[ncl-install] Mysterious missing symbol error in NCL libraries
Mary Haley
haley at ucar.edu
Mon May 11 20:05:43 MDT 2015
Hi Rich,
I was offline for most of the day, so I'm glad you figured out a solution.
The other way you can get around this problem is to edit the
$NCARG/config/Site.local file and add the -I/usr/include/freetype2 path to
the end of the "#define IncSearch" line that you hopefully already have in
that file.
Then, you can either run "make Everything" from the top $NCARG directory to
make sure all the Makefiles get regenerated, or else you can simply just
remake the Makefiles and start the build from where you left off with:
cd $NCARG
make Makefiles includes depend all install
This is pretty much like doing a "make Everything", except the "make clean"
step is omitted.
--Mary
On Mon, May 11, 2015 at 6:34 PM, Cook, Rich <cook47 at llnl.gov> wrote:
> ... and I figured a way to do this. It's not elegant:
>
> sed -i'' -E -e "s:(-ansi -openmp):\1 -I/usr/include/freetype2:"
> config/LINUX
>
> Problem solved; thanks for the help!
> -- Rich
>
>
> On May 11, 2015, at 1:46 PM, Cook, Rich <cook47 at llnl.gov> wrote:
>
> I'm attaching my entire build log per your request.
> I've looked at
> https://www.ncl.ucar.edu/Download/build_from_src.shtml#ConfigurationFiles
> but I just can't seem to figure out which files to add the include flags I
> need to make it see freetype on our system.
> I tried
> make Everything CFLAGS=-I/usr/include/freetype2
> but this caused problems.
> Thanks
> -- Rich
>
>
> On May 11, 2015, at 12:33 PM, Cook, Rich <cook47 at llnl.gov> wrote:
>
> What's the easy way top tell NCAR where freetype lives? I see
> /usr/include/freetype2/freetype/config/ftheader.h
> but I guess that's not NCAR's assumed location.
> Thanks
> -- Rich
>
> On May 11, 2015, at 11:25 AM, Cook, Rich <cook47 at llnl.gov> wrote:
>
> Hi, aha, yes, you are correct.
> I guess looking for the word "Error" in my build log was too obvious an
> exercise for me. :-|
> It would be good if the build would fail instead of appearing to complete,
> but it looks like I have a way forward here. I need to install freetype it
> looks like...
>
> intel: icc-14.0.174 -ansi -openmp -O -I../../../.././include
> -I/usr/include/X11 -DLinux -DCTXT -DX11 -DPS -DPDF -DPIX -DSYSV
> -D_POSIX_SOURCE -D_XOPEN_SOURCE -DByteSwapped -DNeedFuncProto -c -o
> cro_device.o cro_device.c
> intel: In file included from /usr/include/cairo/cairo-ft.h(47),
> intel: from cro.h(147),
> intel: from cro_device.c(26):
> intel: /usr/include/ft2build.h(56): catastrophic error: cannot open source
> file "freetype/config/ftheader.h"
> intel: #include <freetype/config/ftheader.h>
> intel: ^
> intel:
> intel: compilation aborted for cro_device.c (code 4)
> intel: make[5]: *** [cro_device.o] Error 4
> intel: make[5]: Leaving directory
> `/tmp/dpkg-mkdeb.ljmPKZOP1X/src/ncl_ncarg-6.3.0/ncarg2d/src/libncarg_gks/cdrivers'
>
>
>
> On May 11, 2015, at 11:01 AM, Mary Haley <haley at ucar.edu> wrote:
>
> Hi Richard,
>
> The likely issue is that the GKS library didn't get fully built, and the
> culprit is probably the "cdrivers" directory under the
> "$NCARG/ncarg2d/src/libncarg_gks" directory. There's some source code in
> that directory that depends on cairo, which is an external package required
> by NCL V6.3.0. It wasn't required by NCL V6.0.0. My guess is that the build
> failed because it couldn't find some required include files by cairo and/or
> freetype.
>
> Can you email me the full build log so I can see where the error is?
>
> --Mary
>
>
> On Mon, May 11, 2015 at 10:26 AM, Cook, Rich <cook47 at llnl.gov> wrote:
>
> Hello,
> I'm sorry if this is a known issue; I am the maintainer of our cluster
> installation of NCAR on our machines. A user recently complained to me
> that he is having linker errors when trying build against ncar:
>
> //
> -------------------------------------------------------------------------
> ifort shok3.o /usr/local/lib/libmbase.a
> /usr/local/tools/ncar-intel-6.3.0/lib/libncarg.a
> /usr/local/tools/ncar-intel-6.3.0/lib/libncarg_gks.a
> /usr/local/tools/ncar-intel-6.3.0/lib/libncarg_c.a
> /usr/local/tools/ncar-intel-6.3.0/lib/libcgm.a /usr/lib64/libX11.so -o shok3
> /usr/local/tools/ncar-intel-6.3.0/lib/libncarg_gks.a(gziqwk.o): In
> function `gziqwk_':
> gziqwk.f:(.text+0x123): undefined reference to `ggkwdr_'
> /usr/local/tools/ncar-intel-6.3.0/lib/libncarg_gks.a(gztowk.o): In
> function `gztowk_':
> gztowk.f:(.text+0x2ce): undefined reference to `ggkwdr_'
> gztowk.f:(.text+0x5a2): undefined reference to `ggkwdr_'
> gztowk.f:(.text+0x984): undefined reference to `ggkwdr_'
> make: *** [shok3] Error 1
> //
> -------------------------------------------------------------------------
>
> Naturally I googled to find a solution but none of the postings I found
> seemed relevant to me -- they all referenced some w_char problem from ages
> past, which I don't see any hint of in my build logs.
>
> If the user tries building against our 6.0.0 build, he does not have
> this problem -- nm reveals that the symbol lives in libncarg_c.a
> I looked and ggkwdr() is a function from file fort_c.c
> When I compared the build logs of the two versions, I see that in 6.0.0,
> fort_c.o gets archived into libncarg_c.a, which then gets installed into
> the INSTALL_DIR/lib:
>
> //
> -------------------------------------------------------------------------
> ar vru ../libncarg_gks.a fort_c.o gksc.o transform.o gksP.o gks_device.o
> ctxt_device.o ctxt.o ctxt_conv.o xdevice.o font.o text.o x_conv.o
> xattribute.o xcontrol.o xinquiry.o xoutput.o psdevice.o ps.o ps_conv.o
> psfill.o pdf.o pdfdevice.o pdf_conv.o pdffill.o pixcontrol.o
> pixoutput.o pixdevice.o pix_conv.o pixattribute.o pixinquiry.o pixwrite_xwd.o
>
> ....
> intel: ranlib libncarg_gks.a
> intel: Installing libncarg_gks.a
> intel: ranlib /usr/local/tools/ncar-intel-6.3.0/lib/libncarg_gks.a
> //
> -------------------------------------------------------------------------
>
> But in the build log for version 6.3.0, fort_c.o gets stuffed into a
> library called libbasegks.a, and this library never seems to be installed
> anywhere or used:
>
> //
> -------------------------------------------------------------------------
> intel: ar vru ../libbasegks.a fort_c.o gksc.o transform.o gksP.o argb.o
> ....
> (no more mention of libbasegks.a in the build log from here)
> //
> -------------------------------------------------------------------------
>
> Can someone help me understand what's wrong with my build process?
> I'm building them both identically, using the config/LINUX.INTEL
> configuration.
>
> Thanks!
>
> --
> ✐Richard Cook
> ✇ Lawrence Livermore National Laboratory
> Bldg-453 Rm-4024, Mail Stop L-557
> 7000 East Avenue, Livermore, CA, 94550, USA
> <emoji_u260e.png> (office) (925) 423-9605
> <emoji_u260e.png> (fax) (925) 423-6961
> ---
> Information Management & Graphics Grp., Services & Development Div.,
> Integrated Computing & Communications Dept.
> (opinions expressed herein are mine and not those of LLNL)
>
>
>
>
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>
>
> --
> ✐Richard Cook
> ✇ Lawrence Livermore National Laboratory
> Bldg-453 Rm-4024, Mail Stop L-557
> 7000 East Avenue, Livermore, CA, 94550, USA
> [image: ☎] (office) (925) 423-9605
> [image: ☎] (fax) (925) 423-6961
> ---
> Information Management & Graphics Grp., Services & Development Div.,
> Integrated Computing & Communications Dept.
> (opinions expressed herein are mine and not those of LLNL)
>
>
>
>
> --
> ✐Richard Cook
> ✇ Lawrence Livermore National Laboratory
> Bldg-453 Rm-4024, Mail Stop L-557
> 7000 East Avenue, Livermore, CA, 94550, USA
> [image: ☎] (office) (925) 423-9605
> [image: ☎] (fax) (925) 423-6961
> ---
> Information Management & Graphics Grp., Services & Development Div.,
> Integrated Computing & Communications Dept.
> (opinions expressed herein are mine and not those of LLNL)
>
>
>
>
> --
> ✐Richard Cook
> ✇ Lawrence Livermore National Laboratory
> Bldg-453 Rm-4024, Mail Stop L-557
> 7000 East Avenue, Livermore, CA, 94550, USA
> [image: ☎] (office) (925) 423-9605
> [image: ☎] (fax) (925) 423-6961
> ---
> Information Management & Graphics Grp., Services & Development Div.,
> Integrated Computing & Communications Dept.
> (opinions expressed herein are mine and not those of LLNL)
>
>
>
> <intel-log.txt.gz>
>
>
> --
> ✐Richard Cook
> ✇ Lawrence Livermore National Laboratory
> Bldg-453 Rm-4024, Mail Stop L-557
> 7000 East Avenue, Livermore, CA, 94550, USA
> [image: ☎] (office) (925) 423-9605
> [image: ☎] (fax) (925) 423-6961
> ---
> Information Management & Graphics Grp., Services & Development Div.,
> Integrated Computing & Communications Dept.
> (opinions expressed herein are mine and not those of LLNL)
>
>
>
>
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