Re: NAMD compiling problem

From: Faramarz Joodaki (fjoodaki_at_my.uri.edu)
Date: Thu Dec 06 2018 - 14:08:52 CST

Dear Giacomo and Laurent,

Thank you for your guidaces! I checked four weeks ago mailing list and I
found the solution.
I need to enable PIE. I added -no-pie to CXXOPTS in Linux-x86_64-g++.arch
and it works!

Best Regards,
Faramarz

On Thu, Dec 6, 2018 at 12:13 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
wrote:

> Sorry, it's actually a thread from about 4 weeks ago.
>
> On Thu, Dec 6, 2018 at 12:11 PM Giacomo Fiorin <giacomo.fiorin_at_gmail.com>
> wrote:
>
>> Check the mailing list archive in the last 2 weeks.
>>
>> On Thu, Dec 6, 2018 at 12:01 PM Faramarz Joodaki <fjoodaki_at_my.uri.edu>
>> wrote:
>>
>>> Hi Everyone!
>>> I always install NAMD easily on my computer. But recently when I
>>> switched to Ubuntu 18.04, I could not compile it, and I received the blow
>>> error during compiling.
>>>
>>> /usr/bin/ld: .rootdir/fftw/lib/libsrfftw.a(rfftwnd.o): relocation
>>> R_X86_64_32 against `.rodata.str1.32' can not be used when making a PIE
>>> object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsrfftw.a(rplanner.o): relocation
>>> R_X86_64_32 against symbol `rfftw_config' can not be used when making a PIE
>>> object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsrfftw.a(rexec.o): relocation
>>> R_X86_64_32 against `.rodata.str1.32' can not be used when making a PIE
>>> object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(planner.o): relocation
>>> R_X86_64_32 against symbol `fftw_config' can not be used when making a PIE
>>> object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(executor.o): relocation
>>> R_X86_64_32 against `.rodata.str1.32' can not be used when making a PIE
>>> object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(fftwnd.o): relocation
>>> R_X86_64_32 against `.rodata.str1.32' can not be used when making a PIE
>>> object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(malloc.o): relocation
>>> R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE
>>> object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(wisdom.o): relocation
>>> R_X86_64_32 against `.rodata.str1.1' can not be used when making a PIE
>>> object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(wisdomio.o): relocation
>>> R_X86_64_32 against `.text' can not be used when making a PIE object;
>>> recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(putils.o): relocation
>>> R_X86_64_32S against `.rodata' can not be used when making a PIE object;
>>> recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(rader.o): relocation
>>> R_X86_64_32 against symbol `fftw_twiddle_rader' can not be used when making
>>> a PIE object; recompile with -fPIC
>>> /usr/bin/ld: .rootdir/fftw/lib/libsfftw.a(twiddle.o): relocation
>>> R_X86_64_32 against `.bss' can not be used when making a PIE object;
>>> recompile with -fPIC
>>> /usr/bin/ld: final link failed: Nonrepresentable section on output
>>> collect2: error: ld returned 1 exit status
>>> Fatal Error by charmc in directory
>>> /home/faramarz/Software/NAMD/NAMD_2.11_Source/Linux-x86_64-g++
>>>
>>> I searched a lot about this problem but I could not figure it out the
>>> problem. I reinstalled fftw, g++, and gcc but it did not help!
>>>
>>> I would be so grateful if you could tell me your idea about this issue?
>>>
>>> Best Regards,
>>>
>>> Faramarz
>>>
>>>
>>
>> --
>> Giacomo Fiorin
>> Associate Professor of Research, Temple University, Philadelphia, PA
>> Contractor, National Institutes of Health, Bethesda, MD
>> http://goo.gl/Q3TBQU
>> https://github.com/giacomofiorin
>>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research, Temple University, Philadelphia, PA
> Contractor, National Institutes of Health, Bethesda, MD
> http://goo.gl/Q3TBQU
> https://github.com/giacomofiorin
>

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