VMD-L Mailing List

From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Tue Mar 07 2017 - 19:31:27 CST

I just realised that John actually replied to my email.

Apologies John, I didn't see it with my email program, but just found
it on the vmd-l archive page ....
Catch ya,

Dr. Dallas Warren

Drug Delivery, Disposition and Dynamics

Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.warren_at_monash.edu

+61 3 9903 9304
---------------------------------
When the only tool you own is a hammer, every problem begins to resemble a nail.

On 8 March 2017 at 12:21, Dallas Warren <dallas.warren_at_monash.edu> wrote:
> 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.