[GRASS-user] Compilation issues on Scientific Linux 6.6

GRASS GRASS user
, ,
1

Hi there!
I’m trying to compile GRASS GIS and ist components (proj, libtiff, geotiff, geos, gdal, netcdf, hdf5, laszip) from source on Scientific Linux. I’ve done that routine like a 100 times on Ubuntu with root access where it worked fine. The current machine has a lot of restrictions, that might be one of the issues.

This is my config:

CFLAGS=“-g” ./configure
–prefix=/path/to/releasebranch_7_0/build
–enable-64bit
–enable-debug
–enable-largefile
–with-freetype --with-freetype-includes=/usr/include/freetype2
–with-gdal=/path/to/gdal-2.0.1/build/bin/gdal-config
–with-geos=/path/to/geos-3.4.2/build/bin/geos-config
–with-netcdf=/path/to/netcdf-4.3.3.1/build/bin/nc-config
–with-openmp
–with-proj-includes=/path/to/proj-4.9.1/build/include
–with-proj-libs=/path/to/proj-4.9.1/build/lib
–with-proj-share=/path/to/proj-4.9.1/build/share
–with-python
–with-readline
–with-sqlite
–with-tiff-includes=/path/to/tiff-4.0.6/build/include
–with-tiff-libs=/path/to/tiff-4.0.6/build/lib
–without-fftw
–without-blas
–without-ffmpeg
–without-lapack
–without-mysql
–without-odbc
–without-opengl
–without-postgres

This is the errormessage after make -j16:

GRASS GIS 7.0.2svn r66747 compilation log

Started compilation: Thu Nov 5 12:02:49 CET 2015

Errors in:
/path/to/releasebranch_7_0/raster/r.gwflow
/path/to/releasebranch_7_0/raster/r.param.scale
/path/to/releasebranch_7_0/raster/r.proj
/path/to/releasebranch_7_0/raster/r.series.accumulate
/path/to/releasebranch_7_0/raster/r.resamp.bspline
/path/to/releasebranch_7_0/raster/r.resamp.rst
/path/to/releasebranch_7_0/raster/r.solute.transport
/path/to/releasebranch_7_0/raster/r.surf.gauss
/path/to/releasebranch_7_0/raster/r.sim/r.sim.water
/path/to/releasebranch_7_0/raster/r.surf.random
/path/to/releasebranch_7_0/raster/r.sim/r.sim.sediment
/path/to/releasebranch_7_0/raster3d/r3.gwflow
/path/to/releasebranch_7_0/vector/v.extract
/path/to/releasebranch_7_0/vector/v.kernel
/path/to/releasebranch_7_0/vector/v.lidar.correction
/path/to/releasebranch_7_0/vector/v.lidar.edgedetection
/path/to/releasebranch_7_0/vector/v.lidar.growing
/path/to/releasebranch_7_0/vector/v.outlier
/path/to/releasebranch_7_0/vector/v.rectify
/path/to/releasebranch_7_0/vector/v.surf.rst
/path/to/releasebranch_7_0/vector/v.surf.bspline
/path/to/releasebranch_7_0/imagery/i.cca
/path/to/releasebranch_7_0/imagery/i.gensigset
/path/to/releasebranch_7_0/imagery/i.ortho.photo/i.ortho.camera
/path/to/releasebranch_7_0/imagery/i.ortho.photo/i.ortho.elev
/path/to/releasebranch_7_0/imagery/i.pca
/path/to/releasebranch_7_0/imagery/i.smap
/path/to/releasebranch_7_0/imagery/i.ortho.photo/i.ortho.rectify

In case of errors please change into the directory with error and run ‘make’.
If you get multiple errors, you need to deal with them in the order they
appear in the error log. If you get an error building a library, you will
also get errors from anything which uses the library.

Finished compilation: Thu Nov 5 12:04:15 CET 2015
make: *** [default] Error 1

It already had some more errors, but those I could solve with various export PATH and LD_LIBRARY commands.

When I enter one of the dirs and try to do make, this happens:

[user@l33 r.gwflow]$ make
: && icc -L/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib -L/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib -Wl,–export-dynamic -Wl,-rpath-link,/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib -o /path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/bin/r.gwflow OBJ.x86_64-unknown-linux-gnu/main.o -lgrass_gpde.7.0.2svn -lgrass_raster.7.0.2svn -lgrass_gis.7.0.2svn -lgrass_gmath.7.0.2svn
/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib/libgrass_gmath.7.0.2svn.so: undefined reference to __kmpc_reduce_nowait' /path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib/libgrass_gmath.7.0.2svn.so: undefined reference to __kmpc_end_reduce_nowait’
/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib/libgrass_gpde.7.0.2svn.so: undefined reference to __kmpc_end_serialized_parallel' ... /home/lv70836/avaflow/src/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib/libgrass_gpde.7.0.2svn.so: undefined reference to __kmpc_for_static_init_4’

Any pointers would be much appreciated!

Regards, Matthias

2

Hi,

sorry for the delay, some questions below:

On Thu, Nov 5, 2015 at 12:17 PM, Matthias Benedikt
<matthias.benedikt@boku.ac.at> wrote:

Hi there!
I'm trying to compile GRASS GIS and ist components (proj, libtiff, geotiff,
geos, gdal, netcdf, hdf5, laszip) from source on Scientific Linux.

Same system here - do you use SL6 or SL7?

I've done
that routine like a 100 times on Ubuntu with root access

In general you don't need root access at all in order to compile GRASS GIS.

where it worked
fine. The current machine has a lot of restrictions, that might be one of
the issues.

This is my config:

CFLAGS="-g" ./configure \
--prefix=/path/to/releasebranch_7_0/build \
--enable-64bit \
--enable-debug \
--enable-largefile \
--with-freetype --with-freetype-includes=/usr/include/freetype2 \
--with-gdal=/path/to/gdal-2.0.1/build/bin/gdal-config \
--with-geos=/path/to/geos-3.4.2/build/bin/geos-config \
--with-netcdf=/path/to/netcdf-4.3.3.1/build/bin/nc-config \
--with-openmp \
--with-proj-includes=/path/to/proj-4.9.1/build/include \
--with-proj-libs=/path/to/proj-4.9.1/build/lib \
--with-proj-share=/path/to/proj-4.9.1/build/share \
--with-python \
--with-readline \
--with-sqlite \
--with-tiff-includes=/path/to/tiff-4.0.6/build/include \
--with-tiff-libs=/path/to/tiff-4.0.6/build/lib \
--without-fftw \
--without-blas \
--without-ffmpeg \
--without-lapack \
--without-mysql \
--without-odbc \
--without-opengl \
--without-postgres

This is the errormessage after make -j16:

GRASS GIS 7.0.2svn r66747 compilation log
--------------------------------------------------
Started compilation: Thu Nov 5 12:02:49 CET 2015
--
Errors in:
/path/to/releasebranch_7_0/raster/r.gwflow

ok, so here is the first issue, it may be related to GMATHLIB (lib/gmath/)

/path/to/releasebranch_7_0/raster/r.param.scale

[...]

/path/to/releasebranch_7_0/imagery/i.ortho.photo/i.ortho.rectify
--
In case of errors please change into the directory with error and run
'make'.

[...]

It already had some more errors, but those I could solve with various export
PATH and LD_LIBRARY commands.

Mhh, perhaps something "bad" crept in. Please post the very initial
error if it still occurs with the current 7.0. If you can, take it
from SVN or the weekly snapshot.

When I enter one of the dirs and try to do make, this happens:

[user@l33 r.gwflow]$ make
: && icc -L/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib
-L/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib
-Wl,--export-dynamic
-Wl,-rpath-link,/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib
-o /path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/bin/r.gwflow
OBJ.x86_64-unknown-linux-gnu/main.o -lgrass_gpde.7.0.2svn
-lgrass_raster.7.0.2svn -lgrass_gis.7.0.2svn -lgrass_gmath.7.0.2svn
/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib/libgrass_gmath.7.0.2svn.so:
undefined reference to `__kmpc_reduce_nowait'
/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib/libgrass_gmath.7.0.2svn.so:
undefined reference to `__kmpc_end_reduce_nowait'
/path/to/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib/libgrass_gpde.7.0.2svn.so:
undefined reference to `__kmpc_end_serialized_parallel'
...
/home/lv70836/avaflow/src/releasebranch_7_0/dist.x86_64-unknown-linux-gnu/lib/libgrass_gpde.7.0.2svn.so:
undefined reference to `__kmpc_for_static_init_4'

Which compiler do you use?

I am frequently compiling GRASS GIS on Scientific Linux 6 and 7
systems, no problems so far.

best
Markus