5), Ptr{UInt8}, (hid_t,), type_id)
pc = ccall(:H5Tget_tag, Ptr{UInt8}, (hid_t,), type_id)
if pc == C_NULL
error("Error getting opaque tag")
end
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5 changes: 2 additions & 3 deletions src/mpio.jl
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Expand Up @@ -2,9 +2,8 @@ using .MPI
import Libdl

# Check whether the HDF5 libraries were compiled with parallel support.
HAS_PARALLEL[] = Libdl.dlopen(libhdf5) do lib
Libdl.dlsym(lib, :H5Pget_fapl_mpio, throw_error=false) !== nothing
end
HAS_PARALLEL[] = Libdl.dlsym(dlhdf5[], :H5Pget_fapl_mpio, throw_error=false) !== nothing


# Low-level MPI handles.
const MPIHandle = Union{MPI.MPI_Comm, MPI.MPI_Info}
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2 changes: 1 addition & 1 deletion test/plain.jl
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Expand Up @@ -709,7 +709,7 @@ dspace_scal = HDF5.Dataspace(HDF5.h5s_create(HDF5.H5S_SCALAR))
dspace_norm = dataspace((100, 4))
dspace_maxd = dataspace((100, 4), max_dims = (256, 4))
dspace_slab = HDF5.hyperslab(dataspace((100, 4)), 1:20:100, 1:4)
if HDF5.libversion ≥ v"1.10.7"
if HDF5.h5_get_libversion() ≥ v"1.10.7"
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Call the function instead of using the const global (to do the latter, it would need to be HDF5.libversion[] since it's a Ref).

dspace_irrg = HDF5.Dataspace(HDF5.h5s_combine_select(
HDF5.h5s_copy(dspace_slab), HDF5.H5S_SELECT_OR,
HDF5.hyperslab(dataspace((100, 4)), 2, 2)))
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