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Use set_preferences to set system hdf5 #111

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Merged
sloede merged 6 commits into from
Sep 12, 2023
Merged

Use set_preferences to set system hdf5 #111

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81d0b87
use set_preferences to set system hdf5
benegee Sep 12, 2023
8109789
Remove `LD_PRELOAD` for libcurl
sloede Sep 12, 2023
021ff8f
Fancy LD_PRELOAD dancing
sloede Sep 12, 2023
933eb09
Continue the LD_PRELOAD dance
sloede Sep 12, 2023
ed91195
Properly unset LD_PRELOAD in init script only when running in CI
sloede Sep 12, 2023
4225f45
Update utils/libtrixi-init-julia
benegee Sep 12, 2023
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1 change: 1 addition & 0 deletions .github/workflows/ci.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -160,6 +160,7 @@ jobs:
check_bounds: 'auto'
env:
LIBTRIXI_DEBUG: all
LD_PRELOAD: "" # Disable preloading libcurl.so since it does not work with the JLL-provided libhdf5.so

- name: Run examples
run: |
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29 changes: 18 additions & 11 deletions utils/libtrixi-init-julia
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Expand Up @@ -314,17 +314,24 @@ echo

# Set system HDF5 library
echo "Use system HDF5 for Julia... "
JULIA_HDF5_PATH="$hdf5_libdir" JULIA_DEPOT_PATH="$julia_depot" $julia_exec --project=. \
-e 'using Pkg; Pkg.build("HDF5"; verbose = true)'
# Note: The following code replaces the previous line for HDF5 v0.17+, which has not yet
# been released at the time of writing
# -e "
# using Preferences, UUIDs
# set_preferences!(UUID(\"f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f\"),
# \"libhdf5\" => \"$hdf5_library\",
# \"libhdf5_hl\" => \"$hdf5_hl_library\",
# force = true)
# "
# Disable preloading libcurl.so if it has been set when running within the GitHub runner,
# since it does not work with the JLL-provided libhdf5.so
if [ "$CI" = "true" ] && [ -n "$LD_PRELOAD" ]; then
store_ld_preload="$LD_PRELOAD"
LD_PRELOAD=""
fi
JULIA_DEPOT_PATH="$julia_depot" $julia_exec --project=. \
-e "
using Preferences, UUIDs
set_preferences!(UUID(\"f67ccb44-e63f-5c2f-98bd-6dc0ccc4ba2f\"),
\"libhdf5\" => \"$hdf5_library\",
\"libhdf5_hl\" => \"$hdf5_hl_library\",
force = true)
"
# Restore LD_PRELOAD if it had been set before
if [ "$CI" = "true" ] && [ -n "$store_ld_preload" ]; then
LD_PRELOAD="$store_ld_preload"
fi
[ $? -eq 0 ] || die "could not configure system HDF5 library for Julia"
echo

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