Can you send a simple test that reproduces these errors?
I.e., if there's a single, simple package that you can send
instructions on how to build, it would be most helpful if we could
reproduce the error (and therefore figure out how to fix it).
Thanks!
On May 9, 2007, at 2:19 PM, Steven Truong wrote:
Oh, no. I tried with ACML and had the same set of errors.
Steven.
On 5/9/07, Steven Truong <midai...@gmail.com> wrote:
Hi, Kevin and all. I tried with the following:
./configure --prefix=/usr/local/openmpi-1.2.1 --disable-ipv6
--with-tm=/usr/local/pbs --enable-mpirun-prefix-by-default
--enable-mpi-f90 --with-threads=posix --enable-static
and added the mpi.o in my VASP's makefile but i still got error.
I forgot to mention that our environment has Intel MKL 9.0 or 8.1 and
my machines are dual proc dual core Xeon 5130 .
Well, I am going to try acml too.
Attached is my makefile for VASP and I am not sure if I missed
anything again.
Thank you very much for all your helps.
On 5/9/07, Steven Truong <midai...@gmail.com> wrote:
Thank Kevin and Brook for replying to my question. I am going to
try
out what Kevin suggested.
Steven.
On 5/9/07, Kevin Radican <radi...@tcd.ie> wrote:
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 a...@my.com
#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.
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
_______________________________________________
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users
--
Jeff Squyres
Cisco Systems
