Hi Jason,
I retracted the previous message because I realised that pmemd.MPI was not found in /bin.
sander.MPI was installed. The version of amber is 11.
I checked a 2nd machine running OSX in which I've also installed amber11. pmemd.MPI is installed in this machine.
Is there a way to install pmemd.MPI without trying to reinstall amber11?
Thanks for the advice
George
On Sep 16, 2010, at 7:50 PM, Jason Swails wrote:
> What version of amber are you using? If you're using amber11, pmemd.MPI
> should be installed automatically alongside sander.MPI. Moreover, if
> pmemd.MPI was not installed, you'd see something about "command not found",
> not
>
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> MPI version of PMEMD must be used with 2 or more processors!
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
> MPI version of PMEMD must be used with 2 or more processors!
> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>
> I still think my previous response is the most likely. The above messages
> are basically 4 threads of pmemd.MPI that are unaware of any kind of MPI
> world. i.e. mpirun from, say, openMPI not playing nice with pmemd.MPI
> compiled from an mpich2 mpif90. Do you have MPI_HOME set? What is
> $MPI_HOME/bin/mpirun and `which mpirun` ? Are they different?
>
> Good luck!
> Jason
>
> On Thu, Sep 16, 2010 at 1:46 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> I'd like to retract the previous message.
>>
>> It seems that pmemd.MPI was not installed during the installation.
>> sander.MPI was
>>
>> So my question is whether there's a special procedure to install it?
>>
>> George
>>
>>
>> On Sep 16, 2010, at 7:35 PM, George Tzotzos wrote:
>>
>>> Hi everybody
>>>
>>> amber11 parallel has been installed and passed all tests.
>>>
>>> I'm running OSX on a 4 Core 2.8 GHz Intel Core i7 machine.
>>>
>>> Running: mpirun -np 4 sander.MPI etc. works smoothly
>>>
>>> Running: mpirun -np 4 pmemd.MPI produces the following error.
>>>
>>> MPI version of PMEMD must be used with 2 or more processors!
>>> MPI version of PMEMD must be used with 2 or more processors!
>>> MPI version of PMEMD must be used with 2 or more processors!
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>> MPI version of PMEMD must be used with 2 or more processors!
>>> application called MPI_Abort(MPI_COMM_WORLD, 1) - process 0
>>>
>>> Any ideas as to why?
>>>
>>> Thanks in advance and regards
>>>
>>> George
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Graduate Student
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Sep 16 2010 - 11:30:04 PDT
