[overture] Re: Installing Overture.v24 on Mac OS X

  • From: Bill Henshaw <henshaw@xxxxxxxx>
  • To: "kmaki@xxxxxxx" <kmaki@xxxxxxx>, freelists <overture@xxxxxxxxxxxxx>
  • Date: Mon, 09 Jan 2012 11:37:43 -0800

Hi Kara,
It seems likely that you have a problem with mixing different versions of gcc, g++, 
and gfortran and/or the libraries.
Normally I would change my path to include the gcc 4.3 bin directory (I have 
forgotten what I do on the Mac). You may need to make sure that the g++ and
gfortran commands are also being found in the right directory (in additon to gcc). 

...Bill

Kara L. Maki wrote:

Hi Bill,
Thanks again for your help. In /opt/local/lib, I don't see a different version of libgfortran.a or libgfortran.so. libgfortran.a is in /opt/local/lib/gcc43. Do I need to change one of the environment variables to reflect this? Using macports, I installed gcc4.3 and then I made a soft link following the instruction (ln -s gcc-mp-4.3 gcc). Could I have done this incorrectly? 
Kara


On 1/2/12 6:11 PM, Bill Henshaw wrote:

Hi Professor Kara,
Happy New Year! Note that your post to the overture mailing list was not allowed since kmaki@xxxxxxx is not subscribed. It looks like you have subscribed as kara.l.maki@xxxxxxxxx and klmsma@xxxxxxx 

Regarding your trouble below.  The loader cannot find a gfortran routine
  Undefined symbols:
   "__gfortran_transfer_real_write"

I wonder if there is some confusion as to the location of the gfortran
libraries. From the load line:
    -L/opt/local/lib -lhdf5 -ljpeg -lz  -lgfortran
the loader may be looking in /opt/local/lib for the gfortran libs.
It could be there is a version of libgfortran.a (or .so?) in /opt/local/lib which is not the same as the one in /opt/local/lib/gcc43
I wonder, did you install your own version of gcc 4.3.6 ? 
Regards,
  Bill
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Date: Mon, 02 Jan 2012 13:55:54 -0500
From: "Kara L. Maki" <kmaki@xxxxxxx>
Subject: Installing Overture.v24 on Mac OS X
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Hello,

I am running into a problem building Overture on my new machine.
Unfortunately, I have not been able to find a fix searching the web or
the Overture mailing list. In the make process in the installation of
Overture, I am getting the following complaint:

touch Ogmg_date
ar ruv   libOverture_static.a ../static/*.o ../boxlib/*.o
r - ../static/GLwDrawA.o
r - ../static/GLwMDrawA.o
r - ../static/OvertureInit.o
r - ../static/RapsodiInit.o
r - ../static/ReferenceCounting.o
r - ../static/initOvertureGlobalVariables.o
r - ../static/initStaticMappingVariables.o
r - ../static/memoryUsage.o
r - ../static/mogl.o
r - ../static/xColours.o
r - ../boxlib/AliasedDPtr.o
r - ../boxlib/ArithFab.o
r - ../boxlib/Box.o
r - ../boxlib/BoxArray.o
r - ../boxlib/BoxAssoc.o
r - ../boxlib/BoxDomain.o
r - ../boxlib/BoxLib.o
r - ../boxlib/BoxList.o
r - ../boxlib/FArrayBox.o
r - ../boxlib/FPC.o
r - ../boxlib/FabConv.o
r - ../boxlib/IndexType.o
r - ../boxlib/IntVect.o
r - ../boxlib/MultiFab.o
r - ../boxlib/OrderedFab.o
r - ../boxlib/Orientation.o
r - ../boxlib/ParmParse.o
r - ../boxlib/Utility.o
r - ../boxlib/aString.o
/usr/bin/ranlib: file: libOverture_static.a(AliasedDPtr.o) has no symbols
/usr/bin/ranlib: file: libOverture_static.a(Pointers.o) has no symbols
ranlib libOverture_static.a
ranlib: file: libOverture_static.a(AliasedDPtr.o) has no symbols
ranlib: file: libOverture_static.a(Pointers.o) has no symbols
touch lib_date
g++ -o libOverture.dylib -dynamiclib -single_module -Wl-bind_at_load
-L/Users/klmsma/Overture/Overture.v24/lib
-L/opt/local/lib/perl5/5.12.3/darwin-multi-2level/CORE -lperl -ldl -lm
-lutil -lc -L/opt/local/lib -lGL -lGLU  -L/opt/local/lib -lXm
-L/opt/local/lib -lXpm -lXp -lXt -lXmu -lXi -lXext -lX11  -lm
-L/opt/local/lib -lhdf5 -ljpeg -lz  -lgfortran
-L/Users/klmsma/Overture/A++P++-0.8.0/gcc-4.3/A++/install/lib -lApp
-lApp_static  ../DataBase/*.o ../GridFunction/*.o ../templates/*.o \
              ../Grid/*.o ../Mapping/*.o ../Oges/*.o
../GridGenerator/*.o ../Ogshow/*.o ../mapUtil/*.o \
          ../otherStuff/*.o
-L/opt/local/lib/perl5/5.12.3/darwin-multi-2level/CORE -lperl -ldl -lm
-lutil -lc -L/opt/local/lib -lGL -lGLU  -L/opt/local/lib -lXm
-L/opt/local/lib -lXpm -lXp -lXt -lXmu -lXi -lXext -lX11  -lm
-L/Users/klmsma/Overture/Overture.v24/lib -lOverture_static
-L/opt/local/lib -lhdf5 -ljpeg -lz  -lgfortran
-L/Users/klmsma/Overture/A++P++-0.8.0/gcc-4.3/A++/install/lib -lApp
-lApp_static  -Wl-weak-framework,vecLib
Undefined symbols:
   "__gfortran_transfer_real_write", referenced from:
_rdplt3dqs_ in dpm.o
_rdplt3dqs_ in dpm.o
_rdplt3dqs_ in dpm.o
_rdplt3dqd_ in dpm.o

followed by a long list of .o files.  The final error message reads

ld: symbol(s) not found
collect2: ld returned 1 exit status
make[1]: *** [libso_date] Error 1
make: *** [all] Error 2

I am using version 4.3.6 of gcc.

MATHKLMIMAC:Overture.v24 klmsma$ gfortran -v
Using built-in specs.
Target: x86_64-apple-darwin10
Configured with: ../gcc-4.3.6/configure --prefix=/opt/local
--build=x86_64-apple-darwin10
--enable-languages=c,c++,objc,obj-c++,java,fortran
--libdir=/opt/local/lib/gcc43 --includedir=/opt/local/include/gcc43
--infodir=/opt/local/share/info --mandir=/opt/local/share/man
--datadir=/opt/local/share/gcc43 --with-local-prefix=/opt/local
--with-system-zlib --disable-nls --program-suffix=-mp-4.3
--with-gxx-include-dir=/opt/local/include/gcc43/c++/
--with-gmp=/opt/local --with-mpfr=/opt/local --disable-multilib
Thread model: posix
gcc version 4.3.6 (GCC)

I would greatly appreciate any suggestions.

Happy New Year,
Kara

--
Kara L. Maki, Ph.D.
Assistant Professor
School of Mathematical Sciences
Rochester Institute of Technology
Gosnell Hall (Bldg. 8), Room 3250
P: (585) 475-2541
kmaki@xxxxxxx
http://people.rit.edu/klmsma


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<html>
  <head>

    <meta http-equiv="content-type" content="text/html; ">
  </head>
  <body bgcolor="#FFFFFF" text="#000000">
    Hello,
    <br>
    <br>
    I am running into a problem building Overture on my new machine.
    Unfortunately, I have not been able to find a fix searching the web
    or the Overture mailing list. In the make process in the
    installation of Overture, I am getting the following complaint:
    <br>
    <br>
    touch Ogmg_date
    <br>
    ar ruv&nbsp;&nbsp; libOverture_static.a ..<i class="moz-txt-slash"><span
        class="moz-txt-tag">/</span>static<span 
class="moz-txt-tag">/</span></i>*.o
    ..<i class="moz-txt-slash"><span class="moz-txt-tag">/</span>boxlib<span
        class="moz-txt-tag">/</span></i>*.o
    <br>
    r - ../static/GLwDrawA.o
    <br>
    r - ../static/GLwMDrawA.o
    <br>
    r - ../static/OvertureInit.o
    <br>
    r - ../static/RapsodiInit.o
    <br>
    r - ../static/ReferenceCounting.o
    <br>
    r - ../static/initOvertureGlobalVariables.o
    <br>
    r - ../static/initStaticMappingVariables.o
    <br>
    r - ../static/memoryUsage.o
    <br>
    r - ../static/mogl.o
    <br>
    r - ../static/xColours.o
    <br>
    r - ../boxlib/AliasedDPtr.o
    <br>
    r - ../boxlib/ArithFab.o
    <br>
    r - ../boxlib/Box.o
    <br>
    r - ../boxlib/BoxArray.o
    <br>
    r - ../boxlib/BoxAssoc.o
    <br>
    r - ../boxlib/BoxDomain.o
    <br>
    r - ../boxlib/BoxLib.o
    <br>
    r - ../boxlib/BoxList.o
    <br>
    r - ../boxlib/FArrayBox.o
    <br>
    r - ../boxlib/FPC.o
    <br>
    r - ../boxlib/FabConv.o
    <br>
    r - ../boxlib/IndexType.o
    <br>
    r - ../boxlib/IntVect.o
    <br>
    r - ../boxlib/MultiFab.o
    <br>
    r - ../boxlib/OrderedFab.o
    <br>
    r - ../boxlib/Orientation.o
    <br>
    r - ../boxlib/ParmParse.o
    <br>
    r - ../boxlib/Utility.o
    <br>
    r - ../boxlib/aString.o
    <br>
    /usr/bin/ranlib: file: libOverture_static.a(AliasedDPtr.o) has no
    symbols
    <br>
    /usr/bin/ranlib: file: libOverture_static.a(Pointers.o) has no
    symbols
    <br>
    ranlib libOverture_static.a
    <br>
    ranlib: file: libOverture_static.a(AliasedDPtr.o) has no symbols
    <br>
    ranlib: file: libOverture_static.a(Pointers.o) has no symbols
    <br>
    touch lib_date
    <br>
    g++ -o libOverture.dylib -dynamiclib -single_module -Wl-bind_at_load
    -L/Users/klmsma/Overture/Overture.v24/lib&nbsp;
    -L/opt/local/lib/perl5/5.12.3/darwin-multi-2level/CORE -lperl -ldl
    -lm -lutil -lc -L/opt/local/lib -lGL -lGLU&nbsp; -L/opt/local/lib -lXm&nbsp;
    -L/opt/local/lib -lXpm -lXp -lXt -lXmu -lXi -lXext -lX11&nbsp; -lm
    -L/opt/local/lib -lhdf5 -ljpeg -lz&nbsp; -lgfortran
    -L/Users/klmsma/Overture/A++P++-0.8.0/gcc-4.3/A++/install/lib -lApp
    -lApp_static&nbsp; ..<i class="moz-txt-slash"><span 
class="moz-txt-tag">/</span>DataBase<span
        class="moz-txt-tag">/</span></i>*.o ..<i class="moz-txt-slash"><span
        class="moz-txt-tag">/</span>GridFunction<span
        class="moz-txt-tag">/</span></i>*.o ..<i class="moz-txt-slash"><span
        class="moz-txt-tag">/</span>templates<span 
class="moz-txt-tag">/</span></i>*.o
    \
    <br>
    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ..<i 
class="moz-txt-slash"><span class="moz-txt-tag">/</span>Grid<span
        class="moz-txt-tag">/</span></i>*.o ..<i class="moz-txt-slash"><span
        class="moz-txt-tag">/</span>Mapping<span 
class="moz-txt-tag">/</span></i>*.o
    ..<i class="moz-txt-slash"><span class="moz-txt-tag">/</span>Oges<span
        class="moz-txt-tag">/</span></i>*.o&nbsp; ..<i 
class="moz-txt-slash"><span
        class="moz-txt-tag">/</span>GridGenerator<span
        class="moz-txt-tag">/</span></i>*.o ..<i class="moz-txt-slash"><span
        class="moz-txt-tag">/</span>Ogshow<span 
class="moz-txt-tag">/</span></i>*.o
    ..<i class="moz-txt-slash"><span class="moz-txt-tag">/</span>mapUtil<span
        class="moz-txt-tag">/</span></i>*.o \
    <br>
    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; ..<i class="moz-txt-slash"><span 
class="moz-txt-tag">/</span>otherStuff<span
        class="moz-txt-tag">/</span></i>*.o
    -L/opt/local/lib/perl5/5.12.3/darwin-multi-2level/CORE -lperl -ldl
    -lm -lutil -lc -L/opt/local/lib -lGL -lGLU&nbsp; -L/opt/local/lib -lXm&nbsp;
    -L/opt/local/lib -lXpm -lXp -lXt -lXmu -lXi -lXext -lX11&nbsp; -lm
    -L/Users/klmsma/Overture/Overture.v24/lib -lOverture_static
    -L/opt/local/lib -lhdf5 -ljpeg -lz&nbsp; -lgfortran
    -L/Users/klmsma/Overture/A++P++-0.8.0/gcc-4.3/A++/install/lib -lApp
    -lApp_static&nbsp; -Wl-weak-framework,vecLib
    <br>
    Undefined symbols:
    <br>
    &nbsp; "__gfortran_transfer_real_write", referenced from:
    <br>
    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <span class="moz-txt-underscore"><span 
class="moz-txt-tag">_</span>rdplt3dqs<span
        class="moz-txt-tag">_</span></span> in dpm.o
    <br>
    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <span class="moz-txt-underscore"><span 
class="moz-txt-tag">_</span>rdplt3dqs<span
        class="moz-txt-tag">_</span></span> in dpm.o
    <br>
    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <span class="moz-txt-underscore"><span 
class="moz-txt-tag">_</span>rdplt3dqs<span
        class="moz-txt-tag">_</span></span> in dpm.o
    <br>
    &nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <span class="moz-txt-underscore"><span 
class="moz-txt-tag">_</span>rdplt3dqd<span
        class="moz-txt-tag">_</span></span> in dpm.o
    <br>
    <br>
    followed by a long list of .o files.&nbsp; The final error message reads
    <br>
    <br>
    ld: symbol(s) not found
    <br>
    collect2: ld returned 1 exit status
    <br>
    make[1]: *** [libso_date] Error 1
    <br>
    make: *** [all] Error 2
    <br>
    <br>
    I am using version 4.3.6 of gcc.
    <br>
    <br>
    MATHKLMIMAC:Overture.v24 klmsma$ gfortran -v
    <br>
    Using built-in specs.
    <br>
    Target: x86_64-apple-darwin10
    <br>
    Configured with: ../gcc-4.3.6/configure --prefix=/opt/local
    --build=x86_64-apple-darwin10
    --enable-languages=c,c++,objc,obj-c++,java,fortran
    --libdir=/opt/local/lib/gcc43 --includedir=/opt/local/include/gcc43
    --infodir=/opt/local/share/info --mandir=/opt/local/share/man
    --datadir=/opt/local/share/gcc43 --with-local-prefix=/opt/local
    --with-system-zlib --disable-nls --program-suffix=-mp-4.3
    --with-gxx-include-dir=/opt/local/include/gcc43/c++/
    --with-gmp=/opt/local --with-mpfr=/opt/local --disable-multilib
    <br>
    Thread model: posix
    <br>
    gcc version 4.3.6 (GCC)
    <br>
    <br>
    I would greatly appreciate any suggestions.
    <br>
    <br>
    Happy New Year,
    <br>
    Kara
    <pre class="moz-signature" cols="72">--
Kara L. Maki, Ph.D.
Assistant Professor
School of Mathematical Sciences
Rochester Institute of Technology
Gosnell Hall (Bldg. 8), Room 3250
P: (585) 475-2541
<a class="moz-txt-link-abbreviated" 
href="mailto:kmaki@xxxxxxx";>kmaki@xxxxxxx</a>
<a class="moz-txt-link-freetext" 
href="http://people.rit.edu/klmsma";>http://people.rit.edu/klmsma</a></pre>
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--------------020201050603070804090407--
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.






--
Kara L. Maki, Ph.D.
Assistant Professor
School of Mathematical Sciences
Rochester Institute of Technology
Gosnell Hall (Bldg. 8), Room 3250
P: (585) 475-2541
kmaki@xxxxxxx
http://people.rit.edu/klmsma

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