Re: [OMPI users] qsub - mpirun problem

On Mon, 2008-09-29 at 17:30 -0500, Zhiliang Hu wrote: > >As you blank out some addresses: have the nodes and the headnode one > >or two network cards installed? All the names like node001 et al. are > >known on neach node by the correct address? I.e. 172.16.100.1 = node001? > > > >-- Reuti >

Re: [OMPI users] qsub - mpirun problem

Am 30.09.2008 um 00:30 schrieb Zhiliang Hu: At 12:10 AM 9/30/2008 +0200, you wrote: Can you please try this jobscript instead: #!/bin/sh set | grep PBS /path/to/mpirun /path/to/my_program All should be handled by Open MPI automatically. With the "set" bash command you will get a list with

Re: [OMPI users] qsub - mpirun problem

At 12:10 AM 9/30/2008 +0200, you wrote: >>Can you please try this jobscript instead: >> >>#!/bin/sh >>set | grep PBS >>/path/to/mpirun /path/to/my_program >> >>All should be handled by Open MPI automatically. With the "set" >>bash >>command you will get a

Re: [OMPI users] qsub - mpirun problem

Am 29.09.2008 um 23:15 schrieb Doug Reeder: It sounds like you may not have setup paswordless ssh between all your nodes. If you have a tight intergration of Open MPI and use the task manager from torque this shiouldn't be necessary. Continued below... Doug Reeder On Sep 29, 2008, at

Re: [OMPI users] qsub - mpirun problem

References: <200809290102.m8t12ic5022...@despam-11.iastate.edu> <5118_1222651029_m8t1h7c9014112_297d3668-bbfa-480c-8aa3-4dfe9a7dc...@lanl.gov> <200809290207.m8t27hg6030...@despam-10.iastate.edu> <19464_1222702229_m8tfursa024528_a4205240-a331-4854-b32c-bfb27b24d...@cisco.com>

Re: [OMPI users] qsub - mpirun problem

At 02:15 PM 9/29/2008 -0700, you wrote: >It sounds like you may not have setup paswordless ssh between all >your nodes. > >Doug Reeder That's not the case. paswordless ssh is set up and it works fine. -- that's how I can do "mpirun -np 6 -machinefiles .." fine. Zhiliang >On Sep 29,

Re: [OMPI users] qsub - mpirun problem

It sounds like you may not have setup paswordless ssh between all your nodes. Doug Reeder On Sep 29, 2008, at 2:12 PM, Zhiliang Hu wrote: At 10:45 PM 9/29/2008 +0200, you wrote: Am 29.09.2008 um 22:33 schrieb Zhiliang Hu: At 07:37 PM 9/29/2008 +0200, Reuti wrote: "-l nodes=6:ppn=2" is

Re: [OMPI users] qsub - mpirun problem

At 10:45 PM 9/29/2008 +0200, you wrote: >Am 29.09.2008 um 22:33 schrieb Zhiliang Hu: > >>At 07:37 PM 9/29/2008 +0200, Reuti wrote: >> "-l nodes=6:ppn=2" is all I have to specify the node requests: >>> >>>this might help: http://www.open-mpi.org/faq/?category=tm >> >>Essentially the examples

Re: [OMPI users] qsub - mpirun problem

Am 29.09.2008 um 22:33 schrieb Zhiliang Hu: At 07:37 PM 9/29/2008 +0200, Reuti wrote: "-l nodes=6:ppn=2" is all I have to specify the node requests: this might help: http://www.open-mpi.org/faq/?category=tm Essentially the examples given on this web is no difference from what I did.

Re: [OMPI users] qsub - mpirun problem

At 07:37 PM 9/29/2008 +0200, Reuti wrote: >>"-l nodes=6:ppn=2" is all I have to specify the node requests: > >this might help: http://www.open-mpi.org/faq/?category=tm Essentially the examples given on this web is no difference from what I did. Only thing new is, I suppose "qsub -I " is for

Re: [OMPI users] Execution in multicore machines

Hi, > A) The execution time in case "1" should be smaller (only sm > communication, no?) than case "2" and "3", no? Cache problems? Shot in the dark from working on Sun T1 (also 8 real cores): from time to time the OS wants to do something (interrupt handling, wake up cron, ...). Leaving one or

Re: [OMPI users] Execution in multicore machines

Jed Brown escribió: On Mon 2008-09-29 20:30, Leonardo Fialho wrote: 1) If I use one node (8 cores) the "user" % is around 100% per core. The execution time is around 430 seconds. 2) If I use 2 nodes (4 cores in each node) the "user" % is around 95% per core and the "sys" % is 5%. The

Re: [OMPI users] Execution in multicore machines

On Mon 2008-09-29 20:30, Leonardo Fialho wrote: > 1) If I use one node (8 cores) the "user" % is around 100% per core. The > execution time is around 430 seconds. > > 2) If I use 2 nodes (4 cores in each node) the "user" % is around 95% > per core and the "sys" % is 5%. The execution time is

[OMPI users] Execution in multicore machines

Hi All, I´m doing some probes in a multi core (8 cores per node) machine with NAS benchmarks. Something that I consider strange is occurring... I´m using only one NIC and paffinity: ./bin/mpirun -n 8 --hostfile ./hostfile --mca mpi_paffinity_alone 1 --mca btl_tcp_if_include eth1

Re: [OMPI users] MPI_THREAD_INIT

Gabriele, If you want to write portable MPI applications then I think you should stick with what the standard say. In other words for hybrid programming, and if only one thread will make MPI calls you need either MPI_THREAD_FUNNELED or MPI_THREAD_SERIALIZED. Now, that being said, I don't

Re: [OMPI users] qsub - mpirun problem

Hi, Am 29.09.2008 um 19:06 schrieb Zhiliang Hu: At 06:55 PM 9/29/2008 +0200, Reuti wrote: Am 29.09.2008 um 18:27 schrieb Zhiliang Hu: How you run that command line from *inside a Torque* job? -- I am only a poor biologist, reading through the manuals/ tutorials but still don't have good

[OMPI users] OpenMPI portability problems: debug info isn't helpful

Hello! I'm trying to build OpenMPI on NetBSD 4.99.72, I'm getting next message either when I'm building in debug mode or without it: [asau.local:27880] [NO-NAME] ORTE_ERROR_LOG: Not found in file runtime/orte_init_stage1.c at line 182

Re: [OMPI users] qsub - mpirun problem

At 06:55 PM 9/29/2008 +0200, Reuti wrote: >Am 29.09.2008 um 18:27 schrieb Zhiliang Hu: > >>How you run that command line from *inside a Torque* job? >> >>-- I am only a poor biologist, reading through the manuals/ tutorials but >>still don't have good clues... (thanks in advance ;-) > >What is

Re: [OMPI users] qsub - mpirun problem

I am the "system admin" here (so far so good on several servers over several years but this PBS thing appear to be daunting ;-) I suppose **run ... from *inside a Torque*** is to run things with a PBS script. I thought "qsub -l nodes=6:ppn=2 mpirun ..." already bring things into a PBS

Re: [OMPI users] qsub - mpirun problem

Am 29.09.2008 um 18:27 schrieb Zhiliang Hu: How you run that command line from *inside a Torque* job? -- I am only a poor biologist, reading through the manuals/ tutorials but still don't have good clues... (thanks in advance ;-) What is the content of your jobscript? Did you request more

Re: [OMPI users] qsub - mpirun problem

On Sep 29, 2008, at 12:27 PM, Zhiliang Hu wrote: How you run that command line from *inside a Torque* job? -- I am only a poor biologist, reading through the manuals/tutorials but still don't have good clues... (thanks in advance ;-) Ah, gotcha. I'm guessing that you're running OMPI

Re: [OMPI users] qsub - mpirun problem

How you run that command line from *inside a Torque* job? -- I am only a poor biologist, reading through the manuals/tutorials but still don't have good clues... (thanks in advance ;-) Zhiliang At 11:48 AM 9/29/2008 -0400, you wrote: >We need to see that command line from *inside a Torque*

Re: [OMPI users] qsub - mpirun problem

We need to see that command line from *inside a Torque* job. That's the only place where those PBS_* environment variables will exists -- OMPI's mpirun should be seeing these environment variables (when inside a Torque job) and then reacting to them by using the Torque native launcher,

Re: [OMPI users] qsub - mpirun problem

At 11:29 AM 9/29/2008 -0400, Jeff Squyres wrote: >On Sep 28, 2008, at 10:07 PM, Zhiliang Hu wrote: > >>Indeed as you expected, "printenv | grep PBS" produced nothing. > >Are you *sure*? I find it very hard to believe that if you run that >command ***in a Torque job*** that you will get no

Re: [OMPI users] qsub - mpirun problem

On Sep 28, 2008, at 10:07 PM, Zhiliang Hu wrote: Indeed as you expected, "printenv | grep PBS" produced nothing. Are you *sure*? I find it very hard to believe that if you run that command ***in a Torque job*** that you will get no output. Torque would have to be *seriously* misbehaving

Re: [OMPI users] MPI_THREAD_INIT

Hi George. So is it dangerous to use hybrid program ( MPI+OpenMP) without enable threads support? 2008/9/29 George Bosilca > Gabriele, > > The thread support has to be explicitly requested at build time, or it will > be disabled. Add --enable-mpi-threads (configure --help

Re: [OMPI users] MPI_THREAD_INIT

Gabriele, The thread support has to be explicitly requested at build time, or it will be disabled. Add --enable-mpi-threads (configure --help will give you more info) to your configure. If you plan to use threads with Open MPI I strongly suggest to update to the 1.3. This version is not

Re: [OMPI users] MPI_THREAD_INIT

Another question about MPI_INIT_THREAD. At the moment, as said, my OpenMPi version supports only level 0: MPI_THREAD_SINGLE. Suppose that i have this code: #pragma omp barrier #pragma omp master MPI_Send(buf,...); #pragma omp barrier Due my OpenMPI configuration, is it dangerous use this

[OMPI users] MPI_THREAD_INIT

Dear OpenMPi developers, i've noted that OpenMPI 1.25 and 1.2.6 version doesn't supports thread initialization function shows below: int MPI_Init_thread(int *argc, char *((*argv)[]), int required, int *provided) used in hybrid programming MPI+OpenMP. Returned vales provided is 0, so the unique

Re: [OMPI users] qsub - mpirun problem

Hi Zhiliang This has nothing to do with how you configured Open MPI. The issue is that your Torque queue manager isn't setting the expected environment variables to tell us the allocation. I'm not sure why it wouldn't be doing so, and I'm afraid I'm not enough of a Torque person to know