Hi, Tom,
I tried it. The problem is still there.
Lakee
2008/8/24 Thomas Sadowski <[EMAIL PROTECTED]>
That might be your problem...Try linking against libmpi_f90.a
-Tom
Date: Sat, 23 Aug 2008 10:13:43 +0800
From: [EMAIL PROTECTED]
Subject: Re: [SIESTA-L] Strange mpi problem
To: SIESTA-L@listserv.uam.es
Hi, Dear Tom,
I tried "mpirun -np 4 siesta < input.fdf > output.out &". What I get
is the following:
libibverbs: Fatal: couldn't read uverbs ABI version.
--------------------------------------------------------------------------
[0,1,0]: OpenIB on host node1 was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
libibverbs: Fatal: couldn't read uverbs ABI version.
--------------------------------------------------------------------------
[0,1,1]: OpenIB on host node1 was unable to find any HCAs.
Another transport will be used instead, although this may result in
lower performance.
--------------------------------------------------------------------------
[node1:11756] *** An error occurred in MPI_Comm_group
[node1:11757] *** An error occurred in MPI_Comm_group
[node1:11757] *** on communicator MPI_COMM_WORLD
[node1:11757] *** MPI_ERR_COMM: invalid communicator
[node1:11757] *** MPI_ERRORS_ARE_FATAL (goodbye)
[node1:11756] *** on communicator MPI_COMM_WORLD
[node1:11756] *** MPI_ERR_COMM: invalid communicator
[node1:11756] *** MPI_ERRORS_ARE_FATAL (goodbye)
From the FAQ of openmpi official site, it seems that we should use
the option "--mca btl tcp,self" for TCP network?
My machines are also x86-64 architecture with RedHat Enterprise
Linux 4. The compiler is pgi-7.1.4. My configure options are:
./configure --prefix=/usr/local/math_library/pgi-7.1.4/openmpi-1.2.6
CC=cc CXX=c++ F77=pgf90 F90=pgf90 FC=pgf90 CFLAGS="-O2" FFLAGS="-O2"
Do you think there is anything wrong here, please?
By the way, when I compile BLACS and scalapack, in the "lib"
directory of openmpi-1.2.6, I can not see the file "libmpich.a", but
I can see it in both mpich2 and mvapich2. So I set MPILIB in
Bmake.inc of BLACS and SMPLIB in SLmake.inc of scalapack to
"openmpi-1.2.6/lib/libmpi.la", since only this file looks similar to
libmpich.a. Is it wrong here, please?
I will appreciate it very much if you can send your log file for
configuring openmpi, the Bmake.inc and SLmake.inc.
Sincerely,
Lakee
2008/8/23 Thomas Sadowski <[EMAIL PROTECTED]>
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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