Lakee,
Glad to hear everything worked well with MVAPICH. In regards to OpenMPI, I am
confused. You are running on a machine with eight CPUs correct? Why supply a
host file then? Try it without the -hostfile <filename>. Typically, my routines
are input
mpirun -np 4 siesta < input.fdf > output.out &
If this still doesn't work, it may have to do with how you configured OpenMPI.
The machines I run SIESTA on are x86_64 architecture with SuSE 10.x. OpenMPI
was compiled with Intel Fortran, C compilers. I can send the log file, if
necessary
-Tom
Date: Fri, 22 Aug 2008 22:47:25 +0800
From: [EMAIL PROTECTED]
Subject: Re: [SIESTA-L] Strange mpi problem
To: SIESTA-L@listserv.uam.es
Hello, Dear Tom,
Thank you so much for your experience and suggestion. I also have tried MVAPICH
and OpenMPI today.
For me, MVAPICH also works very well! :-)
However, OpenMPI does not work for more than 1 processor. Every time after I
run the command:
mpirun --mca btl tcp,self -np 4 --hostfile hostfile siesta <input.fdf >output
I always got the following error message
[node1:10222] *** An error occurred in MPI_Comm_group
[node1:10222] *** on communicator MPI_COMM_WORLD
[node1:10222] *** MPI_ERR_COMM: invalid communicator
[node1:10222] *** MPI_ERRORS_ARE_FATAL (goodbye)
[node1:10223] *** An error occurred in MPI_Comm_group
[node1:10223] *** on communicator MPI_COMM_WORLD
[node1:10223] *** MPI_ERR_COMM: invalid communicator
[node1:10223] *** MPI_ERRORS_ARE_FATAL (goodbye)
[node1:10224] *** An error occurred in MPI_Comm_group
[node1:10224] *** on communicator MPI_COMM_WORLD
[node1:10224] *** MPI_ERR_COMM: invalid communicator
[node1:10224] *** MPI_ERRORS_ARE_FATAL (goodbye)
[node1:10225] *** An error occurred in MPI_Comm_group
[node1:10225] *** on communicator MPI_COMM_WORLD
[node1:10225] *** MPI_ERR_COMM: invalid communicator
[node1:10225] *** MPI_ERRORS_ARE_FATAL (goodbye)
[node1:10219] [0,0,0] ORTE_ERROR_LOG: Timeout in file
base/pls_base_orted_cmds.c at line 275
[node1:10219] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line
1166
[node1:10219] [0,0,0] ORTE_ERROR_LOG: Timeout in file errmgr_hnp.c at line 90
[node1:10219] [0,0,0] ORTE_ERROR_LOG: Timeout in file
base/pls_base_orted_cmds.c at line 188
[node1:10219] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line
1198
--------------------------------------------------------------------------
mpirun was unable to cleanly terminate the daemons for this job. Returned value
Timeout instead of ORTE_SUCCESS.
--------------------------------------------------------------------------
[1]+ Exit 1 mpirun --mca btl tcp,self -np 4 --hostfile
hostfile siesta <input.fdf >output
But when I check the output file, I can get the following lines at the end:
...
* Maximum dynamic memory allocated = 1 MB
siesta: ==============================
Begin CG move = 0
==============================
outcell: Unit cell vectors (Ang):
12.000000 0.000000 0.000000
0.000000 12.000000 0.000000
0.000000 0.000000 41.507400
outcell: Cell vector modules (Ang) : 12.000000 12.000000 41.507400
outcell: Cell angles (23,13,12) (deg): 90.0000 90.0000 90.0000
outcell: Cell volume (Ang**3) : 5977.0656
InitMesh: MESH = 108 x 108 x 360 = 4199040
InitMesh: Mesh cutoff (required, used) = 200.000 207.901 Ry
* Maximum dynamic memory allocated = 163 MB
So, the calculation started normally, but it stopped suddengly. I dit it on a
single machine with 8 cores. Do you have any idea about it, please?
Sincerely,
Lakee
2008/8/20 Thomas Sadowski <[EMAIL PROTECTED]>
Lakee,
I cannt speak about the serial sleep, but I have encountered similar problems
trying to run parallel SIESTA using MPICH2 as my MPI interface. I would
recommend considering one of the other MPI programs and see if this doesn't
solve the problem. Myself I use both OpenMPI and MVAPICH. Depending on how
aggressively the libraries are compiled, the latter tends to run a little
faster than the former, but it is not really that significant of a difference.
I would be interested to hear what the other users have to say concerning this
issue.
Tom Sadowski
University of Connecticut
Date: Wed, 20 Aug 2008 22:06:20 +0800
From: [EMAIL PROTECTED]
Subject: [SIESTA-L] Strange mpi problem
To: SIESTA-L@listserv.uam.es
Hello, Dear all,
These days, I was trying to run a calculation with the parallel version of
siesta on a PC cluster. It was compiled by mpich2 and pgi compiler. What
surprises me is that, sometimes, it runs normally, and sometimes, the task
enters a sleeping status right after I submit the job by "mpiexec -n 8 siesta
<input> output". In the output of the command "top", I can see "S" as the
status on the line of my job. At this time ,it never goes on. This happens
very frequently, even for the same input file. I do not know why. Could you
tell me how to avoid entering a sleeping state right after the submission of
the job, please?
Thank you very much!!
Sincerely,
Lakee
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