[MITgcm-support] domain size limit?

Ryan Abernathey ryan.abernathey at gmail.com
Tue Dec 3 13:46:05 EST 2013


Ok, so now I am really confused. In order to eliminate the possibility of a
compiler mismatch, I upgraded to the latest set of gcc / gfortran (4.8)
from the mac hpc website:
http://hpc.sourceforge.net/
I stuck them all in a special directory (/usr/local/gcc-4.8)
$ file /usr/local/gcc-4.8/bin/gcc
/usr/local/gcc-4.8/bin/gcc: Mach-O 64-bit executable x86_64
$ file /usr/local/gcc-4.8/bin/gfortran
/usr/local/gcc-4.8/bin/gfortran: Mach-O 64-bit executable x86_64
I am no longer using the gcc that comes with Xcode.

I put this in my optfile
BASEDIR="/usr/local/gcc-4.8"
CC="$BASEDIR/bin/gcc"
FC="$BASEDIR/bin/gfortran"
F90C=$FC
LINK=$FC
CPP="$BASEDIR/bin/cpp -traditional -P"
# and libaries / includes
INCLUDEDIR="$BASEDIR/include"
INCLUDES="-I$BASEDIR/include"
LIBDIR="$BASEDIR/lib"
LIBS="-L$BASEDIR/lib"
FFLAGS="$FFLAGS -arch x86_64"
CFLAGS="-arch x86_64"

I am *still* getting the same error about:
ld: 32-bit RIP relative reference out of range (2149180116 max is +/-4GB):
from _find_alpha_ (0x1001ADD60) to _rholoc.3148 (0x18034E880) in
'_find_alpha_' from find_alpha.o for architecture x86_64

Full optfile is attached. It is a modified version of the
darwin_amd64_gfortran.

-Ryan






On Tue, Dec 3, 2013 at 1:39 PM, Gus Correa <gus at ldeo.columbia.edu> wrote:

> Hi Ryan
>
> Sorry, I meant:
>
> $ file /usr/bin/gcc
>
> or
>
> $ file `which gcc`
>
> This should tell if it is 32-bit or 64-bit
>
> Cheers,
> Gus
>
> On 12/03/2013 01:25 PM, Ryan Abernathey wrote:
>
>> $ which gcc
>> /usr/bin/gcc
>>
>>
>> On Tue, Dec 3, 2013 at 1:21 PM, Gus Correa <gus at ldeo.columbia.edu
>> <mailto:gus at ldeo.columbia.edu>> wrote:
>>
>>     Hi Ryan
>>
>>     Because of the output of 'gcc -v' that you sent.
>>
>>     It says:
>>      >         $ gcc -v
>>      >         Using built-in specs.
>>      >         Target: i686-apple-darwin11\
>>     ...
>>      >         --program-prefix=i686-apple-____darwin11-
>>
>>     --host=x86_64-apple-darwin11
>>      >         --target=i686-apple-darwin11
>>
>>     All the "i686" refer to 32-bit Pentium-type (and later) processors.
>>     Normally 64 bit shows as "x86_64" instead.
>>
>>     If you want to make sure, please send the output of
>>
>>     file `which gcc`
>>
>>     [please note the backquotes]
>>     That would be the best check.
>>
>>     This will tell what type of executable your default gcc 4.2.1 is.
>>
>>     Cheers,
>>     Gus
>>
>>
>>     On 12/03/2013 01:11 PM, Ryan Abernathey wrote:
>>
>>         Gus,
>>
>>         How do you know that my gcc is not 64 bit? This gcc 4.2.1 is the
>>         latest
>>         version available through Apple and, according to this
>>         documentation,
>>         should be able to compile 64 bit no problem:
>>         https://developer.apple.com/__library/mac/documentation/__
>> Darwin/Conceptual/__64bitPorting/building/__building.html
>>
>>         <https://developer.apple.com/library/mac/documentation/
>> Darwin/Conceptual/64bitPorting/building/building.html>
>>
>>         I don't have gcc 4.7.1 installed.
>>
>>         -Ryan
>>
>>
>>         On Tue, Dec 3, 2013 at 12:59 PM, Gus Correa
>>         <gus at ldeo.columbia.edu <mailto:gus at ldeo.columbia.edu>
>>         <mailto:gus at ldeo.columbia.edu <mailto:gus at ldeo.columbia.edu>>__>
>>
>>         wrote:
>>
>>              Hi Ryan
>>
>>              Your gfortran is 64-bit and seems to have been built with
>>         gcc 4.7.1.
>>              However, that is not the gcc 4.2.1, which is 32-bit,
>>              and which seems to take precedence in your PATH.
>>
>>              I wonder if you can locate your gcc 4.7.1, and modify your
>>         PATH to
>>              point to it (Would this break other Mac functionality?
>>         Maybe ...),
>>              and/or point to gcc 4.7.1 full path in the MITgcm
>>         build_options file.
>>              Hopefully this will take care of the link error.
>>
>>              I hope this helps,
>>              Gus Correa
>>
>>
>>              On 12/03/2013 09:13 AM, Ryan Abernathey wrote:
>>
>>                  Thanks guys for the quick response.
>>
>>                  The full error is
>>
>>                  Creating mitgcmuv ...
>>                  gfortran  -o mitgcmuv -fsecond-underscore
>>         -fconvert=big-endian
>>                  -Wunused
>>                  -Wuninitialized  -O3 -funroll-loops chksum_tiled.o
>>         [...all the
>>                  objects...] timer_stats.o  -L/usr/local/lib
>>                  final section layout:
>>                        __TEXT/__text addr=0x100001620, size=0x0029268D,
>>                  fileOffset=0x00001620, type=1
>>                        __TEXT/__text_startup addr=0x100293CB0,
>>         size=0x00000029,
>>                  fileOffset=0x00293CB0, type=1
>>                        __TEXT/__stubs addr=0x100293CDA, size=0x0000013E,
>>                  fileOffset=0x00293CDA, type=27
>>                        __TEXT/__stub_helper addr=0x100293E18,
>>         size=0x00000222,
>>                  fileOffset=0x00293E18, type=31
>>                        __TEXT/__cstring addr=0x100294040, size=0x00002840,
>>                  fileOffset=0x00294040, type=12
>>                        __TEXT/__const addr=0x100296880, size=0x00018440,
>>                  fileOffset=0x00296880, type=0
>>                        __TEXT/__eh_frame addr=0x1002AECC0,
>> size=0x00018330,
>>                  fileOffset=0x002AECC0, type=18
>>                        __DATA/__program_vars addr=0x1002C7000,
>>         size=0x00000028,
>>                  fileOffset=0x002C7000, type=29
>>                        __DATA/__got addr=0x1002C7028, size=0x00000198,
>>                  fileOffset=0x002C7028, type=28
>>                        __DATA/__nl_symbol_ptr addr=0x1002C71C0,
>>         size=0x00000010,
>>                  fileOffset=0x002C71C0, type=28
>>                        __DATA/__la_symbol_ptr addr=0x1002C71D0,
>>         size=0x000001A8,
>>                  fileOffset=0x002C71D0, type=26
>>                        __DATA/__data addr=0x1002C7380, size=0x00000078,
>>                  fileOffset=0x002C7380, type=0
>>                        __DATA/__bss addr=0x1002C73F8, size=0x00000010,
>>                  fileOffset=0x00000000, type=24
>>                        __DATA/__bss4 addr=0x1002C7410, size=0x00000024,
>>                  fileOffset=0x00000000, type=24
>>                        __DATA/__bss5 addr=0x1002C7440, size=0x00007238,
>>                  fileOffset=0x00000000, type=24
>>                        __DATA/__bss3 addr=0x1002CE678, size=0x00000018,
>>                  fileOffset=0x00000000, type=24
>>                        __DATA/__common addr=0x1002CE6A0, size=0x00152F90,
>>                  fileOffset=0x00000000, type=24
>>                        __DATA/__huge addr=0x100421640, size=0x15D3D3B88,
>>                  fileOffset=0x00000000, type=24
>>                  ld: 32-bit RIP relative reference out of range
>>         (2162237024 <tel:%282162237024>
>>         <tel:%282162237024> max is
>>                  +/-4GB): from _find_beta__ (0x100227200) to _rhoden.4514
>>                  (0x18103AE80)
>>                  in '_find_beta__' from find_alpha.o for architecture
>> x86_64
>>                  collect2: error: ld returned 1 exit status
>>                  make[1]: *** [mitgcmuv] Error 1
>>                  make: *** [fwd_exe_target] Error 2
>>
>>                  My detailed compiler versions.
>>
>>                  $ gcc -v
>>                  Using built-in specs.
>>                  Target: i686-apple-darwin11
>>                  Configured with:
>>
>>         /private/var/tmp/llvmgcc42/____llvmgcc42-2336.11~182/src/___
>> _configure
>>                  --disable-checking --enable-werror
>>
>>         --prefix=/Applications/Xcode.____app/Contents/Developer/usr/
>> ____llvm-gcc-4.2
>>                  --mandir=/share/man
>>         --enable-languages=c,objc,c++,____obj-c++
>>                  --program-prefix=llvm-
>>                  --program-transform-name=/^[____cg][^.-]*$/s/$/-4.2/
>>                  --with-slibdir=/usr/lib --build=i686-apple-darwin11
>>
>>         --enable-llvm=/private/var/____tmp/llvmgcc42/llvmgcc42-2336.
>> ____11~182/dst-llvmCore/__Developer/__usr/local
>>                  --program-prefix=i686-apple-____darwin11-
>>         --host=x86_64-apple-darwin11
>>                  --target=i686-apple-darwin11
>>                  --with-gxx-include-dir=/usr/____include/c++/4.2.1
>>
>>
>>                  Thread model: posix
>>                  gcc version 4.2.1 (Based on Apple Inc. build 5658)
>>         (LLVM build
>>                  2336.11.00)
>>                  localhost:build rpa$
>>
>>                  $ gfortran -v
>>                  Using built-in specs.
>>                  COLLECT_GCC=gfortran
>>
>>         COLLECT_LTO_WRAPPER=/usr/____local/libexec/gcc/x86_64-____
>> apple-darwin11.4.0/4.7.1/lto-____wrapper
>>
>>
>>                  Target: x86_64-apple-darwin11.4.0
>>                  Configured with: ../gcc-4.7.1/configure
>>         --enable-languages=fortran
>>                  Thread model: posix
>>                  gcc version 4.7.1 (GCC)
>>
>>
>>                  On Tue, Dec 3, 2013 at 8:53 AM, fancer lancer
>>         <fancer.lancer at gmail.com <mailto:fancer.lancer at gmail.com>
>>         <mailto:fancer.lancer at gmail.__com <mailto:fancer.lancer at gmail.com
>> >>
>>         <mailto:fancer.lancer at gmail. <mailto:fancer.lancer at gmail.>____com
>>
>>
>>         <mailto:fancer.lancer at gmail.__com
>>         <mailto:fancer.lancer at gmail.com>>>> wrote:
>>
>>                       Martin,
>>                       Is it the only error produced by the
>>         compiler/linker or
>>                  there are
>>                       some additional warnings or messages? If so could
>> you,
>>                  please, post
>>                       them here? It can be useful.
>>
>>                       Sincerely,
>>                       -Sergey
>>
>>
>>                       On Tue, Dec 3, 2013 at 4:50 PM, Martin Losch
>>         <Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>>>>
>> wrote:
>>
>>                           Hi Sergey,
>>
>>                           The compiler flags are the ones that you can
>>         find in
>>                           tools/build_options/darwin_____amd64_gfortran,
>>
>>         so no
>>
>>                  32bit related
>>                           parameters (-arch i386 is commented out).
>>
>>                           I saw that thread earlier today, but I cannot
>>         extract
>>                  solution
>>                           for the MITgcm. I have no idea about C, and as
>>         far as I
>>                  know/can
>>                           see, including headers is always the first
>>         stuff in all
>>                  files.
>>
>>                             Martin
>>
>>                           On Dec 3, 2013, at 1:38 PM, fancer lancer
>>         <fancer.lancer at gmail.com <mailto:fancer.lancer at gmail.com>
>>         <mailto:fancer.lancer at gmail.__com <mailto:fancer.lancer at gmail.com
>> >>
>>         <mailto:fancer.lancer at gmail. <mailto:fancer.lancer at gmail.>____com
>>
>>
>>         <mailto:fancer.lancer at gmail.__com
>>         <mailto:fancer.lancer at gmail.com>>>> wrote:
>>
>>          > Hi Martin,
>>          > Ok, you use x86_64 version of compiler. And I suppose you
>>                           don't specify any additional parameters to the
>>         compiler
>>                  like '-m32'.
>>          > Alas I don't have an Apple computer nearby to check the
>>                           actual cause of the problem. But I guess the
>>         clue to
>>                  solve the
>>                           issue may be found in the thread:
>>          >
>>         http://lists.apple.com/____archives/xcode-users/2012/Jun/
>> ____msg00118.html
>>         <http://lists.apple.com/__archives/xcode-users/2012/Jun/
>> __msg00118.html>
>>
>>
>>         <http://lists.apple.com/__archives/xcode-users/2012/Jun/
>> __msg00118.html
>>         <http://lists.apple.com/archives/xcode-users/2012/Jun/
>> msg00118.html>>
>>          > And additional explanation is here:
>>          >
>>         http://lists.apple.com/____archives/xcode-users/2012/Jun/
>> ____msg00126.html
>>         <http://lists.apple.com/__archives/xcode-users/2012/Jun/
>> __msg00126.html>
>>
>>
>>         <http://lists.apple.com/__archives/xcode-users/2012/Jun/
>> __msg00126.html
>>         <http://lists.apple.com/archives/xcode-users/2012/Jun/
>> msg00126.html>>
>>          >
>>          > Sincerely,
>>          > -Sergey
>>          >
>>          >
>>          >
>>          >
>>          > On Tue, Dec 3, 2013 at 3:43 PM, Martin Losch
>>         <Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>
>>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>>>>
>> wrote:
>>          > Hi Sergey,
>>          >
>>          > I don’t know if Ryan’s compiler is the same (probably
>>                           similar), but here’s mine:
>>          >
>>          > csysm15::build> gfortran -v
>>          > Using built-in specs.
>>          > COLLECT_GCC=gfortran
>>          >
>>
>>
>>         COLLECT_LTO_WRAPPER=/usr/____local/libexec/gcc/x86_64-____
>> apple-darwin13.0.0/4.9.0/lto-____wrapper
>>
>>
>>          > Target: x86_64-apple-darwin13.0.0
>>          > Configured with: ../gcc-4.9-20130929/configure
>>                           --enable-languages=c,c++,____fortran
>>
>>
>>          > Thread model: posix
>>          > gcc version 4.9.0 20130929 (experimental) (GCC)
>>          >
>>          > Martin
>>          >
>>          > On Dec 3, 2013, at 9:48 AM, fancer lancer
>>         <fancer.lancer at gmail.com <mailto:fancer.lancer at gmail.com>
>>         <mailto:fancer.lancer at gmail.__com <mailto:fancer.lancer at gmail.com
>> >>
>>         <mailto:fancer.lancer at gmail. <mailto:fancer.lancer at gmail.>____com
>>
>>
>>         <mailto:fancer.lancer at gmail.__com
>>         <mailto:fancer.lancer at gmail.com>>>> wrote:
>>          >
>>          > > Hi Ryan,
>>          > >
>>          > > Could you please, show the result of the command "gfortran
>>                           -v". I suppose, that you used the 32-bit
>>         version of the
>>                  compiler
>>                           that is why you overcame the limit.
>>          > >
>>          > > Sincerely,
>>          > > -Sergey
>>          > >
>>          > >
>>          > > On Tue, Dec 3, 2013 at 12:29 PM, Martin Losch
>>         <Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>
>>
>>         <mailto:Martin.Losch at awi.de <mailto:Martin.Losch at awi.de>>>>
>> wrote:
>>          > > Hi Ryan,
>>          > >
>>          > > I can only reproduce the problem with
>>                           tutorial_barotropic_gyre (and gcc/gfortran 4.9
>>         on OSX
>>                  10.9).
>>          > >
>>          > > By how much do you have to repduce the domain size to make
>>                           it work?
>>          > >
>>          > > The simplest solution that I found: instead of sNy=1600 and
>>                           nSy = 1 use sNy=800 and nSy = 2. It’s a little
>>         bit of
>>                  cheating,
>>                           isn’t it?
>>          > >
>>          > > Martin
>>          > >
>>          > > On Dec 3, 2013, at 6:00 AM, Ryan Abernathey
>>         <ryan.abernathey at gmail.com <mailto:ryan.abernathey at gmail.com>
>>         <mailto:ryan.abernathey at gmail.__com
>>         <mailto:ryan.abernathey at gmail.com>>
>>         <mailto:ryan.abernathey at gmail.
>>         <mailto:ryan.abernathey at gmail.>____com
>>
>>
>>         <mailto:ryan.abernathey at gmail.__com
>>         <mailto:ryan.abernathey at gmail.com>>>>
>>
>>                           wrote:
>>          > >
>>          > > > Dear Super Modelers,
>>          > > >
>>          > > > I found a weird error when trying to compile a large
>>                           domain (500 x 1600 x 1) on a single processor.
>>         On the
>>                  final link
>>                           stage of the build, I get:
>>          > > > ld: 32-bit RIP relative reference out of range
>>         (2162237024 <tel:%282162237024> <tel:%282162237024>
>>         <tel:%282162237024> max is
>>
>>                  +/-4GB): from
>>
>>                           _find_beta__ (0x100227200) to _rhoden.4514
>>         (0x18103AE80) in
>>         '_find_beta__' from find_alpha.o for architecture x86_64
>>          > > > The error disappears if I just reduce sNx * sNy. I guess
>>                           this has something to do with running out of
>>         memory address
>>                           space? Is it weird that "32-bit RIP" is being
>>         used even
>>                  though
>>                           my platform is 64 bit?
>>          > > >
>>          > > > My one weak attempt to overcome this was by adding -fPIC
>>                           to my FFLAGS. No success.
>>          > > >
>>          > > > Is there any way to overcome this problem, or am I
>>                           hitting some kind of fundamental limit to the
>>         domain size?
>>          > > >
>>          > > > Thanks for your suggestions,
>>          > > > Ryan
>>          > > >
>>          > > >
>>          > > > My platform is Mac OX 10.8.5, Intel Core i7, gcc version
>>                           4.2.1 (via xcode), gfortran GNU Fortran (GCC)
>>         4.7.1. My
>>                  optfile
>>                           is the default darwin_amd64_gfortran.
>>          > > >
>>          > > > From my SIZE.h:
>>          > > > &           sNx = 500,
>>          > > > &           sNy = 1600,
>>          > > > &           OLx =   4,
>>          > > > &           OLy =   4,
>>          > > > &           nSx =   1,
>>          > > > &           nSy =   1,
>>          > > > &           nPx =   1,
>>          > > > &           nPy =   1,
>>          > > > &           Nx  = sNx*nSx*nPx,
>>          > > > &           Ny  = sNy*nSy*nPy,
>>          > > > &           Nr  =   1)
>>          > > >
>>          > > >
>>          > > >
>>          > > >
>>          > > > ___________________________________________________
>>
>>
>>          > > > MITgcm-support mailing list
>>          > > > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.
>> org>
>>         <mailto:MITgcm-support at mitgcm.__org
>>         <mailto:MITgcm-support at mitgcm.org>>
>>         <mailto:MITgcm-support at mitgcm.
>>         <mailto:MITgcm-support at mitgcm.>____org
>>         <mailto:MITgcm-support at mitgcm.__org
>>         <mailto:MITgcm-support at mitgcm.org>>>
>>
>>          > > > http://mitgcm.org/mailman/____listinfo/mitgcm-support
>>         <http://mitgcm.org/mailman/__listinfo/mitgcm-support>
>>         <http://mitgcm.org/mailman/__listinfo/mitgcm-support
>>         <http://mitgcm.org/mailman/listinfo/mitgcm-support>>
>>          > >
>>          > >
>>          > > ___________________________________________________
>>
>>
>>          > > MITgcm-support mailing list
>>          > > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
>>         <mailto:MITgcm-support at mitgcm.__org
>>         <mailto:MITgcm-support at mitgcm.org>>
>>         <mailto:MITgcm-support at mitgcm.
>>         <mailto:MITgcm-support at mitgcm.>____org
>>         <mailto:MITgcm-support at mitgcm.__org
>>         <mailto:MITgcm-support at mitgcm.org>>>
>>
>>          > > http://mitgcm.org/mailman/____listinfo/mitgcm-support
>>         <http://mitgcm.org/mailman/__listinfo/mitgcm-support>
>>         <http://mitgcm.org/mailman/__listinfo/mitgcm-support
>>         <http://mitgcm.org/mailman/listinfo/mitgcm-support>>
>>          > >
>>          > > ___________________________________________________
>>
>>
>>          > > MITgcm-support mailing list
>>          > > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org>
>>         <mailto:MITgcm-support at mitgcm.__org
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>>         <mailto:MITgcm-support at mitgcm.>____org
>>         <mailto:MITgcm-support at mitgcm.__org
>>         <mailto:MITgcm-support at mitgcm.org>>>
>>
>>          > > http://mitgcm.org/mailman/____listinfo/mitgcm-support
>>         <http://mitgcm.org/mailman/__listinfo/mitgcm-support>
>>         <http://mitgcm.org/mailman/__listinfo/mitgcm-support
>>         <http://mitgcm.org/mailman/listinfo/mitgcm-support>>
>>          >
>>          >
>>          > ___________________________________________________
>>
>>
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>>         <mailto:MITgcm-support at mitgcm.>____org
>>         <mailto:MITgcm-support at mitgcm.__org
>>         <mailto:MITgcm-support at mitgcm.org>>>
>>
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>>         <http://mitgcm.org/mailman/__listinfo/mitgcm-support
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>>          >
>>          > ___________________________________________________
>>
>>
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>>
>>           ___________________________________________________
>>
>>
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