Re: [OMPI users] Help: Program Terminated

[Lee Amy]

2008/5/30 Jeff Squyres :

> I'd also like to re-emphasize something Andreas said earlier: SIGTERM
> *usually* means that some external entity is killing your
> application.  It *could* be coming from within the application itself,
> but that's not too common.
>
> You might want to look into that to find out where the SIGTERM is
> coming from.  The Microtar maintainers might have some better ideas.
>
>
> On May 30, 2008, at 9:17 AM, Andreas Schäfer wrote:
>
> > On 12:28 Fri 30 May , Lee Amy wrote:
> >> 2008/5/29 Andreas Schäfer :
> >> Thank you very much. If I do a shorter job it seems run well. And
> >> the job
> >> dosen't repeatedly fail at the same time, but it will fail at this
> >> error
> >> messages. Anyway, I'm not using a scheduling system. So any
> >> suggestions?
> >
> > At least no easy ones, sorry. ;-) You could ask the Microtar guys if
> > they know anything about that problem. And of course you could use a
> > debugger to dig into Microtar and find the problem yourself. ^^ Open
> > MPI has some doc how to attach gdb to a parallel job: (and how to use
> > valgrind etc.)
> >
> > http://www.open-mpi.org/faq/?category=debugging
> >
> > Good luck!
> > -Andi
> >
> >
> > --
> > 
> > Andreas Schäfer
> > Cluster and Metacomputing Working Group
> > Friedrich-Schiller-Universität Jena, Germany
> > PGP/GPG key via keyserver
> > I'm a bright... http://www.the-brights.net
> > 
> >
> > (\___/)
> > (+'.'+)
> > (")_(")
> > This is Bunny. Copy and paste Bunny into your
> > signature to help him gain world domination!
> > ___
> > users mailing list
> > us...@open-mpi.org
> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>
>
> --
> Jeff Squyres
> Cisco Systems
>
>
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>
Thank you very much. I will try.

Amy

Re: [OMPI users] eigenvalue problem

[Brock Palen]

arpack

http://www.caam.rice.edu/software/ARPACK/

maybe some of the functions from scalapack also.  Any MPI eigenvalue  
package should work with OPMPI as its just another MPI library  
(though my current fav)


Brock Palen
www.umich.edu/~brockp
Center for Advanced Computing
bro...@umich.edu
(734)936-1985



On May 30, 2008, at 4:05 PM, Radovan Herchel wrote:

Hello, does anyone has a Fortran program or a link to Fortran code to
calculate eigenvalues of real/complex symmetric matrices using OpenMPI
package? Would be very thankful for help.
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[OMPI users] eigenvalue problem

[Radovan Herchel]

Hello, does anyone has a Fortran program or a link to Fortran code to
calculate eigenvalues of real/complex symmetric matrices using OpenMPI
package? Would be very thankful for help.

Re: [OMPI users] specifying hosts in mpi_spawn()

[Bruno Coutinho]

I'm using open mpi 1.2.6 from the open mpi site, but I can switch to another
version if necessary.


2008/5/30 Ralph H Castain :

> I'm afraid I cannot answer that question without first knowing what version
> of Open MPI you are using. Could you provide that info?
>
> Thanks
> Ralph
>
>
>
> On 5/29/08 6:41 PM, "Bruno Coutinho"  wrote:
>
> > How mpi handles the host string passed in the info argument to
> > mpi_comm_spawn() ?
> >
> > if I set host to:
> > "host1,host2,host3,host2,host2,host1"
> >
> > then ranks 0 and 5 will run in host1, ranks 1,3,4 in host 2 and rank 3
> > in host3?
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>
>
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[OMPI users] Problem with X forwarding

[Cally K]

hi, I have some problem running DistributedData.cxx ( it is a VTK file ) , I
need to be able to see the rendering from my computer

I, however have problem running the executable, I loaded both the executabe
into 2 machines

and I am accesing it from my computer( DHCP enabled )

after running the following command - I use OpenMPI

mpirun -hostfile myhostfile -np 2 -bynode ./DistributedData

and I keep getting these errors

ERROR: In
/home/kalpanak/Installation_Files/VTKProject/VTK/Rendering/vtkXOpenGLRenderWindow.cxx,
line 326
vtkXOpenGLRenderWindow (0x8664438): bad X server connection.


ERROR: In
/home/kalpanak/Installation_Files/VTKProject/VTK/Rendering/vtkXOpenGLRenderWindow.cxx,
line 169
vtkXOpenGLRenderWindow (0x8664438): bad X server connection.


[vrc1:27394] *** Process received signal ***
[vrc1:27394] Signal: Segmentation fault (11)
[vrc1:27394] Signal code: Address not mapped (1)
[vrc1:27394] Failing at address: 0x84
[vrc1:27394] [ 0] [0xe440]
[vrc1:27394] [ 1]
./DistributedData(_ZN22vtkXOpenGLRenderWindow20GetDesiredVisualInfoEv+0x229)
[0x8227e7d]
[vrc1:27394] [ 2]
./DistributedData(_ZN22vtkXOpenGLRenderWindow16WindowInitializeEv+0x340)
[0x8226812]
[vrc1:27394] [ 3]
./DistributedData(_ZN22vtkXOpenGLRenderWindow10InitializeEv+0x29)
[0x82234f9]
[vrc1:27394] [ 4]
./DistributedData(_ZN22vtkXOpenGLRenderWindow5StartEv+0x29) [0x82235eb]
[vrc1:27394] [ 5]
./DistributedData(_ZN15vtkRenderWindow14DoStereoRenderEv+0x1a) [0x82342ac]
[vrc1:27394] [ 6]
./DistributedData(_ZN15vtkRenderWindow10DoFDRenderEv+0x427) [0x8234757]
[vrc1:27394] [ 7]
./DistributedData(_ZN15vtkRenderWindow10DoAARenderEv+0x5b7) [0x8234d19]
[vrc1:27394] [ 8] ./DistributedData(_ZN15vtkRenderWindow6RenderEv+0x690)
[0x82353b4]
[vrc1:27394] [ 9]
./DistributedData(_ZN22vtkXOpenGLRenderWindow6RenderEv+0x52) [0x82245e2]
[vrc1:27394] [10] ./DistributedData [0x819e355]
[vrc1:27394] [11]
./DistributedData(_ZN16vtkMPIController19SingleMethodExecuteEv+0x1ab)
[0x837a447]
[vrc1:27394] [12] ./DistributedData(main+0x180) [0x819de78]
[vrc1:27394] [13] /lib/libc.so.6(__libc_start_main+0xe0) [0xb79c0fe0]
[vrc1:27394] [14] ./DistributedData [0x819dc21]
[vrc1:27394] *** End of error message ***
mpirun noticed that job rank 0 with PID 27394 on node  exited on signal
11 (Segmentation fault).



Maybe I am not doing the xforwading properly, but has anyone ever
encountered the same problem, it works fine on one pc, and I read the
mailing list but I just don't know if my prob is similiar to their, I even
tried changing the DISPLAY env


This is what I want to do

my mpirun should run on 2 machines ( A and B ) and I should be able to view
the output ( on my PC ),
are there any specfic commands to use.

Re: [OMPI users] Problem with NFS + PVFS2 + OpenMPI

[Davi Vercillo C. Garcia]

Hi,

Sorry but I made a mistake... I'm not trying to use PVFS over NFS but
PVFS over EXT3. I still don't know this error message...

On Thu, May 29, 2008 at 5:33 PM, Robert Latham  wrote:
> On Thu, May 29, 2008 at 04:48:49PM -0300, Davi Vercillo C. Garcia wrote:
>> > Oh, I see you want to use ordered i/o in your application.  PVFS
>> > doesn't support that mode.  However, since you know how much data each
>> > process wants to write, a combination of MPI_Scan (to compute each
>> > processes offset) and MPI_File_write_at_all (to carry out the
>> > collective i/o) will give you the same result with likely better
>> > performance (and has the nice side effect of working with pvfs).
>>
>> I don't understand very well this... what do I need to change in my code ?
>
> MPI_File_write_ordered has an interesting property (which you probably
> know since you use it, but i'll spell it out anyway):  writes end up
> in the file in rank-order, but are not necessarily carried out in
> rank-order.
>
> Once each process knows the offsets and lengths of the writes the
> other process will do, that process can writes its data.  Observe that
> rank 0 can write immediately.  Rank 1 only needs to know how much data
> rank 0 will write.  and so on.
>
> Rank N can compute its offset by knowing how much data the proceeding
> N-1 processes want to write.  The most efficent way to collect this is
> to use MPI_Scan and collect a sum of data:
>
> http://www.mpi-forum.org/docs/mpi-11-html/node84.html#Node84
>
> Once you've computed these offsets, MPI_File_write_at_all has enough
> information to cary out a collective write of the data.
>
> ==rob
>
> --
> Rob Latham
> Mathematics and Computer Science DivisionA215 0178 EA2D B059 8CDF
> Argonne National Lab, IL USA B29D F333 664A 4280 315B
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-- 
Davi Vercillo Carneiro Garcia

Universidade Federal do Rio de Janeiro
Departamento de Ciência da Computação
DCC-IM/UFRJ - http://www.dcc.ufrj.br

"Good things come to those who... wait." - Debian Project

"A computer is like air conditioning: it becomes useless when you open
windows." - Linus Torvalds

"Há duas coisas infinitas, o universo e a burrice humana. E eu estou
em dúvida quanto o primeiro." - Albert Einstein

[OMPI users] File download sizes

[Ashley Pittman]

I notice on the download page all file sizes are listed as 0KB, this is
presumably an error somewhere.

http://www.open-mpi.org/software/ompi/v1.2/

Ashley,

Re: [OMPI users] specifying hosts in mpi_spawn()

[Ralph H Castain]

I'm afraid I cannot answer that question without first knowing what version
of Open MPI you are using. Could you provide that info?

Thanks
Ralph



On 5/29/08 6:41 PM, "Bruno Coutinho"  wrote:

> How mpi handles the host string passed in the info argument to
> mpi_comm_spawn() ?
> 
> if I set host to:
> "host1,host2,host3,host2,host2,host1"
> 
> then ranks 0 and 5 will run in host1, ranks 1,3,4 in host 2 and rank 3
> in host3?
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Re: [OMPI users] Open MPI instructional videos

[Andreas Schäfer]

I've never really dig into Open MPI's guts, not because I wasn't
interested, but mainly because the time required to get my bearings
seemed just too much. Until now. I've watched a couple of the videos
while coding and it was pretty awesome. Easy to understand, structured
and well spoken.

On 12:41 Tue 27 May , Jeff Squyres wrote:
> Note that "receiving permission" is very different than receiving  
> funding or additional staff to publish said training material.  :-)   

Put them on itunes and talk some lectures into making them suggested
materials for their parallel computing courses. ;-)

> - Do you like the format?
>  - Is the (slides+narration) format useful?

Yes, I like it a lot. I guess a pure podcast would be insufficient for
complex issues where you simply need diagrams. Maybe a small
suggestion: maybe it's just me, but I'd actually prefer (even) leaner
slides. Currently you're basically duplicating on screen what you're
saying, which is good when you're a nervous, moumbling college student
and might lose your audience somewhere. But when you're an experenced
speaker (which you obviously are), the audience does rarely need this
redundancy and might rather get confused when trying to digest both
streams of information (visual and auditory) simultaneously. But this
is of course a question of personal preference.

>  - Would terminal screen-scrape sessions be useful?

I'd prefer how-to pages for this, as you can copy the commands
directly into your own shell.

>  - ...other [low-budget] suggestions?

Maybe an a tad higher audio bitrate. And some people don't like the
.mov format, but that isn't really important. 

Thanks!
-Andreas


-- 

Andreas Schäfer
Cluster and Metacomputing Working Group
Friedrich-Schiller-Universität Jena, Germany
PGP/GPG key via keyserver
I'm a bright... http://www.the-brights.net


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Re: [OMPI users] Help: Program Terminated

[Jeff Squyres]

I'd also like to re-emphasize something Andreas said earlier: SIGTERM  
*usually* means that some external entity is killing your  
application.  It *could* be coming from within the application itself,  
but that's not too common.


You might want to look into that to find out where the SIGTERM is  
coming from.  The Microtar maintainers might have some better ideas.



On May 30, 2008, at 9:17 AM, Andreas Schäfer wrote:


On 12:28 Fri 30 May , Lee Amy wrote:

2008/5/29 Andreas Schäfer :
Thank you very much. If I do a shorter job it seems run well. And  
the job
dosen't repeatedly fail at the same time, but it will fail at this  
error
messages. Anyway, I'm not using a scheduling system. So any  
suggestions?


At least no easy ones, sorry. ;-) You could ask the Microtar guys if
they know anything about that problem. And of course you could use a
debugger to dig into Microtar and find the problem yourself. ^^ Open
MPI has some doc how to attach gdb to a parallel job: (and how to use
valgrind etc.)

http://www.open-mpi.org/faq/?category=debugging

Good luck!
-Andi


--

Andreas Schäfer
Cluster and Metacomputing Working Group
Friedrich-Schiller-Universität Jena, Germany
PGP/GPG key via keyserver
I'm a bright... http://www.the-brights.net


(\___/)
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--
Jeff Squyres
Cisco Systems

Re: [OMPI users] Help: Program Terminated

[Andreas Schäfer]

On 12:28 Fri 30 May , Lee Amy wrote:
> 2008/5/29 Andreas Schäfer :
> Thank you very much. If I do a shorter job it seems run well. And the job
> dosen't repeatedly fail at the same time, but it will fail at this error
> messages. Anyway, I'm not using a scheduling system. So any suggestions?

At least no easy ones, sorry. ;-) You could ask the Microtar guys if
they know anything about that problem. And of course you could use a
debugger to dig into Microtar and find the problem yourself. ^^ Open
MPI has some doc how to attach gdb to a parallel job: (and how to use
valgrind etc.)
  
http://www.open-mpi.org/faq/?category=debugging

Good luck!
-Andi


-- 

Andreas Schäfer
Cluster and Metacomputing Working Group
Friedrich-Schiller-Universität Jena, Germany
PGP/GPG key via keyserver
I'm a bright... http://www.the-brights.net


(\___/)
(+'.'+)
(")_(")
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Re: [OMPI users] Help: Program Terminated

[Lee Amy]

2008/5/29 Andreas Schäfer :

> Hi Amy,
>
> On 16:10 Thu 29 May , Lee Amy wrote:
> > MicroTar parallel version was terminated after 463 minutes with following
> > error messages:
> > 
> > [gnode5:31982] [ 0] /lib64/tls/libpthread.so.0 [0x345460c430]
> > [gnode5:31982] [ 1] microtar(LocateNuclei+0x137) [0x403037]
> > [gnode5:31982] [ 2] microtar(main+0x4ac) [0x40431c]
> > [gnode5:31982] [ 3] /lib64/tls/libc.so.6(__libc_start_main+0xdb)
> > [0x3453b1c3fb]
> > [gnode5:31982] [ 4] microtar [0x402e6a]
> > [gnode5:31982] *** End of error message ***
> > mpirun noticed that job rank 0 with PID 18710 on node gnode1 exited on
> > signal 15 (Terminated).
> > 19 additional processes aborted (not shown)
> > 
>
> if I'm not mistaken, signal 15 is SIGTERM, which is sent to processes
> to terminate them. To me this sounds like your application is
> terminated from an external instance, maybe because your job exceeded
> the wall clock time limit of your scheduling system. Does the job
> repeatedly fail at the same time? Do shorter jobs finish successfully?
>
> Just my 0.02 Euros (-8
>
> Cheers
> -Andreas
>
>
> --
> 
> Andreas Schäfer
> Cluster and Metacomputing Working Group
> Friedrich-Schiller-Universität Jena, Germany
> PGP/GPG key via keyserver
> I'm a bright... http://www.the-brights.net
> 
>
> (\___/)
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> signature to help him gain world domination!
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>
Thank you very much. If I do a shorter job it seems run well. And the job
dosen't repeatedly fail at the same time, but it will fail at this error
messages. Anyway, I'm not using a scheduling system. So any suggestions?

Thank you again.

Regards,

Amy