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Incomplete plugin filters instalation #3055

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mannreis opened this issue Nov 25, 2024 · 0 comments
Open

Incomplete plugin filters instalation #3055

mannreis opened this issue Nov 25, 2024 · 0 comments

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@mannreis
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I believe the current CMake build is missing some plugin installation that were removed in https://github.com/Unidata/netcdf-c/pull/3034/files#diff-1abf564a84becf73b24c833a7300a9fcaf5ff9df6427cb54fd53b297806669a0L141

Using automake:

$ rm -f /usr/local/hdf5/lib/plugin/*.so
$ sudo make install
...
libtool: install: /usr/bin/install -c .libs/lib__nch5fletcher32.so /usr/local/hdf5/lib/plugin/lib__nch5fletcher32.so
libtool: install: /usr/bin/install -c .libs/lib__nch5fletcher32.lai /usr/local/hdf5/lib/plugin/lib__nch5fletcher32.la
libtool: install: /usr/bin/install -c .libs/lib__nch5shuffle.so /usr/local/hdf5/lib/plugin/lib__nch5shuffle.so
libtool: install: /usr/bin/install -c .libs/lib__nch5shuffle.lai /usr/local/hdf5/lib/plugin/lib__nch5shuffle.la
libtool: install: /usr/bin/install -c .libs/lib__nch5deflate.so /usr/local/hdf5/lib/plugin/lib__nch5deflate.so
libtool: install: /usr/bin/install -c .libs/lib__nch5deflate.lai /usr/local/hdf5/lib/plugin/lib__nch5deflate.la
libtool: install: /usr/bin/install -c .libs/lib__nch5szip.so /usr/local/hdf5/lib/plugin/lib__nch5szip.so
libtool: install: /usr/bin/install -c .libs/lib__nch5szip.lai /usr/local/hdf5/lib/plugin/lib__nch5szip.la
libtool: install: /usr/bin/install -c .libs/lib__nch5blosc.so /usr/local/hdf5/lib/plugin/lib__nch5blosc.so
libtool: install: /usr/bin/install -c .libs/lib__nch5blosc.lai /usr/local/hdf5/lib/plugin/lib__nch5blosc.la
libtool: install: /usr/bin/install -c .libs/lib__nch5zstd.so /usr/local/hdf5/lib/plugin/lib__nch5zstd.so
libtool: install: /usr/bin/install -c .libs/lib__nch5zstd.lai /usr/local/hdf5/lib/plugin/lib__nch5zstd.la
...
$ ls /usr/local/hdf5/lib/plugin/*.so
/usr/local/hdf5/lib/plugin/lib__nch5blosc.so  /usr/local/hdf5/lib/plugin/lib__nch5deflate.so     /usr/local/hdf5/lib/plugin/lib__nch5shuffle.so  /usr/local/hdf5/lib/plugin/lib__nch5zstd.so        /usr/local/hdf5/lib/plugin/lib__nczstdfilters.so
/usr/local/hdf5/lib/plugin/lib__nch5bzip2.so  /usr/local/hdf5/lib/plugin/lib__nch5fletcher32.so  /usr/local/hdf5/lib/plugin/lib__nch5szip.so     /usr/local/hdf5/lib/plugin/lib__nczhdf5filters.so

Using CMake:

$ rm -f /usr/local/hdf5/lib/plugin/*.so
$ sudo cmake --install .
...
-- Installing: /usr/local/hdf5/lib/plugin/lib__nch5bzip2.so
-- Installing: /usr/local/hdf5/lib/plugin/lib__nch5zstd.so
-- Installing: /usr/local/hdf5/lib/plugin/lib__nch5blosc.so
...
$ ls /usr/local/hdf5/lib/plugin/*.so
/usr/local/hdf5/lib/plugin/lib__nch5blosc.so  /usr/local/hdf5/lib/plugin/lib__nch5bzip2.so  /usr/local/hdf5/lib/plugin/lib__nch5zstd.so

The current state of this makes reading some pure Zarr dataset impossible. ncdump -v tas -L11 file:///var/tmp/ngc4008_P1D_0.zarr#mode=zarr,file fails here:

#0  NCZ_applyfilterchain (file=0x5555556f4f00, var=0x5555559049c0, chain=0x555555906160, inlen=308522, indata=0x55555597f3e0, outlenp=0x7ffffffc6168, outdatap=0x7ffffffc6160, encode=0) at /home/reis/repos/netcdf-c/libnczarr/zfilter.c:773
#1  0x00007ffff7d3b95a in get_chunk (cache=0x555555907570, entry=0x555555974e20) at /home/reis/repos/netcdf-c/libnczarr/zxcache.c:810
#2  0x00007ffff7d3a4ad in NCZ_read_cache_chunk (cache=0x555555907570, indices=0x55555597ee00, datap=0x7ffffffc6290) at /home/reis/repos/netcdf-c/libnczarr/zxcache.c:306
#3  0x00007ffff7d57a75 in readfromcache (source=0x555555907570, chunkindices=0x55555597ee00, chunkdatap=0x7ffffffc6290) at /home/reis/repos/netcdf-c/libnczarr/zwalk.c:717
#4  0x00007ffff7d569c6 in NCZ_transfer (common=0x7ffffffe8350, slices=0x7ffffffe0350) at /home/reis/repos/netcdf-c/libnczarr/zwalk.c:322
#5  0x00007ffff7d562c7 in NCZ_transferslice (var=0x5555559049c0, reading=1, start=0x7fffffff5ca0, count=0x7fffffff1ca0, stride=0x7fffffff7ca0, memory=0x55555597f1e0, typecode=5) at /home/reis/repos/netcdf-c/libnczarr/zwalk.c:181
#6  0x00007ffff7d54f27 in NCZ_get_vars (ncid=65537, varid=91, startp=0x555555707980, countp=0x555555704760, stridep=0x0, data=0x55555597f1e0, mem_nc_type=5) at /home/reis/repos/netcdf-c/libnczarr/zvar.c:2065
#7  0x00007ffff7d534ec in NCZ_get_vara (ncid=65537, varid=91, startp=0x555555707980, countp=0x555555704760, ip=0x55555597f1e0, memtype=5) at /home/reis/repos/netcdf-c/libnczarr/zvar.c:1441
#8  0x00007ffff7c826ae in NC_get_vara (ncid=65537, varid=91, start=0x555555707980, edges=0x555555704760, value=0x55555597f1e0, memtype=5) at /home/reis/repos/netcdf-c/libdispatch/dvarget.c:104
#9  0x00007ffff7c83ce4 in nc_get_vara (ncid=65537, varid=91, startp=0x555555707980, countp=0x555555704760, ip=0x55555597f1e0) at /home/reis/repos/netcdf-c/libdispatch/dvarget.c:755
#10 0x000055555555fd2c in print_rows (level=1, ncid=65537, varid=91, vp=0x7fffffffc0e0, vdims=0x55555594aa20, cor=0x555555707980, edg=0x555555704760, vals=0x55555597f1e0, marks_pending=0) at /home/reis/repos/netcdf-c/ncdump/vardata.c:483
#11 0x000055555555fc47 in print_rows (level=0, ncid=65537, varid=91, vp=0x7fffffffc0e0, vdims=0x55555594aa20, cor=0x55555597f1a0, edg=0x55555597f1c0, vals=0x55555597f1e0, marks_pending=0) at /home/reis/repos/netcdf-c/ncdump/vardata.c:468
#12 0x00005555555602a8 in vardata (vp=0x7fffffffc0e0, vdims=0x55555594aa20, ncid=65537, varid=91) at /home/reis/repos/netcdf-c/ncdump/vardata.c:590
#13 0x000055555555d3c2 in do_ncdump_rec (ncid=65537, path=0x0) at /home/reis/repos/netcdf-c/ncdump/ncdump.c:1973
#14 0x000055555555d650 in do_ncdump_rec (ncid=65536, path=0x55555559f940 "file:///var/tmp/ngc4008_P1D_0.zarr#mode=zarr,file") at /home/reis/repos/netcdf-c/ncdump/ncdump.c:2015
#15 0x000055555555d7f3 in do_ncdump (ncid=65536, path=0x55555559f940 "file:///var/tmp/ngc4008_P1D_0.zarr#mode=zarr,file") at /home/reis/repos/netcdf-c/ncdump/ncdump.c:2056
#16 0x000055555555ea50 in main (argc=1, argv=0x7fffffffdd28) at /home/reis/repos/netcdf-c/ncdump/ncdump.c:2505
mannreis added a commit to mannreis/netcdf-c that referenced this issue Nov 25, 2024
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