...
| Code Block |
|---|
melody.zhu@mahuika02 ~/gmt> mkdir build melody.zhu@mahuika02 ~/gmt> cd build melody.zhu@mahuika02 ~/gmt/build> cmake .. |
Error:
...
cannot
...
find
...
CURL_INCLUDE_DIR
...
error
Solution:
...
check
...
if
...
you
...
install
...
your
...
custom
...
curl
edit ccmake..
| Code Block |
|---|
melody.zhu@mahuika02 ~/gmt/build> ccmake .. # hardcode the path for following variables. Enforce using custom curl and zlib. Editing ConfigUser.cmake will not solve the issue. CURL_INCLUDE_DIR /home/melody.zhu/bin/curl/include CURL_LIBRARY /home/melody.zhu/bin/curl/lib/libcurl.so ZLIB_INCLUDE_DIR /home/melody.zhu/bin/zlib/include ZLIB_LIBRARY /home/melody.zhu/bin/zlib/lib/libz.so |
...
| Code Block |
|---|
$find . -name "link.txt" | xargs grep lmkl_gf_lp64 | cut -d: -f1 | xargs -I % sed -i -e 's?-lmkl_gf_lp64??g' % |
Error:
| Code Block |
|---|
/opt/nesi/mahuika/binutils/2.28-GCCcore-7.1.0/bin/ld: warning: libopenjp2.so.7, needed by /opt/nesi/mahuika/GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1/lib/libgdal.so, not found (try using -rpath or -rpath-link) |
...
/opt/nesi/mahuika/binutils/2.28-GCCcore-7.1.0/bin/ld: warning: libpq.so.5, needed by /opt/nesi/mahuika/GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1/lib/libgdal.so, not found (try using -rpath or -rpath-link) |
...
/opt/nesi/mahuika/binutils/2.28-GCCcore-7.1.0/bin/ld: warning: libkea.so.1.4.6, needed by /opt/nesi/mahuika/GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1/lib/libgdal.so, not found (try using -rpath or -rpath-link) |
...
/opt/nesi/mahuika/GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1/lib/libgdal.so: undefined reference to `kealib::KEAImageIO::setImageBandClrInterp(unsigned int, kealib::KEABandClrInterp)' |
...
/opt/nesi/mahuika/GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1/lib/libgdal.so: undefined reference to `PQputCopyEnd' |
...
/opt/nesi/mahuika/GDAL/2.2.2-gimkl-2017a-GEOS-3.5.1/lib/libgdal.so: undefined reference to `opj_create_compress' |
Solution:
Check
...
modules:OpenJPEG/2.3.0-gimkl-2017a,
...
KEALib/1.4.6-gimkl-2017a
...
and
...
PostgreSQL/9.6.2-gimkl-2017a
...
are
...
loaded.
Check
...
the
...
above
...
modules
...
are
...
in
...
PATH;
...
Their
...
libs
...
are
...
in
...
LD_LIBRARY_PATH
| Code Block |
|---|
melody.zhu@mahuika02 /scale_wlg_persistent/filesets/project/nesi00213/share> module show KEALib/1.4.6-gimkl-2017a
prepend_path("LD_LIBRARY_PATH","/opt/nesi/mahuika/KEALib/1.4.6-gimkl-2017a/lib")
prepend_path("LIBRARY_PATH","/opt/nesi/mahuika/KEALib/1.4.6-gimkl-2017a/lib")
prepend_path("PATH","/opt/nesi/mahuika/KEALib/1.4.6-gimkl-2017a/bin")
# Add missing libs to LD_LIBRARY_PATH: (use 'module show' to see each module path)
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/nesi/mahuika/PostgreSQL/9.6.2-gimkl-2017a/lib
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/nesi/mahuika/OpenJPEG/2.3.0-gimkl-2017a/lib
LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/opt/nesi/mahuika/KEALib/1.4.6-gimkl-2017a/lib |
Error:
...
| Code Block |
|---|
Linking C executable gmt /opt/nesi/mahuika/libpng/1.6.28-gimkl-2017a/lib/libpng16.so.16: undefined reference to `inflateValidate@ZLIB_1.2.9 |
Solution:
...
check
...
if
...
you
...
install
...
your
...
custom
...
libpng
...
using
...
your
...
custom
...
zlib
...
(see
...
point
...
3)
check if you have the correct ZLIB_INCLUDE_DIR and ZLIB_LIBRARY in ccmake
check src/CMakeFiles/gmt.dir/link.txt and edit so cmake can find libs for your custom curl and zlib
| Code Block |
|---|
melody.zhu@mahuika02 ~/gmt/build> vim src/CMakeFiles/gmt.dir/link.txt /usr/bin/cc -std=gnu99 -ggdb3 -O2 -Wuninitialized CMakeFiles/gmt.dir/gmt.c.o -o gmt -rdynamic libgmt.so.6.0.0 /cm/shared/apps/netcdf/gcc/64/4.4.0/lib/libnetcdf.so /home/melody.zhu/bin/curl/lib/libcurl.so -lgdal -lpcre -lfftw3f -lfftw3f_threads -lblas libpostscriptlight.so.6.0.0 /home/melody.zhu/bin/zlib/lib/libz.so -lm -ldl -Wl,-rpath,/home/melody.zhu/gmt/build/src:/cm/shared/apps/netcdf/gcc/64/4.4.0/lib:/home/melody.zhu/bin/curl/lib:/home/melody.zhu/bin/zlib/lib |
When
...
no
...
error
...
running
...
cmake ..
Do
| Code Block |
|---|
melody.zhu@mahuika02 ~/gmt/build> cmake .. melody.zhu@mahuika02 ~/gmt/build> make melody.zhu@mahuika02 ~/gmt/build> make install DESTDIR=/home/melody.zhu/bin |
...