Re: namd and Fedora14

From: Michael S. Sellers (Cont, ARL/WMRD) (michael.s.sellers.ctr_at_us.army.mil)
Date: Mon Mar 28 2011 - 09:16:51 CDT

Sorry, disregard that Fedora comment. It's only for ../sbin's.

Michael S. Sellers (Cont, ARL/WMRD) wrote:
> 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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