VMD-L Mailing List

From: Epiphaniou, Nicholas (n.epiphaniou_at_cranfield.ac.uk)
Date: Thu Jan 25 2007 - 04:57:09 CST

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