VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Thu Jan 25 2007 - 14:49:56 CST

Hi,
  Are you compiling from CVS, or from a release version source package?
Also, which build target did you use? If you didn't use LINUXAMD64, this
may explain some of what's happening there. Let me know exactly what
commands you ran, and I should be able to help solve your problem.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Thu, Jan 25, 2007 at 10:57:09AM -0000, Epiphaniou, Nicholas wrote:
>
> Dear All,
>
> I have recently downloaded the source code VMD. I am getting the following error when compiling the plugins for source code which is:
>
> Building Molecule File Reader plugins
> src/cpmdplugin.c: In function `vmdplugin_register':
> src/cpmdplugin.c:200: warning: dereferencing type-punned pointer will break strict-aliasing rules
> src/cpmdplugin.c: At top level:
> src/cpmdplugin.c:82: warning: `read_cpmd_structure' defined but not used
> /usr/lib64/gcc-lib/x86_64-suse-linux/3.3.5/../../../../x86_64-suse-linux/bin/ld: ../compile/lib_LINUX/molfile/cpmdplugin.o: relocation R_X86_64_32 against `a local symbol' can not be used when making a shared object; recompile with -fPIC
> ../compile/lib_LINUX/molfile/cpmdplugin.o: could not read symbols: Bad value
> collect2: ld returned 1 exit status
> make[2]: *** [cpmdplugin.so] Error 1
> /bin/sh: line 0: cd: apbsrun: No such file or directory
> /bin/sh: line 0: cd: autoimd: No such file or directory
> /bin/sh: line 0: cd: autoionize: No such file or directory
> /bin/sh: line 0: cd: catdcd: No such file or directory
> /bin/sh: line 0: cd: cliptool: No such file or directory
> /bin/sh: line 0: cd: contactmap: No such file or directory
> /bin/sh: line 0: cd: exectool: No such file or directory
> /bin/sh: line 0: cd: imdmenu: No such file or directory
> /bin/sh: line 0: cd: membrane: No such file or directory
> /bin/sh: line 0: cd: navigate: No such file or directory
> /bin/sh: line 0: cd: pdbtool: No such file or directory
> /bin/sh: line 0: cd: pmepot: No such file or directory
> /bin/sh: line 0: cd: psfgen: No such file or directory
> /bin/sh: line 0: cd: ramaplot: No such file or directory
> /bin/sh: line 0: cd: rmsd: No such file or directory
> /bin/sh: line 0: cd: solvate: No such file or directory
> /bin/sh: line 0: cd: timeline: No such file or directory
> /bin/sh: line 0: cd: viewmaster: No such file or directory
> /bin/sh: line 0: cd: vmdmovie: No such file or directory
> /bin/sh: line 0: cd: vmdtkcon: No such file or directory
> /bin/sh: line 0: cd: zoomseq: No such file or directory
> make[1]: *** [dynlibs] Error 1
> make: *** [LINUX] Error 2
>
>
> Could anyone help me to fix this error?
>
> Nicholas Epiphaniou
>
> PhD student
>
> Aerospace Sciences
> Fluid Mechanics and Computational Science Group
> Cranfield University
> School of Engineering
> Cranfield,Bedfordshire MK43 0AL
> UK
> Email: n.epiphaniou_at_cranfield.ac.uk
> 

-- 
NIH Resource for Macromolecular Modeling and Bioinformatics
Beckman Institute for Advanced Science and Technology
University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
Email: johns_at_ks.uiuc.edu                 Phone: 217-244-3349
  WWW: http://www.ks.uiuc.edu/~johns/      Fax: 217-244-6078