CDO

Hi Gianluca,

I cannot see the error you are having. Can you try to find the log file? Also, I noticed that your libraries are in the root directory. Could it be a permission problem? Most of the building issues are related with paths or not found libraries. If you can find the log file (blabla.log), we will be able to spot the problem

Kind regards,

Estanislao

Hi Estanislao,
First of all it cannot be a permission problem as I'm operating as root, also i cannot access a log as the "make" command doesn't generate any log but system response is what I reported in my previous message.

Kind Regards,
Gianluca

Hi Gianluca,

I am not sure if this is the issue, but that post says that you have to add that setting to CFLAGS and CXXFLAGS. Did you try to include "export CXXFLAGS=-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H"?

Kind regards,

Estanislao

hi!

Gianluca, you can call make V=1 instead of make for more output. uploading the config.log would also be helpful, because it describes the relevant parts of your system.

In general: Why do you compile CDO? Did you check an installation with conda instead?

Hi Estanislao, Ralf,
in the attachments you can find the config.log file.

I've tried to set the environment variable "CXXFLAGS=-DACCEPT_USE_OF_DEPRECATED_PROJ_API_H" and to use the "make V=1", and now the output is:

libtool: link: /opt/intel/oneapi/compiler/latest/linux/bin/intel64/icpc -std=gnu++17 -DACCEPT_USE_OF_DEPRECATED_PROJ_API_H -fopenmp -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-Query.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 -L/usr/local/netcdf4/lib -L/usr/local/lib -L/root/temp/proj-6.1.0/build/lib -L/root/temp/hdf5-1.8.22/build/lib ./.libs/libcdo.a ../libcdi/src/.libs/libcdi.a ../src/lib/yac/.libs/libyac.a ../src/lib/gradsdes/.libs/libgradsdes.a -L/root/temp/proj-5.0.0/build//lib ../src/lib/healpix/.libs/libhealpix.a /usr/local/lib/libproj.so /usr/local/netcdf4/lib/libnetcdf.so -lbz2 -lcurl /root/temp/hdf5-1.8.22/build/lib/libhdf5_hl.so /root/temp/hdf5-1.8.22/build/lib/libhdf5.so -lz -ldl /usr/local/lib/libsz.so -lm -lpthread -pthread -fopenmp -Wl,-rpath,/usr/local/lib -Wl,-rpath,/usr/local/netcdf4/lib -Wl,-rpath,/root/temp/hdf5-1.8.22/build/lib -Wl,-rpath,/usr/local/lib -Wl,-rpath,/usr/local/netcdf4/lib -Wl,-rpath,/root/temp/hdf5-1.8.22/build/lib
ld: warning: libhdf5_hl.so.8, needed by /usr/local/netcdf4/lib/libnetcdf.so, may conflict with libhdf5_hl.so.10
ld: warning: libhdf5.so.8, needed by /usr/local/netcdf4/lib/libnetcdf.so, may conflict with libhdf5.so.10
ld: warning: libhdf5_hl.so.8, needed by /usr/local/netcdf4/lib/libnetcdf.so, may conflict with libhdf5_hl.so.10
ld: warning: libhdf5.so.8, needed by /usr/local/netcdf4/lib/libnetcdf.so, may conflict with libhdf5.so.10
./.libs/libcdo.a(libcdo_la-grid_proj.o): In function `cdo_lcc_to_lonlat(int, unsigned long, double*, double*)':
grid_proj.cc:(.text+0x328e): undefined reference to `proj_errno_string'
grid_proj.cc:(.text+0x33db): undefined reference to `proj_errno_string'
./.libs/libcdo.a(libcdo_la-grid_proj.o): In function `cdo_stere_to_lonlat(int, unsigned long, double*, double*)':
grid_proj.cc:(.text+0x588e): undefined reference to `proj_errno_string'
grid_proj.cc:(.text+0x59db): undefined reference to `proj_errno_string'
./.libs/libcdo.a(libcdo_la-grid_proj.o): In function `cdo_sinu_to_lonlat(unsigned long, double*, double*)':
grid_proj.cc:(.text+0x65cf): undefined reference to `proj_errno_string'
./.libs/libcdo.a(libcdo_la-grid_proj.o):grid_proj.cc:(.text+0x720b): more undefined references to `proj_errno_string' follow
make[2]: *** [cdo] Error 1
make[2]: Leaving directory `/root/temp/cdo-2.1.1/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/root/temp/cdo-2.1.1/src'
make: *** [all-recursive] Error 1

P.S: a customer asked me to compile CDO, i don't know what they have to do with it; I can't install conda on this host, I've already tried for some pyhton packages but doesn't work as well and broke the entire host

1. CDO itseld needs netcdf
2. CDO can be build with direct hdf5 support (for a single operator)
3. netcdf itself needs hdf5 in case it is build with cdf4 support

In order to get this right, you need to use the indentical hdf5 version for netcdf AND cdo. I recommend removeing --with-hdf5 options from the configure call. I am sure you don't need it.

Regarding undefined reference to `proj_errno_string
For the sake of getting a working CDO binary, I would again drop the proj4 support for now. It might be that there is a version problem with proj, since your are using 5.0.0. Another option is to check different proj version, but you seem to do that already

Why can't you install conda?

Hi Ralf,

after changing hdf5 and removed proj the compilation completed successfully.

I don't know why I can't install conda, but the guy who has configured the system told me not install conda, in fact when I've tried it broke yum and other packages.

Thanks

alright - thx for posting the solution. good luck with the binary ;-)

cheers + a weekend
ralf