...
| Code Block |
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$find . -name "link.txt" | xargs grep lmkl_gf_lp64 | cut -d: -f1 | xargs -I % sed -i -e 's?-lmkl_gf_lp64??g' % |
Error:
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undefined reference to 'dsyev_' |
this error often happens when LAPACK is not linked properly.
Solution:
edit the link.txt for gmt and manually add in the liblapack.so
NOTE: the lapack modules provided in modules on Mahuika is built using f77 instead of f90. using this module may result in crashes.
use try use the one located in /usr/lib64
see below for an example.
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$vim src/CMakeFiles/gmt.dir/link.txt
/opt/nesi/mahuika/GCCcore/5.4.0/bin/cc -std=gnu99 -ggdb3 -O2 -Wuninitialized CMakeFiles/gmt.dir/gmt.c.o -o gmt -rdynamic libgmt.so.5.4.4 /cm/shared/apps/netcdf/gcc/64/4.4.0/lib/libnetcdf.so /nesi/project/nesi00213/opt/mahuika/curl/7.63.0-DEV-gcc-5.4.0/lib/libcurl.so /usr/lib64/liblapack.so.3.4.2 -lgdal -lpcre -lfftw3f -lfftw3f_threads -lblas -lpthread -lm libpostscriptlight.so.5.4.4 /nesi/project/nesi00213/opt/mahuika/zlib/1.2.11/lib/libz.so -lm -ldl -Wl,-rpath,/home/ykh22/deploy/gmt/build/src:/cm/shared/apps/netcdf/gcc/64/4.4.0/lib:/nesi/project/nesi00213/opt/mahuika/curl/7.63.0-DEV-gcc-5.4.0/lib:/nesi/project/nesi00213/opt/mahuika/zlib/1.2.11/lib: |
Error:
| Code Block |
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/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' |
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