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ee509ff4f3
corresponding HDF5 operations. re: github issue https://github.com/Unidata/netcdf-c/issues/908 also in reference to https://github.com/pydata/xarray/issues/2004 The netcdf-c library has implemented the nc_get_vars and nc_put_vars operations as element at a time. This has resulted in very slow operation. This pr attempts to improve the situation for netcdf-4/hdf5 files by using the slab operations provided by the hdf5 library. The new implementation passes the get/put vars stride information down to the hdf5 slab operations. The result appears to improve performance significantly. Some simple tests on large 2-D arrays shows speedups in excess of 150. Misc. other changes: 1. fix bug in ncgen/semantics.c; using a list's allocated length instead of actual length. 2. Added a temporary hook in the netcdf library plus a performance test case (tst_varsperf.c) to estimate the speedup. After users have had some experience with this, I will remove it, probably after the 4.7 release.
52 lines
1012 B
Plaintext
52 lines
1012 B
Plaintext
# Test c output
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T=tst_varsperf
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#SRC=hdf5plugins/H5Zmisc.c
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#CMD=valgrind --leak-check=full
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#CMD=gdb --args
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#FILTER=H5Zmisc
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#FILTEROBJ=hdf5plugins/${FILTER}.o
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#PAR=1
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#SZIP=1
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CFLAGS = -Wall -Wno-unused-variable -Wno-unused-function -g -O0 -I.. -I../include
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LDFLAGS = ../liblib/.libs/libnetcdf.a -L/usr/local/lib -lhdf5_hl -lhdf5 -lz -ldl -lcurl -lm -lmfhdf -ldf
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ifdef PAR
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CC=mpicc
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LDFLAGS += -lmpich
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else
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CC=gcc
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endif
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ifdef SZIP
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LDFLAGS += -lsz -laec
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endif
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LLP=/usr/local/lib:${LD_LIBRARY_PATH}
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all:: cmp
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export LD_LIBRARY_PATH=${LLP}; export CFLAGS; export LDFLAGS; \
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${CMD} ./t ${ARGS}
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cmp::
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export LD_LIBRARY_PATH=${LLP}; export CFLAGS; export LDFLAGS; \
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${CC} -o t ${CFLAGS} ${T}.c ${SRC} ${FILTEROBJ} ${LDFLAGS}
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filter::
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${CC} ${CFLAGS} -c hdf5plugins/${FILTER}.c ${LDFLAGS}
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cpp::
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${CC} -E ${CFLAGS} ${T}.c > ${T}.txt
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H5=h5testszip
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EXT=testszip.nc
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h5::
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export LD_LIBRARY_PATH=${LLP}; export CFLAGS; export LDFLAGS; \
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${CC} -o h5 ${CFLAGS} ${H5}.c ${SRC} ${LDFLAGS}; \
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${CMD} ./h5 ${EXT}
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