[MITgcm-support] domain size limit?

Ryan Abernathey ryan.abernathey at gmail.com
Tue Dec 3 13:12:38 EST 2013


p.s I tried adding "-arch x86_64" to my CFLAGS and FFLAGS, but it did not
change anything.
-R


On Tue, Dec 3, 2013 at 1:11 PM, Ryan Abernathey
<ryan.abernathey at gmail.com>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> 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 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>> 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>> 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>>
>>> 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
>>>          > And additional explanation is here:
>>>          >
>>>         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>> 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>>
>>> 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>> 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>>
>>>
>>>         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> 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>
>>>
>>>          > > > http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>          > >
>>>          > >
>>>          > > _______________________________________________
>>>          > > MITgcm-support mailing list
>>>          > > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org
>>> >
>>>
>>>          > > http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>          > >
>>>          > > _______________________________________________
>>>          > > MITgcm-support mailing list
>>>          > > MITgcm-support at mitgcm.org <mailto:MITgcm-support at mitgcm.org
>>> >
>>>
>>>          > > http://mitgcm.org/mailman/listinfo/mitgcm-support
>>>          >
>>>          >
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>>
>>
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