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Installation fails Ubuntu

Added by Marco Bacci over 1 year ago

After
./configure --with-netcdf=yes --with-eccodes=yes
make
fails with
/usr/bin/ld: cdo-cdo.o: undefined reference to symbol 'H5dont_atexit@@HDF5_SERIAL_1.8.7'
/usr/bin/ld: /lib/x86_64-linux-gnu/libhdf5_serial.so.103: error adding symbols: DSO missing from command line

Suggestions?

Full command that fails is:
/bin/bash ../libtool --tag=CXX --mode=link g++ -std=gnu++17 -g -O2 -fopenmp -pthread -L/usr/include/hdf5 -o cdo cdo-cdo.o cdo-Adisit.o cdo-Afterburner.o cdo-Arith.o cdo-Arithc.o cdo-Arithdays.o cdo-Arithlat.o cdo-Bitrounding.o cdo-Cat.o cdo-CDIread.o cdo-CDItest.o cdo-CDIwrite.o cdo-Change.o cdo-Change_e5slm.o cdo-Cloudlayer.o cdo-CMOR.o cdo-CMOR_lite.o cdo-CMOR_table.o cdo-Collgrid.o cdo-Command.o cdo-Comp.o cdo-Compc.o cdo-Complextorect.o cdo-Cond.o cdo-Cond2.o cdo-Condc.o cdo-Consecstat.o cdo-Copy.o cdo-DCW_util.o cdo-Dayarith.o cdo-Deltat.o cdo-Deltime.o cdo-Depth.o cdo-Derivepar.o cdo-Detrend.o cdo-Diff.o cdo-Distgrid.o cdo-Duplicate.o cdo-EOFs.o cdo-Eof3d.o cdo-EcaIndices.o cdo-EcaEtccdi.o cdo-Echam5ini.o cdo-Enlarge.o cdo-Enlargegrid.o cdo-Ensstat.o cdo-Ensstat3.o cdo-Ensval.o cdo-Eofcoeff.o cdo-Eofcoeff3d.o cdo-EstFreq.o cdo-Exprf.o cdo-FC.o cdo-Filedes.o cdo-Fillmiss.o cdo-Filter.o cdo-Fldrms.o cdo-Fldstat.o cdo-Fldstat2.o cdo-Fourier.o cdo-Gengrid.o cdo-Gradsdes.o cdo-Gridboxstat.o cdo-Gridcell.o cdo-Gridsearch.o cdo-Harmonic.o cdo-Hi.o cdo-Histogram.o cdo-Importamsr.o cdo-Importbinary.o cdo-Importcmsaf.o cdo-Importobs.o cdo-Importfv3grid.o cdo-Info.o cdo-Input.o cdo-Intgrid.o cdo-Intgridtraj.o cdo-Intlevel.o cdo-Intlevel3d.o cdo-Intntime.o cdo-Inttime.o cdo-Intyear.o cdo-Invert.o cdo-Invertlev.o cdo-Lic.o cdo-MapReduce.o cdo-Maskbox.o cdo-Mastrfu.o cdo-Math.o cdo-Merge.o cdo-Mergegrid.o cdo-Mergetime.o cdo-Merstat.o cdo-Monarith.o cdo-Mrotuv.o cdo-Mrotuvb.o cdo-NCL_wind.o cdo-Ninfo.o cdo-Nmldump.o cdo-Output.o cdo-Outputgmt.o cdo-Pack.o cdo-Pardup.o cdo-Pinfo.o cdo-Pressure.o cdo-Recttocomplex.o cdo-Regres.o cdo-Remap.o cdo-Remapweights.o cdo-Remapeta.o cdo-Remapstat.o cdo-Replace.o cdo-Replacevalues.o cdo-Rhopot.o cdo-Rotuv.o cdo-Runpctl.o cdo-Runstat.o cdo-Samplegrid.o cdo-Samplegridicon.o cdo-Seascount.o cdo-Seaspctl.o cdo-Seasstat.o cdo-Seasmonstat.o cdo-Selbox.o cdo-Selgridcell.o cdo-Select.o cdo-Selmulti.o cdo-Seloperator.o cdo-Selrec.o cdo-Selregion.o cdo-Selsurface.o cdo-Seltime.o cdo-Selvar.o cdo-Selyearidx.o cdo-Set.o cdo-Setattribute.o cdo-Setbox.o cdo-Setgrid.o cdo-Setgridcell.o cdo-Sethalo.o cdo-Setmiss.o cdo-Setpartab.o cdo-Setrcaname.o cdo-Settime.o cdo-Setzaxis.o cdo-Shiftxy.o cdo-Showinfo.o cdo-Showattribute.o cdo-Sinfo.o cdo-Smooth.o cdo-Sort.o cdo-Sorttimestamp.o cdo-Specinfo.o cdo-Spectral.o cdo-Spectrum.o cdo-Split.o cdo-Splitrec.o cdo-Splitsel.o cdo-Splittime.o cdo-Splityear.o cdo-Tee.o cdo-Templates.o cdo-Test.o cdo-Tests.o cdo-Timcount.o cdo-Timcumsum.o cdo-Timfill.o cdo-Timpctl.o cdo-Timselpctl.o cdo-Timselstat.o cdo-Timsort.o cdo-Timstat.o cdo-Timstat2.o cdo-Timstat3.o cdo-Tinfo.o cdo-Tocomplex.o cdo-Transpose.o cdo-Trend.o cdo-Trendarith.o cdo-Tstepcount.o cdo-Unpack.o cdo-Vargen.o cdo-Varrms.o cdo-Varsstat.o cdo-Vertintap.o cdo-Vertintgh.o cdo-Vertintml.o cdo-Vertintzs.o cdo-Vertstat.o cdo-Vertcum.o cdo-Vertwind.o cdo-Verifygrid.o cdo-Wct.o cdo-Wind.o cdo-WindTrans.o cdo-Writegrid.o cdo-Writerandom.o cdo-XTimstat.o cdo-Yeararith.o cdo-Yearmonstat.o cdo-Ydayarith.o cdo-Ydaypctl.o cdo-Ydaystat.o cdo-Ydrunpctl.o cdo-Ydrunstat.o cdo-Yhourarith.o cdo-Yhourstat.o cdo-Ymonarith.o cdo-Ymonpctl.o cdo-Ymonstat.o cdo-Yseaspctl.o cdo-Yseasstat.o cdo-Zonstat.o cdo-Maggraph.o cdo-Magplot.o cdo-Magvector.o cdo-template_parser.o cdo-results_template_parser.o cdo-magics_template_parser.o cdo-string_utilities.o cdo-cdo_magics_mapper.o libcdo.la ../libcdi/src/libcdi.la ../src/lib/yac/libyac.la ../src/lib/gradsdes/libgradsdes.la ../src/lib/ncl/libncl.la -leccodes -lnetcdf -lpthread -leccodes -lnetcdf -lpthread


Replies (6)

RE: Installation fails Ubuntu - Added by Marco Bacci over 1 year ago

Additional information:
dpkg -l | grep eccodes
ii libeccodes-data 2.16.0-1 all GRIB and BUFR enecoding/encoding software library - data
ii libeccodes-dev:amd64 2.16.0-1 amd64 GRIB and BUFR decoding/encoding software library (development)
ii libeccodes-tools 2.16.0-1 amd64 GRIB decoding/encoding software (utilities)
ii libeccodes0:amd64 2.16.0-1 amd64 GRIB and BUFR enecoding/encoding software library

dpkg -l | grep hdf5
ii hdf5-helpers 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - Helper tools
ii libhdf5-103:amd64 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - runtime files - serial version
ii libhdf5-cpp-103:amd64 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - C++ libraries
ii libhdf5-dev 1.10.4+repack-11ubuntu1 amd64 Hierarchical Data Format 5 (HDF5) - development files - serial version

dpkg -l | grep netcdf
ii libnetcdf-dev 1:4.7.3-1 amd64 creation, access, and sharing of scientific data
ii libnetcdf15:amd64 1:4.7.3-1 amd64 Interface for scientific data access to large binary data
ii netcdf-bin 1:4.7.3-1 amd64 Programs for reading and writing NetCDF files

Thanks!

RE: Installation fails Ubuntu - Added by Uwe Schulzweida over 1 year ago

Looks like the hdf5 library is not automatically found by netcdf. Try this:

LIBS="-lhdf5" ./configure --with-netcdf=yes --with-eccodes=yes
make

RE: Installation fails Ubuntu - Added by Estanislao Gavilan over 1 year ago

Hi Marco,

I also noticed that your hdf5 library path (-L/....) is set to the include subfolder inside usr. Should not it be the lib subfolder?

Regards,

Estanislao

RE: Installation fails Ubuntu - Added by Marco Bacci over 1 year ago

With this one:
export LIBS="-lhdf5"; ./configure --with-netcdf=yes --with-eccodes=yes
I had the same error as before.
Thank you very much for your support.
I will try to go ahead with just ./configure && make && make install # which runs

RE: Installation fails Ubuntu - Added by Marco Bacci over 1 year ago

Marco Bacci wrote in RE: Installation fails Ubuntu:

With this one:
LIBS="-lhdf5"; ./configure --with-netcdf=yes --with-eccodes=yes
I had the same error as before.
Thank you very much for your support.
I will try to go ahead with just ./configure && make && make install # which runs

RE: Installation fails Ubuntu - Added by Gianluca Falconi about 1 year ago

Ciao Marco, sei riuscito a trovare la soluzione? Ho il tuo stesso problema
Grazie

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