VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 21 2016 - 09:56:02 CDT

Hi,
  I haven't added the "-lrt" by default yet as I still have a 32-bit linux
build that is compiled against an older rev of CUDA. That being said, it's
probably time to drop the old 32-bit build, or at least eliminate its
outdated CUDA linkage. I will add the "-lrt" before the final release.

Cheers,
  John

On Wed, Sep 21, 2016 at 03:26:17PM +0200, Vlad Cojocaru wrote:
> Thanks Axel,
>
> The glibc version is 2.19 and is the same as the one CUDA was installed
> against ....
>
> But I could not find "-lrt" in the linking options ... In the VMD
> configure file in only appears at arch = SUMMIT or SOLARIS under
> "cuda_libs" ... I will try to add it to the general $cuda_libs and see
> if it works
>
> Best
> Vlad
>
> On 09/21/2016 03:10 PM, Axel Kohlmeyer wrote:
> >On Wed, Sep 21, 2016 at 8:42 AM, Vlad Cojocaru
> ><vlad.cojocaru_at_mpi-muenster.mpg.de> wrote:
> >>Dear all,
> >>
> >>I am trying to compile VMD (CVS today) on a LINUXAMD64 arch with openSUSE
> >>42.1 (gcc 4.8.5), cuda 7.5.18 but I get the following error:
> >>
> >>
> >>/usr/lib64/gcc/x86_64-suse-linux/4.8/../../../../x86_64-suse-linux/bin/ld:
> >>/apps/nvidia/cuda/7.5.18/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:608: recipe for target 'vmd_LINUXAMD64' failed
> >>make: *** [vmd_LINUXAMD64] Error 1
> >>
> >>
> >>Did anybody experience this and knows a way to resolve the issue?
> >this most likely means, that you either didn't link with -lrt
> >correctly or that your glibc version is too old compared with the one
> >used to compile the CUDA toolkit.
> >
> >axel.
> >
> >>Thanks a lot
> >>
> >>Best wishes
> >>Vlad
> >>
> >>--
> >>Dr. Vlad Cojocaru
> >>Computational Structural Biology Laboratory
> >>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
> >>
> >
> >
>
> --
> Dr. Vlad Cojocaru
> Computational Structural Biology Laboratory
> 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/