[MITgcm-support] domain size limit?

Gus Correa gus at ldeo.columbia.edu
Tue Dec 3 13:39:05 EST 2013


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
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>         <mailto:MITgcm-support at mitgcm.org>>
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>         <mailto:MITgcm-support at mitgcm.>____org
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>         <mailto:MITgcm-support at mitgcm.org>>>
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