[visit-users] FW: SILO error

Mark Miller miller86 at llnl.gov
Fri Apr 17 17:05:10 EDT 2009


Hi Matt,

Ok, so, whatever worked for my Intel installation didn't work for yours.

Is there a 'for_main.o' in the lib dir for your intel compiler set?

If so, try adding that to the link line manually, WITHOUT -lifcore_pic.

Also, ultimately what I did on my system was find all libs in intel
compiler's lib dir, add them all to the link line, confirmed it built
without error (which it thankfully did) and then I started removing them
one by one.

I see you've got a 10.1 intel compiler. Let me see if I can find a
system here at LLNL with 10.1 on it and see if I can duplicate with
newer compiler.

Sorry you're having so much difficulty.

Mark

On Fri, 2009-04-17 at 12:55, Jessee, Matthew Anderson wrote:
> Hi Mark,
> 
> I'm still having some trouble.
> 
> 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
> 
> Then, after "make; cd tests;make arrayf77", I get
> 
> /bin/sh ../libtool --tag=CXX   --mode=link
> /opt/intel/cce/10.1.015/bin/icpc  -fPIC  -L/home/m8j/pkgs/64/intel/lib
> -i-static -o arrayf77   -lhdf5 -ldl  -lm
> mkdir .libs
> /opt/intel/cce/10.1.015/bin/icpc -fPIC -i-static -o arrayf77
> -L/home/m8j/pkgs/64/intel/lib /home/m8j/pkgs/64/intel/lib/libhdf5.a -lz
> -ldl -lm  
> /usr/lib/gcc/x86_64-redhat-linux/3.4.6/../../../../lib64/crt1.o(.text+0x
> 21): In function `_start':
> : undefined reference to `main'
> make: *** [arrayf77] Error 1
> 
> Note that my -lifcore_pic is not on the line, so when I manually add it,
> I get:
> 
> [m8j at node37 /home/m8j/pkgs/silo-4.6.2/tests]$
> /opt/intel/cce/10.1.015/bin/icpc -fPIC -i-static -o arrayf77
> /opt/intel/fce/10.1.015/lib/libifcore_pic.a
> -L/home/m8j/pkgs/64/intel/lib /home/m8j/pkgs/64/intel/lib/libhdf5.a -lz
> -ldl -lm
> /opt/intel/fce/10.1.015/lib/libifcore_pic.a(for_main.o)(.text+0x38): In
> function `main':
> : undefined reference to `MAIN__'
> 
> So then, I tried the fortran compiler, just to see if it compiles:
> 
> [m8j at node37 /home/m8j/pkgs/silo-4.6.2/tests]$ ifort -c arrayf77.f -o
> arrayf77.o -I ../src/silo
> arrayf77.f(72): (col. 7) remark: LOOP WAS VECTORIZED.
> arrayf77.f(104): (col. 7) remark: LOOP WAS VECTORIZED.
> 
> After creating arrayf77.o, I try to link w/ ifort (and icpc and icc),
> and I get the same error above:
> 
> [m8j at node37 /home/m8j/pkgs/silo-4.6.2/tests]$ ifort -fPIC -i-static -o
> arrayf77 /opt/intel/fce/10.1.015/lib/libifcore_pic.a
> -L/home/m8j/pkgs/64/intel/lib /home/m8j/pkgs/64/intel/lib/libhdf5.a -lz
> -ldl -lm
> /opt/intel/fce/10.1.015/lib/for_main.o(.text+0x26): In function `main':
> : undefined reference to `MAIN__'
> 
> 
> Thoughts?
> 
> 
> -----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://   
> > > email.ornl.gov/mailman/listinfo/visit-users
> > > > Searchable list archives: https://   
> > > email.ornl.gov/pipermail/visit-users
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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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