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From: Kevin Radican (radicak_at_[hidden])
Date: 2007-05-09 05:15:28


Hi,

We use VASP 4.6 in parallel with opemmpi 1.1.2 without any problems on
x86_64 with opensuse and compiled with gcc and Intel fortran and use
torque PBS.

I used standard configure to build openmpi something like

./configure --prefix=/usr/local --enable-static --with-threads
--with-tm=/usr/local --with-libnuma

I used the ACLM math lapack libs and built Blacs and Scalapack with them
too.

I attached my vasp makefile, I might of added

mpi.o : mpi.F
        $(CPP)
        $(FC) -FR -lowercase -O0 -c $*$(SUFFIX)

to the end of the make file, It doesn't look like it is in the example
makefiles they give, but I compiled this a while ago.

Hope this helps.

Cheers,
Kevin

On Tue, 2007-05-08 at 19:18 -0700, Steven Truong wrote:
> Hi, all. I am new to OpenMPI and after initial setup I tried to run
> my app but got the followign errors:
>
> [node07.my.com:16673] *** An error occurred in MPI_Comm_rank
> [node07.my.com:16673] *** on communicator MPI_COMM_WORLD
> [node07.my.com:16673] *** MPI_ERR_COMM: invalid communicator
> [node07.my.com:16673] *** MPI_ERRORS_ARE_FATAL (goodbye)
> [node07.my.com:16674] *** An error occurred in MPI_Comm_rank
> [node07.my.com:16674] *** on communicator MPI_COMM_WORLD
> [node07.my.com:16674] *** MPI_ERR_COMM: invalid communicator
> [node07.my.com:16674] *** MPI_ERRORS_ARE_FATAL (goodbye)
> [node07.my.com:16675] *** An error occurred in MPI_Comm_rank
> [node07.my.com:16675] *** on communicator MPI_COMM_WORLD
> [node07.my.com:16675] *** MPI_ERR_COMM: invalid communicator
> [node07.my.com:16675] *** MPI_ERRORS_ARE_FATAL (goodbye)
> [node07.my.com:16676] *** An error occurred in MPI_Comm_rank
> [node07.my.com:16676] *** on communicator MPI_COMM_WORLD
> [node07.my.com:16676] *** MPI_ERR_COMM: invalid communicator
> [node07.my.com:16676] *** MPI_ERRORS_ARE_FATAL (goodbye)
> mpiexec noticed that job rank 2 with PID 16675 on node node07 exited
> on signal 60 (Real-time signal 26).
>
> /usr/local/openmpi-1.2.1/bin/ompi_info
> Open MPI: 1.2.1
> Open MPI SVN revision: r14481
> Open RTE: 1.2.1
> Open RTE SVN revision: r14481
> OPAL: 1.2.1
> OPAL SVN revision: r14481
> Prefix: /usr/local/openmpi-1.2.1
> Configured architecture: x86_64-unknown-linux-gnu
> Configured by: root
> Configured on: Mon May 7 18:32:56 PDT 2007
> Configure host: neptune.nanostellar.com
> Built by: root
> Built on: Mon May 7 18:40:28 PDT 2007
> Built host: neptune.my.com
> C bindings: yes
> C++ bindings: yes
> Fortran77 bindings: yes (all)
> Fortran90 bindings: yes
> Fortran90 bindings size: small
> C compiler: gcc
> C compiler absolute: /usr/bin/gcc
> C++ compiler: g++
> C++ compiler absolute: /usr/bin/g++
> Fortran77 compiler: /opt/intel/fce/9.1.043/bin/ifort
> Fortran77 compiler abs: /opt/intel/fce/9.1.043/bin/ifort
> Fortran90 compiler: /opt/intel/fce/9.1.043/bin/ifort
> Fortran90 compiler abs: /opt/intel/fce/9.1.043/bin/ifort
> C profiling: yes
> C++ profiling: yes
> Fortran77 profiling: yes
> Fortran90 profiling: yes
> C++ exceptions: no
> Thread support: posix (mpi: no, progress: no)
> Internal debug support: no
> MPI parameter check: runtime
> Memory profiling support: no
> Memory debugging support: no
> libltdl support: yes
> Heterogeneous support: yes
> mpirun default --prefix: yes
> MCA backtrace: execinfo (MCA v1.0, API v1.0, Component v1.2.1)
> MCA memory: ptmalloc2 (MCA v1.0, API v1.0, Component v1.2.1)
> MCA paffinity: linux (MCA v1.0, API v1.0, Component v1.2.1)
> MCA maffinity: first_use (MCA v1.0, API v1.0, Component v1.2.1)
> MCA maffinity: libnuma (MCA v1.0, API v1.0, Component v1.2.1)
> MCA timer: linux (MCA v1.0, API v1.0, Component v1.2.1)
> MCA installdirs: env (MCA v1.0, API v1.0, Component v1.2.1)
> MCA installdirs: config (MCA v1.0, API v1.0, Component v1.2.1)
> MCA allocator: basic (MCA v1.0, API v1.0, Component v1.0)
> MCA allocator: bucket (MCA v1.0, API v1.0, Component v1.0)
> MCA coll: basic (MCA v1.0, API v1.0, Component v1.2.1)
> MCA coll: self (MCA v1.0, API v1.0, Component v1.2.1)
> MCA coll: sm (MCA v1.0, API v1.0, Component v1.2.1)
> MCA coll: tuned (MCA v1.0, API v1.0, Component v1.2.1)
> MCA io: romio (MCA v1.0, API v1.0, Component v1.2.1)
> MCA mpool: rdma (MCA v1.0, API v1.0, Component v1.2.1)
> MCA mpool: sm (MCA v1.0, API v1.0, Component v1.2.1)
> MCA pml: cm (MCA v1.0, API v1.0, Component v1.2.1)
> MCA pml: ob1 (MCA v1.0, API v1.0, Component v1.2.1)
> MCA bml: r2 (MCA v1.0, API v1.0, Component v1.2.1)
> MCA rcache: vma (MCA v1.0, API v1.0, Component v1.2.1)
> MCA btl: self (MCA v1.0, API v1.0.1, Component v1.2.1)
> MCA btl: sm (MCA v1.0, API v1.0.1, Component v1.2.1)
> MCA btl: tcp (MCA v1.0, API v1.0.1, Component v1.0)
> MCA topo: unity (MCA v1.0, API v1.0, Component v1.2.1)
> MCA osc: pt2pt (MCA v1.0, API v1.0, Component v1.2.1)
> MCA errmgr: hnp (MCA v1.0, API v1.3, Component v1.2.1)
> MCA errmgr: orted (MCA v1.0, API v1.3, Component v1.2.1)
> MCA errmgr: proxy (MCA v1.0, API v1.3, Component v1.2.1)
> MCA gpr: null (MCA v1.0, API v1.0, Component v1.2.1)
> MCA gpr: proxy (MCA v1.0, API v1.0, Component v1.2.1)
> MCA gpr: replica (MCA v1.0, API v1.0, Component v1.2.1)
> MCA iof: proxy (MCA v1.0, API v1.0, Component v1.2.1)
> MCA iof: svc (MCA v1.0, API v1.0, Component v1.2.1)
> MCA ns: proxy (MCA v1.0, API v2.0, Component v1.2.1)
> MCA ns: replica (MCA v1.0, API v2.0, Component v1.2.1)
> MCA oob: tcp (MCA v1.0, API v1.0, Component v1.0)
> MCA ras: dash_host (MCA v1.0, API v1.3, Component v1.2.1)
> MCA ras: gridengine (MCA v1.0, API v1.3, Component v1.2.1)
> MCA ras: localhost (MCA v1.0, API v1.3, Component v1.2.1)
> MCA ras: slurm (MCA v1.0, API v1.3, Component v1.2.1)
> MCA ras: tm (MCA v1.0, API v1.3, Component v1.2.1)
> MCA rds: hostfile (MCA v1.0, API v1.3, Component v1.2.1)
> MCA rds: proxy (MCA v1.0, API v1.3, Component v1.2.1)
> MCA rds: resfile (MCA v1.0, API v1.3, Component v1.2.1)
> MCA rmaps: round_robin (MCA v1.0, API v1.3, Component v1.2.1)
> MCA rmgr: proxy (MCA v1.0, API v2.0, Component v1.2.1)
> MCA rmgr: urm (MCA v1.0, API v2.0, Component v1.2.1)
> MCA rml: oob (MCA v1.0, API v1.0, Component v1.2.1)
> MCA pls: gridengine (MCA v1.0, API v1.3, Component v1.2.1)
> MCA pls: proxy (MCA v1.0, API v1.3, Component v1.2.1)
> MCA pls: rsh (MCA v1.0, API v1.3, Component v1.2.1)
> MCA pls: slurm (MCA v1.0, API v1.3, Component v1.2.1)
> MCA pls: tm (MCA v1.0, API v1.3, Component v1.2.1)
> MCA sds: env (MCA v1.0, API v1.0, Component v1.2.1)
> MCA sds: pipe (MCA v1.0, API v1.0, Component v1.2.1)
> MCA sds: seed (MCA v1.0, API v1.0, Component v1.2.1)
> MCA sds: singleton (MCA v1.0, API v1.0, Component v1.2.1)
> MCA sds: slurm (MCA v1.0, API v1.0, Component v1.2.1)
>
> As you can see, I used Gnu gcc and g++ with Intel Fortran Compiler to
> compile Open MPI and I am not sure if there are any special flags that
> I need to have.
> ./configure --prefix=/usr/local/openmpi-1.2.1 --disable-ipv6
> --with-tm=/usr/local/pbs --enable-mpirun-prefix-by-default
> --enable-mpi-f90
>
> After getting mpif90, I compiled my application (VASP) with this new
> parellel compiler but then I could not run it through PBS.
>
> #PBS -N Pt.CO.bridge.25ML
> ### Set the number of nodes that will be used. Ensure
> ### that the number "nodes" matches with the need of your job
> ### DO NOT MODIFY THE FOLLOWING LINE FOR SINGLE-PROCESSOR JOBS!
> #PBS -l nodes=node07:ppn=4
> #PBS -l walltime=96:00:00
> ##PBS -M asit_at_[hidden]
> #PBS -m abe
> export NPROCS=`wc -l $PBS_NODEFILE |gawk '//{print $1}'`
> echo $NPROCS
> echo The master node of this job is `hostname`
> echo The working directory is `echo $PBS_O_WORKDIR`
> echo The node file is $PBS_NODEFILE
> echo This job runs on the following $NPROCS nodes:
> echo `cat $PBS_NODEFILE`
> echo "=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-=-"
> echo
> echo command to EXE:
> echo
> echo
> cd $PBS_O_WORKDIR
>
> echo "cachesize=4000 mpiblock=500 npar=4 procgroup=4 mkl ompi"
>
> date
> /usr/local/openmpi-1.2.1/bin/mpiexec -mca mpi_paffinity_alone 1 -np
> $NPROCS /hom e/struong/bin/vaspmpi_mkl_ompi >"$PBS_JOBID".out
> date
> ------------
>
> My environment is CentOS 4.4 x86_64, Intel Xeon, Torque, Maui.
>
> Could somebody here tell me what I missed or did incorrectly?
>
> Thank you very much.
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