VMD-L Mailing List

From: Vermaas, Joshua (Joshua.Vermaas_at_nrel.gov)
Date: Wed Mar 01 2017 - 10:35:37 CST

Hi Dallas,

Here is my make command on a Ubuntu 16.04 system to compile the plugins:

make LINUXAMD64 TCLINC=-I/usr/include/tcl8.6 TCLLIB=-L/usr/lib
NETCDFLIB=-L/usr/lib NETCDFINC=-I/usr/include/ -j 1

Now one thing you may want to change here is to use tcl 8.5, as some of
the plugins behave strangely under 8.6, but otherwise you made the same
mistake I did the first time I did this, and forgot about the -I and -L,
since these flags are used directly by the compiler.

-Josh

On 02/28/2017 07:14 PM, Dallas Warren wrote:
> From what I can tell, the no version information error is due to fact
> vmd was complied with a latter (or different) version of libGL than
> which I have installed on my machine. In order to solve that issue,
> meant to compile vmd, so that it uses the local libraries etc.
>
> Instructions on how to compile vmd here:
> http://www.ks.uiuc.edu/Research/vmd/doxygen/compiling.html
>
> Have following installed, so that appears to tick the boxes of what is required.
> tcl 8.6.1-4.2.1
> FLTK 1.33-1.6
> Mesa-libGL 11.2.2-166.1
>
> Next step is to compile the plugins, as documented here:
> http://www.ks.uiuc.edu/Research/vmd/plugins/doxygen/compiling.html
>
> Issue I have here is where exactly are TCLINC and TCLLIB meant to be
> pointing to? From what the instructions say, initially thought was
> within what comes with vmd, but no .../lib/tcl or ..../lib/tcl/include
> directories.
>
> There is a tcl.h file in /usr/include so set TCLINC to that location.
> But stumped where TCLLIB should be pointing to. There is a
> /usr/lib64/tcl/tcl8.6 directory but pointing to that get a "file not
> recognized: Is a directory" error when run "gmake LINUXAMD64
> TCLINC=$TCLINC TCLLIB=$TCLLIB"
>
> I can normally work my way through compiling things, but it's beyond
> me this time.
> 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 28 February 2017 at 11:32, Dallas Warren <dallas.warren_at_monash.edu> wrote:
>> Suspect they are all related? A point in the direction of what I
>> should be looking at, updating, compiling etc would be appreciated.
>> Thank you.
>>
>> Seen mentioned on the list that the CUDA message came up for older
>> versions of vmd (1.9.1), but it was being fixed in 1.9.2
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22958.html
>>
>> The libGL issue something about old versions of the nvidia driver left
>> hanging around?
>> http://www.ks.uiuc.edu/Research/vmd/mailing_list/vmd-l/22907.html
>>
>> Opensuse: 42.1
>> Kernel: 4.1.36-44
>> NVIDIA Driver: 375.26
>>
>> Upon starting vmd:
>> /usr/local/lib/vmd/vmd_LINUXAMD64: /usr/lib64/libGL.so.1: no version
>> information available (required by /usr/local/lib/vmd/vmd_LINUXAMD64)
>> Info) VMD for LINUXAMD64, version 1.9.3 (November 30, 2016)
>> 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) CPU features: SSE2 AVX
>> Info) Free system memory: 35GB (97%)
>> 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, 956MB 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
>>
>> Upon selecting QuickSurf, other representations appear to work fine:
>> terminate called after throwing an instance of 'thrust::system::system_error'
>> what(): after cub_::DeviceRadixSort::SortPairs(0): invalid device function
>> Abort
>>
>> 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.
>>
>