VMD-L Mailing List

From: Ajasja Ljubetič (ajasja.ljubetic_at_gmail.com)
Date: Fri Dec 11 2015 - 11:24:18 CST

>
> One needs to type "*E:\VMD\nanotubes-files" *and not
> *"E:/VMD/nanotubes-files". *That's one problem.

Sorry, but that is not correct.

Forward slashes work just fine in Win7.

Best,
Ajasja

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On 11 December 2015 at 15:51, Richard Wood <Richard.Wood_at_purduecal.edu>
wrote:

>
> ------------------------------
> *From:* owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of
> Ajasja Ljubetič [ajasja.ljubetic_at_gmail.com]
> *Sent:* Friday, December 11, 2015 2:31 AM
> *To:* Ashar Malik
> *Cc:* Julio Cantu; VMD Mailing List
> *Subject:* Re: vmd-l: Unable to access config file
>
> Yes, that's a windows "feature". To change drives you have to enter "E:".
> Or install Git for windows <https://git-scm.com/download/win> and you
> will get a fully functional bash shell:)
>
> Best,
> Ajasja
>
> On 11 December 2015 at 05:57, Ashar Malik <asharjm_at_gmail.com> wrote:
>
>> As you can see when you do:
>>
>> *C:\Users\Julio>cd E:/VMD/nanotubes-files*
>>
>> your next prompt still reads this
>>
>> *C:\Users\Julio>*
>>
>> when it should read
>>
>> *E:\VMD\nanotubes-files>*
>>
>> in short your attempt at changing path doesn't work. Meaning when you run
>> NAMD, it tries to look for the conf file in the wrong folder and hence
>> fail.
>>
>> Solution: Make sure you are in the same folder as your conf file before
>> you run NAMD.
>>
>>
>> On Fri, Dec 11, 2015 at 12:36 PM, Julio Cantu <julio.c.cantu03_at_utrgv.edu>
>> wrote:
>>
>>> Hello all,
>>>
>>>
>>>
>>> I am attempting to follow the nanotubes tutorial, but have trouble when
>>> submitting my own namd job. I receive the following error once I initiate
>>> the simulation:
>>>
>>>
>>>
>>> *C:\Users\Julio>cd E:/VMD/nanotubes-files*
>>>
>>> *C:\Users\Julio>E:/VMD/NAMD/namd2 sim_short.conf*
>>> *Charm++: standalone mode (not using charmrun)*
>>> *Charm++ warning> fences and atomic operations not available in native
>>> assembly*
>>> *Converse/Charm++ Commit ID:
>>> v6.6.1-rc1-1-gba7c3c3-namd-charm-6.6.1-build-2014-De*
>>> *c-08-28969*
>>> *[0] isomalloc.c> Disabling isomalloc because mmap() does not work*
>>> *CharmLB> Load balancer assumes all CPUs are same.*
>>> *Charm++> Running on 1 unique compute nodes (4-way SMP).*
>>> *Charm++> cpu topology info is gathered in 0.000 seconds.*
>>> *Info: NAMD 2.10 for Win64-multicore*
>>> *Info:*
>>> *Info: Please visit http://www.ks.uiuc.edu/Research/namd/
>>> <http://www.ks.uiuc.edu/Research/namd/>*
>>> *Info: for updates, documentation, and support information.*
>>> *Info:*
>>> *Info: Please cite Phillips et al., J. Comp. Chem. 26:1781-1802 (2005)*
>>> *Info: in all publications reporting results obtained with NAMD.*
>>> *Info:*
>>> *Info: Based on Charm++/Converse 60601 for multicore-win64*
>>> *Info: Built Tue, Dec 09, 2014 3:31:31 PM by jim on europa*
>>> *Info: Running on 1 processors, 1 nodes, 1 physical nodes.*
>>> *Info: CPU topology information available.*
>>> *Info: Charm++/Converse parallel runtime startup completed at 0 s*
>>> *Info: 4.49219 MB of memory in use based on GetProcessMemoryInfo*
>>> *Info: Configuration file is sim_short.conf*
>>> *FATAL ERROR: Unable to access config file sim_short.conf*
>>> *------------- Processor 0 Exiting: Called CmiAbort ------------*
>>> *Reason: FATAL ERROR: Unable to access config file sim_short.conf*
>>>
>>> *Charm++ fatal error:*
>>> *FATAL ERROR: Unable to access config file sim_short.conf*
>>>
>>>
>>> I apologize if the solution if trivial, but if anyone may have some
>>> insight as to what I am doing wrong, I would greatly appreciate it.
>>>
>>>
>>> Thank you for your time and consideration.
>>>
>>>
>>> Julio
>>>
>>>
>>
>>
>> --
>> Best,
>> /A
>>
>
>


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