installation problem: compiling cdo 1.9.6 with --enable-cdi-lib fails

Added by Natalja Rakowsky about 6 years ago

It is my first visit in this forum, and I hope, it is at the right place here. Or is it so specific that I should move to "Issues" immediately?

With cdo 1.9.5, everything works fine. I have never had any issues installing cdo on our Linux cluster (CentOS, now 7.5) so far. Nicht geschimpft ist genug gelobt

But now, with gcc 4.8.5 (also tried with gcc 7.4.0, same issue) and our own installation of netcdf, hdf5, eccodes, grib_api:

Configure with

export ECCDIR=/global/AWIsoft/eccodes/2.8.0
export UDUNITSDIR=/global/AWIsoft/udunits/2.2.26
export NETCDFDIR=/global/AWIsoft/netcdf/4.6.1_gnu
export HDF5DIR=/global/AWIsoft/hdf5/1.10.2_gnu
export GRIBDIR=/global/AWIsoft/grib_api/1.28.0
export PROJDIR=/global/AWIsoft/proj/5.1.0

LDFLAGS="-L$ECCDIR/lib -Wl,-rpath=$ECCDIR/lib -Wl,-rpath=$UDUNITSDIR/lib -Wl,-rpath=$NETCDFDIR/lib -Wl,-rpath=HDF5DIR/lib -Wl,-rpath,$GRIBDIR/lib -Wl,-rpath,$PROJDIR/lib" CXXFLAGS="-fpic" CFLAGS="-fpic" FFLAGS="-fpic" ./configure --prefix=/global/AWIsoft/cdo/1.9.6 --with-gnu-ld --with-fftw3 --with-pic --with-hdf5=$HDF5DIR --with-proj=$PROJDIR --with-netcdf=$NETCDFDIR --enable-python --with-eccodes=$ECCDIR --with-udunits2=$UDUNITSDIR --enable-cdi-lib --enable-all-static --with-grib_api=$GRIBDIR --enable-grib

works, expected output. Compilation starts fine, too, but

[...]
libtool: link: g++ -fpic -Wl,-rpath=/global/AWIsoft/eccodes/2.8.0/lib -Wl,-rpath=/global/AWIsoft/udunits/2.2.26/lib -Wl,-rpath=/global/AWIsoft/netcdf/4.6.1_gnu/lib -Wl,-rpath=HDF5DIR/lib -Wl,-rpath -Wl,/global/AWIsoft/grib_api/1.28.0/lib -Wl,-rpath -Wl,/global/AWIsoft/proj/5.1.0/lib -Wl,-rpath=/global/AWIsoft/eccodes/2.8.0/lib -Wl,-rpath=/global/AWIsoft/udunits/2.2.26/lib -Wl,-rpath=/global/AWIsoft/netcdf/4.6.1_gnu/lib -Wl,-rpath=HDF5DIR/lib -Wl,-rpath -Wl,/global/AWIsoft/grib_api/1.28.0/lib -Wl,-rpath -Wl,/global/AWIsoft/proj/5.1.0/lib -o .libs/CdiInfo CdiInfo.o -L/global/AWIsoft/netcdf/4.6.1_gnu/lib -L/global/AWIsoft/hdf5/1.10.2_gnu/lib -L/global/AWIsoft/grib_api/1.28.0/lib -L/global/AWIsoft/eccodes/2.8.0/lib ./.libs/libcdipp.a /global/AWIbuild/cdo/cdo-1.9.6/libcdi/src/.libs/libcdi.so -leccodes /global/AWIsoft/netcdf/4.6.1_gnu/lib/libnetcdf.so /global/AWIsoft/hdf5/1.10.2_gnu/lib/libhdf5_hl.so /global/AWIsoft/hdf5/1.10.2_gnu/lib/libhdf5.so -ldl -lz -lcurl -lm -luuid -pthread -Wl,-rpath -Wl,/global/AWIsoft/cdo/1.9.6/lib -Wl,-rpath -Wl,/global/AWIsoft/netcdf/4.6.1_gnu/lib -Wl,-rpath -Wl,/global/AWIsoft/hdf5/1.10.2_gnu/lib
/global/AWIbuild/cdo/cdo-1.9.6/libcdi/src/.libs/libcdi.so: undefined reference to `strIsEqual'
collect2: error: ld returned 1 exit status
make²: * [CdiInfo] Error 1
make²: Leaving directory `/global/AWIbuild/cdo/cdo-1.9.6/libcdi/interfaces'
make¹: [all-recursive] Error 1
make¹: Leaving directory `/global/AWIbuild/cdo/cdo-1.9.6/libcdi'
make: ** [all-recursive] Error 1

If I compare to cdo-1.9.5, strIsEqual is new in 1.9.6. It appears quite often in libcdi/src/cdilib.c and libcdi/src/stream_cdf_i.c. At the first glance, I cannot spot any obvious bug, but, well, my knowledge of C is limited. Time to hand it over to the experts!

Shall I attach config.log and the output of make?

Replies (5)

RE: installation problem: compiling cdo 1.9.6 with --enable-cdi-lib fails - Added by Uwe Schulzweida about 6 years ago

Unfortunately the declaration of strIsEqual() is not 100% correct. This function will be inline expanded only if the compiler optimization (-O) is enabled. Otherwise the keyword static is necessary:

static inline bool
strIsEqual(const char *x, const char *y)

RE: installation problem: compiling cdo 1.9.6 with --enable-cdi-lib fails - Added by Natalja Rakowsky about 6 years ago

Thank you for the very fast reply! Adding optimization is generally a good idea, why did I miss that at all?! Thanks to this minor strIsEqual-bug, we get faster cdo in 1.9.6 and all following releases!

RE: installation problem: compiling cdo 1.9.6 with --enable-cdi-lib fails - Added by Matt Thompson about 6 years ago

Uwe,

I believe I just hit this issue or something similar:

../src/.libs/libcdi.a(stream_cdf_i.o): In function `cdf_time_dimid':
stream_cdf_i.c:(.text+0x12ff): undefined reference to `strIsEqual'
stream_cdf_i.c:(.text+0x1319): undefined reference to `strIsEqual'
../src/.libs/libcdi.a(stream_cdf_i.o): In function `scan_hybrid_formulaterms':
stream_cdf_i.c:(.text+0x215a): undefined reference to `strIsEqual'
stream_cdf_i.c:(.text+0x2185): undefined reference to `strIsEqual'
stream_cdf_i.c:(.text+0x21b0): undefined reference to `strIsEqual'
../src/.libs/libcdi.a(stream_cdf_i.o):stream_cdf_i.c:(.text+0x21db): more undefined references to `strIsEqual' follow
collect2: error: ld returned 1 exit status

What is the preferred fix? Should I edit files in my cdo source tree?

Thanks,
Matt

RE: installation problem: compiling cdo 1.9.6 with --enable-cdi-lib fails - Added by Uwe Schulzweida almost 6 years ago

You can fix this problem by editing the file libcdi/src/cdi_int.h line 44, and change

inline bool
strIsEqual(const char *x, const char *y)

static inline bool
strIsEqual(const char *x, const char *y)

Another solution is to use the compiler flag -O to enable the optimization, but this is normally the default. Here is an example for the GNU C compiler:

./configure ...  CC=gcc CFLAGS="-g -O2" CXX=g++ CXXFLAGS="-g -O2"

RE: installation problem: compiling cdo 1.9.6 with --enable-cdi-lib fails - Added by Matt Thompson almost 6 years ago

Uwe,

Okay. I'll see about altering the source. I suppose it'll be fixed in 1.9.7, so it's temporary for now.

Thanks,
Matt

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