[OMPI users] calling a customized MPI_Allreduce with MPI_PACKED datatype
Dear all, in one of my C codes developed using Open MPI v1.4.3 I need to call MPI_Allreduce() passing as sendbuf and recvbuf arguments two MPI_PACKED arrays. The reduction requires my own MPI_User_function that needs to MPI_Unpack() its first and second argument, process them and finally MPI_Pack() the result in the second argument. I need to use MPI_Pack/MPI_Unpack because I am not able to create a derived datatype, since many data I need to send are dynamically allocated. However, the code fails at runtime with the following message: An error occurred in MPI_Unpack on communicator MPI_COMM_WORLD MPI_ERR_TRUNCATE: message truncated MPI_ERRORS_ARE_FATAL (your MPI job will now abort) I have verified that, after unpacking the data in my own reduction function, all of the data are wrong. Is this possible in MPI? I did not find anything on the "MPI reference Volume 1" and "Using MPI" that prevents this. This should just require using as datatype MPI_PACKED in MPI_Allreduce() . However, searching on the web I did not find any examples. Thank you in advance for any clue/suggestions/source code examples. This is driving me crazy now ;-( Massimo Cafaro - *** Massimo Cafaro, Ph.D. Additional affiliations: Assistant Professor Euro-Mediterranean Centre for Climate Change Dept. of Engineering for Innovation SPACI Consortium University of Salento, Lecce, Italy E-mail massimo.caf...@unisalento.it Via per Monteroni massimo.caf...@cmcc.it 73100 Lecce, Italy caf...@ieee.org Voice/Fax +39 0832 297371 caf...@acm.org Web http://sara.unisalento.it/~cafaro *** smime.p7s Description: S/MIME cryptographic signature
[OMPI users] Default hostfile not being used by mpirun
There have been many postings about openmpi-default-hostfile on the list, but I haven't found one that answers my question, so I hope you won't mind one more. When I use mpirun, openmpi-default-hostfile does not appear to get used. I've added three lines to the default host file: node0 slots=3 node1 slots=4 node2 slots=4 'node0' is the local (master) host. If I explicitly list the hostfile in the mpirun command, everything works correctly. E.g. mpirun -np 15 -hostfile /full/path/to/openmpi-default-hostfile hello_c works correctly - hello_c gets run using all three nodes. However, if I don't specify the hostfile, only the local node, node0, is used. E.g. mpirun -np 15 hello_c creates all 15 processes on node0. I was under the impression that all machines listed in openmpi-default-hostfile should get used by default. Is that correct? Unfortunately I can't use the hostfile command line option. I'm going to be using a mpi app (npRmpi) that doesn't let me pass params to mpirun. So I need all my nodes used by default. Configuration details: openmpi 1.4.3, built from source. OS: Debian lenny (but the Debian openmpi package is NOT installed). Installation dir: /home/omu/openmpi The default host file has pathname /home/omu/openmpi/etc/openmpi-default-hostfile I've set two envirnmental variables to support open mpi: PATH=/home/omu/openmpi/bin:... LD_LIBRARY_PATH=/home/omu/openmpi/lib:... Are there any other environmental variables that need to be set? I'd appreciate any suggestions about this. thanks, Barnet Wagman
Re: [OMPI users] Default hostfile not being used by mpirun
Barnet, This isn't the most straightforward solution, but as a workaround, create a bash script and run that script through npRmpi? Something like: !#/bin/bash openmpi -np 15 -hostfile /path/to/hostfile $1 Cheers, Ethan -- Dr. Ethan Deneault Assistant Professor of Physics The University of Tampa 401 W Kennedy Blvd Tampa, FL 33606 (813) 732-3718 Barnet Wagman wrote: There have been many postings about openmpi-default-hostfile on the list, but I haven't found one that answers my question, so I hope you won't mind one more. When I use mpirun, openmpi-default-hostfile does not appear to get used. I've added three lines to the default host file: node0 slots=3 node1 slots=4 node2 slots=4 'node0' is the local (master) host. If I explicitly list the hostfile in the mpirun command, everything works correctly. E.g. mpirun -np 15 -hostfile /full/path/to/openmpi-default-hostfile hello_c works correctly - hello_c gets run using all three nodes. However, if I don't specify the hostfile, only the local node, node0, is used. E.g. mpirun -np 15 hello_c creates all 15 processes on node0. I was under the impression that all machines listed in openmpi-default-hostfile should get used by default. Is that correct? Unfortunately I can't use the hostfile command line option. I'm going to be using a mpi app (npRmpi) that doesn't let me pass params to mpirun. So I need all my nodes used by default. Configuration details: openmpi 1.4.3, built from source. OS: Debian lenny (but the Debian openmpi package is NOT installed). Installation dir: /home/omu/openmpi The default host file has pathname /home/omu/openmpi/etc/openmpi-default-hostfile I've set two envirnmental variables to support open mpi: PATH=/home/omu/openmpi/bin:... LD_LIBRARY_PATH=/home/omu/openmpi/lib:... Are there any other environmental variables that need to be set? I'd appreciate any suggestions about this. thanks, Barnet Wagman
Re: [OMPI users] Default hostfile not being used by mpirun
The easiest solution is to take advantage of the fact that the default hostfile is an MCA parameter - so you can specify it in several ways other than on the cmd line. It can be in your environment, in the default MCA parameter file, or in an MCA param file in your home directory. See http://www.open-mpi.org/faq/?category=tuning#setting-mca-params for a full description on how to do this. On Feb 5, 2011, at 3:14 PM, ETHAN DENEAULT wrote: > Barnet, > > This isn't the most straightforward solution, but as a workaround, create a > bash script and run that script through npRmpi? Something like: > > !#/bin/bash > > openmpi -np 15 -hostfile /path/to/hostfile $1 > > Cheers, > Ethan > > -- > Dr. Ethan Deneault > Assistant Professor of Physics > The University of Tampa > 401 W Kennedy Blvd > Tampa, FL 33606 > (813) 732-3718 > > Barnet Wagman wrote: > > There have been many postings about openmpi-default-hostfile on the > list, but I haven't found one that answers my question, so I hope you > won't mind one more. > > When I use mpirun, openmpi-default-hostfile does not appear to get used. > I've added three lines to the default host file: > >node0 slots=3 >node1 slots=4 >node2 slots=4 > > 'node0' is the local (master) host. > > If I explicitly list the hostfile in the mpirun command, everything > works correctly. E.g. > >mpirun -np 15 -hostfile /full/path/to/openmpi-default-hostfile hello_c > > works correctly - hello_c gets run using all three nodes. > > However, if I don't specify the hostfile, only the local node, node0, is > used. E.g. > >mpirun -np 15 hello_c > > creates all 15 processes on node0. I was under the impression that all > machines listed in openmpi-default-hostfile should get used by default. > Is that correct? > > Unfortunately I can't use the hostfile command line option. I'm going > to be using a mpi app (npRmpi) that doesn't let me pass params to > mpirun. So I need all my nodes used by default. > > Configuration details: > >openmpi 1.4.3, built from source. > >OS: Debian lenny (but the Debian openmpi package is NOT installed). > >Installation dir: /home/omu/openmpi > >The default host file has pathname >/home/omu/openmpi/etc/openmpi-default-hostfile > >I've set two envirnmental variables to support open mpi: > >PATH=/home/omu/openmpi/bin:... >LD_LIBRARY_PATH=/home/omu/openmpi/lib:... > > > Are there any other environmental variables that need to be set? > > I'd appreciate any suggestions about this. > > thanks, > > Barnet Wagman > > > > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users
