Re: mpirun was unable to find the specified executable file

From: Adupa Vasista (adupavasista_at_gmail.com)
Date: Fri Aug 02 2019 - 11:29:28 CDT

Thanks for the reply
I tried using namd2 instead of namd and the following error popped up
--------------------------------------------------------------------------------------------------------------------
Charm++: standalone mode (not using charmrun)
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++: standalone mode (not using charmrun)
Charm++: standalone mode (not using charmrun)
Charm++> Running in Multicore mode: 1 threads
Charm++> Running in Multicore mode: 1 threads
Charm++> Running in Multicore mode: 1 threads
--------------------------------------------------------------------------
Primary job terminated normally, but 1 process returned
a non-zero exit code. Per user-direction, the job has been aborted.
--------------------------------------------------------------------------
--------------------------------------------------------------------------
mpirun noticed that process rank 0 with PID 0 on node vasi exited on signal
11 (Segmentation fault).

-----------------------------------------------------------------------------------------------------------------------------

Its the tutorial file. in the tutorial, it says for 16 replicas and I
changed it to 4 replicas and did the necessary changes in other files too.

On Fri, Aug 2, 2019 at 8:45 PM Roshan Shrestha <roshanpra_at_gmail.com> wrote:

> Using namd2 command instead of namd alone should solve the issue I guess.
> Best regards
>
> On Fri, 2 Aug 2019, 20:48 mariano spivak, <mariano_at_ks.uiuc.edu> wrote:
>
>> Hi, I believe that the problem is that the command that you want is not
>> "namd".
>> Try in the terminal: which namd
>> If it does not find the command, then you might want to try "namd2"
>> instead.
>> Otherwise you should find where NAMD is installed and write the full path
>> in the mpirun call.
>>
>> Best
>>
>> Mariano Spivak, Ph.D.
>>
>> Theoretical and Computational Biophysics Group
>>
>> Beckman Institute, University of Illinois.
>>
>> mariano_at_ks.uiuc.edu
>>
>> mspivak_at_illinois.edu
>>
>>
>> On Fri, Aug 2, 2019 at 8:29 AM Adupa Vasista <adupavasista_at_gmail.com>
>> wrote:
>>
>>> Dear NAMD users
>>>
>>> I am learning replica-exchange umbrella sampling MD. I am using the
>>> tutorial files. I copied umbrella.namd file into my working directory.
>>>
>>> Tutorial says to use the command "mpirun -np 4 namd +replicas 4
>>> job0.conf +stdout output/%d/job0.%d.log"
>>>
>>> But when i execute it the error is as follows :
>>>
>>> -------------------------------------------------------------------------------------------------------
>>> mpirun was unable to find the specified executable file, and therefore
>>> did not launch the job. This error was first reported for process
>>> rank 0; it may have occurred for other processes as well.
>>>
>>> NOTE: A common cause for this error is misspelling a mpirun command
>>> line parameter option (remember that mpirun interprets the first
>>> unrecognized command line token as the executable).
>>>
>>> Node: vasi
>>> Executable: namd
>>>
>>> -----------------------------------------------------------------------------------------------------------
>>>
>>> job0.conf file details are as follows :
>>>
>>> ------------------------------------------------------------------------------------------------------------
>>> source stretch_alanin.conf
>>>
>>> # prevent VMD from reading umbrella.namd by trying command only NAMD has
>>> if { ! [catch numPes] } { source ./umbrella.namd }
>>>
>>> ------------------------------------------------------------------------------------------------------------
>>>
>>> Can anyone point out the mistake I am making?
>>>
>>> Thank You in advance.
>>>
>>>
>>>
>>>

-- 
*A.VasistaM.Tech,Department Of Chemical Engineering,*
*IIT Guwahati.*

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