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-   -   MPI problmes (http://www.cfd-online.com/Forums/openfoam/111120-mpi-problmes.html)

sharonyue December 27, 2012 22:56

MPI problmes
 
Hi Foamers.

According to this http://www.openfoam.org/download/git.php
After I compiled OF 21x and paraview, there is totally nothing wrong and successfully run solvers.
But I want to run parallel. so I tried, there are some errors:

Code:

cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$ mpirun -np 4 interFoam -parallel
[cfd:08509] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 121
--------------------------------------------------------------------------
Sorry!  You were supposed to get help about:
    orte_init:startup:internal-failure
But I couldn't open the help file:
    /home/cfd/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/share/openmpi/help-orte-runtime: No such file or directory.  Sorry!
--------------------------------------------------------------------------
[cfd:08509] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 572
cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$

Code:

cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$ mpirun
--------------------------------------------------------------------------
Sorry!  You were supposed to get help about:
    orterun:usage
But I couldn't open the help file:
    /home/cfd/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/share/openmpi/help-orterun.txt: No such file or directory.  Sorry!
--------------------------------------------------------------------------
cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$

Code:

cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$ sudo mpirun
[sudo] password for cfd:
mpirun (Open MPI) 1.5.3

Usage: mpirun [OPTION]...  [PROGRAM]...
Start the given program using Open RTE

  -am <arg0>            Aggregate MCA parameter set file list
  --app <arg0>          Provide an appfile; ignore all other command line
                        options
  -bind-to-board|--bind-to-board
                        Whether to bind processes to specific boards
                        (meaningless on 1 board/node)
  -bind-to-core|--bind-to-core
                        Whether to bind processes to specific cores
  -bind-to-none|--bind-to-none
                        Do not bind processes to cores or sockets
                        (default)
  -bind-to-socket|--bind-to-socket
                        Whether to bind processes to sockets
  -byboard|--byboard    Whether to assign processes round-robin by board
                        (equivalent to bynode if only 1 board/node)
  -bycore|--bycore      Alias for byslot
  -bynode|--bynode      Whether to assign processes round-robin by node
  -byslot|--byslot      Whether to assign processes round-robin by slot
                        (the default)
  -bysocket|--bysocket  Whether to assign processes round-robin by socket
-c|-np|--np <arg0>      Number of processes to run
  -cf|--cartofile <arg0> 
                        Provide a cartography file
  -cpu-set|--cpu-set <arg0> 
                        Comma-separated list of ranges specifying logical
                        cpus allocated to this job [default: none]
  -cpus-per-proc|--cpus-per-proc <arg0> 
                        Number of cpus to use for each process [default=1]
  -cpus-per-rank|--cpus-per-rank <arg0> 
                        Synonym for cpus-per-proc
-d|-debug-devel|--debug-devel
                        Enable debugging of OpenRTE
  -debug|--debug        Invoke the user-level debugger indicated by the
                        orte_base_user_debugger MCA parameter
  -debug-daemons|--debug-daemons
                        Enable debugging of any OpenRTE daemons used by
                        this application
  -debug-daemons-file|--debug-daemons-file
                        Enable debugging of any OpenRTE daemons used by
                        this application, storing output in files
  -debugger|--debugger <arg0> 
                        Sequence of debuggers to search for when "--debug"
                        is used
  -default-hostfile|--default-hostfile <arg0> 
                        Provide a default hostfile
  -display-allocation|--display-allocation
                        Display the allocation being used by this job
  -display-devel-allocation|--display-devel-allocation
                        Display a detailed list (mostly intended for
                        developers) of the allocation being used by this
                        job
  -display-devel-map|--display-devel-map
                        Display a detailed process map (mostly intended for
                        developers) just before launch
  -display-map|--display-map
                        Display the process map just before launch
  -do-not-launch|--do-not-launch
                        Perform all necessary operations to prepare to
                        launch the application, but do not actually launch
                        it
  -do-not-resolve|--do-not-resolve
                        Do not attempt to resolve interfaces
  -gmca|--gmca <arg0> <arg1> 
                        Pass global MCA parameters that are applicable to
                        all contexts (arg0 is the parameter name; arg1 is
                        the parameter value)
-h|--help                This help message
-H|-host|--host <arg0>  List of hosts to invoke processes on
  --hetero              Indicates that multiple app_contexts are being
                        provided that are a mix of 32/64 bit binaries
  -hostfile|--hostfile <arg0> 
                        Provide a hostfile
  -launch-agent|--launch-agent <arg0> 
                        Command used to start processes on remote nodes
                        (default: orted)
  -leave-session-attached|--leave-session-attached
                        Enable debugging of OpenRTE
  -loadbalance|--loadbalance
                        Balance total number of procs across all allocated
                        nodes
  -machinefile|--machinefile <arg0> 
                        Provide a hostfile
  -mca|--mca <arg0> <arg1> 
                        Pass context-specific MCA parameters; they are
                        considered global if --gmca is not used and only
                        one context is specified (arg0 is the parameter
                        name; arg1 is the parameter value)
  -n|--n <arg0>        Number of processes to run
  -nolocal|--nolocal    Do not run any MPI applications on the local node
  -nooversubscribe|--nooversubscribe
                        Nodes are not to be oversubscribed, even if the
                        system supports such operation
  --noprefix            Disable automatic --prefix behavior
  -nperboard|--nperboard <arg0> 
                        Launch n processes per board on all allocated
                        nodes
  -npernode|--npernode <arg0> 
                        Launch n processes per node on all allocated nodes
  -npersocket|--npersocket <arg0> 
                        Launch n processes per socket on all allocated
                        nodes
  -num-boards|--num-boards <arg0> 
                        Number of processor boards/node (1-256) [default:
                        1]
  -num-cores|--num-cores <arg0> 
                        Number of cores/socket (1-256) [default: 1]
  -num-sockets|--num-sockets <arg0> 
                        Number of sockets/board (1-256) [default: 1]
  -ompi-server|--ompi-server <arg0> 
                        Specify the URI of the Open MPI server, or the name
                        of the file (specified as file:filename) that
                        contains that info
  -output-filename|--output-filename <arg0> 
                        Redirect output from application processes into
                        filename.rank
  -path|--path <arg0>  PATH to be used to look for executables to start
                        processes
  -pernode|--pernode    Launch one process per available node on the
                        specified number of nodes [no -np => use all
                        allocated nodes]
  --prefix <arg0>      Prefix where Open MPI is installed on remote nodes
  --preload-files <arg0> 
                        Preload the comma separated list of files to the
                        remote machines current working directory before
                        starting the remote process.
  --preload-files-dest-dir <arg0> 
                        The destination directory to use in conjunction
                        with --preload-files. By default the absolute and
                        relative paths provided by --preload-files are
                        used.
-q|--quiet              Suppress helpful messages
  -report-bindings|--report-bindings
                        Whether to report process bindings to stderr
  -report-events|--report-events <arg0> 
                        Report events to a tool listening at the specified
                        URI
  -report-pid|--report-pid <arg0> 
                        Printout pid on stdout [-], stderr [+], or a file
                        [anything else]
  -report-uri|--report-uri <arg0> 
                        Printout URI on stdout [-], stderr [+], or a file
                        [anything else]
  -rf|--rankfile <arg0> 
                        Provide a rankfile file
-s|--preload-binary      Preload the binary on the remote machine before
                        starting the remote process.
  -server-wait-time|--server-wait-time <arg0> 
                        Time in seconds to wait for ompi-server (default:
                        10 sec)
  -show-progress|--show-progress
                        Output a brief periodic report on launch progress
  -slot-list|--slot-list <arg0> 
                        List of processor IDs to bind MPI processes to
                        (e.g., used in conjunction with rank files)
  -stdin|--stdin <arg0> 
                        Specify procs to receive stdin [rank, all, none]
                        (default: 0, indicating rank 0)
  -stride|--stride <arg0> 
                        When binding multiple cores to a rank, the step
                        size to use between cores [default: 1]
  -tag-output|--tag-output
                        Tag all output with [job,rank]
  -timestamp-output|--timestamp-output
                        Timestamp all application process output
  -tmpdir|--tmpdir <arg0> 
                        Set the root for the session directory tree for
                        orterun ONLY
  -tv|--tv              Deprecated backwards compatibility flag; synonym
                        for "--debug"
  -use-regexp|--use-regexp
                        Use regular expressions for launch
-v|--verbose            Be verbose
-V|--version            Print version and exit
  -wait-for-server|--wait-for-server
                        If ompi-server is not already running, wait until
                        it is detected (default: false)
  -wd|--wd <arg0>      Synonym for --wdir
  -wdir|--wdir <arg0>  Set the working directory of the started processes
-x <arg0>                Export an environment variable, optionally
                        specifying a value (e.g., "-x foo" exports the
                        environment variable foo and takes its value from
                        the current environment; "-x foo=bar" exports the
                        environment variable name foo and sets its value to
                        "bar" in the started processes)
  -xml|--xml            Provide all output in XML format
  -xml-file|--xml-file <arg0> 
                        Provide all output in XML format to the specified
                        file
  -xterm|--xterm <arg0> 
                        Create a new xterm window and display output from
                        the specified ranks there

Report bugs to http://www.open-mpi.org/community/help/
cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$

Code:

cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$ sudo su
root@cfd:/home/cfd/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak# mpirun -np 4 interFoam -parallel
--------------------------------------------------------------------------
mpirun was unable to launch the specified application as it could not find an executable:

Executable: interFoam
Node: cfd

while attempting to start process rank 0.
--------------------------------------------------------------------------
4 total processes failed to start
root@cfd:/home/cfd/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak#

How to fix this? Thanks in advance

Tushar@cfd December 28, 2012 00:31

Dear sharonyue,
 
Have you done? "decomposePar" properly?..

I think you should check your file "decomposeParDict"...

All the best...

sharonyue December 28, 2012 01:36

Quote:

Originally Posted by Tushar_Mtechcfd (Post 399269)
Have you done? "decomposePar" properly?..

I think you should check your file "decomposeParDict"...

All the best...

~Yes,I have done that~

Tushar@cfd December 28, 2012 02:42

Can you please copy-paste the "decomposeParDict" code here... So that I will have a better idea...

sharonyue December 28, 2012 04:40

Quote:

Originally Posted by Tushar_Mtechcfd (Post 399276)
Can you please copy-paste the "decomposeParDict" code here... So that I will have a better idea...


Code:

numberOfSubdomains 4;

method          simple;

simpleCoeffs
{
    n              ( 2 2 1 );
    delta          0.001;
}

hierarchicalCoeffs
{
    n              ( 1 1 1 );
    delta          0.001;
    order          xyz;
}

manualCoeffs
{
    dataFile        "";
}

distributed    no;

roots          ( );


// ************************************************************************* //



I think its tough to install openmpi for myself.

sharonyue December 28, 2012 04:56

I do strictly according to this page. http://www.openfoam.org/download/git.php
But I can NOT install openmpi correctly. Its driving me crazy and upset!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!! !!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!

Tushar@cfd December 28, 2012 05:14

1) Install "openmpi-bin" and after that

2) Try running this command...
mpirun -np 4 interFoam -parallel

sharonyue December 28, 2012 05:16

Quote:

Originally Posted by Tushar_Mtechcfd (Post 399287)
1) Install "openmpi-bin" and after that

2) Try running this command...
mpirun -np 4 interFoam -parallel


Code:

cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$ mpirun -np 4 interFoam -parallel
[cfd:08509] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 121
--------------------------------------------------------------------------
Sorry!  You were supposed to get help about:
    orte_init:startup:internal-failure
But I couldn't open the help file:
    /home/cfd/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc/openmpi-1.5.3/share/openmpi/help-orte-runtime: No such file or directory.  Sorry!
--------------------------------------------------------------------------
[cfd:08509] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 572
cfd@cfd:~/OpenFOAM/tutorials/multiphase/interFoam/laminar/damBreak$

yeah, I have installed that...

l_r_mcglashan December 28, 2012 05:17

What is the result of:

Code:

ls $WM_THIRD_PARTY_DIR/platforms/linux64Gcc/openmpi-1.5.3/share/openmpi/
Does that path exist?

And also post the output of the Allwmake script that you ran in $WM_THIRD_PARTY_DIR.

Code:

cd $WM_THIRD_PARTY_DIR
./Allwmake > log.make 2>&1 &

Nobody can help you unless you provide more information.

P.S. Do not run stuff as root.

sharonyue December 28, 2012 05:28

Quote:

Originally Posted by l_r_mcglashan (Post 399290)
What is the result of:

Code:

ls $WM_THIRD_PARTY_DIR/platforms/linux64Gcc/openmpi-1.5.3/share/openmpi/
Does that path exist?

And also post the output of the Allwmake script that you ran in $WM_THIRD_PARTY_DIR.

Code:

cd $WM_THIRD_PARTY_DIR
./Allwmake > log.make 2>&1 &

Nobody can help you unless you provide more information.

P.S. Do not run stuff as root.


no it does not exits.

Code:

cfd@cfd:~/OpenFOAM/ThirdParty-2.1.x/platforms/linux64Gcc$ ls
paraview-3.12.0

I installed openmpi153 this way:

cd OpenFOAM/ThirdParty-2.1.x/openmpi1.5.3
./configure
make all install

then I set the .bashrc but it does not work. actually I dont know how to set the .bashrc. I search the internet.............




forget it !!!!! I just re-install my ubuntu and compile Openfoam.. I am totally pissed off! I am running interFoam on a mesh with 3,000,000 cells. thats too slow! I cant endure that. now I am so upset. I got have a rest.

anyway Thank you guys very much. I will update my problem later after I reinstall my ubuntu and foam.

l_r_mcglashan December 28, 2012 05:38

Quote:

Originally Posted by sharonyue (Post 399297)
forget it !!!!! I just re-install my ubuntu and compile Openfoam.. I am totally pissed off!.

Don't do that, it will take even longer!

Unpack the openmpi sources into $WM_THIRD_PARTY_DIR and then just run the Allwmake script in $WM_THIRD_PARTY_DIR. That will install openmpi for you.

Tushar@cfd December 28, 2012 05:40

Check this link...
http://auriza.site40.net/notes/mpi/o...on-ubuntu-904/

Try installing it from the command prompt..


Best of luck...


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