[gmx-users] GROMACS 4.6.3 Static Linking

[Dr. Vitaly Chaban]

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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