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