Re: Building with GCC on Ubuntu 18

From: Jérôme Hénin (jerome.henin_at_ibpc.fr)
Date: Fri Nov 09 2018 - 07:00:43 CST

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>
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 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> 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%7Cd65bb448805e4f24cd2d08d6459fbfe3%7Ca0f29d7e28cd4f5484427885aee7c080%7C0%7C0%7C636772949761307269&sdata=rZOMh70qljZ3BA8KdyJTm9EqxV7bmT4%2FuVs%2FwY8Ebjg%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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