VMD-L Mailing List

From: Vlad Cojocaru (vlad.cojocaru_at_mpi-muenster.mpg.de)
Date: Tue Jan 10 2017 - 08:51:33 CST

Yes, adding -lrt solved the issue ...

Thanks
Vlad

On 01/10/2017 03:44 PM, John Stone wrote:
> 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 

-- 
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