VMD-L Mailing List

From: Brian Bennion (brian_at_youkai.llnl.gov)
Date: Tue Sep 16 2003 - 10:17:13 CDT

Hello Phuong,

I must admit I have never compiled this program before (last advice was
from a google search), but now the compiler seems
to have found the correct c++ libraries. Now the compiler can't find
certain specific trio functions in the object files when linking.

Do the .o files exist (possibly dump question)?
Is there a makefile for this particular program?

Brian

On Tue, 16 Sep 2003, Nguyen Hoang Phuong wrote:

> > Hi
> >
> > Are you using suse linux?
> >
> >
> > try using g++ in the makefile...instead of gcc
> >
> >
> > Brian
> >
> > On Fri, 12 Sep 2003, John Stone wrote:
> >
>
> Dear Brian,
>
> thanks for help. I'm using suse linux. The results of the using of g++:
>
> g++ -O Trio.C MDFile.o MDFile_I.o MDFile_O.o MDFile_GRO.o MDFile_G96.o
> MDFile_TRR.o MDFile_PDB.o MDFile_DCD.o -o trio
> /tmp/cc2sq1TW.o: In function `main':
> /tmp/cc2sq1TW.o(.text+0x6c2): undefined reference to
> `MDFile_I::read_step(md_timestep*, md_structure*)'
> /tmp/cc2sq1TW.o(.text+0x6f3): undefined reference to
> `free_traj(md_timestep*)'
> /tmp/cc2sq1TW.o(.text+0x740): undefined reference to
> `free_traj(md_timestep*)'
> /tmp/cc2sq1TW.o(.text+0x783): undefined reference to
> `MDFile_O::write_step(md_timestep*, md_structure*)'
> /tmp/cc2sq1TW.o(.text+0x7d4): undefined reference to
> `MDFile_O::write_step(md_timestep*, md_structure*)'
> /tmp/cc2sq1TW.o(.text+0x80f): undefined reference to
> `MDFile_O::write_step(md_timestep*, md_structure*)'
> /tmp/cc2sq1TW.o(.text+0x886): undefined reference to
> `free_traj(md_timestep*)'
> collect2: ld returned 1 exit status
> make: *** [trio] Error 1
>
> Did it work well for you?
>
> Phuong
>
>
> > >
> > > Hi,
> > > I've got no idea what the cause of that error is, I've never
> > > seen it before. Have you succesfully compiled any other programs
> > > on your machine? That error looks like some problem with gcc itself...
> > > Has anyone else seen this error before?
> > >
> > > Thanks,
> > > John Stone
> > > vmd_at_ks.uiuc.edu
> > >
> > >
> > > On Fri, Sep 12, 2003 at 03:19:38PM +0200, Nguyen Hoang Phuong wrote:
> > > >
> > > > Dear All,
> > > >
> > > > I have downloaded the trio program and tried to compile it. I just run:
> > > >
> > > > make
> > > >
> > > > and then I got the error:
> > > >
> > > > gcc -O Trio.C MDFile.o MDFile_I.o MDFile_O.o MDFile_GRO.o MDFile_G96.o
> > > > MDFile_TRR.o MDFile_PDB.o MDFile_DCD.o -o trio
> > > > /tmp/ccyuZG1y.o(.eh_frame+0x12): undefined reference to
> > > > `__gxx_personality_v0'
> > > > MDFile_I.o(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
> > > > MDFile_O.o(.eh_frame+0x12): undefined reference to `__gxx_personality_v0'
> > > > MDFile_GRO.o(.eh_frame+0x11): undefined reference to
> > > > `__gxx_personality_v0'
> > > > MDFile_G96.o(.eh_frame+0x11): undefined reference to
> > > > `__gxx_personality_v0'
> > > > MDFile_TRR.o(.eh_frame+0x11): more undefined references to
> > > > `__gxx_personality_v0' follow
> > > > collect2: ld returned 1 exit status
> > > > make: *** [trio] Error 1
> > > >
> > > > Can anyone help me how to solve this?
> > > >
> > > > Thank you very much in advance.
> > > >
> > > > Phuong
> > > >
> > > >
> > >
> > >
> >
> > --
> > *****************************************************************
> > **Brian Bennion, Ph.D. **
> > **Computational and Systems Biology Division **
> > **Biology and Biotechnology Research Program **
> > **Lawrence Livermore National Laboratory **
> > **P.O. Box 808, L-448 bennion1_at_llnl.gov **
> > **7000 East Avenue phone: (925) 422-5722 **
> > **Livermore, CA 94550 fax: (925) 422-6605 **
> > *****************************************************************
> >
> >
> >
> 

-- 
*****************************************************************
**Brian Bennion, Ph.D.                                         **
**Computational and Systems Biology Division                   **
**Biology and Biotechnology Research Program                   **
**Lawrence Livermore National Laboratory                       **
**P.O. Box 808, L-448    bennion1_at_llnl.gov                     **
**7000 East Avenue       phone: (925) 422-5722                 **
**Livermore, CA  94550   fax:   (925) 422-6605                 **
*****************************************************************