Re: [OMPI users] No output from mpirun
On 12/31/07, Varun R <nig...@gmail.com> wrote: > Yes, the 'mpirun' is the one from OpenMPI. And btw mpich worked perfectly > for me. It's only ompi that's giving me these problems. Do I have to setup > ssh or something? Because I remember doing that for mpich. You have to set up password less SSH login on each of the 'remote' host you are planning to spawn your tasks. HTH, Amit -- Amit Kumar Saha Writer, Programmer, Researcher http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
Re: [OMPI users] Theoretical Differences: Cluster Computing, Distributed Computing, Grid Computing
On 12/19/07, Jeff Squyres <jsquy...@cisco.com> wrote: > On Dec 19, 2007, at 11:33 AM, Amit Kumar Saha wrote: > > > This probably is the same as saying that : In Distributed computing, > > the member nodes are *not* dedicated machines solely for executing the > > specific HPC task, where as in a Cluster we have a dedicated set of > > nodes, specifically working on a particular task. > > > Those are common models, yes. But probably not the only ones (notice > how I used "usually" liberally in my definitions :-) ). > > Given the differences between Aurelien's answers and mine, I think the > community really only has general ideas about what exactly those terms > mean. Yes, I shall accept that, since time and again I have thought about this terms- I have always had to end up getting confused, searching for the _exact_, clear-cut difference. Thanks again! Amit -- Amit Kumar Saha *NetBeans Community Docs Coordinator* http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
Re: [OMPI users] Theoretical Differences: Cluster Computing, Distributed Computing, Grid Computing
On 12/19/07, Aurelien Bouteiller <boute...@eecs.utk.edu> wrote: > I have quite different definitions than Jeff. > > Distributed computing is encompassing all the "parallel computing" > models, including clusters, grids, master-slave, shared memory... > Everything that basically implies using several collaborating > processes to solve a problem (whatever collaborating means, network, > shared memory, RPC, data dependencies... ). > > Cluster computing simply refers simply to computations that occurs on > a cluster type machine. A cluster is -usually- a distributed memory > computer based on commodity hardware (but counter examples exist). It > may include commodity network (like giga ethernet) or more specific > nics (like myrinet, infiniband, quadrics and so on). As said Jeff, > usually the best way to use such a machine is to have a kind of > tightly coupled application. > > Grid computing refers to gathering several clusters (and sometimes > large databases and scientific instruments like telescopes that > generate data) and use them altogether. Compared to a cluster or a > supercomputer, this introduces several issues related to password > administration, user domains, firewall bypass, several different > scheduler collaborating, and quite slow network between the sites. I understand that a major difference between Distributed Computing and Grid Computing is that whereas we *usually* have a set of trusted nodes in the former, in the latter case, we generally have geographically dispersed computers which use a separate authentication mechanism to come together and form a Grid. Please correct me if I am wrong Thanks, Amit -- Amit Kumar Saha Writer, Programmer, Researcher http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
Re: [OMPI users] Theoretical Differences: Cluster Computing, Distributed Computing, Grid Computing
On 12/19/07, Jeff Squyres <jsquy...@cisco.com> wrote: > It's a pretty hazy difference; I don't think there are formal > definitions for each. > > Cluster computing *usually* (but not always) implies a bit more > tightly coupled set of computing: the app communicates and coordinates > between itself more than your standard manager/worker computation > model. Distributed computing *usually* focuses on the manager/worker > model -- send some work to anyone who asks for it and then eventually > get some results back from them (or not -- then you have to send the > same work out to someone else). > > But you can certainly use the manager/worker model in cluster > computing, too. Not all cluster computing is tightly coupled. This probably is the same as saying that : In Distributed computing, the member nodes are *not* dedicated machines solely for executing the specific HPC task, where as in a Cluster we have a dedicated set of nodes, specifically working on a particular task. Correct me, if I am wrong. Thanks, Amit -- Amit Kumar Saha Writer, Programmer, Researcher http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
[OMPI users] Theoretical Differences: Cluster Computing, Distributed Computing, Grid Computing
Hi all! I am a bit hazy about the differences between Distributed Computing and Cluster Computing. This document here http://www.ibm.com/developerworks/grid/library/gr-heritage/ is a nice read on Grid Computing and it also has few lines about important differences from Cluster Computing. Hints will be duly appreciated! Thanks, Amit -- Amit Kumar Saha Writer, Programmer, Researcher http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
Re: [OMPI users] Hi
On 12/18/07, SaiGiridhar Ramasamy <r.saigirid...@gmail.com> wrote: > > Can you elaborate it still? http://www-fp.mcs.anl.gov/CCST/research/reports_pre1998/comp_bio/stalk/pgapack.html HTH, Amit -- Amit Kumar Saha Writer, Programmer, Researcher http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
Re: [OMPI users] Hi
On 12/18/07, SaiGiridhar Ramasamy <r.saigirid...@gmail.com> wrote: > > > Great.I have few on hand experience with MPI(tracking target) it involved > GA.We jus had an intro on parallel GA too.I prefer any kind of application > which can be finished in 2 or 3 months. How about trying out 'PGAPack' then? > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > -- Amit Kumar Saha Writer, Programmer, Researcher http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
Re: [OMPI users] Hi
On 12/18/07, SaiGiridhar Ramasamy <r.saigirid...@gmail.com> wrote: > hi, > As a project for final year.Not just to test. Okay, so are you experienced with parallel programming? What kind of HPC applications are you looking for? 3-months back, I had no exposure to parallel programming. Subsequently, I worked on a project titled "Review of Parallel Computing" where I got familiar with PVM, MPI (Open MPI) and then implemented a simple Parallel Search algorithm and also reviewed some stuffs, issues related to Parallel Image processing. Now, I am starting work with "Parallel Genetic Algorithms", since it is one of my research areas. So, it really depends on what you want to do. There a lot of HPC applications you can work on - Mathematical, Biological, Computer Vision, etc. HTH, Amit -- Amit Kumar Saha Writer, Programmer, Researcher http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
Re: [OMPI users] Hi
On 12/18/07, SaiGiridhar Ramasamy <r.saigirid...@gmail.com> wrote: > Hi all, >I've an operational cluster and soon about to form a cluster can > anyone suggest any hpc application. A HPC application to do a test run on your cluster? --Amit -- Amit Kumar Saha Writer, Programmer, Researcher http://amitsaha.in.googlepages.com http://amitksaha.blogspot.com
Re: [OMPI users] How to construct a datatype over two different arrays?
On 10/31/07, Oleg Morajko <olegmora...@gmail.com> wrote:
>
> Hello,
>
> I have the following problem. There areI two arrays somewere in the
> program:
>
> double weights [MAX_SIZE];
> ...
> int values [MAX_SIZE];
> ...
>
> I need to be able to send a single pair { weights [i], values [i] } with a
> single MPI_Send call Or receive it directly into both arrays at at given
> index i. How can I define a datatype that spans this pair over both arrays?
Did you have a look at topics like - MPI derived data types, MPI packing?
May be they can help.
>
>
--
Amit Kumar Saha
*NetBeans Community Docs
Contribution Coordinator*
me blogs@ http://amitksaha.blogspot.com
URL:http://amitsaha.in.googlepages.com
Re: [OMPI users] Parallel Genetic Algorithms - Open MPI Implementation
Hi Dirk, On 10/24/07, Dirk Eddelbuettel <e...@debian.org> wrote: > > > On 24 October 2007 at 01:01, Amit Kumar Saha wrote: > | Hello all! > | > | After some background research, I am soon going to start working on > | "Parallel Genetic Algorithms". When I reach the point of practical > | implementation, I am going to use Open MPI for the purpose. > | > | Has anyone here worked on similar things? It would be nice if you could > | share some views/comments. > > Yes. PGAPACK, developend in the mid-1990s by David Levine while at > Argonne, > works perfectly well in parallel under various MPI implementations. > > I have been in contact with David and Argonne to coordinate a re-release > under a newer license [1], but we're not quite there yet, and I have > been the one holding this up. Hopefully more news 'soon' but I've been > mumbling that all summer while I kept busy... > > You may want to look at PGAPACK and study it for possible extensions and > refactorings, rather than to start again from scratch. Had come across PGAPack some time back, did not spend much time with it though. But after I am through with some of the theoretical aspects of both Genetic algorithms, parallel genetic algorithms. I shall definitely start off with PGAPack By the way, if time permits could you kindly point me to some relevant resources you may know of, though I shall turn to Google soon. Will get back to you after I have started looking at PGAPack. Thanks, Amit -- Amit Kumar Saha *NetBeans Community Docs Contribution Coordinator* me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
[OMPI users] Parallel Genetic Algorithms - Open MPI Implementation
Hello all! After some background research, I am soon going to start working on "Parallel Genetic Algorithms". When I reach the point of practical implementation, I am going to use Open MPI for the purpose. Has anyone here worked on similar things? It would be nice if you could share some views/comments. Regards, Amit -- Amit Kumar Saha *NetBeans Community Docs Contribution Coordinator* me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
Re: [OMPI users] Compile test programs
On 18 Oct 2007 08:44:36 -, Neeraj Chourasia <neeraj_...@rediffmail.com> wrote: > > Hi all, > > Could someone suggest me, how to compile programs given in test > directory of the source code? There are couple of directories within test > which contains sample programs about the usage of datastructures being used > by open-MPI. I am able to compile some of the directories at it was having > Makefile created on running configure script, but few of them like runtime > doesn't have the Makefile. > > Please help me compiling it. Did you try doing doing it using 'mpicc'? Sorry, I cant try it now. --Amit -- Amit Kumar Saha me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
Re: [OMPI users] [OT] Newbie seeks clarification about Parallel Computing Terminologies
On 10/8/07, Bill Rankin <wran...@duke.edu> wrote: > > Yes, you have created a cluster. > > More information on general parallel/cluster computing topics can be > found at the Beowulf website: > > http://www.beowulf.org/ > > Hope this helps, > Thanks, bill! -- Amit Kumar Saha *NetBeans Community Docs Coordinator* me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
Re: [OMPI users] problem with 'orted'
On 10/4/07, Tim Prins <tpr...@open-mpi.org> wrote: > So you did: > ssh which orted > > and it found the orted? Yes. it reported it in '/usr/bin/orted' Regards, Amit -- Amit Kumar Saha *NetBeans Community Docs Coordinator* me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
Re: [OMPI users] Tool communication
Hello Oleg :-) I am a newbie as far as MPI is concerned. Still I will take a shot: On 10/2/07, Oleg Morajko <olegmora...@gmail.com> wrote: > Hello, > > In the context of my PhD research, I have been developing a run-time > performance analyzer for MPI-based applications. > My tool provides a controller process for each MPI task. In particular, when > a MPI job is started, a special wrapper script is generated that first > starts my controller processes and next each controller spawns an actual MPI > task (that performs MPI_Init etc.). I use dynamic instrumentation API > (DynInst API) to control and instrument MPI tasks. > > The point is I need to intercommunicate my controller processes, in > particular I need a point-to-point communication between arbitrary pair of > controllers. So it seems reasonable to take advantage of MPI itself and use > it for communication. However I am not sure what would be the impact of > calling MPI_Init and communicating from controller processes taking into > account both controllers and actual MPI processes where started with the > same mpirun invocation. Actually I would need to assure that controllers > have a separate MPI execution enviroment while the application has another > one. Have you thought about using a separate MPI Communicator? Sorry if that was lame! Regards, Amit -- Amit Kumar Saha me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
Re: [OMPI users] problem with 'orted'
Hi sebi! On 10/2/07, Sebastian Schulz <sham...@mac.com> wrote: > Amit Kumar Saha wrote: > > what i find bizarre is that I used Open MPI 1.2.3 to install on all my > > 4 machines. whereas, 'orted' is installed in /usr/local/bin on all the > > other 3 machines, the 4th machine which is giving me trouble has got > > it installed in '/usr/bin' . Yes, 'orted' is accessible from a ssh > > login as well. > > Note that on Ubuntu (at least on 7.04) the default ~/.bashrc contains the > following line: > > # If not running interactively, don't do anything > [ -z "$PS1" ] && return > Unfortunately, this does not solve the problem. I have got all 2 of my other 3 machines running Ubuntu 7.04 as well. but they are doing fine! Hope you can provide me some more info! Thanks, --Amit -- Amit Kumar Saha *NetBeans Community Docs Coordinator* me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
Re: [OMPI users] problem with 'orted'
On 10/1/07, Si Hammond <simon.hamm...@gmail.com> wrote: > Can you make sure that orted is in the PATH variable for each machine? > You can do this by adding it to /etc/bash.bashrc or an appropriate file? > what i find bizarre is that I used Open MPI 1.2.3 to install on all my 4 machines. whereas, 'orted' is installed in /usr/local/bin on all the other 3 machines, the 4th machine which is giving me trouble has got it installed in '/usr/bin' . Yes, 'orted' is accessible from a ssh login as well. Regards, Amit -- Amit Kumar Saha *NetBeans Community Docs Coordinator* me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
[OMPI users] problem with 'orted'
hello, I am using Open MPI 1.2.3 to run a task on 4 hosts as follows: amit@ubuntu-desktop-1:~/mpi-exec$ mpirun --np 4 --hostfile mpi-host-file ParallelSearch bash: /usr/local/bin/orted: No such file or directory The problem is that 'orted' is not found on one of the 4 hosts. I investigated the problem and found out that whereas 'orted' is stored in /usr/local/bin on all the other 3 hosts, it is in /usr/bin/orted on the erroneous host. I tried to create a soft link to solve the problem but sadly it is not so simple, it seems. It would be nice to know how to get around this problem. Thanks, Amit -- Amit Kumar Saha *NetBeans Community Docs Coordinator* me blogs@ http://amitksaha.blogspot.com URL:http://amitsaha.in.googlepages.com
Re: [OMPI users] OpenMPI Documentation?
> > Docbook gets my vote, especially when one considers the html and pdf > output. I'd prefer LaTeX, but then I come from an academic background > :-) I prefer LaTex too, the reason is same. Academic background :) and new found love in LaTex Regards, Amit -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
Re: [OMPI users] OpenMPI Documentation?
Hi Richard and all concerned, On 9/12/07, richard.fried...@sun.com <rc...@sun.com> wrote: > Thanks for the reply. Actually, I'm working with the MPI team at Sun and > I was wondering if there was already a team within the OpenMPI community > thinking about developing a doc set for OpenMPI. Such doc communities > exist for the other open source communities I've worked with, such as > OpenSolaris.org and netbeans.org. > > Sounds like the answer to the question is no, or, not yet. > > So, maybe we need to start one. I would like to play a role in the documentation community, if that is allowed. I am no expert in MPI but I am slowly learning it for the past 1.5 months or so. So, may be I have something to contribute. Regards, Amit -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
Re: [OMPI users] Basic problems with OpenMPI
Hello, On 8/29/07, Jeff Squyres <jsquy...@cisco.com> wrote: > Amit -- > > I think you want to have a look at the "setup" FAQ -- many of the > questions you have asked are answered there: > > http://www.open-mpi.org/faq/?category=running Thanks Jeff for pointing that out. I am sorry for not having looked up the FAQ before asking the mailing list. Regards -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
Re: [OMPI users] Basic problems with OpenMPI
Hi Gleb, > The above output shows that you have a problem on host ubuntu-desktop-2. > Have you setup login without a password from ubuntu-desktop-1 to > ubuntu-desktop-2? Thank you very much. It works! Regards -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
Re: [OMPI users] Basic problems with OpenMPI
Hi Glib, i am sending a sample trace of my program: amit@ubuntu-desktop-1:~/mpi-exec$ mpirun --np 3 --hostfile mpi-host-file HellMPI amit@debian-desktop-1's password: [ubuntu-desktop-1:28575] [0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 275 [ubuntu-desktop-1:28575] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1164 [ubuntu-desktop-1:28575] [0,0,0] ORTE_ERROR_LOG: Timeout in file errmgr_hnp.c at line 90 [ubuntu-desktop-1:28575] ERROR: A daemon on node ubuntu-desktop-2 failed to start as expected. [ubuntu-desktop-1:28575] ERROR: There may be more information available from [ubuntu-desktop-1:28575] ERROR: the remote shell (see above). [ubuntu-desktop-1:28575] ERROR: The daemon exited unexpectedly with status 255. [ubuntu-desktop-1:28575] [0,0,0] ORTE_ERROR_LOG: Timeout in file base/pls_base_orted_cmds.c at line 188 [ubuntu-desktop-1:28575] [0,0,0] ORTE_ERROR_LOG: Timeout in file pls_rsh_module.c at line 1196 -- mpirun was unable to cleanly terminate the daemons for this job. Returned value Timeout instead of ORTE_SUCCESS. -- this is what I get when i run the program. However when i use "--np 2 " it works perfectly which of course means that it is not a problem with "debian-desktop-1" as the above output may show. Please refer to the host file as well. (attached). I am using the same openMPI version 1.2.3 and compiled all the executables using that. Waiting for your suggestions. Thanks -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com mpi-host-file Description: Binary data
Re: [OMPI users] Basic problems with OpenMPI
Hi gleb, > Have you installed Open MPI at the same place on all nodes? What command > line are you using to run app on more then one host? this is a sample run amit@ubuntu-desktop-1:~/mpi-exec$ mpirun --np 2 --hostfile mpi-host-file HellMPI amit@ubuntu-desktop-2's password: HellMPI: error while loading shared libraries: liborte.so.0: cannot open shared object file: No such file or directory I have them installed at the same place, (I have used the 'configure' switch that you told me earlier) Hope that helps. Thanks -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
Re: [OMPI users] Basic problems with OpenMPI
Hi all,
I have installed OpenMPI 1.2.3 on all my hosts (3).
Now when I try to start a simple demo program ("hello world") using
./a.out I get the error. When I run my program using "mpirun" on more
than one host it gives me similar error:
error while loading shared libraries: libopen-rte.so.0: cannot open
shared object file: No such file or directory
However when I do a mpirun a.out , it gives me no error.
Please suggest
Thanks
Amit
--
Amit Kumar Saha
[URL]:http://amitsaha.in.googlepages.com
Re: [OMPI users] Basic problems with OpenMPI
Hi Gleb, On 8/29/07, Gleb Natapov <gl...@voltaire.com> wrote: > Where have you installed it? If in /usr/local/ then try to run > mpirun --prefix /usr/local/ --np 1 --hostfile hostfile ./a.out Thanks again. It solves the problem. > > If this helps then you may want to re-run configure script with flag > --enable-orterun-prefix-by-default and recompile. Also, is open MPI 1.1 compatible with MPI 1.2.3, I mean to ask is whether a MPI executable generated using 1.1 is executable by 1.2.3? i am trying to run a 1.1 generated executable on a remote 1.2.3 host when i get the following: amit@ubuntu-desktop-1:~/mpi-exec$ mpirun -np 3 --hostfile /home/amit/junk/mpi-codes/mpi-host-file --mca btl ^openib ./HellMPI amit@debian-desktop-1's password: amit@ubuntu-desktop-2's password: [ubuntu-desktop-1:13202] [0,0,0] ORTE_ERROR_LOG: Data unpack failed in file dss/dss_peek.c at line 59 [ubuntu-desktop-1:13202] [0,0,0] ORTE_ERROR_LOG: Data unpack failed in file dss/dss_peek.c at line 59 [ubuntu-desktop-1:13202] [0,0,0] ORTE_ERROR_LOG: Data unpack failed in file dss/dss_peek.c at line 59 Note that the host "debian-desktop-1" is 1.2.3 and the other 2 is 1.1 Regards -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
Re: [OMPI users] Basic problems with OpenMPI
Hello all, I have installed Open MPI 1.2.3 from source on Debian 4.0. I did the "make all install" using root privileges. Now when I try to execute a simple program , I get the following: debian-desktop-1:/home/amit/junk/mpi-codes# mpirun --np 1 --hostfile hostfile ./a.out ./a.out: error while loading shared libraries: libmpi.so.0: cannot open shared object file: No such file or directory I get the error whether I do it as "normal user" or "root user" Please suggest. Thanks -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
Re: [OMPI users] Basic problems with OpenMPI
On 8/29/07, Gleb Natapov <gl...@voltaire.com> wrote: > On Wed, Aug 29, 2007 at 11:42:29AM +0530, Amit Kumar Saha wrote: > > hello all, > > > > I am just trying to get started with OpenMPI (version 1.1) on Linux. > Vesrion 1.1 is old an no longer supported. > > > > > When I try to run a simple MPI - "Hello World" program, here is what i get: > > > > amit@ubuntu-desktop-1:~/junk/mpi-codes$ mpirun -np 1 --hostfile > > mpi-host-file ./a.out > > libibverbs: Fatal: couldn't read uverbs ABI version. > > -- > > [0,1,0]: OpenIB on host ubuntu-desktop-1 was unable to find any HCAs. > > Another transport will be used instead, although this may result in > > lower performance. > > -- > > Processor 0 of 1: Hello World! > > > > Please explain the statements above. > Open MPI has Infiniband module compiled but there is no IB device found > on your host. Try to add "--mca btl ^openib" string to your command > line. > > > > > Also, when I am trying to launch the above process on 2 processors, > > instead of one, it gives me: > > > > Failed to find or execute the following executable: > > > > Host: ubuntu-desktop-2 > > Executable: ./a.out > > > > Cannot continue. > > > > Does that mean I have to place a copy of the executable on the other > > node as well? Where should I place the executable? > > > Yes. At the same location on each host. Thank you very much Gleb. It works! Regards -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
[OMPI users] Basic problems with OpenMPI
hello all, I am just trying to get started with OpenMPI (version 1.1) on Linux. When I try to run a simple MPI - "Hello World" program, here is what i get: amit@ubuntu-desktop-1:~/junk/mpi-codes$ mpirun -np 1 --hostfile mpi-host-file ./a.out libibverbs: Fatal: couldn't read uverbs ABI version. -- [0,1,0]: OpenIB on host ubuntu-desktop-1 was unable to find any HCAs. Another transport will be used instead, although this may result in lower performance. -- Processor 0 of 1: Hello World! Please explain the statements above. Also, when I am trying to launch the above process on 2 processors, instead of one, it gives me: Failed to find or execute the following executable: Host: ubuntu-desktop-2 Executable: ./a.out Cannot continue. Does that mean I have to place a copy of the executable on the other node as well? Where should I place the executable? Thanks in advance. Regards -- Amit Kumar Saha [URL]:http://amitsaha.in.googlepages.com
