Re: Building with GCC on Ubuntu 18

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Mon Nov 12 2018 - 09:14:01 CST

Yup, that's my experience. Josh, do you have symlinked directories
somewhere that you didn't mention? ;-)

On Mon, 12 Nov 2018 at 16:08, Jim Phillips <jim_at_ks.uiuc.edu> wrote:

>
> Sorry, actually the config script magic just checks for a tcl[-threaded]
> directory in namd/ and $HOME. It's up to the compiler to find system
> libraries or you can specify the directory manually with --tcl-prefix
>
> Jim
>
> On Mon, 12 Nov 2018, Jérôme Hénin wrote:
>
> > The magic is not working for me... GCC says it can't find tcl.h.
> >
> >> I don't change anything in arch/ other than CUDA locations
> > Here I'm trying a non-CUDA build, changing precisely nothing from the git
> > repo.
> >
> > Jerome
> >
> > On Fri, 9 Nov 2018 at 23:21, Jim Phillips <jim_at_ks.uiuc.edu> wrote:
> >
> >>
> >> The config script is magic like that. -Jim
> >>
> >> On Fri, 9 Nov 2018, Vermaas, Joshua wrote:
> >>
> >>> Hi Jerome,
> >>>
> >>> Weird. When I build NAMD with 18.04, gnu compilers looks in the system
> >> directories by default, so I don't change anything in arch/ other than
> CUDA
> >> locations when I rebuild NAMD with a new release.
> >>>
> >>> -Josh
> >>>
> >>>
> >>> On 2018-11-09 06:01:10-07:00 Jérôme Hénin wrote:
> >>>
> >>> Thanks Josh!
> >>> That said, in my tests the system library locations are not searched,
> as
> >> the default line in the arch file is:
> >>> TCLDIR=/Projects/namd2/tcl/tcl8.5.9-linux-x86_64-threaded
> >>> Jerome
> >>>
> >>> On Thu, 8 Nov 2018 at 18:51, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov
> >> <mailto:Joshua.Vermaas_at_nrel.gov>> wrote:
> >>> The other option is to use dynamically loaded fftw and tcl. On ubuntu,
> I
> >> think the relevant packages are "fftw-dev" or "libfftw3-dev" and either
> >> "tcl8.5-dev" or "tcl8.6-dev", which put things where the default
> Makefile
> >> expects to find them.
> >>>
> >>> -Josh
> >>>
> >>>
> >>>
> >>> On 2018-11-08 10:29:37-07:00 owner-namd-l_at_ks.uiuc.edu<mailto:
> >> owner-namd-l_at_ks.uiuc.edu> wrote:
> >>>
> >>> We’ll look into it. Thanks for reporting that, Jerome.
> >>> Julio
> >>>
> >>> On Nov 8, 2018, at 11:18 AM, Jérôme Hénin <jerome.henin_at_ibpc.fr
> <mailto:
> >> jerome.henin_at_ibpc.fr>> wrote:
> >>>
> >>> Dear all,
> >>> just an announcement to anyone who'd run into trouble building NAMD
> with
> >> GCC as shipped with recent Ubuntu distros. They enable PIE by default:
> >> https://wiki.ubuntu.com/SecurityTeam/PIE<
> >>
> https://na01.safelinks.protection.outlook.com/?url=https%3A%2F%2Furldefense.proofpoint.com%2Fv2%2Furl%3Fu%3Dhttps-3A__wiki.ubuntu.com_SecurityTeam_PIE%26d%3DDwMFaQ%26c%3DOCIEmEwdEq_aNlsP4fF3gFqSN-E3mlr2t9JcDdfOZag%26r%3DjUfnSyKkfkyVRBIUzlG1GSGGZAZGcznwr8YliSSCjPc%26m%3DfvL2HxXBc0Wm9o6bm9n18giKJj9NVVjzK9Hhr5h9tCg%26s%3DZIZpjLxaNPamXi49qEfd3tYsc1VcVChfhldG_UD1W1s%26e%3D&data=02%7C01%7CJoshua.Vermaas%40nrel.gov%7Cc432f9193ff14a45f2bd08d6464369c2%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636773652699132132&sdata=UwzoxQ4JOA1qDf7Rrx2L%2BX%2BCUONJ9BvbNq%2FR038X17Y%3D&reserved=0
> >>>
> >>> which will break if you try to link NAMD with, say, a static FFTW that
> >> wasn't built with that option. Then you'll see errors like this:
> >>>> relocation R_X86_64_32 against `.rodata.str1.1' can not be used when
> >> making a PIE object; recompile with -fPIC
> >>> This can be fixed by adding the option -no-pie to CXXOPTS in the
> >> relevant arch file (eg. Linux-x86_64-g++.arch).
> >>>
> >>> Jerome
> >>>
> >

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