VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Tue Jan 10 2017 - 08:44:15 CST

Hi,
  For compilation on Suse, you may need to add "-lrt" and/or "-ldl"
to the link flags (either at the end, or at least after "-lcuda_static"
in the vmd/src/Makefile that was generated by the configure script,
if they aren't there already. You're looking for the line of the Makefile
that looks similar to this (I just added "-lrt" below as an example):

LIBS = -lGL -L/usr/X11R6/lib64 -lGL -lX11 -lactc -Wl,-rpath -Wl,$$ORIGIN/ -lcudart_static -lrt -lsball -lXinerama -lXi -loptixu -loptix -lospray -lospray_common -lembree -ltbb -ltbbmalloc -ltachyon -lvrpn -lquat -lpython2.5 -lpthread -lpthread -ltk8.5 -lX11 -ltcl8.5 -lmolfile_plugin -lnetcdf -lfltk -lX11 -lm -ldl -lutil $(VMDEXTRALIBS)

See if that addresses the remaining linkage issue or not.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Tue, Jan 10, 2017 at 03:32:55PM +0100, Vlad Cojocaru wrote:
> HI John,
>
> Thanks ...The ospray support compiles fine with the source you sent
> ... However, I get another issue (see error below) ...
>
> Thanks for any hints
> Vlad
>
>
>
> /usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld: /apps/nvidia/cuda/8.0.44/lib64/libcudart_static.a(libcudart_static.a.o):
> undefined reference to symbol 'shm_unlink@@GLIBC_2.2.5'
> /lib64/librt.so.1: error adding symbols: DSO missing from command line
> collect2: error: ld returned 1 exit status
> Makefile:620: recipe for target 'vmd_LINUXAMD64' failed
> make: *** [vmd_LINUXAMD64] Error 1
>
>
> On 01/10/2017 02:59 PM, John Stone wrote:
> >Hi,
> > Please try using the attached source file in place of the original,
> >and let me know if you still have difficulties.
> >
> >Cheers,
> > John Stone
> > vmd_at_ks.uiuc.edu
> >
> >On Tue, Jan 10, 2017 at 02:25:10PM +0100, Vlad Cojocaru wrote:
> >>Dear VMDers,
> >>
> >>I am trying to compile VMD 1.9.3 with OSPRay support. However, I get
> >>the compilation error below:
> >>
> >>Some details:
> >>OS: openSUSE 42.2 (arch x86_64)
> >>GCC 4.8.5
> >>OSPRay 1.1.2 (downloaded and built successfully according to their
> >>instructions)
> >>
> >>Has anybody observed such an errror and has a fix for it ?
> >>
> >>Thanks for letting me know
> >>
> >>Best wishes
> >>Vlad
> >>
> >>Compiling OSPRayRenderer.C --> OSPRayRenderer.o ...
> >>OSPRayRenderer.C: In member function ???void
> >>OSPRayRenderer::render_compile_and_validate()???:
> >>OSPRayRenderer.C:662:12: error: redeclaration of ???int i???
> >> for (int i = 0; i < directional_lights.num(); ++i) {
> >> ^
> >>OSPRayRenderer.C:552:7: error: ???int i??? previously declared here
> >> int i;
> >> ^
> >>OSPRayRenderer.C: In member function ???void
> >>OSPRayRenderer::cylinder_array(Matrix4*, float, float*, int, float*,
> >>int)???:
> >>OSPRayRenderer.C:2027:38: warning: comparison between signed and
> >>unsigned integer expressions [-Wsign-compare]
> >> for (i=0,ind4=0,ind6=0,ind7=0; i<cylnum;
> >>i++,ind4+=4,ind6+=6,ind7+=7) {
> >> ^
> >>OSPRayRenderer.C:2035:38: warning: comparison between signed and
> >>unsigned integer expressions [-Wsign-compare]
> >> for (i=0,ind4=0,ind6=0,ind7=0; i<cylnum;
> >>i++,ind4+=4,ind6+=6,ind7+=7) {
> >> ^
> >>OSPRayRenderer.C: In member function ???void
> >>OSPRayRenderer::trimesh_c4u_n3f_v3f(Matrix4&, unsigned char*,
> >>float*, float*, int, int)???:
> >>OSPRayRenderer.C:2474:11: warning: unused variable ???norm???
> >>[-Wunused-variable]
> >> float norm[9];
> >> ^
> >>OSPRayRenderer.C:2472:15: warning: unused variable ???cn2f???
> >>[-Wunused-variable]
> >> const float cn2f = 1.0f / 127.5f;
> >> ^
> >>OSPRayRenderer.C: In member function ???void
> >>OSPRayRenderer::trimesh_n3f_v3f(Matrix4&, float*, float*, float*,
> >>int, int)???:
> >>OSPRayRenderer.C:2630:14: warning: unused variable ???c??? [-Wunused-variable]
> >> const rgba c = { uniform_color[0],
> >> ^
> >>Makefile:595: recipe for target 'OSPRayRenderer.o' failed
> >>make: *** [OSPRayRenderer.o] Error 1
> >>
> >>--
> >>Vlad Cojocaru, Ph.D., Project Group Leader
> >>Department of Cell and Developmental Biology
> >>Max Planck Institute for Molecular Biomedicine
> >>Röntgenstrasse 20, 48149 Münster, Germany
> >>Tel: +49-251-70365-324; Fax: +49-251-70365-399
> >>Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> >>http://www.mpi-muenster.mpg.de/43241/cojocaru
>
> --
> Vlad Cojocaru, Ph.D., Project Group Leader
> Department of Cell and Developmental Biology
> Max Planck Institute for Molecular Biomedicine
> Röntgenstrasse 20, 48149 Münster, Germany
> Tel: +49-251-70365-324; Fax: +49-251-70365-399
> Email: vlad.cojocaru[at]mpi-muenster.mpg.de
> http://www.mpi-muenster.mpg.de/43241/cojocaru 

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