Re: [OMPI users] Symbol not found: _evsignal_base

2011-05-26 Thread charles reid
You can disregard, the problem has been resolved by re-running the
configure/make/make install procedure.  Thanks again for the help!


Charles


On Thu, May 26, 2011 at 13:16, charles reid  wrote:

> Hi Jeff & others -
>
> Thanks for the response.  OpenMPI compiles fine, so there are no problems
> with the make process, but I can't run "mpirun" because the program won't
> compile with mpicc - this case isn't really covered by the "Getting Help"
> page.  However, I have provided the output of configure/make/make install,
> even though it was successful.  The .tar.gz file is here:
>
> http://files.charlesmartinreid.com/openmpi_out.tar.gz
>
> If there is any additional info that would be helpful, please let me know.
>
>
> Charles
>
>
>
> On Wed, May 25, 2011 at 17:27, Jeff Squyres  wrote:
>
>> This looks like your installation is busted somehow.  Can you send all the
>> information listed here:
>>
>>http://www.open-mpi.org/community/help/
>>
>>
>> On May 24, 2011, at 4:05 PM, charles reid wrote:
>>
>> > Hi -
>> >
>> > I'm trying to compile a simple hello world program with mpicc,
>> >
>> > $ cat test.c
>> > #include 
>> >
>> > main()
>> > {
>> >   printf ("Hello World!\n");
>> > }
>> >
>> >
>> > but I'm seeing this issue:
>> >
>> > $ ~/pkg/openmpi/1.4.3_bigmac/bin/mpicc test.c
>> > dyld: Symbol not found: _evsignal_base
>> >   Referenced from: /uufs/
>> chpc.utah.edu/common/home/u0552682/pkg/openmpi/1.4.3_bigmac/lib/libopen-pal.0.dylib
>> >   Expected in: flat namespace
>> >  in /uufs/
>> chpc.utah.edu/common/home/u0552682/pkg/openmpi/1.4.3_bigmac/lib/libopen-pal.0.dylib
>> > Trace/BPT trap
>> >
>> >
>> > I found this previous thread,
>> http://comments.gmane.org/gmane.comp.clustering.open-mpi.user/13033 ,
>> which suggested adding the installation directory's lib/ to LD_LIBRARY_PATH
>> would fix things, but it did not:
>> >
>> > $ export
>> LD_LIBRARY_PATH="${HOME}/pkg/openmpi/1.4.3_bigmac/lib:${LD_LIBRARY_PATH}";
>> ~/pkg/openmpi/1.4.3_bigmac/bin/mpicc test.c
>> > dyld: Symbol not found: _evsignal_base
>> >   Referenced from: /uufs/
>> chpc.utah.edu/common/home/u0552682/pkg/openmpi/1.4.3_bigmac/lib/libopen-pal.0.dylib
>> >   Expected in: flat namespace
>> >  in /uufs/
>> chpc.utah.edu/common/home/u0552682/pkg/openmpi/1.4.3_bigmac/lib/libopen-pal.0.dylib
>> > Trace/BPT trap
>> >
>> >
>> > Any suggestions on what I might be doing wrong?
>> >
>> >
>> > Charles
>> > ___
>> > users mailing list
>> > us...@open-mpi.org
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>>
>> --
>> Jeff Squyres
>> jsquy...@cisco.com
>> For corporate legal information go to:
>> http://www.cisco.com/web/about/doing_business/legal/cri/
>>
>>
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>


Re: [OMPI users] Symbol not found: _evsignal_base

2011-05-26 Thread charles reid
Hi Jeff & others -

Thanks for the response.  OpenMPI compiles fine, so there are no problems
with the make process, but I can't run "mpirun" because the program won't
compile with mpicc - this case isn't really covered by the "Getting Help"
page.  However, I have provided the output of configure/make/make install,
even though it was successful.  The .tar.gz file is here:

http://files.charlesmartinreid.com/openmpi_out.tar.gz

If there is any additional info that would be helpful, please let me know.


Charles


On Wed, May 25, 2011 at 17:27, Jeff Squyres  wrote:

> This looks like your installation is busted somehow.  Can you send all the
> information listed here:
>
>http://www.open-mpi.org/community/help/
>
>
> On May 24, 2011, at 4:05 PM, charles reid wrote:
>
> > Hi -
> >
> > I'm trying to compile a simple hello world program with mpicc,
> >
> > $ cat test.c
> > #include 
> >
> > main()
> > {
> >   printf ("Hello World!\n");
> > }
> >
> >
> > but I'm seeing this issue:
> >
> > $ ~/pkg/openmpi/1.4.3_bigmac/bin/mpicc test.c
> > dyld: Symbol not found: _evsignal_base
> >   Referenced from: /uufs/
> chpc.utah.edu/common/home/u0552682/pkg/openmpi/1.4.3_bigmac/lib/libopen-pal.0.dylib
> >   Expected in: flat namespace
> >  in /uufs/
> chpc.utah.edu/common/home/u0552682/pkg/openmpi/1.4.3_bigmac/lib/libopen-pal.0.dylib
> > Trace/BPT trap
> >
> >
> > I found this previous thread,
> http://comments.gmane.org/gmane.comp.clustering.open-mpi.user/13033 ,
> which suggested adding the installation directory's lib/ to LD_LIBRARY_PATH
> would fix things, but it did not:
> >
> > $ export
> LD_LIBRARY_PATH="${HOME}/pkg/openmpi/1.4.3_bigmac/lib:${LD_LIBRARY_PATH}";
> ~/pkg/openmpi/1.4.3_bigmac/bin/mpicc test.c
> > dyld: Symbol not found: _evsignal_base
> >   Referenced from: /uufs/
> chpc.utah.edu/common/home/u0552682/pkg/openmpi/1.4.3_bigmac/lib/libopen-pal.0.dylib
> >   Expected in: flat namespace
> >  in /uufs/
> chpc.utah.edu/common/home/u0552682/pkg/openmpi/1.4.3_bigmac/lib/libopen-pal.0.dylib
> > Trace/BPT trap
> >
> >
> > Any suggestions on what I might be doing wrong?
> >
> >
> > Charles
> > ___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> jsquy...@cisco.com
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>


[OMPI users] BLCR support not building on 1.5.3

2011-05-26 Thread Bill Johnstone
Hello all.

I'm building 1.5.3 from source on a Debian Squeeze AMD64 system, and trying to 
get BLCR support built-in.  I've installed all the packages that I think should 
be relevant to BLCR support, including:

+blcr-dkms
+libcr0
+libcr-dev
+blcr-util

I've also installed blcr-testuite .  I only run Open MPI's configure after 
loading the blcr modules, and the tests in blcr-testsuite pass.  The relevant 
headers seem to be in /usr/include and the relevant libraries in /usr/lib .

I've tried three different invocations of configure:

1. No BLCR-related arguments.

Output snippet from configure:
checking --with-blcr value... simple ok (unspecified)
checking --with-blcr-libdir value... simple ok (unspecified)
checking if MCA component crs:blcr can compile... no

2. With --with-blcr=/usr only

Output snippet from configure:
checking --with-blcr value... sanity check ok (/usr)
checking --with-blcr-libdir value... simple ok (unspecified)
configure: WARNING: BLCR support requested but not found.  Perhaps you need to 
specify the location of the BLCR libraries.
configure: error: Aborting.

3. With --with-blcr-libdir=/usr/lib only

Output snippet from configure:
checking --with-blcr value... simple ok (unspecified)
checking --with-blcr-libdir value... sanity check ok (/usr/lib)
checking if MCA component crs:blcr can compile... no


config.log only seems to contain the output of whatever tests were run to 
determine whether or not blcr support could be compiled, but I don't see any 
way to get details on what code and compile invocation actually failed, in 
order to get to the root of the problem.  I'm not a configure or m4 expert, so 
I'm not sure how to go further in troubleshooting this.

Help would be much appreciated.

Thanks!




Re: [OMPI users] huge VmRSS on rank 0 after MPI_Init when using "btl_openib_receive_queues" option

2011-05-26 Thread Eloi Gaudry

hi,
does anyone have a clue here ?
éloi

On 22/04/2011 08:52, Eloi Gaudry wrote:
it varies with the receive_queues specification *and* with the number 
of mpi processes:  memory_consumed = nb_mpi_process * nb_buffers * 
(buffer_size + low_buffer_count_watermark + credit_window_size )


éloi


On 04/22/2011 12:26 AM, Jeff Squyres wrote:

Does it vary exactly according to your receive_queues specification?

On Apr 19, 2011, at 9:03 AM, Eloi Gaudry wrote:


hello,

i would like to get your input on this:
when launching a parallel computation on 128 nodes using openib and 
the "-mca btl_openib_receive_queues P,65536,256,192,128" option, i 
observe a rather large resident memory consumption (2GB: 
65336*256*128) on the process with rank 0 (and only this process) 
just after a call to MPI_Init.


i'd like to know why the other processes doesn't behave the same:
- other processes located on the same nodes don't use that amount of 
memory

- all others processes (i.e. located on any other nodes) neither

i'm using OpenMPI-1.4.2, built with gcc-4.3.4 and 
'--enable-cxx-exceptions --with-pic --with-threads=posix' options.


thanks for your help,
éloi

--
Eloi Gaudry
Senior Product Development Engineer

Free Field Technologies
Company Website: http://www.fft.be
Direct Phone Number: +32 10 495 147

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--
Eloi Gaudry
Senior Product Development Engineer

Free Field Technologies
Company Website: http://www.fft.be
Direct Phone Number: +32 10 495 147



Re: [OMPI users] problem using mpirun over multiple nodes

2011-05-26 Thread Jagannath Mondal
Hi Jeff,
  Thanks to you, I figured the problem . As you suspected, it was iptables
which was  acting as firewalls in some machines. So, after I stopped the
iptable, the MPI communication is going fine. Even I tried with 5 machines
together and the communication is going allright.
Thanks again,
Jagannath

On Thu, May 26, 2011 at 5:19 AM, Jeff Squyres  wrote:

> ssh may be allowed but other random TCP ports may not.
>
> iptables is the typical firewall software that most Linux installations
> use; it may have been enabled by default.
>
> I'm a little doubtful that this is your problem, though, because you're
> apparently able to *launch* your application, which means that OMPI's
> out-of-band communication system was able to make some sockets.  So it's a
> little weird that the MPI layer's TCP sockets were borked.  But let's check
> for firewall software, first...
>
>
> On May 26, 2011, at 12:42 AM, Jagannath Mondal wrote:
>
> > Hi Jeff,
> > I was wondering how I can check whether there is any firewall
> software . In fact I can use ssh to go from one machine to another . But,
> only with mpirun , it does not work. I was wondering whether it is possible
> that even in presence of firewall ssh may work but mpirun may not.
> > Jagannath
> >
> > On Wed, May 25, 2011 at 10:42 PM, Jeff Squyres (jsquyres) <
> jsquy...@cisco.com> wrote:
> > Are you running any firewall software?
> >
> > Sent from my phone. No type good.
> >
> > On May 25, 2011, at 10:41 PM, "Jagannath Mondal" <
> jagannath.mon...@gmail.com> wrote:
> >
> >> Hi,
> >> I am having a problem in running mpirun  over multiple nodes.
> >> To run a job  over two 8-core processors, I generated a hostfile as
> follows:
> >>  yethiraj30 slots=8 max_slots=8
> >>   yethiraj31 slots=8 max_slots=8
> >>
> >> These two machines are intra-connected and I have installed openmpi
> 1.3.3.
> >> Then If I try to run the replica exchange simulation using the following
> command:
> >> mpirun -np 16 --hostfile  hostfile  mdrun_4mpi -s topol_.tpr -multi 16
> -replex 100 >& log_replica_test
> >>
> >> But I find following error and job does not proceed at all :
> >> btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect()
> to 192.168.0.31 failed: No route to host (113)
> >>
> >> Here is the full details:
> >>
> >> NNODES=16, MYRANK=0, HOSTNAME=yethiraj30
> >> NNODES=16, MYRANK=1, HOSTNAME=yethiraj30
> >> NNODES=16, MYRANK=4, HOSTNAME=yethiraj30
> >> NNODES=16, MYRANK=2, HOSTNAME=yethiraj30
> >> NNODES=16, MYRANK=6, HOSTNAME=yethiraj30
> >> NNODES=16, MYRANK=3, HOSTNAME=yethiraj30
> >> NNODES=16, MYRANK=5, HOSTNAME=yethiraj30
> >> NNODES=16, MYRANK=7, HOSTNAME=yethiraj30
> >>
> [yethiraj30][[22604,1],0][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
> connect() to 192.168.0.31 failed: No route to host (113)
> >>
> [yethiraj30][[22604,1],4][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
> connect() to 192.168.0.31 failed: No route to host (113)
> >>
> [yethiraj30][[22604,1],6][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
> connect() to 192.168.0.31 failed: No route to host (113)
> >>
> [yethiraj30][[22604,1],1][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
> connect() to 192.168.0.31 failed: No route to host (113)
> >>
> [yethiraj30][[22604,1],3][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
> connect() to 192.168.0.31 failed: No route to host (113)
> >>
> [yethiraj30][[22604,1],2][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
> connect() to 192.168.0.31 failed: No route to host (113)
> >> NNODES=16, MYRANK=10, HOSTNAME=yethiraj31
> >> NNODES=16, MYRANK=12, HOSTNAME=yethiraj31
> >>
> >> I am not sure how to resolve this issue. In general, I can go from one
> machine to another without any problem using ssh. But, when I am trying to
> run openmpi over both the machines, I get this error. Any help will be
> appreciated.
> >>
> >> Jagannath
> >> ___
> >> 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
> jsquy...@cisco.com
> For corporate legal information go to:
> http://www.cisco.com/web/about/doing_business/legal/cri/
>
>
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>


Re: [OMPI users] problem using mpirun over multiple nodes

2011-05-26 Thread Jeff Squyres
ssh may be allowed but other random TCP ports may not.

iptables is the typical firewall software that most Linux installations use; it 
may have been enabled by default.

I'm a little doubtful that this is your problem, though, because you're 
apparently able to *launch* your application, which means that OMPI's 
out-of-band communication system was able to make some sockets.  So it's a 
little weird that the MPI layer's TCP sockets were borked.  But let's check for 
firewall software, first...


On May 26, 2011, at 12:42 AM, Jagannath Mondal wrote:

> Hi Jeff,
> I was wondering how I can check whether there is any firewall software . 
> In fact I can use ssh to go from one machine to another . But, only with 
> mpirun , it does not work. I was wondering whether it is possible that even 
> in presence of firewall ssh may work but mpirun may not. 
> Jagannath
> 
> On Wed, May 25, 2011 at 10:42 PM, Jeff Squyres (jsquyres) 
>  wrote:
> Are you running any firewall software?
> 
> Sent from my phone. No type good. 
> 
> On May 25, 2011, at 10:41 PM, "Jagannath Mondal"  
> wrote:
> 
>> Hi, 
>> I am having a problem in running mpirun  over multiple nodes. 
>> To run a job  over two 8-core processors, I generated a hostfile as follows:
>>  yethiraj30 slots=8 max_slots=8
>>   yethiraj31 slots=8 max_slots=8
>> 
>> These two machines are intra-connected and I have installed openmpi 1.3.3.
>> Then If I try to run the replica exchange simulation using the following 
>> command:
>> mpirun -np 16 --hostfile  hostfile  mdrun_4mpi -s topol_.tpr -multi 16 
>> -replex 100 >& log_replica_test
>> 
>> But I find following error and job does not proceed at all : 
>> btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 
>> 192.168.0.31 failed: No route to host (113)
>> 
>> Here is the full details:
>> 
>> NNODES=16, MYRANK=0, HOSTNAME=yethiraj30
>> NNODES=16, MYRANK=1, HOSTNAME=yethiraj30
>> NNODES=16, MYRANK=4, HOSTNAME=yethiraj30
>> NNODES=16, MYRANK=2, HOSTNAME=yethiraj30
>> NNODES=16, MYRANK=6, HOSTNAME=yethiraj30
>> NNODES=16, MYRANK=3, HOSTNAME=yethiraj30
>> NNODES=16, MYRANK=5, HOSTNAME=yethiraj30
>> NNODES=16, MYRANK=7, HOSTNAME=yethiraj30
>> [yethiraj30][[22604,1],0][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>>  connect() to 192.168.0.31 failed: No route to host (113)
>> [yethiraj30][[22604,1],4][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>>  connect() to 192.168.0.31 failed: No route to host (113)
>> [yethiraj30][[22604,1],6][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>>  connect() to 192.168.0.31 failed: No route to host (113)
>> [yethiraj30][[22604,1],1][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>>  connect() to 192.168.0.31 failed: No route to host (113)
>> [yethiraj30][[22604,1],3][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>>  connect() to 192.168.0.31 failed: No route to host (113)
>> [yethiraj30][[22604,1],2][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>>  connect() to 192.168.0.31 failed: No route to host (113)
>> NNODES=16, MYRANK=10, HOSTNAME=yethiraj31
>> NNODES=16, MYRANK=12, HOSTNAME=yethiraj31
>> 
>> I am not sure how to resolve this issue. In general, I can go from one 
>> machine to another without any problem using ssh. But, when I am trying to 
>> run openmpi over both the machines, I get this error. Any help will be 
>> appreciated.
>> 
>> Jagannath
>> ___
>> 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
jsquy...@cisco.com
For corporate legal information go to:
http://www.cisco.com/web/about/doing_business/legal/cri/




Re: [OMPI users] MPI_COMM_DUP freeze with OpenMPI 1.4.1

2011-05-26 Thread Jeff Squyres
On May 26, 2011, at 4:43 AM, francoise.r...@obs.ujf-grenoble.fr wrote:

 CALL MPI_COMM_SIZE(id%COMM, id%NPROCS, IERR )
 IF ( id%PAR .eq. 0 ) THEN
IF ( id%MYID .eq. MASTER ) THEN
   color = MPI_UNDEFINED
ELSE
   color = 0
END IF
CALL MPI_COMM_SPLIT( id%COMM, color, 0, id%COMM_NODES, IERR )
id%NSLAVES = id%NPROCS - 1
 ELSE
CALL MPI_COMM_DUP( id%COMM, id%COMM_NODES, IERR )
id%NSLAVES = id%NPROCS
 END IF
 
 IF (id%PAR .ne. 0 .or. id%MYID .NE. MASTER) THEN
CALL MPI_COMM_DUP( id%COMM_NODES, id%COMM_LOAD, IERR
 ENDIF
 
> Yes, id%myid is relative to id%comm. It is assigned, just before in the code, 
> by all the processes, by the following call :
> CALL MPI_COMM_RANK(id%COMM, id%MYID, IERR)

I'm out of ideas.  :-(

Can you create a short reproducer code?

-- 
Jeff Squyres
jsquy...@cisco.com
For corporate legal information go to:
http://www.cisco.com/web/about/doing_business/legal/cri/




Re: [OMPI users] problem using mpirun over multiple nodes

2011-05-26 Thread Jeff Squyres (jsquyres)
Are you running any firewall software?

Sent from my phone. No type good. 

On May 25, 2011, at 10:41 PM, "Jagannath Mondal"  
wrote:

> Hi, 
> I am having a problem in running mpirun  over multiple nodes. 
> To run a job  over two 8-core processors, I generated a hostfile as follows:
>  yethiraj30 slots=8 max_slots=8
>   yethiraj31 slots=8 max_slots=8
> 
> These two machines are intra-connected and I have installed openmpi 1.3.3.
> Then If I try to run the replica exchange simulation using the following 
> command:
> mpirun -np 16 --hostfile  hostfile  mdrun_4mpi -s topol_.tpr -multi 16 
> -replex 100 >& log_replica_test
> 
> But I find following error and job does not proceed at all : 
> btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect] connect() to 
> 192.168.0.31 failed: No route to host (113)
> 
> Here is the full details:
> 
> NNODES=16, MYRANK=0, HOSTNAME=yethiraj30
> NNODES=16, MYRANK=1, HOSTNAME=yethiraj30
> NNODES=16, MYRANK=4, HOSTNAME=yethiraj30
> NNODES=16, MYRANK=2, HOSTNAME=yethiraj30
> NNODES=16, MYRANK=6, HOSTNAME=yethiraj30
> NNODES=16, MYRANK=3, HOSTNAME=yethiraj30
> NNODES=16, MYRANK=5, HOSTNAME=yethiraj30
> NNODES=16, MYRANK=7, HOSTNAME=yethiraj30
> [yethiraj30][[22604,1],0][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>  connect() to 192.168.0.31 failed: No route to host (113)
> [yethiraj30][[22604,1],4][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>  connect() to 192.168.0.31 failed: No route to host (113)
> [yethiraj30][[22604,1],6][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>  connect() to 192.168.0.31 failed: No route to host (113)
> [yethiraj30][[22604,1],1][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>  connect() to 192.168.0.31 failed: No route to host (113)
> [yethiraj30][[22604,1],3][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>  connect() to 192.168.0.31 failed: No route to host (113)
> [yethiraj30][[22604,1],2][btl_tcp_endpoint.c:636:mca_btl_tcp_endpoint_complete_connect]
>  connect() to 192.168.0.31 failed: No route to host (113)
> NNODES=16, MYRANK=10, HOSTNAME=yethiraj31
> NNODES=16, MYRANK=12, HOSTNAME=yethiraj31
> 
> I am not sure how to resolve this issue. In general, I can go from one 
> machine to another without any problem using ssh. But, when I am trying to 
> run openmpi over both the machines, I get this error. Any help will be 
> appreciated.
> 
> Jagannath
> ___
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