Subject: [Dorsal-dev] Error building dolfin-0.9.0. with Dorsal on Mac OS Tiger

From: Aron Wahlberg <[email-masked]>
Date: Fri, 20 Feb 2009 15:29:43 +0100

Ok,

I've removed mtl from platforms/tiger.platform in order to be able to  
continue with the installation. I also had to do a "make clean" in  
the folder for Trilinos to be able to rerun ./dorsal.sh. Though, a  
new problem arised, now when building Dolfin. Any suggestions?

Aron

#############################################################
...
/usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: internal link edit  
command failed
scons: *** [dolfin/libdolfin.dylib] Error 1
scons: building terminated because of errors.
---------------------------------------------------------
If there were no errors, run

     scons install

to install DOLFIN on your system. Note that you may need
to be root in order to install. To specify an alternative
installation directory, run

     scons install prefix=<path>

You may also run ./scons.local for a local installation
in the DOLFIN source tree.

You can compile all the demo programs in the subdirectory
demo by running

    scons enableDemos=yes

---------------------------------------------------------
Failure with exit status: 2
Exit message: There was a problem building dolfin-0.9.0.
##############################################################

---

From: Harish Narayanan <[email-masked]>
Date: Fri, 20 Feb 2009 16:09:52 +0100

> new problem arised, now when building Dolfin. Any suggestions?

Good, so I presume you've made it all the way down to the final package,
DOLFIN (plus or minus a couple of things along the way :)). You need to
install libtool via fink, and then create symlinks for glibtool and
glibtoolize called libtool and libtoolize.

Do the same sort of thing you needed to do to get mpi working.

Harish

---

From: Aron Wahlberg <[email-masked]>
Date: Fri, 20 Feb 2009 21:41:55 +0100

I have tried to make the right symlinks after installing libtool via  
fink successfully. It still doesn't work though. But there are a lot  
of files with the names glibtool(ize) and I'm not sure of which to  
make symlinks for. ("sudo ln -s /sw/bin/glibtoolize /sw/bin/ 
libtoolize"  and similar, right?) I have also dubbel checked so I'm  
really sure I gave them the right names, no typos...

I've tried with the following
/sw/bin/glibtool
/usr/bin/glibtoolize
/Developer/usr/bin/glibtoolize

Also, for the following I get "file exist" when trying to create  
symlinks
/sw/bin/glibtoolize
/usr/bin/glibtool
/Developer/usr/bin/glibtool
/Developer/usr/bin/glibtoolize

But it still doesn't work. Same error as before. Exit status 2.

Below are the files I find with name glibtool, which also seems to  
include glibtoolize...

-Aron

###################################################################

bash-3.2$ locate glibtool
/Developer/ADC Reference Library/documentation/DeveloperTools/glibtool
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_1.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_10.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_11.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_12.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_13.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_14.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_15.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_16.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_17.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_18.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_2.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_3.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_4.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_5.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_6.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_7.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_8.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_9.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_abt.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_fot.html
/Developer/ADC Reference Library/documentation/DeveloperTools/ 
glibtool/libtool_toc.html
/Developer/usr/bin/glibtool
/Developer/usr/bin/glibtoolize
/Developer/usr/share/man/man1/glibtool.1
/sw/bin/glibtool
/sw/bin/glibtoolize
/usr/bin/glibtool
/usr/bin/glibtoolize
/usr/share/man/man1/glibtool.1

######################################################################## 
####

---

From: Aron Wahlberg <[email-masked]>
Date: Mon, 23 Feb 2009 11:12:00 +0100

Hi again,

So it seems libtool and libtoolize  are pointing to the right files  
then. But I still get the same error though.
I find libtriutils.dylib (and .a) when looking through finder, but  
not with 'locate', 'which' or 'find' in the terminal.
Any suggestions of what may be wrong?

Aron

###################

ld: warning can't open dynamic library: libtriutils.dylib referenced  
from: /Users/aronwahlberg/Work/FEniCS/build/lib/libml.dylib (checking  
for undefined symbols may be affected) (No such file or directory,  
errno = 2)
ld: common symbols not allowed with MH_DYLIB output format with the - 
multi_module option
/Users/aronwahlberg/Work/FEniCS/build/lib/libscotch.a(parser_yy.o)  
definition of common _yychar (size 16)
/Users/aronwahlberg/Work/FEniCS/build/lib/libscotch.a(parser_yy.o)  
definition of common _yylval (size 256)
/Users/aronwahlberg/Work/FEniCS/build/lib/libscotch.a(parser_yy.o)  
definition of common _yynerrs (size 16)
/Users/aronwahlberg/Work/FEniCS/build/lib/libscotch.a(parser_ll.o)  
definition of common _yyleng (size 16)
/Users/aronwahlberg/Work/FEniCS/build/lib/libscotch.a(parser_ll.o)  
definition of common _yytext (size 16)
/usr/libexec/gcc/i686-apple-darwin8/4.0.1/libtool: internal link edit  
command failed
scons: *** [dolfin/libdolfin.dylib] Error 1
scons: building terminated because of errors.
---------------------------------------------------------
If there were no errors, run

     scons install

    scons enableDemos=yes

######################

21 feb 2009 kl. 20.12 skrev Harish Narayanan:

> Aron Wahlberg wrote:
>> I'm not sure if they point to the right versions in fink? Seems like
>> they point towards the files in the same folder...  I've tried to  
>> figure
>> out where they should point but didn't manage to. This is how it  
>> looks...
>>
>> --------------------------------------------------------------------- 
>> --------------------------------
>>
>> bash-3.2$ which libtool
>> /sw/bin/libtool
>> bash-3.2$ which libtoolize
>> /sw/bin/libtoolize
>> bash-3.2$ ls -l /sw/bin/libtool
>> lrwxr-xr-x   1 root  admin  16 Feb 20 18:40 /sw/bin/libtool ->
>> /sw/bin/glibtool
>> bash-3.2$ ls -l /sw/bin/libtoolize
>> lrwxr-xr-x   1 root  admin  19 Feb 20 18:26 /sw/bin/libtoolize ->
>> /sw/bin/glibtoolize
>> --------------------------------------------------------------------- 
>> ---------------------------------
>>
>>
>> How do I change where they point in case I need to?
>
> You've made them point to the versions in fink, since everything  
> in /sw
> is fink related.
>
> If you need to change a link to another file, you do 'ln -sf something
> somewhere', where 'somewhere' is the new location.
>
> Harish

---

From: Anders Logg <[email-masked]>
Date: Mon, 23 Feb 2009 13:26:31 +0100

Have you tried without SCOTCH and Trilinos? I doubt you will be using
any of them for your project.

-- 
Anders

On Mon, Feb 23, 2009 at 11:12:00AM +0100, Aron Wahlberg wrote:
> _______________________________________________
> Dorsal-dev mailing list
> [email-masked]
> http://fenics.org/mailman/listinfo/dorsal-dev

---

From: Erik Larsson <[email-masked]>
Date: Mon, 23 Feb 2009 13:36:02 +0100 (CET)

> any of them for your project.

Yes, I have tried both with all the package that originally was included 
in rhel4.platform and with excluding gmp, mtl, trilinos, parmetis and 
scotch. 
Neither this is included in the manual install list at 
http://www.fenics.org/wiki/A_detailed_guide_to_installing_DOLFIN

The result is still the same. I am not able to build dolfin itself.

Regards, Erik.

---

From: Harish Narayanan <[email-masked]>
Date: Mon, 23 Feb 2009 13:39:13 +0100

> The result is still the same. I am not able to build dolfin itself.

I have a feeling the gcc is too old, and it is unable to handle some of
the fancier C++. Could you do a 'gcc --version'?

Harish

---

From: Anders Logg <[email-masked]>
Date: Mon, 23 Feb 2009 13:40:53 +0100

>> any of them for your project.

This was actually in response to Aron Wahlberg, but I guess it applies
to you as well. :-)

-- 
Anders

> scotch. Neither this is included in the manual install list at

---

From: Harish Narayanan <[email-masked]>
Date: Mon, 23 Feb 2009 13:42:30 +0100

> Any suggestions of what may be wrong?

One of the libtools will work, but I don't have a Tiger machine to
quickly test this. Try:

a. Installing different libtools via fink ('fink list libtool' provides
three options), and pointing the symlinks libtool, libtoolize to each of
them in turn.
b. Point libtool, libtoolize to the system glibtool, glibtoolize (in
/usr/bin).

Harish

---

From: Erik Larsson <[email-masked]>
Date: Mon, 23 Feb 2009 13:43:21 +0100 (CET)

> the fancier C++. Could you do a 'gcc --version'?

gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9)

/Erik.
--

---

From: Anders Logg <[email-masked]>
Date: Mon, 23 Feb 2009 13:45:03 +0100

> gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9)

That's almost three years old! I wouldn't expect that to work.

-- 
Anders

---

From: Harish Narayanan <[email-masked]>
Date: Mon, 23 Feb 2009 13:46:17 +0100

> gcc (GCC) 3.4.6 20060404 (Red Hat 3.4.6-9)

I thought this might be your problem, but I looked at your build log
again, and it not using this gcc (it is using gcc4, by dorsal design).

Do a gcc4 --version also.

Harish

---

From: Erik Larsson <[email-masked]>
Date: Mon, 23 Feb 2009 13:52:58 +0100 (CET)

> Do a gcc4 --version also.

Sorry Aron that I missmatched our two cases.

The gcc4 version that I have is
gcc4 (GCC) 4.1.2 20070626 (Red Hat 4.1.2-14)

/Erik.
--