AMBER Archive (2008)

Subject: Re: AMBER: PROBLEM: AmberTools Installation using Ubuntu

From: Jens Lattig (Jens.Lattig_at_toulouse.inserm.fr)
Date: Wed Jun 11 2008 - 03:59:12 CDT

Thank you very much for the fast and furious help. The compilation of
AmberTools worked.

Now, I was trying to test this using the proposed

   sudo make -f Makefile_at test

in the test-directory.

Almost everything went fine but I got a new problem, which is out of
my range of knowledge - unfortunately I was never installing Amber
software by my own so far.

The Problem occurs in Antechamber, saying:

   ==============================================================
   cd antechamber/c60 && ./Run.c60
   *** stack smashing detected ***: ../../../exe/antechamber terminated
   ======= Backtrace: =========
   /lib/tls/i686/cmov/libc.so.6(__fortify_fail+0x48)[0x40142138]
   /lib/tls/i686/cmov/libc.so.6(__fortify_fail+0x0)[0x401420f0]
   ../../../exe/antechamber[0x806faf6]
   ../../../exe/antechamber[0x8076db7]
   /lib/tls/i686/cmov/libc.so.6(__libc_start_main+0xe0)[0x4006b450]
   ../../../exe/antechamber[0x8048c41]
   ======= Memory map: ========
   08048000-08082000 r-xp 00000000 08:05 5573684
/opt/amber10/bin/antechamber
   08082000-08083000 rw-p 0003a000 08:05 5573684
/opt/amber10/bin/antechamber
   08083000-080bc000 rw-p 08083000 00:00 0 [heap]
   40000000-4001a000 r-xp 00000000 08:05 1916947 /lib/ld-2.7.so
   4001a000-4001c000 rw-p 00019000 08:05 1916947 /lib/ld-2.7.so
   4001c000-4001d000 r-xp 4001c000 00:00 0 [vdso]
   4001d000-4001f000 rw-p 4001d000 00:00 0
   40030000-40053000 r-xp 00000000 08:05 1934698
/lib/tls/i686/cmov/libm-2.7.so
   40053000-40055000 rw-p 00023000 08:05 1934698
/lib/tls/i686/cmov/libm-2.7.so
   40055000-4019e000 r-xp 00000000 08:05 1934690
/lib/tls/i686/cmov/libc-2.7.so
   4019e000-4019f000 r--p 00149000 08:05 1934690
/lib/tls/i686/cmov/libc-2.7.so
   4019f000-401a1000 rw-p 0014a000 08:05 1934690
/lib/tls/i686/cmov/libc-2.7.so
   401a1000-401a5000 rw-p 401a1000 00:00 0
   401a5000-401af000 r-xp 00000000 08:05 1916992 /lib/libgcc_s.so.1
   401af000-401b0000 rw-p 0000a000 08:05 1916992 /lib/libgcc_s.so.1
   bfdd6000-bfdeb000 rw-p bffeb000 00:00 0 [stack]
   Aborted
     ./Run.c60: Program error
   make: *** [test.antechamber] Error 1

I assume, there some more libraries missing, Anyhow, the ones I
searched for and installed are obviously not the right ones.

Would anybody of you give me some more help?

Thanks a lot in advance ( again :-/ )

Jens 

-- 
U858 INSERM I2MR, Equipe 13
1 avenue Jean Poulhès, BP 84225
31432 TOULOUSE Cedex 4
Phone   : +33(0)5.61.32.30.57
Email   : Jens.Lattig_at_toulouse.inserm.fr
Internet: http://i2mr.toulouse.inserm.fr

Zitat von Mark Williamson <mark.williamson_at_imperial.ac.uk>:

> Jens Lattig wrote:
>> Thank you for the help, I solved this problem but - unfortunately -  
>>  found a new one.
>
>>  /usr/bin/ld: cannot find -lXext
>>  collect2: ld returned 1 exit status
>
> To resolve that specific error, you need to install libxext-dev. To do
> this under ubuntu, you need to execute:
>
>  sudo apt-get install libxext-dev
>
> This is under the premise that you've already run:
>
>  sudo apt-get update
>
> at some point in the past.
>
>
> regards,
>
> Mark
>
> -----------------------------------------------------------------------
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
>      to majordomo_at_scripps.edu

----------------------------------------------------------------
This message was sent using IMP, the Internet Messaging Program.

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu