mpiuser.node1:~/amber11/test$ make test.parallel.MM < /dev/null
If I omit sudo I got the following:
mpiuser.node1:~/amber11/test$ make test.parallel.MM < /dev/null
export TESTsander=/home/mpiuser/amber11/exe/sander.MPI; make test.sander.BASIC
make[1]: Entering directory `/home/mpiuser/amber11/test'
cd cytosine && ./Run.cytosine
diffing cytosine.out.save with cytosine.out
PASSED
==============================================================
cd nonper && ./Run.nonper
gbin: Permission denied.
diffing mdout.nonper.save with mdout.nonper
PASSED
==============================================================
cd nonper && ./Run.nonper.belly
diffing mdout.belly.save with mdout.belly
PASSED
==============================================================
cd nonper && ./Run.nonper.belly.mask
--------------------------------------------------------------------------
MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD
with errorcode 1.
NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes.
You may or may not see output from other processes, depending on
exactly when Open MPI kills them.
--------------------------------------------------------------------------
Unit 6 Error on OPEN: mdout.belly.mask
--------------------------------------------------------------------------
mpirun has exited due to process rank 0 with PID 2051 on
node node1 exiting without calling "finalize". This may
have caused other processes in the application to be
terminated by signals sent by mpirun (as reported here).
--------------------------------------------------------------------------
Program error
make[1]: *** [test.sander.BASIC] Error 1
make[1]: Leaving directory `/home/mpiuser/amber11/test'
make: *** [test.sander.BASIC.MPI] Error 2
mpiuser.node1:~/amber11/test$
> From: nyam100.hotmail.com
> To: amber.ambermd.org
> Date: Fri, 30 Mar 2012 06:25:32 +0000
> Subject: [AMBER] Amber10 parallel test example run error
>
>
> Hi
> I know this is little bit off topic question, but I thought someone might help me.
> I am trying to run Amber10 parallel test example on my Beowulf cluster(Ubuntu 11.10, OpenMPI)
> It is asking slave node's password for every example. I noticed this kind of behaviour for Ubuntu +NFS4
> when I test example C++/C programs,but I found a workaround using NFS3 instead of NFS4(they don't ask for password).
> But this time even I use NFS3 , the slave asks its password.Whole amber11 is owned by mpiuser.
> Do test Makefile has some option for debugging or verbose?
>
> The result of my test is:
>
> mpiuser.node1:~/amber11/test$ sudo make test.parallel.MM < /dev/null
> export TESTsander=/home/mpiuser/amber11/exe/sander.MPI; make test.sander.BASIC
> make[1]: Entering directory `/home/mpiuser/amber11/test'
> cd cytosine && ./Run.cytosine
> mpiuser.node2's password:
> diffing cytosine.out.save with cytosine.out
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper
> mpiuser.node2's password:
> diffing mdout.nonper.save with mdout.nonper
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper.belly
> mpiuser.node2's password:
> diffing mdout.belly.save with mdout.belly
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper.belly.mask
> mpiuser.node2's password:
> diffing mdout.belly.mask.save with mdout.belly.mask
> PASSED
> ==============================================================
> cd nonper && ./Run.nonper.min
> mpiuser.node2's password: mpirun: killing job...
>
>
> --------------------------------------------------------------------------
> mpirun noticed that the job aborted, but has no info as to the process
> that caused that situation.
> --------------------------------------------------------------------------
> mpirun: clean termination accomplished
>
> make[1]: *** [test.sander.BASIC] Interrupt
> make: *** [test.sander.BASIC.MPI] Interrupt
> mpiuser.node1:~/amber11/test$
>
>
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Received on Fri Mar 30 2012 - 01:30:03 PDT
