[netcdfgroup] Error while compiling netcdf with netcdf-4, hdf4 and hdf5

• To: netcdfgroup@xxxxxxxxxxxxxxxx
• Subject: [netcdfgroup] Error while compiling netcdf with netcdf-4, hdf4 and hdf5
• From: Ronald Opio <opioronald123@xxxxxxxxx>
• Date: Tue, 28 Sep 2021 11:32:22 +0300

Hello colleagues.

I am trying to install netcdf (4.1.3) with netcdf-4 enabled and with hdf4
(4.2.9) and hdf5 (1.8.12) but I get this error in the make stage:

/bin/bash ../libtool --tag=CC   --mode=link gcc  -g -O2
 -L/home/opio/wrf/libraries/hdf/lib -o ncgen3 main.o load.o escapes.o
getfill.o init.o genlib.o ncgentab.o ../liblib/libnetcdf.la  -lhdf5_hl
-lhdf5 -lm -lz
libtool: link: gcc -g -O2 -o ncgen3 main.o load.o escapes.o getfill.o
init.o genlib.o ncgentab.o  -L/home/opio/wrf/libraries/hdf/lib
../liblib/.libs/libnetcdf.a -L/home/opio/wrf/libraries/grib2/lib
/home/opio/wrf/libraries/hdf/lib/libhdf5_hl.so
/home/opio/wrf/libraries/hdf/lib/libhdf5.so -ldl -lm -lz -Wl,-rpath
-Wl,/home/opio/wrf/libraries/hdf/lib -Wl,-rpath
-Wl,/home/opio/wrf/libraries/hdf/lib
/usr/bin/ld: ../liblib/.libs/libnetcdf.a(libnetcdf4_la-nc4file.o): in
function `nc4_open_hdf4_file':
/home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2173: undefined
reference to `SDstart'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2177:
undefined reference to `SDfileinfo'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2197:
undefined reference to `SDattrinfo'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2211:
undefined reference to `SDreadattr'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2231:
undefined reference to `SDselect'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2237:
undefined reference to `SDgetinfo'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2256:
undefined reference to `SDgetfillvalue'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2333:
undefined reference to `SDattrinfo'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2347:
undefined reference to `SDreadattr'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2279:
undefined reference to `SDgetdimid'
/usr/bin/ld: /home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2281:
undefined reference to `SDdiminfo'
/usr/bin/ld: ../liblib/.libs/libnetcdf.a(libnetcdf4_la-nc4file.o): in
function `close_netcdf4_file':
/home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4file.c:2702: undefined
reference to `SDend'
/usr/bin/ld: ../liblib/.libs/libnetcdf.a(libnetcdf4_la-nc4var.o): in
function `nc4_get_hdf4_vara':
/home/opio/wrf/libraries/netcdf-4.1.3/libsrc4/nc4var.c:1358: undefined
reference to `SDreaddata'
collect2: error: ld returned 1 exit status
make[2]: *** [Makefile:370: ncgen3] Error 1
make[2]: Leaving directory '/home/opio/wrf/libraries/netcdf-4.1.3/ncgen3'
make[1]: *** [Makefile:551: all-recursive] Error 1
make[1]: Leaving directory '/home/opio/wrf/libraries/netcdf-4.1.3'
make: *** [Makefile:422: all] Error 2


I have read all existing solutions but none has worked for my case yet. I
kindly request help to solve it.


Ronald.

• Follow-Ups:
  • Re: [netcdfgroup] Error while compiling netcdf with netcdf-4, hdf4 and hdf5
    • From: Ed Hartnett