Hi Jason,
You're right. In my hurry I overlooked. Indeed pmemd.MPI is installed.
I'd appreciate if you could shed some light on the following:
1. If as you say, I'm dealing with incompatible MPIs, how come sander.MPI runs and pmemd.MPI does not
pmemd.MPI has passed all tests. Here's a representative example from the installation log file
export TESTsander='../../exe/pmemd.MPI'; cd 4096wat && ./Run.pure_wat
diffing mdout.pure_wat.save with mdout.pure_wat
PASSED
==============================================================
export TESTsander='../../exe/pmemd.MPI'; cd 4096wat && ./Run.pure_wat_nmr_temp_reg
diffing mdout.pure_wat_nmr_temp.save with mdout.pure_wat_nmr_temp
PASSED
==============================================================
2. I've downloaded MPICH2 from MacPorts. 'which mpirun' gives < /opt/mpich2/bin/mpirun>. However, I notice that an mpirun is also in /usr/bin/mpirun
Could there be a conflict between the two? Should I reinstall mpich2?
Thanks in advance and best regards
George
On Sep 16, 2010, at 8:45 PM, Jason Swails wrote:
> Hi George,
>
> If pmemd.MPI wasn't there, it's surprising you got the output I mentioned
> last email instead of "pmemd.MPI: command not found" 4 times. That's what
> you would normally get if pmemd.MPI really didn't exist.
>
> To just build pmemd, you can go to $AMBERHOME/src/pmemd and just run "make
> parallel". That should do it, but you may run into problems if you've done
> a make clean, since that will have gutted netCDF and you'll have trouble
> linking to that (I think). After it's built, though, you'll have to move
> pmemd.MPI into the $AMBERHOME/bin directory.
>
> Keep an eye out for incompatible MPIs, though, since that will cause the
> error you mentioned. Again, if you're using amber11, the only way you would
> NOT have pmemd.MPI is if there was an error while it was compiled that you
> overlooked or if it was deleted from the bin directory, since it's built by
> default.
>
> Hope this helps,
> Jason
>
> On Thu, Sep 16, 2010 at 2:27 PM, George Tzotzos <gtzotzos.me.com> wrote:
>
>> 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
>>>>
>>>> _______________________________________________
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>>>>
>>>
>>>
>>>
>>> --
>>> 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
>>
>> _______________________________________________
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>> 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
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Received on Fri Sep 17 2010 - 05:00:03 PDT
