From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Tue May 19 2015 - 15:18:08 CDT

I need to see the contents of the autoimd/autoimd.log file.

Jim

On Mon, 18 May 2015, Ern Seang Ong wrote:

> Hi Jim,
> Yes, it is the released NAMD_2.10_Win64-multicore binary.
> There is no NAMD output because the namd2.exe crashes before the simulation is started. (I have attached a print screen.)
>
> Cheers,
> Ernest
>
> -----Original Message-----
> From: Jim Phillips [mailto:jim_at_ks.uiuc.edu]
> Sent: Tuesday, 19 May 2015 1:32 AM
> To: Ern Seang Ong
> Cc: John Stone
> Subject: RE: vmd-l: Problems in running AutoIMD
>
>
> I need to see the full NAMD output.
>
> Is this the released NAMD_2.10_Win64-multicore binary or did you build it?
>
> Do you have two +p options on the command line?
>
> Jim
>
>
> On Mon, 18 May 2015, Ern Seang Ong wrote:
>
>> Hi John,
>> Thank you for your help on this. I tried to use the SMP/multicore version of NAMD but I encountered with another problem ie. "namd2.exe has stopped working". Under the problem details, it stated that the problem event name is APPCRASH. I tried to perform system clean-up and error scan, as well as clean boot the Windows but the problem still persists. I also tried to reinstall the NAMD, VMD and the tutorial (I'm running the Simulation of Water Permeation through Nanotubes tutorial) but it still crashes. I have been working on for many hours searching online for solutions but still can't work out. Hope that you have an idea in solving this.
>>
>> Thank you.
>>
>> Cheers,
>> Ernest
>>
>> -----Original Message-----
>> From: John Stone [mailto:johns_at_ks.uiuc.edu]
>> Sent: Thursday, 14 May 2015 6:39 AM
>> To: Ern Seang Ong
>> Cc: vmd-l_at_ks.uiuc.edu
>> Subject: Re: vmd-l: Problems in running AutoIMD
>>
>> Hi,
>> Try running the SMP/multicore version of NAMD and your error should go away.
>> When running NAMD on a cluster/supercomputer, you need to launch it specially, via mpiexec, charmrun, or something similar, and these cases aren't handled by the AutoIMD plugin since they are machine-specific. You can still use the output files that AutoIMD produces for runs like these, but you'll have to launch NAMD yourself.
>>
>> Cheers,
>> John Stone
>> vmd_at_ks.uiuc.edu
>>
>> On Sat, May 09, 2015 at 05:08:44AM +0000, Ern Seang Ong wrote:
>>> Hi John,
>>> Thank you for the reply. I'm running on NAMD 2.10 with parallel build. The error log is as in the following.
>>>
>>> Attempt to connnect to the simulation timed out!
>>>
>>> NAMD Logfile:
>>> Reason: FATAL ERROR: Unknown command-line option +p1
>>> - -type
>>> (procedure "AutoIMD::autoconnect" line 15)
>>> invoked from within
>>> "AutoIMD::autoconnect"
>>> invoked from within
>>> ".autoimd.win.controls.connect invoke"
>>> ("uplevel" body line 1)
>>> invoked from within
>>> "uplevel #0 [list $w invoke]"
>>> (procedure "tk::ButtonUp" line 24)
>>> invoked from within
>>> "tk::ButtonUp .autoimd.win.controls.connect"
>>> (command bound to event)
>>>
>>> Regards,
>>> Ernest
>>>
>>> -----Original Message-----
>>> From: John Stone [mailto:johns_at_ks.uiuc.edu]
>>> Sent: Friday, 8 May 2015 2:13 PM
>>> To: Ern Seang Ong
>>> Cc: vmd-l_at_ks.uiuc.edu
>>> Subject: Re: vmd-l: Problems in running AutoIMD
>>>
>>> Hi,
>>> Sorry for the delay, I'm behind on email and this one is somewhat tricky.
>>> What version of NAMD are you running? Is it an SMP version of NAMD or a parallel build?
>>>
>>> Cheers,
>>> John Stone
>>> vmd_at_ks.uiuc.edu
>>>
>>> On Fri, May 01, 2015 at 05:49:39AM +0000, Ern Seang Ong wrote:
>>>> Hi,
>>>>
>>>>
>>>>
>>>> I have been trying to run AutoIMD but there is an error kept popping out
>>>> "Error connecting to localhost on port XXXX". In the error log, it says
>>>> "Reason: FATAL ERROR: Unknown command-line option +p1". I have tried many
>>>> different ways to solve it but still cannot resolve the problem. Can
>>>> anyone please help?
>>>>
>>>>
>>>>
>>>> Thank you.
>>>>
>>>>
>>>>
>>>> Ernest
>>>>
>>>>
>>>>
>>>>
>>>> --------------------------------------------------------------------
>>>> --
>>>> ----
>>>>
>>>> UNSW AUSTRALIA
>>>> UNSW CANBERRA AT THE AUSTRALIAN DEFENCE FORCE ACADEMY
>>>> PO Box 7916, CANBERRA BC 2610, Australia
>>>> Web: http://unsw.adfa.edu.au
>>>>
>>>> CRICOS Provider no. 00098G
>>>>
>>>> This message is intended for the addressee named and may contain
>>>> confidential information. If you are not the intended recipient, please
>>>> delete it and notify the sender. Views expressed in this message are those
>>>> of the individual sender and are not necessarily the views of UNSW.
>>>
>>> --
>>> NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>>> http://www.ks.uiuc.edu/Research/vmd/
>>> ________________________________
>>>
>>> UNSW AUSTRALIA
>>> UNSW CANBERRA AT THE AUSTRALIAN DEFENCE FORCE ACADEMY PO Box 7916,
>>> CANBERRA BC 2610, Australia
>>> Web: http://unsw.adfa.edu.au
>>>
>>> CRICOS Provider no. 00098G
>>>
>>> This message is intended for the addressee named and may contain confidential information. If you are not the intended recipient, please delete it and notify the sender. Views expressed in this message are those of the individual sender and are not necessarily the views of UNSW.
>>
>> --
>> NIH Center for Macromolecular Modeling and Bioinformatics Beckman Institute for Advanced Science and Technology University of Illinois, 405 N. Mathews Ave, Urbana, IL 61801
>> http://www.ks.uiuc.edu/~johns/ Phone: 217-244-3349
>> http://www.ks.uiuc.edu/Research/vmd/
>>
>