VMD-L Mailing List

From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Tue Mar 07 2017 - 19:21:08 CST

Thank you for the further comments Josh, I'm starting to get my head
around what actually is going on with compiling etc now :)

Added the following packages using Yast, which contain the various
libraries that are required for compiling; python dev, numpy dev, tcl
dev

Change location of python, numpy, OptiX in the configure file, wasn't
automatically finding them with the values defined.

Configure options: LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK CUDA IMD
XINERAMA XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON NETCDF COLVARS TCL
PYTHON PTHREADS NUMPY SILENT ICC

That then goes almost all the way through, and fails with this error:
    Linking vmd_LINUXAMD64 ...
    icpc: error: unrecognized command line option ‘-static-intel’

That is my earlier hack coming back to haunt me, since it was asking
for the ICC compiler and I directed it to gcc manually. I had failed
to realise that there was the configuration option at the end of the
options telling it which compiler to use. So removing that symbolic
link and changing the compiler within the configure options to GCC end
up with ..... the ospray rendering step failing now. Interesting that
it works fine with ICC and fails with GCC? Anyway, onwards .....
    Makefile:585: recipe for target 'OSPRayRenderer.o' failed

So, remove that (LIBOSPRAY) from the configure file.

Next error below, so change location in the configure file to match my 8.6
    cannot find -ltk8.5
    cannot find -ltcl8.5

So, now get an issue with below. These are the system libraries, why
in the world can't it find those? Suspected it should be looking for
-lfl (flex rather than lex,
http://stackoverflow.com/questions/15732155/what-is-ll-gccs-flag ) and
that fixed that issue.
    cannot find -ll

Next is, which seems to be due to the -lrt library not being linked
http://stackoverflow.com/questions/19901934/strange-linking-error-dso-missing-from-command-line
    /lib64/librt.so.1: error adding symbols: DSO missing from command line

Don't know how to add a library via configure, so added it to the
Makefile in the src directory, added it to LIBS = -lrt

And appears that all works. Then swtich to super user (su), make
install and it worked. Yay, that was painful, but got there in the
end.

The start up text is now:

    dallas_at_morph:~> vmd
    Info) VMD for LINUXAMD64, version 1.9.3 (March 8, 2017)
    Info) http://www.ks.uiuc.edu/Research/vmd/
    Info) Email questions and bug reports to vmd_at_ks.uiuc.edu
    Info) Please include this reference in published work using VMD:
    Info) Humphrey, W., Dalke, A. and Schulten, K., `VMD - Visual
    Info) Molecular Dynamics', J. Molec. Graphics 1996, 14.1, 33-38.
    Info) -------------------------------------------------------------
    Info) Multithreading available, 12 CPUs detected.
    Info) Free system memory: 31GB (87%)
    Info) Creating CUDA device pool and initializing hardware...
    CUDA error: invalid device symbol, CUDAClearDevice.cu line 56
    Info) Detected 1 available CUDA accelerator:
    Info) [0] GeForce GTX 550 Ti 4 SM_2.1 @ 1.80 GHz, 960MB RAM, KTO, AE1, ZCP
    Warning) Detected X11 'Composite' extension: if incorrect display occurs
    Warning) try disabling this X server option. Most OpenGL drivers
    Warning) disable stereoscopic display when 'Composite' is enabled.
    Info) OpenGL renderer: GeForce GTX 550 Ti/PCIe/SSE2
    Info) Features: STENCIL MSAA(4) MDE CVA MTX NPOT PP PS GLSL(OVFGS)
    Info) Full GLSL rendering mode is available.
    Info) Textures: 2-D (16384x16384), 3-D (2048x2048x2048), Multitexture (4)
    Info) Dynamically loaded 2 plugins in directory:
    Info) /usr/local/lib/vmd/plugins/LINUXAMD64/molfile
    after#0

So, the /usr/lib64/libGL.so.1: no version error is now gone. One
success, though no idea how much of an issue to behaviour/performance
of vmd that error had.

However, that CUDA error is still there!!! Though again, no idea on
the impact on vmd behaviour/performance it has.

And it still crashes when try to use quicksurf!!! This is the big one,
since I love using this representation for visualising a number of
things quickly etc.

    terminate called after throwing an instance of
'thrust::system::system_error'
      what(): after cub_::DeviceRadixSort::SortPairs(0): invalid
device function
    Abort (core dumped)

With Surf it works, and all the other representations that have
available for a particular system are visualising.