Linking problem when compiling gdalinfo.o: libgdal.so: undefined reference to `MPI::Win::Free()' Reproducible: Always Steps to Reproduce: 1.emerge -av1 =sci-libs/gdal-1.8.0 Actual Results: x86_64-pc-linux-gnu-gcc -march=native -O3 -mmmx -msse -msse2 -msse3 -m3dnow -ftree-vectorize -mfpmath=sse -pipe -ggdb -fPIC -Wall -Wdeclaration-after-statement -I/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/port -I/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/gcore -I/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/alg -I/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/ogr -I/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/ogr/ogrsf_frmts -I/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/frmts -DOGR_ENABLED -I/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/port -I/usr/ -I/usr//include -c -o gdalinfo.o gdalinfo.c x86_64-pc-linux-gnu-g++ -Wl,-O1 -Wl,--as-needed gdalinfo.o -L/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0 -lgdal -L/usr/lib64 -lgeos_c -L/usr/lib -lsqlite3 -lodbc -lodbcinst -lexpat -ljasper -lhdf5 -lgif -ljpeg -lgeotiff -ltiff -lpng -lcfitsio -lz -L/usr/ -L/usr//lib -lpthread -lm -lrt -ldl -lcurl -Wl,-O1 -Wl,--as-needed -L/usr/lib64/mysql -lmysqlclient -L/usr//lib -lz -lcrypt -lnsl -lm -L/usr/lib/ -lssl -lcrypto -o gdalinfo /var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/libgdal.so: undefined reference to `ompi_mpi_cxx_op_intercept' /var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/libgdal.so: undefined reference to `MPI::Datatype::Free()' /var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/libgdal.so: undefined reference to `MPI::Comm::Comm()' /var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/libgdal.so: undefined reference to `MPI::Win::Free()' collect2: ld returned 1 exit status make[1]: *** [gdalinfo] Error 1 make[1]: Leaving directory `/var/tmp/portage/sci-libs/gdal-1.8.0/work/gdal-1.8.0/apps' make: *** [apps-target] Error 2 emake failed Expected Results: emerging of gdal should not fail Portage 2.2.0_alpha23 (default/linux/amd64/10.0/desktop, gcc-4.5.2, glibc-2.13-r0, 2.6.37-pininotebook2 x86_64) ================================================================= System uname: Linux-2.6.37-pininotebook2-x86_64-AMD_Turion-tm-_X2_Ultra_Dual-Core_Mobile_ZM-82-with-gentoo-2.0.1 Timestamp of tree: Sun, 13 Feb 2011 06:45:01 +0000 distcc 3.1 x86_64-pc-linux-gnu [disabled] ccache version 3.1.4 [disabled] app-shells/bash: 4.1_p9 dev-java/java-config: 2.1.11-r3 dev-lang/python: 2.6.6-r1, 2.7.1, 3.1.3 dev-util/ccache: 3.1.4 dev-util/cmake: 2.8.3-r1 sys-apps/baselayout: 2.0.1-r1 sys-apps/openrc: 0.7.0 sys-apps/sandbox: 2.4 sys-devel/autoconf: 2.13, 2.68 sys-devel/automake: 1.8.5-r4, 1.9.6-r3, 1.10.3, 1.11.1 sys-devel/binutils: 2.21 sys-devel/gcc: 4.5.2 sys-devel/gcc-config: 1.4.1 sys-devel/libtool: 2.4-r1 sys-devel/make: 3.82 virtual/os-headers: 2.6.36.1 (sys-kernel/linux-headers) Repositories: gentoo x11 java-overlay qting-edge kde local-repo Installed sets: @kdesdk, @plasmoids, @system 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binpkg-logs distlocks fixlafiles fixpackages metadata-transfer news preserve-libs protect-owned sandbox sfperms splitdebug strict unknown-features-warn unmerge-logs unmerge-orphans userfetch" FFLAGS="-march=native -O3 -mmmx -msse -msse2 -msse3 -m3dnow -ftree-vectorize -mfpmath=sse -pipe -ggdb" GENTOO_MIRRORS="http://trumpetti.atm.tut.fi/gentoo/" LC_ALL="en_US.UTF-8" LDFLAGS="-Wl,-O1 -Wl,--as-needed" LINGUAS="en ru" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_CONFIGROOT="/" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/var/lib/layman/x11 /var/lib/layman/java-overlay /var/lib/layman/qting-edge /var/lib/layman/kde /usr/local/portage" SYNC="rsync://trumpetti.atm.tut.fi/gentoo-portage/" USE="3dnow 3dnowext 3ds 64bit 7zip R X a52 aac accessibility acl acpi addressbook 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symlink sysfs syslog system-sqlite sysvipc szip taglib tcl tcpdump telepathy templates tex4ht theora thin-splines threads threadsafe thumbnail thumbnails tidy tiff timezone timidity tk tls tokenizer toolbar tools translator tremor truetype type3 udev udis86 umfpack unicode unzip upnp urandom usb userlocales utils uuid v4l v4l2 vaapi valgrind verse vga vhosts video vim vim-syntax virtuoso vlc vnc vorbis vpx wav wavpack weather web webdav webdav-neon webinterface webkit webpresence wicd wifi win32 wma wmf wmp wps x264 xattr xcb xcomposite xetex xforms xft xhtml xindy xine xinerama xml xmlpatterns xmlreader xmlrpc xmlwriter xmp xorg xpdf-headers xplanet xpm xrandr xscreensaver xsl xslt xulrunner xv xvid xvmc zeroconf zip zlib" ALSA_CARDS="*" ALSA_PCM_PLUGINS="*" APACHE2_MODULES="actions alias asis auth_basic auth_digest authn_alias authn_anon authn_dbd authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache cern_meta charset_lite dav dav_fs dav_lock dbd deflate dir disk_cache dumpio env expires ext_filter file_cache filter headers ident imagemap include info log_config log_forensic logio mem_cache mime mime_magic negotiation proxy proxy_ajp proxy_balancer proxy_connect proxy_ftp proxy_http rewrite setenvif speling status substitute unique_id userdir usertrack version vhost_alias" APACHE2_MPMS="worker" CAMERAS="canon directory ptp2 template" ELIBC="glibc" GPSD_PROTOCOLS="garmin garmintxt gpsclock" INPUT_DEVICES="evdev synaptics" KERNEL="linux" LINGUAS="en ru" NETBEANS_MODULES="apisupport cnd dlight enterprise ergonomics groovy harness ide identity java mobility nb php profiler ruby webcommon websvccommon" PHP_TARGETS="php5-3" QEMU_SOFTMMU_TARGETS="i386 x86_64" QEMU_USER_TARGETS="i386 x86_64" RUBY_TARGETS="ruby18 jruby" SANE_BACKENDS="*" USERLAND="GNU" VIDEO_CARDS="radeon r600" Unset: CPPFLAGS, CTARGET, INSTALL_MASK, LANG, PORTAGE_BUNZIP2_COMMAND, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS
Created attachment 262321 [details] Build log
After I re-emerged hdf5 without mpi useflag (if its enabled, cxx useflag is turned off by ebuild) and with cxx useflag enabled, gdal was compiled successfully. pininotebook2 ~ # emerge -pv1 sci-libs/hdf5 sci-libs/gdal sci-geosciences/grass sci-geosciences/qgis These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sci-libs/hdf5-1.8.5_p1-r1 USE="cxx examples fortran szip threads zlib -debug -mpi" 0 kB [ebuild R ] sci-libs/gdal-1.8.0 USE="curl doc fits geos gif hdf5 jpeg jpeg2k mysql odbc perl png python ruby sqlite threads -aux_xml -debug -ecwj2k -gml -netcdf -ogdi -postgres" RUBY_TARGETS="ruby18" 0 kB [ebuild R ] sci-geosciences/grass-6.4.0 USE="X cairo cxx ffmpeg fftw gmath jpeg largefile mysql nls odbc opengl png python readline sqlite tiff truetype -debug -motif -postgres -wxwidgets" 0 kB [ebuild R ] sci-geosciences/qgis-1.5.0 USE="examples gps grass gsl python sqlite -postgres" 0 kB Total: 4 packages (4 reinstalls), Size of downloads: 0 kB
gdal should also compile successfully with mpi, which it does if you have mpich2 installed. Try running "ldd -r /path/to/libmpi.so" and see if get any undefined references. If so, then it's a bug in the mpi package and not in gdal (and make sure you know which mpi library is installed).
Sometimes something like the C++ bindings in a dependent package can also be a problem (checking that now on hdf5). Make sure both libmpi and libhdf5 are both compiled with the right USE flags for what you need. $ emerge mpich2 hdf5 gdal -v1p These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] sys-cluster/mpich2-1.2.1_p1-r1 USE="cxx doc fortran mpi-threads romio threads -debug" 0 kB [ebuild R ] sci-libs/hdf5-1.8.5_p1-r1 USE="fortran mpi szip threads zlib -cxx -debug -examples" 0 kB [ebuild R ] sci-libs/gdal-1.8.0 USE="aux_xml curl fits geos gif gml hdf5 jpeg jpeg2k mysql netcdf ogdi perl png postgres python ruby sqlite threads -debug -doc -ecwj2k -odbc" RUBY_TARGETS="ruby18" 0 kB Total: 3 packages (3 reinstalls), Size of downloads: 0 kB $ ldd -r /usr/lib64/libgdal.so linux-vdso.so.1 => (0x00007fffdf91c000) libgeos_c.so.1 => /usr/lib/libgeos_c.so.1 (0x00007ff364b95000) libsqlite3.so.0 => /usr/lib/libsqlite3.so.0 (0x00007ff3648fa000) libexpat.so.1 => /usr/lib/libexpat.so.1 (0x00007ff3646d0000) libjasper.so.1 => /usr/lib/libjasper.so.1 (0x00007ff364477000) libhdf5.so.6 => /usr/lib/libhdf5.so.6 (0x00007ff363fd5000) libogdi.so.3 => /usr/lib/libogdi.so.3 (0x00007ff363db1000) libgif.so.4 => /usr/lib/libgif.so.4 (0x00007ff363ba7000) libjpeg.so.8 => /usr/lib/libjpeg.so.8 (0x00007ff36396c000) libgeotiff.so.2 => /usr/lib/libgeotiff.so.2 (0x00007ff363739000) libtiff.so.5 => /usr/lib/libtiff.so.5 (0x00007ff3634c9000) libpng14.so.14 => /usr/lib/libpng14.so.14 (0x00007ff3632a2000) libnetcdf.so.6 => /usr/lib/libnetcdf.so.6 (0x00007ff362fa4000) libcfitsio.so.3 => /usr/lib/libcfitsio.so.3 (0x00007ff362bf7000) libpq.so.5 => /usr/lib64/postgresql-9.0/lib64/libpq.so.5 (0x00007ff3629cf000) libz.so.1 => /lib/libz.so.1 (0x00007ff3627b8000) libpthread.so.0 => /lib/libpthread.so.0 (0x00007ff36259b000) libdl.so.2 => /lib/libdl.so.2 (0x00007ff362397000) libcurl.so.4 => /usr/lib/libcurl.so.4 (0x00007ff36213e000) libmysqlclient.so.16 => /usr/lib/libmysqlclient.so.16 (0x00007ff361dba000) libm.so.6 => /lib/libm.so.6 (0x00007ff361b38000) libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.5.2/libstdc++.so.6 (0x00007ff36182f000) libgcc_s.so.1 => /lib/libgcc_s.so.1 (0x00007ff361619000) libc.so.6 => /lib/libc.so.6 (0x00007ff3612ba000) libgeos-3.2.2.so => /usr/lib/libgeos-3.2.2.so (0x00007ff360f41000) libsz.so.2 => /usr/lib64/libsz.so.2 (0x00007ff360d2d000) libmpich.so.1.2 => /usr/lib64/libmpich.so.1.2 (0x00007ff36095d000) libproj.so.0 => /usr/lib/libproj.so.0 (0x00007ff360717000) libX11.so.6 => /usr/lib/libX11.so.6 (0x00007ff3603d8000) libjbig.so => /usr/lib/libjbig.so (0x00007ff3601cb000) libhdf5_hl.so.6 => /usr/lib64/libhdf5_hl.so.6 (0x00007ff35ff9d000) libssl.so.1.0.0 => /usr/lib/libssl.so.1.0.0 (0x00007ff35fd40000) libcrypto.so.1.0.0 => /usr/lib/libcrypto.so.1.0.0 (0x00007ff35f992000) libldap_r-2.4.so.2 => /usr/lib/libldap_r-2.4.so.2 (0x00007ff35f746000) /lib64/ld-linux-x86-64.so.2 (0x00007ff365851000) libldap-2.4.so.2 => /usr/lib64/libldap-2.4.so.2 (0x00007ff35f501000) librt.so.1 => /lib/librt.so.1 (0x00007ff35f2f8000) libssl3.so => /usr/lib64/libssl3.so (0x00007ff35f0bf000) libnss3.so => /usr/lib64/libnss3.so (0x00007ff35ed90000) libnspr4.so => /usr/lib64/libnspr4.so (0x00007ff35eb52000) libxcb.so.1 => /usr/lib/libxcb.so.1 (0x00007ff35e933000) liblber-2.4.so.2 => /usr/lib/liblber-2.4.so.2 (0x00007ff35e724000) libresolv.so.2 => /lib/libresolv.so.2 (0x00007ff35e50d000) libsasl2.so.2 => /usr/lib/libsasl2.so.2 (0x00007ff35e2f1000) libgnutls.so.26 => /usr/lib/libgnutls.so.26 (0x00007ff35e045000) libnssutil3.so => /usr/lib/libnssutil3.so (0x00007ff35de25000) libplc4.so => /usr/lib/libplc4.so (0x00007ff35dc1f000) libplds4.so => /usr/lib/libplds4.so (0x00007ff35da1b000) libXau.so.6 => /usr/lib/libXau.so.6 (0x00007ff35d817000) libXdmcp.so.6 => /usr/lib/libXdmcp.so.6 (0x00007ff35d610000) libcrypt.so.1 => /lib/libcrypt.so.1 (0x00007ff35d3d9000) libtasn1.so.3 => /usr/lib/libtasn1.so.3 (0x00007ff35d1c8000) libgcrypt.so.11 => /usr/lib/libgcrypt.so.11 (0x00007ff35cf4d000) libgpg-error.so.0 => /usr/lib/libgpg-error.so.0 (0x00007ff35cd49000)
(In reply to comment #3) > gdal should also compile successfully with mpi, which it does if you have > mpich2 installed. Try running "ldd -r /path/to/libmpi.so" and see if get any > undefined references. If so, then it's a bug in the mpi package and not in > gdal (and make sure you know which mpi library is installed). I use openmpi with USE="cxx", and gdal fails to compile as described above.
I recompiled hdf5 with "-mpi cxx", and gfal compiles now, but I dislike this workaround.
Then you need to get openmpi compiled correctly. Run ldd -r on the openmpi lib and see what it tells you. We've been through this before with mpich2, and I was unable to convince the maintainer of that package to fix it. The upstream guys fixed it at some point, so now it works correctly. At this point, my answer is "go fix openmpi and then gdal will build against it successfully". The problem is not with gdal...
