[MITgcm-support] domain size limit?
Ryan Abernathey
ryan.abernathey at gmail.com
Tue Dec 3 14:20:53 EST 2013
No luck with -mcmodel=medium. Same error at link time.
On Tue, Dec 3, 2013 at 2:13 PM, Oliver Jahn <jahn at mit.edu> wrote:
> Try -mcmodel=medium (and no -fPIC)?
>
> On 2013-12-03 13:46, Ryan Abernathey wrote:
> > 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
> > <mailto: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>
> > <mailto: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
> >
> >
> >
> > <
> 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>>
> > <mailto: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>
> > <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>>>
> > <mailto:fancer.lancer at gmail
> > <mailto:fancer.lancer at gmail>. <mailto:fancer.lancer at gmail
> > <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>>>
> > <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 <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>>>
> > <mailto:fancer.lancer at gmail
> > <mailto:fancer.lancer at gmail>. <mailto:fancer.lancer at gmail
> > <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>>
> >
> >
> >
> > <
> 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>>
> >
> >
> >
> > <
> 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>>>
> > <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 <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>>>
> > <mailto:fancer.lancer at gmail
> > <mailto:fancer.lancer at gmail>. <mailto:fancer.lancer at gmail
> > <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>>>
> > <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 <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>>>
> > <mailto:ryan.abernathey at gmail
> > <mailto:ryan.abernathey at gmail>.
> > <mailto:ryan.abernathey at gmail
> > <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>
> > <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)
> > > > >
> > > > >
> > > > >
> > > > >
> > > > >
> _____________________________________________________
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