Re: namd and Fedora14

From: Michael S. Sellers (Cont, ARL/WMRD) (michael.s.sellers.ctr_at_us.army.mil)
Date: Mon Mar 28 2011 - 09:12:47 CDT

Glad that worked for you.

There are ways to setup links or your path variable so you can refer to
namd2 and charmrun without a full path or copying everything into a
folder...

You could try, as root: ln -s /path/to/NAMD/namd2 /usr/bin/namd2; ln -s
/path/to/NAMD/charmrun /usr/bin/charmrun, if /usr/bin is in your path.
***I believe with Fedora, /usr/bin is not in the path variable by
default. This might have changed in newer releases, or I may be wrong.
echo $PATH.

If you added your NAMD folder to your path variable via .bashrc, as
export PATH=$PATH:/path/to/NAMD/, then it should also work. Remember to
start a new bash session after editing it.

-Mike

flavio seixas wrote:
> Hi Michael,
>
> Thank you for your help.
> I am writing to let the list know that doing as your advice, namd works fine.
> However, I needed to put the namd and charmrun pre compliled files at the same folder were input files were placed:
>
> ./charmrun ++local ./namd2 +p2 input.conf > output.log
>
> setting .bashrc our putting the compiled files on /usr/bin folder does not work.
>
> Thank you again.
>
> Flavio
>
>
>
> --- On Tue, 3/22/11, Michael S. Sellers (Cont, ARL/WMRD) <michael.s.sellers.ctr_at_us.army.mil> wrote:
>
>
>> From: Michael S. Sellers (Cont, ARL/WMRD) <michael.s.sellers.ctr_at_us.army.mil>
>> Subject: Re: namd-l: namd and Fedora14
>> To: "flavio seixas" <oivalf_nix_at_yahoo.com>
>> Cc: namd-l_at_ks.uiuc.edu
>> Date: Tuesday, March 22, 2011, 3:10 PM
>> 1. If this is a pre-compiled
>> version of NAMD (ie Linux-x86_64), I believe they use
>> "net-linux-..." compiled versions of Charm++. So, if
>> you are running locally, you'll want to execute "charmrum
>> ++local namd2 +p2 input.conf"
>>
>> 2. Generally it is not a good idea to run things like
>> this as root.
>>
>>
>> flavio seixas wrote:
>>
>>> Hi,
>>> I was trying to run a namd simulation in an AMD Athlon
>>>
>> X2 Fedora 14 Linux, when I found the following error
>> message:
>>
>>> [root_at_NIR set1]# charmrun namd2 +p2 input.conf >
>>>
>> output.log
>>
>>> Charmrun> Couldn't find rsh program 'rsh'!
>>> Charmrun> Couldn't find rsh program 'rsh'!
>>> Charmrun> Error 1 returned from rsh (localhost:0)
>>>
>>> I do not find anything regarding this error on
>>>
>> google.
>>
>>> Someone have already found an error like this?
>>> Regards,
>>>
>>>
>>> Flavio
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>
>
>
>


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