[MITgcm-support] domain size limit?

Gus Correa gus at ldeo.columbia.edu
Tue Dec 3 13:21:45 EST 2013


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
>
> 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>> 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> 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>>> 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>>> 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>>> 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>
>          > 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>
>          >
>          > 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>>> 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>>> 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>>> 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>>>
>
>                  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> 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>>
>
>          > > > 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>>
>
>          > > http://mitgcm.org/mailman/__listinfo/mitgcm-support
>         <http://mitgcm.org/mailman/listinfo/mitgcm-support>
>          > >
>          > > _________________________________________________
>          > > MITgcm-support mailing list
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>         <mailto:MITgcm-support at mitgcm.org>
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>
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>         <http://mitgcm.org/mailman/listinfo/mitgcm-support>
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