VMD-L Mailing List

From: Sebastian Reiter (reiter.se_at_t-online.de)
Date: Wed Aug 02 2017 - 14:58:58 CDT

Dear Peter,

I am using version 1.9.3 of vmd, specifically the binary distribution
LINUX_64 OpenGL, CUDA, OptiX, OSPRay (Linux (RHEL 6.7 and later) 64-bit
Intel/AMD x86_64 SSE, with CUDA 8.x, OptiX, OSPRay). I installed it by
running configure with the standard options given below, followed by
make install.

LINUXAMD64 OPENGL OPENGLPBUFFER FLTK TK ACTC CUDA IMD LIBSBALL XINERAMA
XINPUT LIBOPTIX LIBOSPRAY LIBTACHYON VRPN NETCDF COLVARS TCL PYTHON
PTHREADS NUMPY SILENT ICC

Also, the startup message of vmd indicates that multithreading is available:

> Info) Multithreading available, 4 CPUs detected.
> Info) CPU features: SSE2 AVX AVX2 FMA

Best regards,
Sebastian

Am 02.08.2017 um 17:35 schrieb Peter Freddolino:
> Dear Sebastien,
> Given where that message is occurring, I suspect that your vmd may
> have been built without multithreading support. Could you confirm what
> version you are running and how you installed it?
> Thanks,
> Peter
>
>
> On 08/02/2017 07:00 AM, Sebastian Reiter wrote:
>> Dear Peter,
>>
>> thank you very much for your quick and helpful reply. You are right: I
>> did not load a psf file, so the charges were missing. Loading the psf
>> fixed the error and the ion positions look reasonable now.
>>
>> In the output, the input parameters are reported correctly at the very
>> beginning:
>>
>> > Running cionize on input file cionize-temp.pqr
>> > Ion-solute distance: 6.000000
>> > Ion-Ion distance: 10.000000
>> > Grid spacing: 0.500000
>> > Boundary size: 10.000000
>> > Max. Processors: 4
>>
>> However, when the actual calculation starts, it does not seem to be
>> running in parallel, which I could also confirm by looking at the system
>> load:
>>
>> > Calculating grid energies...
>> > Multilevel summation for electrostatic potential map
>> > using 1 processors
>>
>> The same happens, when double precision is used instead of multilevel
>> summation.
>>
>> Best regards,
>> Sebastian
>>
>> Am 02.08.2017 um 05:01 schrieb Peter Freddolino:
>>> Dear Sebastian,
>>> Can you confirm how you generated the structure you loaded into vmd?
>>> In particular, are the charges set properly? I suspect that they are
>>> not loaded given the output that you indicate that you have; for
>>> example, you may have forgotten to load a psf file.
>>>
>>> Could you post the output from your job to clarify at which point the
>>> use of only one processor was reported?
>>>
>>> Best,
>>> Peter
>>>
>>>
>>> On 08/01/2017 03:57 PM, Sebastian Reiter wrote:
>>>> Dear all,
>>>>
>>>> I am trying to use the cionize plugin (version 1.0) in vmd 1.9.3 to
>>>> neutralize the charges of an RNA backbone. So far, I have found out
>>>> how
>>>> to start the plugin and the following exemplary command does not yield
>>>> an error message:
>>>>
>>>> cionize -mol 0 -mg -np 4 -go potential.dat -ions "{SOD 85 1}"
>>>>
>>>> However, the output shows that only one processor was used despite the
>>>> option "-np 4" and, more importantly, the generated ions are just
>>>> placed
>>>> cubically around the RNA structure. A quick look into the output file
>>>> "potential.dat" shows that cionize sets the potential to zero at every
>>>> grid point.
>>>>
>>>> I would greatly appreciate your advice on how to use cionize
>>>> correctly,
>>>> so that I can make use of the parallel implementation and the ions are
>>>> placed in sensible positions.
>>>>
>>>> Best regards,
>>>> Sebastian
>>>>
>