[GRASS-dev] g.region "Illegal instruction (core dumped)"

Luca Delucchi lucadeluge at gmail.com
Fri Nov 23 02:05:51 PST 2018 

Hi devs,

I installed GRASS 7.6 on a Singularity container [0] but I have
problems with some commands that return "Illegal instruction (core
dumped)", one of this is g.region.

GRASS 7.6.svn (eu_laea):~ > g.region -p
D1/5: G_set_program_name(): g.region
D2/5: G_file_name(): path = /fem4/pgis/grassdata/eu_laea/sentinel
D2/5: G_file_name(): path = /fem4/pgis/grassdata/eu_laea/PERMANENT/DEFAULT_WIND
D2/5: G_file_name(): path = /fem4/pgis/grassdata/eu_laea/PERMANENT/DEFAULT_WIND
D2/5:     file open: read (mode = r)
D2/5: G__read_Cell_head
D2/5: G__read_Cell_head_array
Illegal instruction (core dumped)

I tried to debug [1] it with ldd but I don't see anything wrong

ldd `which g.region`
    linux-vdso.so.1 (0x00007ffe66981000)
    libgrass_gproj.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_gproj.7.6.svn.so
(0x00002b1a49282000)
    libgrass_vector.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_vector.7.6.svn.so
(0x00002b1a4928f000)
    libgrass_dig2.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_dig2.7.6.svn.so
(0x00002b1a49306000)
    libgrass_g3d.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_g3d.7.6.svn.so
(0x00002b1a49321000)
    libgrass_raster.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_raster.7.6.svn.so
(0x00002b1a49343000)
    libgrass_gis.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_gis.7.6.svn.so
(0x00002b1a49370000)
    libm.so.6 => /lib/x86_64-linux-gnu/libm.so.6 (0x00002b1a493d9000)
    libproj.so.13 => /lib/x86_64-linux-gnu/libproj.so.13 (0x00002b1a4956d000)
    libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x00002b1a495e9000)
    libgdal.so.20 => /lib/libgdal.so.20 (0x00002b1a497a6000)
    libgrass_dbmiclient.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_dbmiclient.7.6.svn.so
(0x00002b1a4a9c1000)
    libgrass_dbmibase.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_dbmibase.7.6.svn.so
(0x00002b1a4a9ce000)
    libgrass_dgl.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_dgl.7.6.svn.so
(0x00002b1a4a9e3000)
    libgrass_linkm.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_linkm.7.6.svn.so
(0x00002b1a4a9fd000)
    libgrass_rtree.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_rtree.7.6.svn.so
(0x00002b1a4aa02000)
    libgeos_c.so.1 => /lib/x86_64-linux-gnu/libgeos_c.so.1 (0x00002b1a4aa0e000)
    libgrass_btree2.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_btree2.7.6.svn.so
(0x00002b1a4aa46000)
    libpq.so.5 => /lib/x86_64-linux-gnu/libpq.so.5 (0x00002b1a4aa4e000)
    libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x00002b1a4aa9b000)
    libgrass_datetime.7.6.svn.so =>
/usr/local/grass-7.6.svn/lib/libgrass_datetime.7.6.svn.so
(0x00002b1a4aaa0000)
    libz.so.1 => /lib/x86_64-linux-gnu/libz.so.1 (0x00002b1a4aaab000)
    libbz2.so.1.0 => /lib/x86_64-linux-gnu/libbz2.so.1.0 (0x00002b1a4acc9000)
    libzstd.so.1 => /lib/x86_64-linux-gnu/libzstd.so.1 (0x00002b1a4acdc000)
    /lib64/ld-linux-x86-64.so.2 (0x00002b1a4924b000)
    libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0
(0x00002b1a4ad77000)
    libarmadillo.so.9 => /lib/libarmadillo.so.9 (0x00002b1a4ad9a000)
    libpoppler.so.80 => /lib/x86_64-linux-gnu/libpoppler.so.80
(0x00002b1a4ada5000)
    libjson-c.so.3 => /lib/x86_64-linux-gnu/libjson-c.so.3 (0x00002b1a4b081000)
    libfreexl.so.1 => /lib/x86_64-linux-gnu/libfreexl.so.1 (0x00002b1a4b28c000)
    libqhull.so.7 => /lib/x86_64-linux-gnu/libqhull.so.7 (0x00002b1a4b297000)
    libwebp.so.6 => /lib/x86_64-linux-gnu/libwebp.so.6 (0x00002b1a4b4f5000)
    libepsilon.so.1 => /lib/x86_64-linux-gnu/libepsilon.so.1
(0x00002b1a4b760000)
    libodbc.so.2 => /lib/x86_64-linux-gnu/libodbc.so.2 (0x00002b1a4b77a000)
    libodbcinst.so.2 => /lib/x86_64-linux-gnu/libodbcinst.so.2
(0x00002b1a4b9ea000)
    libkmlbase.so.1 => /lib/x86_64-linux-gnu/libkmlbase.so.1
(0x00002b1a4bc00000)
    libkmldom.so.1 => /lib/x86_64-linux-gnu/libkmldom.so.1 (0x00002b1a4bc1e000)
    libkmlengine.so.1 => /lib/x86_64-linux-gnu/libkmlengine.so.1
(0x00002b1a4bcd8000)
    libkmlxsd.so.1 => /lib/x86_64-linux-gnu/libkmlxsd.so.1 (0x00002b1a4bd15000)
    libkmlregionator.so.1 =>
/lib/x86_64-linux-gnu/libkmlregionator.so.1 (0x00002b1a4bd2b000)
    libexpat.so.1 => /lib/x86_64-linux-gnu/libexpat.so.1 (0x00002b1a4bd39000)
    libxerces-c-3.2.so => /lib/x86_64-linux-gnu/libxerces-c-3.2.so
(0x00002b1a4bd76000)
    libopenjp2.so.7 => /lib/x86_64-linux-gnu/libopenjp2.so.7
(0x00002b1a4c121000)
    libnetcdf.so.13 => /lib/x86_64-linux-gnu/libnetcdf.so.13
(0x00002b1a4c379000)
    libhdf5_serial_hl.so.100 =>
/lib/x86_64-linux-gnu/libhdf5_serial_hl.so.100 (0x00002b1a4c4bb000)
    libsz.so.2 => /lib/x86_64-linux-gnu/libsz.so.2 (0x00002b1a4c4e1000)
    libhdf5_serial.so.100 =>
/lib/x86_64-linux-gnu/libhdf5_serial.so.100 (0x00002b1a4c6e4000)
    libmfhdfalt.so.0 => /lib/libmfhdfalt.so.0 (0x00002b1a4ca42000)
    libdfalt.so.0 => /lib/libdfalt.so.0 (0x00002b1a4ca6c000)
    libogdi.so.3.2 => /lib/libogdi.so.3.2 (0x00002b1a4cb14000)
    libgif.so.7 => /lib/x86_64-linux-gnu/libgif.so.7 (0x00002b1a4cb39000)
    libCharLS.so.1 => /lib/x86_64-linux-gnu/libCharLS.so.1 (0x00002b1a4cd42000)
    libjpeg.so.62 => /lib/x86_64-linux-gnu/libjpeg.so.62 (0x00002b1a4cd89000)
    libgeotiff.so.2 => /lib/x86_64-linux-gnu/libgeotiff.so.2
(0x00002b1a4cff2000)
    libtiff.so.5 => /lib/x86_64-linux-gnu/libtiff.so.5 (0x00002b1a4d027000)
    libpng16.so.16 => /lib/x86_64-linux-gnu/libpng16.so.16 (0x00002b1a4d0a6000)
    liblzma.so.5 => /lib/x86_64-linux-gnu/liblzma.so.5 (0x00002b1a4d0dd000)
    librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x00002b1a4d303000)
    libdapclient.so.6 => /lib/x86_64-linux-gnu/libdapclient.so.6
(0x00002b1a4d30d000)
    libdapserver.so.7 => /lib/x86_64-linux-gnu/libdapserver.so.7
(0x00002b1a4d354000)
    libdap.so.25 => /lib/x86_64-linux-gnu/libdap.so.25 (0x00002b1a4d365000)
    libspatialite.so.7 => /lib/x86_64-linux-gnu/libspatialite.so.7
(0x00002b1a4d50c000)
    libpcre.so.3 => /lib/x86_64-linux-gnu/libpcre.so.3 (0x00002b1a4dc8f000)
    libcurl-gnutls.so.4 => /lib/x86_64-linux-gnu/libcurl-gnutls.so.4
(0x00002b1a4dd03000)
    libfyba.so.0 => /lib/x86_64-linux-gnu/libfyba.so.0 (0x00002b1a4dd8d000)
    libfygm.so.0 => /lib/x86_64-linux-gnu/libfygm.so.0 (0x00002b1a4dde7000)
    libfyut.so.0 => /lib/x86_64-linux-gnu/libfyut.so.0 (0x00002b1a4ddf0000)
    libxml2.so.2 => /lib/x86_64-linux-gnu/libxml2.so.2 (0x00002b1a4ddfc000)
    libmariadbclient.so.18 =>
/lib/x86_64-linux-gnu/libmariadbclient.so.18 (0x00002b1a4dfa7000)
    libstdc++.so.6 => /lib/x86_64-linux-gnu/libstdc++.so.6 (0x00002b1a4e388000)
    libgcc_s.so.1 => /lib/x86_64-linux-gnu/libgcc_s.so.1 (0x00002b1a4e50b000)
    libgeos-3.7.0.so => /lib/x86_64-linux-gnu/libgeos-3.7.0.so
(0x00002b1a4e525000)
    libssl.so.1.1 => /lib/x86_64-linux-gnu/libssl.so.1.1 (0x00002b1a4e6e2000)
    libcrypto.so.1.1 => /lib/x86_64-linux-gnu/libcrypto.so.1.1
(0x00002b1a4e775000)
    libgssapi_krb5.so.2 => /lib/x86_64-linux-gnu/libgssapi_krb5.so.2
(0x00002b1a4ea5c000)
    libldap_r-2.4.so.2 => /lib/x86_64-linux-gnu/libldap_r-2.4.so.2
(0x00002b1a4eaa9000)
    libblas.so.3 => /lib/x86_64-linux-gnu/libblas.so.3 (0x00002b1a4eafd000)
    liblapack.so.3 => /lib/x86_64-linux-gnu/liblapack.so.3 (0x00002b1a4eb6a000)
    libarpack.so.2 => /lib/x86_64-linux-gnu/libarpack.so.2 (0x00002b1a4f204000)
    libsuperlu.so.5 => /lib/x86_64-linux-gnu/libsuperlu.so.5
(0x00002b1a4f253000)
    libfreetype.so.6 => /lib/x86_64-linux-gnu/libfreetype.so.6
(0x00002b1a4f4c6000)
    libfontconfig.so.1 => /lib/x86_64-linux-gnu/libfontconfig.so.1
(0x00002b1a4f77b000)
    libnss3.so => /lib/x86_64-linux-gnu/libnss3.so (0x00002b1a4f7c1000)
    libsmime3.so => /lib/x86_64-linux-gnu/libsmime3.so (0x00002b1a4f90e000)
    libnspr4.so => /lib/x86_64-linux-gnu/libnspr4.so (0x00002b1a4f93d000)
    liblcms2.so.2 => /lib/x86_64-linux-gnu/liblcms2.so.2 (0x00002b1a4f980000)
    libpopt.so.0 => /lib/x86_64-linux-gnu/libpopt.so.0 (0x00002b1a4f9dd000)
    libltdl.so.7 => /lib/x86_64-linux-gnu/libltdl.so.7 (0x00002b1a4fbea000)
    libminizip.so.1 => /lib/x86_64-linux-gnu/libminizip.so.1
(0x00002b1a4fbf5000)
    liburiparser.so.1 => /lib/x86_64-linux-gnu/liburiparser.so.1
(0x00002b1a4fe01000)
    libkmlconvenience.so.1 =>
/lib/x86_64-linux-gnu/libkmlconvenience.so.1 (0x00002b1a4fe21000)
    libnsl.so.1 => /lib/x86_64-linux-gnu/libnsl.so.1 (0x00002b1a4fe43000)
    libicui18n.so.63 => /lib/x86_64-linux-gnu/libicui18n.so.63
(0x00002b1a4fe5c000)
    libicuuc.so.63 => /lib/x86_64-linux-gnu/libicuuc.so.63 (0x00002b1a50137000)
    libicudata.so.63 => /lib/x86_64-linux-gnu/libicudata.so.63
(0x00002b1a50306000)
    libaec.so.0 => /lib/x86_64-linux-gnu/libaec.so.0 (0x00002b1a51cf8000)
    libjbig.so.0 => /lib/x86_64-linux-gnu/libjbig.so.0 (0x00002b1a51f00000)
    libuuid.so.1 => /lib/x86_64-linux-gnu/libuuid.so.1 (0x00002b1a5210e000)
    libsqlite3.so.0 => /lib/x86_64-linux-gnu/libsqlite3.so.0
(0x00002b1a52117000)
    libnghttp2.so.14 => /lib/x86_64-linux-gnu/libnghttp2.so.14
(0x00002b1a5223a000)
    libidn2.so.0 => /lib/x86_64-linux-gnu/libidn2.so.0 (0x00002b1a52262000)
    librtmp.so.1 => /lib/x86_64-linux-gnu/librtmp.so.1 (0x00002b1a52281000)
    libssh2.so.1 => /lib/x86_64-linux-gnu/libssh2.so.1 (0x00002b1a5249e000)
    libpsl.so.5 => /lib/x86_64-linux-gnu/libpsl.so.5 (0x00002b1a524cc000)
    libnettle.so.6 => /lib/x86_64-linux-gnu/libnettle.so.6 (0x00002b1a524df000)
    libgnutls.so.30 => /lib/x86_64-linux-gnu/libgnutls.so.30
(0x00002b1a52716000)
    libkrb5.so.3 => /lib/x86_64-linux-gnu/libkrb5.so.3 (0x00002b1a52886000)
    libk5crypto.so.3 => /lib/x86_64-linux-gnu/libk5crypto.so.3
(0x00002b1a52963000)
    libcom_err.so.2 => /lib/x86_64-linux-gnu/libcom_err.so.2
(0x00002b1a52997000)
    liblber-2.4.so.2 => /lib/x86_64-linux-gnu/liblber-2.4.so.2
(0x00002b1a5299d000)
    libkrb5support.so.0 => /lib/x86_64-linux-gnu/libkrb5support.so.0
(0x00002b1a529ae000)
    libkeyutils.so.1 => /lib/x86_64-linux-gnu/libkeyutils.so.1
(0x00002b1a529be000)
    libresolv.so.2 => /lib/x86_64-linux-gnu/libresolv.so.2 (0x00002b1a529c4000)
    libsasl2.so.2 => /lib/x86_64-linux-gnu/libsasl2.so.2 (0x00002b1a529dd000)
    libgfortran.so.5 => /lib/x86_64-linux-gnu/libgfortran.so.5
(0x00002b1a529fa000)
    libquadmath.so.0 => /lib/x86_64-linux-gnu/libquadmath.so.0
(0x00002b1a52c67000)
    libnssutil3.so => /lib/x86_64-linux-gnu/libnssutil3.so (0x00002b1a52caa000)
    libplc4.so => /lib/x86_64-linux-gnu/libplc4.so (0x00002b1a52cdc000)
    libplds4.so => /lib/x86_64-linux-gnu/libplds4.so (0x00002b1a52ce3000)
    libunistring.so.2 => /lib/x86_64-linux-gnu/libunistring.so.2
(0x00002b1a52ce8000)
    libhogweed.so.4 => /lib/x86_64-linux-gnu/libhogweed.so.4
(0x00002b1a52e6c000)
    libgmp.so.10 => /lib/x86_64-linux-gnu/libgmp.so.10 (0x00002b1a530a4000)
    libgcrypt.so.20 => /lib/x86_64-linux-gnu/libgcrypt.so.20
(0x00002b1a53328000)
    libp11-kit.so.0 => /lib/x86_64-linux-gnu/libp11-kit.so.0
(0x00002b1a53446000)
    libtasn1.so.6 => /lib/x86_64-linux-gnu/libtasn1.so.6 (0x00002b1a53575000)
    libgpg-error.so.0 => /lib/x86_64-linux-gnu/libgpg-error.so.0
(0x00002b1a53788000)
    libffi.so.6 => /lib/x86_64-linux-gnu/libffi.so.6 (0x00002b1a537ac000)

declare -x LD_LIBRARY_PATH="/usr/local/grass-7.6.svn/lib:/.singularity.d/libs"

I tried to compile GRASS with debug flag to run gdb but I got error in
nviz and I cannot finish the compilation.

Any idea?

[0] https://singularity.lbl.gov/
[1] https://grasswiki.osgeo.org/wiki/GRASS_Debugging#Using_ldd

-- 
ciao
Luca

www.lucadelu.org

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