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Ubuntu 18.04 Makefile problem and gradspy undefined symbol #7

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woodbri opened this issue Jan 9, 2021 · 1 comment · May be fixed by #12
Open

Ubuntu 18.04 Makefile problem and gradspy undefined symbol #7

woodbri opened this issue Jan 9, 2021 · 1 comment · May be fixed by #12

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@woodbri
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woodbri commented Jan 9, 2021

Look like I've run into two issues with building on Ubuntu 18.04.

  1. It looks like the Makefile linking the grads command is failing to add -ludunits2
PKG_CONFIG=/usr/bin/pkg-config ./configure --prefix=/usr/local \
--with-hdf5-include=/usr/include/hdf5/serial \
--with-hdf5-libdir=/usr/lib/x86_64-linux-gnu \
--with-netcdf-include=/usr/include \
--with-netcdf-libdir=/usr/lib/x86_64-linux-gnu \
--with-hdf4-include=/usr/include/hdf \
--with-hdf4-libdir=/usr/lib \
--with-udunits2-include=/usr/lib \
--with-udunits2-libdir=/usr/lib/x86_64-linux-gnu

# works ok but make fails like this:

gcc   -g -O2 -rdynamic   -o grads grads.o gxsubs.o gxmeta.o gxchpl.o gxcntr.o gxstrm.o gxdb.o gxwmap.o gxshad.o gxshad2.o gaexpr.o gafunc.o gautil.o gagx.o gscrpt.o gamach.o gatxt.o galloc.o gaddes.o gacfg.o gaio.o gauser.o gasdf.o bufrstn.o gabufr.o gabufrtbl.o   -L..//lib      -lreadline -lgrib2c -ljasper -lpng15 -lz  -lhdf5 -ljpeg -lz  -lnetcdf  -lgeotiff -ltiff  -lshp    -ldl  -lm
gasdf.o: In function `initUnitSys':
/home/woodbri/work/GrADS-jam/src/gasdf.c:273: undefined reference to `ut_ignore'
/home/woodbri/work/GrADS-jam/src/gasdf.c:273: undefined reference to `ut_set_error_message_handler'
/home/woodbri/work/GrADS-jam/src/gasdf.c:276: undefined reference to `ut_read_xml'
/home/woodbri/work/GrADS-jam/src/gasdf.c:281: undefined reference to `ut_get_unit_by_name'
/home/woodbri/work/GrADS-jam/src/gasdf.c:285: undefined reference to `ut_get_unit_by_name'
/home/woodbri/work/GrADS-jam/src/gasdf.c:289: undefined reference to `ut_get_unit_by_name'
/home/woodbri/work/GrADS-jam/src/gasdf.c:293: undefined reference to `ut_get_unit_by_name'
gasdf.o: In function `compare_units':
/home/woodbri/work/GrADS-jam/src/gasdf.c:1472: undefined reference to `ut_trim'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1475: undefined reference to `ut_parse'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1476: undefined reference to `ut_parse'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1503: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1482: undefined reference to `ut_are_convertible'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1502: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1503: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1502: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1483: undefined reference to `ut_get_converter'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1487: undefined reference to `cv_convert_double'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1488: undefined reference to `cv_convert_double'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1502: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1503: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:1504: undefined reference to `cv_free'
gasdf.o: In function `findZ':
/home/woodbri/work/GrADS-jam/src/gasdf.c:2065: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2020: undefined reference to `ut_parse'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2022: undefined reference to `ut_are_convertible'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2029: undefined reference to `ut_are_convertible'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2037: undefined reference to `ut_are_convertible'
gasdf.o: In function `findT':
/home/woodbri/work/GrADS-jam/src/gasdf.c:2136: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2137: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2105: undefined reference to `ut_parse'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2106: undefined reference to `ut_encode_time'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2106: undefined reference to `ut_offset_by_time'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2109: undefined reference to `ut_are_convertible'
gasdf.o: In function `set_time_type':
/home/woodbri/work/GrADS-jam/src/gasdf.c:2595: undefined reference to `ut_parse'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2597: undefined reference to `ut_encode_time'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2597: undefined reference to `ut_offset_by_time'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2598: undefined reference to `ut_are_convertible'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2602: undefined reference to `ut_free'
/home/woodbri/work/GrADS-jam/src/gasdf.c:2603: undefined reference to `ut_free'
gasdf.o: In function `gadsdf':
/home/woodbri/work/GrADS-jam/src/gasdf.c:880: undefined reference to `ut_parse'
/home/woodbri/work/GrADS-jam/src/gasdf.c:889: undefined reference to `ut_encode_time'
/home/woodbri/work/GrADS-jam/src/gasdf.c:889: undefined reference to `ut_offset_by_time'
/home/woodbri/work/GrADS-jam/src/gasdf.c:892: undefined reference to `ut_are_convertible'
/home/woodbri/work/GrADS-jam/src/gasdf.c:894: undefined reference to `ut_get_converter'
/home/woodbri/work/GrADS-jam/src/gasdf.c:896: undefined reference to `cv_convert_double'
/home/woodbri/work/GrADS-jam/src/gasdf.c:898: undefined reference to `ut_decode_time'
/home/woodbri/work/GrADS-jam/src/gasdf.c:899: undefined reference to `cv_free'
collect2: error: ld returned 1 exit status
Makefile:771: recipe for target 'grads' failed
make[2]: *** [grads] Error 1
make[2]: Leaving directory '/data/work/GrADS-jam/src'
Makefile:614: recipe for target 'all' failed
make[1]: *** [all] Error 2
make[1]: Leaving directory '/data/work/GrADS-jam/src'
Makefile:462: recipe for target 'all-recursive' failed
make: *** [all-recursive] Error 1

but linking like this works by manually adding -ludunits2 to the link command

cd src
gcc   -g -O2 -rdynamic   -o grads grads.o gxsubs.o gxmeta.o gxchpl.o gxcntr.o gxstrm.o gxdb.o gxwmap.o gxshad.o gxshad2.o gaexpr.o gafunc.o gautil.o gagx.o gscrpt.o gamach.o gatxt.o galloc.o gaddes.o gacfg.o gaio.o gauser.o gasdf.o bufrstn.o gabufr.o gabufrtbl.o   -L..//lib      -lreadline -lgrib2c -ljasper -lpng15 -lz  -lhdf5 -ljpeg -lz  -lnetcdf  -lgeotiff -ltiff  -lshp  -ludunits2  -ldl  -lm

cd ..
make  # finishes without any additional errors

notice the manual inclusion of '-ludunits2' to get it to link,
2. but gradspy fails with undefined symbol below:

sudo make install
cd src
sudo python3 setup.py install

python3
Python 3.6.9 (default, Oct  8 2020, 12:12:24)
[GCC 8.4.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import gradspy
/usr/local/lib/libgradspy.so: undefined symbol: ut_ignore
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
SystemError: initialization of gradspy failed without raising an exception
This was referenced Jan 9, 2021
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@woodbri
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woodbri commented Jan 11, 2021

I don't know if this helps but some more info:

woodbri@B1B8B6F:~/work/GrADS-jam/src$ ldconfig -p  | grep units
        libudunits2.so.0 (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libudunits2.so.0
        libudunits2.so (libc6,x86-64) => /usr/lib/x86_64-linux-gnu/libudunits2.so

woodbri@B1B8B6F:~/work/GrADS-jam/src$ nm /usr/local/lib/libgradspy.so | grep ' ut_'
00000000000b0a63 T ut_create_buffer
00000000000b09a3 T ut_delete_buffer
00000000000b09d9 T ut_flush_buffer
00000000000b0a1d T ut_init_buffer
00000000000b0919 T ut_load_buffer_state
00000000000b16d9 T ut_scan_buffer
00000000000b177b T ut_scan_bytes
00000000000b17f0 T ut_scan_string
00000000000b0955 T ut_switch_to_buffer

woodbri@B1B8B6F:~/work/GrADS-jam/src$ grep ut_ignore *
grep: build: Is a directory
gasdf.c:      ut_set_error_message_handler(ut_ignore);
Binary file gasdf.o matches
Binary file grads matches

@opoplawski opoplawski linked a pull request Aug 11, 2023 that will close this issue
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Add UDUNITS2_CFLAGS/_LIBS where needed opoplawski/GrADS
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@woodbri