VMD-L Mailing List

From: Dallas Warren (dallas.warren_at_monash.edu)
Date: Tue Mar 07 2017 - 19:36:13 CST

Would have been nice if I found your message awhile ago John .... oh
dear .... well I have learnt some things while oblivious to what you
had replied ;)

OK, so if I export VMDNOCUDA=1 before executing ......

    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 (86%)
    Info) VMDNOCUDA environment variable is set, CUDA support disabled.
    Info) No CUDA accelerator devices available.
    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

Then if try to use QuickSurf ..... it doesn't CRASH, yay.
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 12:31, Dallas Warren <dallas.warren_at_monash.edu> wrote:
> 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.