[gmx-users] GROMACS 4.6.3 Static Linking
Andrew R Turner
a.turner at epcc.ed.ac.uk
Thu Jul 25 16:21:41 CEST 2013
Mark,
A bit of testing has revealed that it is the
"-DGMX_PREFER_STATIC_LIBS=ON" flag that makes the difference. With
this flag you end up with dynamic executables that do not work (I
think due to some glibc problem I have not yet tracked down) whereas
if I exclude this option then I get working static executables.
Thanks for all your help
Andy
Quoting Mark Abraham <mark.j.abraham at gmail.com> on Thu, 25 Jul 2013
14:18:35 +0200:
> 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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=============================================
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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