[gmx-users] GROMACS 4.6.3 Static Linking

Andrew R Turner a.turner at epcc.ed.ac.uk
Wed Jul 24 08:58:54 CEST 2013


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
>> ==============================**===============
>>
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>> 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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