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cdo-1.8.0 netcdf configure error

Added by namgu yeo almost 10 years ago

To configure,

./configure --with-netcdf=/usr/local/netcdf/363_pgi128 -prefix /home/yeong

but following error occured.

checking netcdf.h usability... yes
checking netcdf.h presence... yes
checking for netcdf.h... yes
checking for library containing nc_open... no
configure: error: Could not link to NetCDF library

I attached config.log
please help me ..

config.log (18.7 KB) config.log

Replies (4)

RE: cdo-1.8.0 netcdf configure error - Added by Ralf Mueller almost 10 years ago

I'm not sure, this is the right config.log file. the stdout of the configure run does not fit to it. Essentially there is not netcdf-test performed in the config.log

RE: cdo-1.8.0 netcdf configure error - Added by namgu yeo almost 10 years ago

I updated config.log file..
please recheck the error.

RE: cdo-1.8.0 netcdf configure error - Added by Ralf Mueller almost 10 years ago

here is the interesting part

configure:19035: gcc -std=gnu99 -o conftest -g -O2 -fopenmp  -I/usr/local/netcdf/363_pgi128/include  -L/usr/local/netcdf/363_pgi128/lib  conftest.c -lnetcdf   -lm  >&5
/usr/local/netcdf/363_pgi128/lib/libnetcdf.a(putget.o): In function `nc_put_vara_text':
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5056: undefined reference to `__builtin_alloca'
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5056: undefined reference to `__builtin_alloca'
/usr/local/netcdf/363_pgi128/lib/libnetcdf.a(putget.o): In function `nc_put_vara_uchar':
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5163: undefined reference to `__builtin_alloca'
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5163: undefined reference to `__builtin_alloca'
/usr/local/netcdf/363_pgi128/lib/libnetcdf.a(putget.o): In function `nc_put_vara_schar':
/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5269: undefined reference to `__builtin_alloca'
/usr/local/netcdf/363_pgi128/lib/libnetcdf.a(putget.o):/etc/.setup/twkit/netcdf/netcdf-3.6.3/libsrc/./putget.c:5269: more undefined references to `__builtin_alloca' follow
collect2: ld returned 1 exit status

although your netcdf installation may be under /usr/local/netcdf/363_pgi128/ it seems to be build somewhere under /etc/.setup. do you build software as root?

I cannot recommend using such an old netcdf installation. if you insist to do so, use a dynamic version. AFAIK __builtin_alloca should have something to do with gcc, which brings to my last point: you use gcc-4.4.7. it was releases 4.5 years ago, so please update or use a different vendor with a newer release. It's not possible to maintain CDO wrt. such old environments. same is true for netcdf-3.6.3 from June 2008.

if updating is not possible, then conda might a way to go: see Anaconda.

hth
ralf

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