VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Fri Dec 11 2015 - 11:36:14 CST

Once you change the drive to "E:", I’d recommend using [file join VMD nanotubes] for specifying folders and files.



On Dec 11, 2015, at 11:32, Richard Wood <Richard.Wood@purduecal.edu> wrote:

Must have started with Win7, then.
From: Ajasja Ljubetič [ajasja.ljubetic@gmail.com]
Sent: Friday, December 11, 2015 11:24 AM
To: Richard Wood
Cc: VMD Mailing List
Subject: Re: vmd-l: Unable to access config file

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

<image.png>

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

From: owner-vmd-l@ks.uiuc.edu [owner-vmd-l@ks.uiuc.edu] on behalf of Ajasja Ljubetič [ajasja.ljubetic@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 and you will get a fully functional bash shell:)

Best,
Ajasja

On 11 December 2015 at 05:57, Ashar Malik <asharjm@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@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: 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