[gmx-users] GROMACS 4.6.3 Static Linking

[Andrew R Turner]

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

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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