[gmx-users] Error while running starting grompp and mdrun

[Mark Abraham]

Ragothaman Yennamalli wrote:
> Dear Mark,
> Thanks for the mail.
> 
> 
>> Since there's three different usages of -np you'd
>> need to be more 
>> precise to make a good description of your problem.
>>
> 
> I was changing the -np option in mdrun and grompp.
>  
>> The symptoms you observe make sense if $NSLOTS==1. Since
>> all three -np 
>> flags need the same value after them, you should use the
>> same variable 
>> each time. You should verify that the "echo" line
>> tells you that has 
>> $NSLOTS==4 like you need.
>>
> Yes. I checked by typing echo $NSLOTS and it says 4.

It's the batch environment that matters, not your terminal environment. 
As I said last time, you'd need to look at the output from the batch 
script to verify its environment.

> So, I changed all the three -np option to -np $NSLOTS..Still the same error. 

That's not possible for any value of $NSLOTS.

For troubleshooting, a (bash) script approach like

command="mpirun -np $NSLOTS <insert the rest of your command line here>"
echo $command
`$command`

will allow you to see in the standard output what you're actually doing, 
and so make a better description of the situation when emailing the list.

Mark