[gmx-users] GROMACS 4.6.3 Static Linking

Mark Abraham mark.j.abraham at gmail.com
Thu Jul 25 14:18:35 CEST 2013 

Vitaly has it upside down - it is normally required to build a static
binary on Crays.

cmake .. -DBUILD_SHARED_LIBS=off just works for building static
binaries for me with 4.6.3 on lindgren, a Cray XE6, when using
PrgEnv-gnu/4.0.46

Mark

On Wed, Jul 24, 2013 at 8:58 AM, Andrew R Turner <a.turner at epcc.ed.ac.uk> wrote:
> Hi Vitaly,
>
> Impossible just for v4.6.3? It was certainly possible to create static
> executables for a Cray XE using v4.6.1 (I know, because I have done it). I
> followed the same procedure for 4.6.3 and have only managed to get dynamic
> executables (which do not work) hence my question.
>
> I will have more of a dig into the build procedure but just wondered if
> anyone was aware of anything that has changed between these two minor
> versions (probably in the build process) that could have precipitated this
> change in behaviour.
>
> Cheers
> Andy
>
>
>
> Quoting "Dr. Vitaly Chaban" <vvchaban at gmail.com> on Sat, 20 Jul 2013
> 09:42:41 +0200:
>
>> Soneone said here that static versions are impossible for Cray...
>>
>>
>>
>> Dr. Vitaly V. Chaban
>>
>>
>> On Fri, Jul 19, 2013 at 12:55 PM, Andrew R Turner
>> <a.turner at epcc.ed.ac.uk>wrote:
>>
>>> Hi
>>>
>>> I am having problems creating static versions of the GROMACS binaries for
>>> a Cray XE6 (www.hector.ac.uk). The build process I am using is documented
>>> at:
>>>
>>> http://www.hector.ac.uk/**support/documentation/**
>>>
>>> software/gromacs/compiling_4-**6-1_phase3.php<http://www.hector.ac.uk/support/documentation/software/gromacs/compiling_4-6-1_phase3.php>
>>>
>>> and successfully produced static binaries for 4.6.1. Has something
>>> changed
>>> in the new version?
>>>
>>> In particular, I am setting:
>>>
>>> -DCMAKE_SKIP_RPATH=YES
>>> -DBUILD_SHARED_LIBS=OFF
>>> -DGMX_PREFER_STATIC_LIBS=ON
>>> -DCMAKE_C_FLAGS="-static -O3 -ftree-vectorize -ffast-math -funroll-loops"
>>> -DCMAKE_CXX_FLAGS="-static -O3 -ftree-vectorize -ffast-math
>>> -funroll-loops"
>>>
>>> but still get dynamic executables:
>>>
>>> gmx at hector-xe6-5:~/4.6.3-**phase3/bin> ldd grompp
>>>         linux-vdso.so.1 =>  (0x00007fff00da2000)
>>>         libm.so.6 => /lib64/libm.so.6 (0x00007f50dc58f000)
>>>         libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f50dc371000)
>>>         libAtpSigHandler.so.0 => /opt/cray/lib64/**libAtpSigHandler.so.0
>>> (0x00007f50dc16b000)
>>>         libgfortran.so.3 => /opt/gcc/4.7.2/snos/lib64/**libgfortran.so.3
>>> (0x00007f50dbe54000)
>>>         libscicpp_gnu.so.2 => /opt/cray/lib64/libscicpp_gnu.**so.2
>>> (0x00007f50dbc4a000)
>>>         libsci_gnu_mp.so.2 => /opt/cray/lib64/libsci_gnu_mp.**so.2
>>> (0x00007f50d72ec000)
>>>         libstdc++.so.6 => /opt/gcc/4.7.2/snos/lib64/**libstdc++.so.6
>>> (0x00007f50d6fdf000)
>>>         libfftw3_mpi.so.3 => /opt/cray/lib64/libfftw3_mpi.**so.3
>>> (0x00007f50d6dc6000)
>>>         libfftw3f_mpi.so.3 => /opt/cray/lib64/libfftw3f_mpi.**so.3
>>> (0x00007f50d6bae000)
>>>         libfftw3_threads.so.3 => /opt/cray/lib64/libfftw3_**threads.so.3
>>> (0x00007f50d69a6000)
>>>         libfftw3f_threads.so.3 =>
>>> /opt/cray/lib64/libfftw3f_**threads.so.3
>>> (0x00007f50d679d000)
>>>         libfftw3.so.3 => /opt/cray/lib64/libfftw3.so.3
>>> (0x00007f50d63a2000)
>>>         libfftw3f.so.3 => /opt/cray/lib64/libfftw3f.so.3
>>> (0x00007f50d5f7c000)
>>>         libmpich_gnu_47.so.1 => /opt/cray/lib64/libmpich_gnu_**47.so.1
>>> (0x00007f50d5add000)
>>>         libmpichf90_gnu_47.so.1 =>
>>> /opt/cray/lib64/libmpichf90_**gnu_47.so.1
>>> (0x00007f50d58da000)
>>>         libmpl.so.0 => /opt/cray/lib64/libmpl.so.0 (0x00007f50d56d5000)
>>>         librt.so.1 => /lib64/librt.so.1 (0x00007f50d54cb000)
>>>         libxpmem.so.0 => /opt/cray/xpmem/default/lib64/**libxpmem.so.0
>>> (0x00007f50d52c9000)
>>>         libdmapp.so.1 => /opt/cray/dmapp/default/lib64/**libdmapp.so.1
>>> (0x00007f50d5092000)
>>>         libugni.so.0 => /opt/cray/ugni/default/lib64/**libugni.so.0
>>> (0x00007f50d4e72000)
>>>         libpmi.so.0 => /opt/cray/pmi/default/lib64/**libpmi.so.0
>>> (0x00007f50d4c51000)
>>>         libalpslli.so.0 => /usr/lib/alps/libalpslli.so.0
>>> (0x00007f50d4a4e000)
>>>         libalpsutil.so.0 => /usr/lib/alps/libalpsutil.so.0
>>> (0x00007f50d4849000)
>>>         libudreg.so.0 => /opt/cray/udreg/default/lib64/**libudreg.so.0
>>> (0x00007f50d4641000)
>>>         libgomp.so.1 => /opt/gcc/4.7.2/snos/lib64/**libgomp.so.1
>>> (0x00007f50d4432000)
>>>         libc.so.6 => /lib64/libc.so.6 (0x00007f50d40d3000)
>>>         libgcc_s.so.1 => /opt/gcc/4.7.2/snos/lib64/**libgcc_s.so.1
>>> (0x00007f50d3ebd000)
>>>         /lib/ld64.so.1 => /lib64/ld-linux-x86-64.so.2
>>> (0x00007f50dc812000)
>>>         libquadmath.so.0 => /opt/gcc/4.7.2/snos/lib64/**libquadmath.so.0
>>> (0x00007f50d3c87000)
>>>         libcray_memcpy.so.0 => /opt/cray/lib64/libcray_**memcpy.so.0
>>> (0x00007f50d3a84000)
>>>         libopa.so.1 => /opt/cray/lib64/libopa.so.1 (0x00007f50d3882000)
>>>         librca.so.0 => /opt/cray/rca/default/lib64/**librca.so.0
>>> (0x00007f50d367d000)
>>>         libdl.so.2 => /lib64/libdl.so.2 (0x00007f50d3479000)
>>>
>>> Any ideas?
>>> Andy
>>>
>>>
>>> ==============================**===============
>>>         Dr Andrew R. Turner
>>>      e: a.turner at epcc.ed.ac.uk
>>>  skype: aturner-epcc
>>>      t: +44 (0)131 651 3578
>>>      p: EPCC, University of Edinburgh EH9 3JZ
>>> ==============================**===============
>>>
>>> --
>>> The University of Edinburgh is a charitable body, registered in
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>
>
>
> =============================================
>
>         Dr Andrew R. Turner
>      e: a.turner at epcc.ed.ac.uk
>  skype: aturner-epcc
>      t: +44 (0)131 651 3578
>      p: EPCC, University of Edinburgh EH9 3JZ
> =============================================
>
>
> --
> The University of Edinburgh is a charitable body, registered in
> Scotland, with registration number SC005336.
>
>
> --
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