That combo is supposed to generate a CMake warning. I also get a warning during linking that some shared library will have to provide some function (getpwuid?) at run time, but the binary is static.
Mark On Thu, Jul 25, 2013 at 4:21 PM, Andrew R Turner <a.tur...@epcc.ed.ac.uk> wrote: > 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.abra...@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.tur...@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" <vvcha...@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.tur...@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@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.tur...@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. >>>>> >>>>> >>>>> -- >>>>> gmx-users mailing list gmx-users@gromacs.org >>>>> >>>>> >>>>> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users> >>>>> * Please search the archive at http://www.gromacs.org/** >>>>> >>>>> >>>>> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before >>>>> posting! >>>>> * Please don't post (un)subscribe requests to the list. Use thewww >>>>> interface or send it to gmx-users-requ...@gromacs.org. >>>>> * Can't post? Read >>>>> >>>>> http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists> >>>>> >>>> -- >>>> gmx-users mailing list gmx-users@gromacs.org >>>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>>> * Please search the archive at >>>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>>> * Please don't post (un)subscribe requests to the list. Use the >>>> www interface or send it to gmx-users-requ...@gromacs.org. >>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >>>> >>>> >>> >>> >>> >>> ============================================= >>> >>> Dr Andrew R. Turner >>> e: a.tur...@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. >>> >>> >>> -- >>> gmx-users mailing list gmx-users@gromacs.org >>> http://lists.gromacs.org/mailman/listinfo/gmx-users >>> * Please search the archive at >>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >>> * Please don't post (un)subscribe requests to the list. Use thewww >>> interface >>> or send it to gmx-users-requ...@gromacs.org. >>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> -- >> gmx-users mailing list gmx-users@gromacs.org >> http://lists.gromacs.org/mailman/listinfo/gmx-users >> * Please search the archive at >> http://www.gromacs.org/Support/Mailing_Lists/Search before posting! >> * Please don't post (un)subscribe requests to the list. Use the >> www interface or send it to gmx-users-requ...@gromacs.org. >> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists >> >> > > > > ============================================= > Dr Andrew R. Turner > e: a.tur...@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. > > > -- > gmx-users mailing list gmx-users@gromacs.org > http://lists.gromacs.org/mailman/listinfo/gmx-users > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/Search before posting! > * Please don't post (un)subscribe requests to the list. Use thewww interface > or send it to gmx-users-requ...@gromacs.org. > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! * Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists