VMD-L Mailing List

From: John Stone (johns_at_ks.uiuc.edu)
Date: Wed Sep 21 2016 - 09:53:14 CDT

Hi Vlad,
  The new version of VMD includes a couple of large Tk GUI components that
take a non-trivial amount of parse time at startup, and this is likely what
you're noticing. I find it is particularly noticable on machines with slow
filesystem access.

Cheers,
  John Stone
  vmd_at_ks.uiuc.edu

On Wed, Sep 21, 2016 at 04:14:48PM +0200, Vlad Cojocaru wrote:
> Indeed, adding the flag -lrt to the general definition of the cuda_libs
> in the configure file solves this issue and the cvs code compiles ...
>
> However, I find that the new VMD starts significantly slower than the
> 1.9.2 version compiled exactly on the same machine with exactly the same
> libs.
>
> Anybody else experiencing this ?
>
> Best
> Vlad
>
> On 09/21/2016 03:26 PM, 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 

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