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[GEMPAK #VTG-818964]: Help building GEMPAK on Cray XT5 with pgi

Hi Mark,

One thing to point out is that pgf77 is an unsupported compiler.  pgf77 does 
not allow a file to be opened by more than once at the same time, at least up 
through version 4.0, which is required for GEMPAK.  You may be able to build 
GEMPAK with pgf77 but you may also run into errors when running the 
executables.  I would suggest using gcc and g77 with openmotif.






> Thanks for all your help so far.  I am still having some problems building
> GEMPAK with PGI 7.2.5 and 8.0.3 on our Cray XT5.  (I can build GEMPAK with
> gcc 4.1.2 and 4.2.4 just fine.)
> 
> The errors are below that I am currently seeing.  I think my question is ­
> can GEMPAK be built with PGI?  If so, what do I need to do to overcome the
> errors below.
> 
> I am now seeing errors like:
> grphgd.o: In function `main':
> /nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/source/pr
> ograms/gd/grphgd/grphgd.c:47: undefined reference to `gg_init_'
> /nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/source/pr
> ograms/gd/grphgd/grphgd.c:60: undefined reference to `gg_sdev_'
> /nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/lib/g
> rphgd.a(ggdriv.o): In function `ggdriv_':
> /nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/source/pr
> ograms/gd/grphgd/ggdriv.f:182: undefined reference to `gg_maps_'
> /nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/lib/g
> dcfil.a(gdcnav.o): In function `gdcnav_':
> /nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/source/pr
> ograms/gd/gdcfil/gdcnav.f:48: undefined reference to `gg_proj_'
> /nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/lib/g
> emlib.a(ipgtpt.o): In function `ip_gtpt_':
> /nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/source/ge
> mlib/ip/ipgtpt.f:103: undefined reference to `gg_zare_'
> 
> 
> I think the undefined references come from:
> pgf77
> -I/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/include
> -I/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/inc
> lude -g -c ggzare.f
> pgf77
> -I/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/include
> -I/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/inc
> lude -g -c ggzsrt.f
> pgcc -DUNDERSCORE -DLinux
> -I/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/include
> -I/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/inc
> lude -I/usr/X11R6/include -g -O  -c ggdvgf.c
> pgcc -DUNDERSCORE -DLinux
> -I/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/include
> -I/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/inc
> lude -I/usr/X11R6/include -g -O  -c ggqbrd.c
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier uchar_t
> by typedef id .Z0000
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 63)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier uchar_t
> by typedef id .Z0001
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 65)
> PGC-S-0040-Illegal use of symbol, uchar_t
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 67)
> PGC-W-0156-Type not specified, 'int' assumed
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 67)
> PGC-S-0035-Syntax error: Recovery attempted by replacing ',' by '='
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 156)
> PGC-S-0035-Syntax error: Recovery attempted by replacing ',' by '!='
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 157)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier uchar_t
> by typedef id .Z0002
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 297)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier uchar_t
> by '}'
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 308)
> PGC-S-0040-Illegal use of symbol, uchar_t
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 309)
> PGC-W-0156-Type not specified, 'int' assumed
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 309)
> PGC-S-0040-Illegal use of symbol, uchar_t
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 310)
> PGC-W-0156-Type not specified, 'int' assumed
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 310)
> PGC-S-0040-Illegal use of symbol, uchar_t
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 311)
> PGC-W-0156-Type not specified, 'int' assumed
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 311)
> PGC-S-0040-Illegal use of symbol, uchar_t
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 324)
> PGC-W-0156-Type not specified, 'int' assumed
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 324)
> .......
> PGC-W-0156-Type not specified, 'int' assumed
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 334)
> PGC-S-0037-Syntax error: Recovery attempted by deleting '}'
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 337)
> PGC-S-0040-Illegal use of symbol, uchar_t
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 335)
> PGC-W-0156-Type not specified, 'int' assumed
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 335)
> PGC-W-0156-Type not specified, 'int' assumed
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 337)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier uchar_t
> by typedef id .Z0003
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 346)
> PGC-S-0035-Syntax error: Recovery attempted by replacing identifier uchar_t
> by '}'
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 357)
> PGC-S-0037-Syntax error: Recovery attempted by deleting '}'
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 376)
> PGC-S-0040-Illegal use of symbol, uchar_t
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 374)
> PGC-F-0008-Error limit exceeded
> (/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/incl
> ude/mel_bufr_types.h: 374)
> PGC/x86-64 Linux 8.0-3: compilation aborted
> make[4]: ***
> [/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/os/linux64/lib/
> gemlib.a(ggqbrd.o)] Error 2
> make[4]: Leaving directory
> `/nics/e/sw/xt5/gempak/5.11.4/sles10.1_pgi7.2.5/GEMPAK5.11.4/gempak/source/g
> emlib/gg'
> 
> 
> 
> 
> 
> On 3/18/09 2:43 PM, "Unidata GEMPAK Support"
> <address@hidden> wrote:
> 
> > Your system configuration is not being guessed correctly by config.guess and
> > config.sub.
> >
> > Try replacing these two files in the directory
> >
> > /sw/xt5/gempak/5.11.4/sl5.2_pgi7.2.5/GEMPAK5.11.4/extlibs/PNG/libpng
> >
> > with the two attached, this may resolve the system configuration.
> >
> >
> > Michael
> >
> >
> >
> >
> >
> >> > The fix you suggested I think is working, but of course a new problem
> >> popped
> >> > up.
> >> >
> >> > Simply, libpng fails during configure:
> >> >
> >> > faheymr@krakenpf8> pwd
> >> > /sw/xt5/gempak/5.11.4/sl5.2_pgi7.2.5/GEMPAK5.11.4/extlibs/PNG/libpng
> >> >
> >> > faheymr@krakenpf8> ./configure
> >> > checking for a BSD-compatible install... /usr/bin/install -c
> >> > checking whether build environment is sane... yes
> >> > checking for gawk... gawk
> >> > checking whether make sets $(MAKE)... yes
> >> > checking whether to enable maintainer-specific portions of Makefiles... 
> >> > no
> >> > checking for gcc... gcc
> >> > checking for C compiler default output file name... a.out
> >> > checking whether the C compiler works... yes
> >> > checking whether we are cross compiling... no
> >> > checking for suffix of executables...
> >> > checking for suffix of object files... o
> >> > checking whether we are using the GNU C compiler... yes
> >> > checking whether gcc accepts -g... yes
> >> > checking for gcc option to accept ISO C89... none needed
> >> > checking for style of include used by make... GNU
> >> > checking dependency style of gcc... gcc3
> >> > checking for a sed that does not truncate output... /usr/bin/sed
> >> > checking build system type... Invalid configuration
> >> `x86_64-unknown-linux-':
> >> > machine `x86_64-unknown-linux' not recognized
> >> > configure: error: /bin/sh ./config.sub x86_64-unknown-linux- failed
> >> >
> >> >
> >> >
> >> > Mark
> >> >
> >> >
> >> >
> >> >
> >> >
> >> > On 3/17/09 4:57 PM, "Unidata GEMPAK Support"
> >> > <address@hidden> wrote:
> >> >
> >>> > > Mark,
> >>> > >
> >>> > > It appears that the environmental variables OS_BIN and OS_LIB are 
> >>> > > being
> >>> > > redefined in your Makeinc.linux64_pgi and that this is the source of 
> >>> > > the
> >>> > > problem.  OS_BIN and OS_LIB are defined in Gemenviron.profile as
> >>> > > $NAWIPS/os/$NA_OS/bin and $NAWIPS/os/$NA_OS/lib, respectively.  If you
> >>> remove
> >>> > > the last two lines from your Makeinc file where these are being
> >>> redefined, I
> >>> > > believe the build will correctly find libnetcdf.a.
> >>> > >
> >>> > >
> >>> > > Michael James
> >>> > > Unidata User Support
> >>> > >
> >>> > >
> >>>>> > >> > GEMPAK Support,
> >>>>> > >> >
> >>>>> > >> > I am having trouble building GEMPAK on a Cray XT5.  I believe I
> >>>>> followed >>
> >> > the
> >>>>> > >> > installation instructions as closely as I could.  I did have to
> >>>>> make a new
> >>>>> > >> > Makeinc (Makeinc.linux64_pgi).  I have attached several files:
> >>>>> build.log
> >>>>> > >> > (which has the error), Makeinc.linux64_pgi, and 
> >>>>> > >> > Gemenviron.profile.
> >>>>> > >> >
> >>>>> > >> > Basically during the make, the make system is unable to find
> >>>>> > >> > /usr/bin/ld:
> >>>>> > >> >
> >>>> > >>
> >>>>
> /nics/e/sw/xt5/gempak/5.11.4/sl5.2_pgi7.2.5/GEMPAK5.11.4/lib/linux64.pgi/lib
> >>>>> > >> > netcdf.a: No such file: No such file or directory
> >>>>> > >> >
> >>>>> > >> > I see that the make system did build libnetcdf.a, just in a
> >>>>> different
> >>>>> > >> > location:
> >>>>> > >> > faheymr@krakenpf7> ls GEMPAK5.11.4/os/linux64/lib
> >>>>> > >> > libexslt.a     libhdf5.la        libnetcdf.la*  libxslt-plugins/
> >>>>> > >> > xsltConf.sh
> >>>>> > >> > libexslt.la*   libhdf5.settings  libxml2.a      libz.a*
> >>>>> > >> > libhdf5.a      libjasper.a       libxml2.la*    pkgconfig/
> >>>>> > >> > libhdf5_hl.a   libjasper.la*     libxslt.a      python2.4/
> >>>>> > >> > libhdf5_hl.la  libnetcdf.a       libxslt.la*    xml2Conf.sh
> >>>>> > >> >
> >>>>> > >> >
> >>>>> > >> > So I am wondering why the make system is looking for all the
> >>>>> libraries in
> >>>>> > >> > one location, yet it places libraries in multiple locations.
> >>>>> > >> >
> >>>>> > >> > Regards,
> >>>>> > >> >
> >>>>> > >> > Mark Fahey
> >>>>> > >> >
> >>>>> > >> >
> >>>>> > >> >
> >>> > >
> >>> > >
> >>> > > Ticket Details
> >>> > > ===================
> >>> > > Ticket ID: VTG-818964
> >>> > > Department: Support GEMPAK
> >>> > > Priority: Normal
> >>> > > Status: Open
> >>> > >
> >>> > >
> >> >
> >> >
> >> >
> >
> >
> > Ticket Details
> > ===================
> > Ticket ID: VTG-818964
> > Department: Support GEMPAK
> > Priority: Normal
> > Status: Open
> >
> 
> 
> 


Ticket Details
===================
Ticket ID: VTG-818964
Department: Support GEMPAK
Priority: Critical
Status: Open