[visit-users] FW: SILO error

Jessee, Matthew Anderson jesseema at ornl.gov
Fri Apr 17 16:31:01 EDT 2009


Thanks Tom,

I reordered the variables to autoconf, as well as substituted LIBS= for
FCLIBS=. 

Autoconf got the make command right this time, but I still get the same
error:

[m8j at node37 /home/m8j/pkgs/silo-4.6.2/tests]$ make arrayf77
/bin/sh ../libtool --tag=CXX   --mode=link icpc  -fPIC
-L/home/m8j/pkgs/64/intel/lib -i-static -o arrayf77   -lhdf5 -ldl
/opt/intel/fce/10.1.015/lib/libifcore_pic.a -lm
mkdir .libs
icpc -fPIC -i-static -o arrayf77  -L/home/m8j/pkgs/64/intel/lib
/home/m8j/pkgs/64/intel/lib/libhdf5.a -lz -ldl
/opt/intel/fce/10.1.015/lib/libifcore_pic.a -lm  
/opt/intel/fce/10.1.015/lib/libifcore_pic.a(for_main.o)(.text+0x38): In
function `main':
: undefined reference to `MAIN__'
make: *** [arrayf77] Error 1

-----Original Message-----
From: tom fogal [mailto:tfogal at alumni.unh.edu] 
Sent: Friday, April 17, 2009 4:11 PM
To: VisIt software users community
Subject: Re: [visit-users] FW: SILO error

"Jessee, Matthew Anderson" <jesseema at ornl.gov> writes:
> I'm using the following configure command  (note that I've added
> -lifcore_pic and --disable-hzip --disable-fpzip):
> 
> ./configure --enable-fortran --enable-static --disable-shared
> --with-readline=no --without-exodus --prefix=/home/m8j/pkgs/64/intel
>
--with-hdf5=/home/m8j/pkgs/64/intel/include,/home/m8j/pkgs/64/intel/lib
> CC=/opt/intel/cce/10.1.015/bin/icc
CXX=/opt/intel/cce/10.1.015/bin/icpc
> FC=/opt/intel/fce/10.1.015/bin/ifort
> F77=/opt/intel/fce/10.1.015/bin/ifort -q
> LD=/opt/intel/fce/10.1.015/bin/ifort LDFLAGS=-i-static --disable-silex
> --disable-hzip --disable-fpzip FCLIBS=-lifcore_pic
[snip]

I don't know about the rest, but do note that autoconf normally wants
variables before options.  Thus you probably want:

  ./configure CC=... ... LDFLAGS=... FCLIBS=... --enable-fortran ... \
              --disable-fpzip

The precious variable for additional linker args is just `LIBS'; there
does not appear to be a separate by-default-precious variable for
autoconf based projects (i.e., no `FCLIBS'.).
This might fix your lack of `-lifcore_pic', for example.

HTH,

-tom

> -----Original Message-----
> From: Mark Miller [mailto:miller86 at llnl.gov] 
> Sent: Wednesday, April 15, 2009 8:09 PM
> To: VisIt software users community
> Subject: Re: [visit-users] FW: SILO error
> 
> Hi Matt,
> 
> Ok, so the problem here on my system turned out to be that Autconf's
> tests for lib dependencies for Intel compilers are simply wrong.
> 
> It decides all of these are needed...
> 
> -lifport -lifcore -limf -lm -lipgo -lirc -lirc_s -ldl
> 
> But it looks like the only one that actually is needed is libifcore.
> 
> Next, if I change that to '-lifcore_pic', then the problem goes away.
> 
> So, solution is to add following when invoking configure...
> 
> FCLIBS=-lifcore_pic
> 
> Mark
> 
> 
> On Wed, 2009-04-15 at 18:14 -0400, Jessee, Matthew Anderson wrote:
> > I'm almost positive icpc is a C++ compiler (not both).
> > 
> > As for and equivalent intel library for gnu/linux's -lftrbegin, I do
> not
> > know if there is one for ifort.  Here is an LS of the ifort lib
> > directory, if it helps:
> > 
> > [m8j at node29 /opt/intel/fce/10.1.015/lib]$ ls
> > ../../../cce/10.1.015/lib/*.a
> > -rw-r--r--  1 root root    2350 Mar 12  2008
> > ../../../cce/10.1.015/lib/libcxaguard.a
> > -rw-r--r--  1 root root  850122 Mar 18  2008
> > ../../../cce/10.1.015/lib/libguide.a
> > -rw-r--r--  1 root root 1119866 Mar 18  2008
> > ../../../cce/10.1.015/lib/libguide_stats.a
> > -rw-r--r--  1 root root 4359816 Mar 12  2008
> > ../../../cce/10.1.015/lib/libimf.a
> > -rw-r--r--  1 root root  892072 Mar 18  2008
> > ../../../cce/10.1.015/lib/libiomp5.a
> > -rw-r--r--  1 root root 1164760 Mar 18  2008
> > ../../../cce/10.1.015/lib/libiompprof5.a
> > -rw-r--r--  1 root root   44328 Mar 18  2008
> > ../../../cce/10.1.015/lib/libiompstubs5.a
> > -rw-r--r--  1 root root   42576 Mar 12  2008
> > ../../../cce/10.1.015/lib/libipgo.a
> > -rw-r--r--  1 root root  373560 Mar 12  2008
> > ../../../cce/10.1.015/lib/libirc.a
> > -rw-r--r--  1 root root   12288 Mar 12  2008
> > ../../../cce/10.1.015/lib/libirc_s.a
> > -rw-r--r--  1 root root   44132 Mar 18  2008
> > ../../../cce/10.1.015/lib/libompstub.a
> > -rw-r--r--  1 root root 1168270 Mar 12  2008
> > ../../../cce/10.1.015/lib/libsvml.a
> > [m8j at node29 /opt/intel/fce/10.1.015/lib]$ ls
> > ../../../fce/10.1.015/lib/*.a
> > -rw-r--r--  1 root root    2350 Mar 12  2008
> > ../../../fce/10.1.015/lib/libcxaguard.a
> > -rw-r--r--  1 root root  850122 Mar 18  2008
> > ../../../fce/10.1.015/lib/libguide.a
> > -rw-r--r--  1 root root 1119866 Mar 18  2008
> > ../../../fce/10.1.015/lib/libguide_stats.a
> > -rw-r--r--  1 root root 1601564 Mar 12  2008
> > ../../../fce/10.1.015/lib/libifcore.a
> > -rw-r--r--  1 root root 1462296 Mar 12  2008
> > ../../../fce/10.1.015/lib/libifcore_pic.a
> > -rw-r--r--  1 root root 1632794 Mar 12  2008
> > ../../../fce/10.1.015/lib/libifcoremt.a
> > -rw-r--r--  1 root root 1491326 Mar 12  2008
> > ../../../fce/10.1.015/lib/libifcoremt_pic.a
> > -rw-r--r--  1 root root  603362 Mar 12  2008
> > ../../../fce/10.1.015/lib/libifport.a
> > -rw-r--r--  1 root root 4359816 Mar 12  2008
> > ../../../fce/10.1.015/lib/libimf.a
> > -rw-r--r--  1 root root  892072 Mar 18  2008
> > ../../../fce/10.1.015/lib/libiomp5.a
> > -rw-r--r--  1 root root 1164760 Mar 18  2008
> > ../../../fce/10.1.015/lib/libiompprof5.a
> > -rw-r--r--  1 root root   44328 Mar 18  2008
> > ../../../fce/10.1.015/lib/libiompstubs5.a
> > -rw-r--r--  1 root root   42576 Mar 12  2008
> > ../../../fce/10.1.015/lib/libipgo.a
> > -rw-r--r--  1 root root  373560 Mar 12  2008
> > ../../../fce/10.1.015/lib/libirc.a
> > -rw-r--r--  1 root root   12288 Mar 12  2008
> > ../../../fce/10.1.015/lib/libirc_s.a
> > -rw-r--r--  1 root root   44132 Mar 18  2008
> > ../../../fce/10.1.015/lib/libompstub.a
> > -rw-r--r--  1 root root 1168270 Mar 12  2008
> > ../../../fce/10.1.015/lib/libsvml.a
> > 
> > 
> > Matt
> > 
> > -----Original Message-----
> > From: Mark Miller [mailto:miller86 at llnl.gov] 
> > Sent: Wednesday, April 15, 2009 5:49 PM
> > To: VisIt software users community
> > Subject: Re: [visit-users] FW: SILO error
> > 
> > Hi Matt,
> > 
> > Ok, apologies for confusion ;)
> > 
> > So, I didn't see a response from you. Is icpc C or C++ compiler or
> both?
> > 
> > Mark
> > 
> > On Wed, 2009-04-15 at 17:13 -0400, Jessee, Matthew Anderson wrote:
> > > No.  I do care about the failed fortran tests, and I still can't
get
> > the
> > > Fortran app to correctly link.
> > > 
> > > Matt
> > > 
> > > 
> > > -----Original Message-----
> > > From: Mark Miller [mailto:miller86 at llnl.gov] 
> > > Sent: Wednesday, April 15, 2009 5:11 PM
> > > To: VisIt software users community
> > > Subject: Re: [visit-users] FW: SILO error
> > > 
> > > Just so I understand, are you saying you don't really care about
> > fortran
> > > at this point? Or, you are saying that even though fortran tests
are
> > > failing in the link step, you can at least get your Fortran app to
> > > correctly link?
> > > 
> > > Mark
> > > 
> > > On Wed, 2009-04-15 at 20:46 +0100, Jonathan Mackey wrote:
> > > > For what it's worth, when I last compiled Silo the fortran tests
> > > didn't 
> > > > compile.  I can't remember if this was just with intel compilers
> or
> > > with 
> > > > gnu also.  I don't use fortran so I just ignored it.  I think it
> was
> > 
> > > > just intel compilers (ifort), but I can't be sure and am a bit
too
> > > busy 
> > > > to look into it at the mo.  I'm almost positive it was in the
> > linking 
> > > > step that it failed.
> > > > Jonathan
> > > > 
> > > > Mark Miller wrote:
> > > > > Hello Matt,
> > > > > 
> > > > > Looked through your logs and didn't find any point where a
> fortran
> > > test
> > > > > was actaully compiled. Can you cd to test dir and do
> following...
> > > > > 
> > > > > rm -f arrayf77.o arrayf77
> > > > > make arrayf77
> > > > > 
> > > > > and report back all the output from the command to make
> (including
> > > the
> > > > > compile and link commands it tried).
> > > > > 
> > > > > Part of what may be going on here is that we are linking C and
> C++
> > > code
> > > > > from silo library into a Fortran silo client (arrayf77) and we
> are
> > > or at
> > > > > least should be using a C++ compiler to perform the actual
link.
> > > And,
> > > > > the Makefile.in in the test dir doesn't necessarily set that
up
> > too
> > > > > well.
> > > > > 
> > > > > Mark
> > > > > 
> > > > > On Wed, 2009-04-15 at 14:58 -0400, Jessee, Matthew Anderson
> wrote:
> > > > >> Hello,  I am having some trouble compiling a silo library for
> use
> > > in a
> > > > >> FORTRAN application.  
> > > > >>
> > > > >> Any suggestions?
> > > > >>
> > > > >> Details in email below and attached log files.
> > > > >>
> > > > >> Thanks,
> > > > >> Matt
> > > > >>
> > > > >>
> > > > >> List subscription information: https://  
> > > email.ornl.gov/mailman/listinfo/visit-users
> > > > >> Searchable list archives: https://  
> > > email.ornl.gov/pipermail/visit-users
> > > > >> VisIt Users Wiki: http://    visitusers.org/
> > > > >> Frequently Asked Questions for VisIt: http://  
> > > visit.llnl.gov/FAQ.html
> > > > >>
> > > > --
> > > > List subscription information: https://  
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> > > > Frequently Asked Questions for VisIt: http:// 
> > visit.llnl.gov/FAQ.html
> > > > 
> > > > 
> -- 
> Mark C. Miller, Lawrence Livermore National Laboratory
> email: mailto:miller86 at llnl.gov
> (M/T/W) (925)-423-5901 (!!LLNL BUSINESS ONLY!!)
> (Th/F)  (530)-753-8511 (!!LLNL BUSINESS ONLY!!)
> 
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