Hello,
On Tue, Feb 23, 2010 at 4:34 AM, Nicee <nicee.srivastava.imtech.res.in> wrote:
> Respected sir,
>
> I have installed amber10 successfully both in serial and parallel with mvapich
> library but while running the test for parallel following error is coming up.
> Kindly look into the problem and please help.
>
> [nicee.master1 test]$ export DO_PARALLEL='mpirun -np 4'
> [nicee.master1 test]$ make test.parallel.MM < /dev/null
> export TESTsander=/home/nicee/amber10/exe/sander.MPI; make test.sander.BASIC
> make[1]: Entering directory `/home/nicee/amber10/test'
> cd cytosine && ./Run.cytosine
> PMGR_COLLECTIVE ERROR: unitialized MPI task: Missing required environment
> variable: MPIRUN_RANK
This looks like an MPI issue. Because mvapich is mpich for infiniband
more or less, I'm assuming you're running this on some kind of HPC
cluster interconnected by this interface. Are you sure that you're
allowed to run parallel jobs interactively? Are you sure that "mpirun
-np 4" is the appropriate way to start a parallel process? Your
system admin may be more helpful than we are in this matter.
> PMGR_COLLECTIVE ERROR: unitialized MPI task: Missing required environment
> variable: MPIRUN_RANK
> PMGR_COLLECTIVE ERROR: unitialized MPI task: Missing required environment
> variable: MPIRUN_RANK
> PMGR_COLLECTIVE ERROR: unitialized MPI task: Missing required environment
> variable: MPIRUN_RANK
> ./Run.cytosine: Program error
> make[1]: *** [test.sander.BASIC] Error 1
> make[1]: Leaving directory `/home/nicee/amber10/test'
> make: *** [test.sander.BASIC.MPI] Error 2
>
> Thanking you,
> Nicee.
Good luck!
Jason
--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Tue Feb 23 2010 - 07:30:05 PST
