On 3 April 2009 at 06:35, Jerome BENOIT wrote:
| It appeared that the file /etc/openmpi/openmpi-mca-params.conf on node green
was the only one
| into the cluster to contain the line
|
| btl_tcp_port_min_v4 = 49152
Great -- so can we now put your claims of 'the Debian package is broken' to
rest
On 3 April 2009 at 03:33, Jerome BENOIT wrote:
| The above submission works the same on my clusters.
| But in fact, my issue involve interconnection between the nodes of the
clusters:
| in the above examples involve no connection between nodes.
|
| My cluster is a cluster of quadcore computers:
: Fri, 03 Apr 2009 02:41:01 +0800
| From: Jerome BENOIT
| Reply-To: ml.jgmben...@mailsnare.net
| To: Dirk Eddelbuettel
| CC: ml.jgmben...@mailsnare.net
| References: <49ce5244.2000...@mailsnare.net>
<49d4ef88.6060...@mailsnare.net> <18901.114.820349.347...@ron.nulle.part&g
To bring closure to this thread, we found that the following simple patch to
Rmpi/src/Rmpi.c fixes the problem:
--- rmpi-0.5-6.orig/src/Rmpi.c
+++ rmpi-0.5-6/src/Rmpi.c
@@ -63,7 +63,7 @@
else {
#ifdef OPENMPI
- dlopen("libmpi.so.0", RTLD_GLOBAL);
+ dlopen("libmpi.so.0", RTL
On 30 January 2009 at 16:15, Jeff Squyres wrote:
| On Jan 26, 2009, at 3:33 PM, Dirk Eddelbuettel wrote:
|
| > Gdb doesn't want to step into the Open MPI code; I used debugging
| > symbols for
| > both R and Open MPI that are available via -dbg packages with the
| > debugg
I am chasing a segfault when I use Open MPI (1.3) with Rmpi (0.5.6), the MPI
add-on package for R that is written and maintained btyby Prof Hao Yu (CC'ed)
I should prefix that the code runs just fine on 32bit Debian system at home.
However, on amd64 running Ubuntu 8.10, I am seeing segfaults upon
On 18 November 2008 at 17:06, Venu Gopal wrote:
| Hello,
|
| I am new into this mailing list, and am trying to install openMPI on Ubuntu
| 8.0.4.1
(That's not an existing version number.)
| Basically my idea is to build a beowulf. Well right now i even dont have
| lots of PC's for this purpose.
On 18 October 2008 at 03:30, Terry Frankcombe wrote:
|
| > Well when I use Open MPI I go with the new convention and call orterun
| > instead of mpirun. I think you should have. Maybe a local alias in your
| > ~/.bashrc can do the trick.
| >
| > Current packages do have mpirun.openmpi but we we
On 18 October 2008 at 00:16, Raymond Wan wrote:
|
| Hi all,
|
| I'm very new to MPI and am trying to install it on to a Debian Etch
| system. I did have mpich installed and I believe that is causing me
Etch is getting old, and its Open MPI 1.1 package were in suboptimal shape.
A few of us ge
On 17 October 2008 at 12:42, Simone Giannerini wrote:
| Dear all,
|
| I managed to install successfully Rmpi 0.5-5 on a quad opteron machine (8
| cores overall) running on OpenSUSE 11.0 and Open MPI 1.5.2.
|
| this is what I get
|
| > library(Rmpi)
| [gauss:24207] mca: base: component_find: una
On Mon, Oct 13, 2008 at 12:18:30PM -0400, Sean Davis wrote:
> On Mon, Oct 13, 2008 at 12:10 PM, Simone Giannerini
> wrote:
> > [...]
> >
> >> Your mail is basically unreadable / impossible to attribute what is
> >> original and what is cited. Please follow convention and indent.
> >
> > I am sorry
On Mon, Oct 13, 2008 at 03:56:19PM +0200, Simone Giannerini wrote:
> Dear Dirk,
>
> many thanks for your reply, please see below,
Your mail is basically unreadable / impossible to attribute what is
original and what is cited. Please follow convention and indent.
> On 13 October 2008 at 11:22, S
On 13 October 2008 at 11:22, Simone Giannerini wrote:
| Dear all,
|
| I have troubles installing rmpi 0.5-5 (or 0.5-6) on a quad opteron machine
| with OpenSUSE 11.0 and
| R 2.7.2
|
| platform x86_64-unknown-linux-gnu
| arch x86_64
| os linux-gnu
| system x86
On 6 September 2008 at 22:13, Davi Vercillo C. Garcia () wrote:
| I'm trying to execute some programs in my notebook (Ubuntu 8.04) using
| OpenMPI, and I always get a warning message like:
|
| libibverbs: Fatal: couldn't read uverbs ABI version.
| -
On 5 August 2008 at 17:01, Ben Payne wrote:
| Hello. I am not sure if this is the correct list to ask this
| question, so if you know of a more appropriate one please let me know.
|
| I think am looking for a LiveCD that supports MPI, specifically one
| that has mpif90 built in, and can easily m
On 24 July 2008 at 14:39, Adam C Powell IV wrote:
| Greetings,
|
| I'm seeing a segfault in a code on Ubuntu 8.04 with gcc 4.2. I
| recompiled the Debian lenny openmpi 1.2.7~rc2 package on Ubuntu, and
| compiled the Debian lenny petsc and libmesh packages against that.
|
| Everything works just
On 15 June 2008 at 17:11, Brian Barrett wrote:
| On Jun 15, 2008, at 2:20 PM, Dirk Eddelbuettel wrote:
|
| > Yup: I still suspect compiler / linker changes in Ubuntu between Gutsy
| > (released Oct 2007) and Hardy (April 2008).
| >
| > Why? Because the exactly same source package
t; contains my stack trace).
| >
| > Anybody have an idea what could cause this?
| >
| > Thanks,
| > Andreas
| >
| > [1] http://www.open-mpi.org/community/lists/users/2007/08/3844.php
| > [2] https://bugs.launchpad.net/bugs/210273
|
| Dirk Eddelbuettel has pinpointed this t
On 25 April 2008 at 20:10, Barry Smith wrote:
|
|
| A smarter colleague then I, has reminded me that is very difficult
| to obtain all the
| Fortran libraries and linker options that would be needed to allow the
| mpicc compiler to
| also link against the MPI fortran libraries successful
On 22 April 2008 at 00:12, Vincent Rotival wrote:
| Sorry to bother you all about that but I am quite lost with a puzzling
| problem concerning openMPI + Ubuntu 7.10. I could not find similar
| threads on the archive
[...]
| I am using openMPI version 1.2.6 (but same bug occured with 1.2.5),
|
On Wed, Jan 30, 2008 at 09:13:28AM -0500, Sang Chul Choi wrote:
> I am wondering which version of open mpi I should install. I am using the
> latest version of Ubuntu. Is debian package 1.1-2.5 the relatively latest
> version of open mpi?
No -- and a simple way of getting selected packages from De
On 18 December 2007 at 16:08, Randy Heiland wrote:
| The pkg in question is here: http://www.stats.uwo.ca/faculty/yu/Rmpi/
|
| The question is: has anyone on this list got OpenMPI working for
| this pkg? Any suggestions?
Yes -- I happen to maintain GNU R, a number of R packages (eg r-cran-*
On 13 December 2007 at 13:17, Lisandro Dalcin wrote:
| Perhaps I was not clear enough. There are many public ways of
| importing modules in Python. Modules can came mainly from two sources:
| pure Python code, or C compiled code. In the later case (called
| extension modules), they are normally a
On 22 November 2007 at 17:08, yh sun wrote:
| hi ,
|Recently i am practising with PGAPack. Have anyone do the similiar work?
I have using PGApack with Open MPI. I have also prepared a draft of what
should "soon" become a new / updated PGApack releases, primarily with an
updated / newer lice
Yay, three cheers for Jeff.
Reverting to the stock libibverbs package (still at 1.0-4 for the version of
Ubuntu I'm running at work as I haven't upgraded to last week's Ubuntu 7.10
release) and rebuilding the Open MPI 1.2.4 deb packages under it fixes the
openib error message issue.
So even fo
On 25 October 2007 at 07:54, Jeff Squyres wrote:
| We will not dlopen libibverbs.so directly -- we will only dlopen the
| mca_btl_openib.so file. The dynamic linker will automatically open
| all of its dependencies. If those dependencies cannot be found /
| symbols cannot be resolved, the
On 24 October 2007 at 21:31, Jeff Squyres wrote:
| On Oct 24, 2007, at 9:23 PM, Dirk Eddelbuettel wrote:
|
| > | If I had to guess, the systems where you don't see the warning are
| > | systems that have OFED loaded.
| >
| > I am pretty sure that none of the systems
On 24 October 2007 at 16:22, Jeff Squyres wrote:
| On Oct 24, 2007, at 4:16 PM, Dirk Eddelbuettel wrote:
|
| > I buy that explanation any day, but what is funny is that the
| > btl = ^openib
| > does suppress the warning on some of my systems (all running 1.2.4)
| > but no
and that's what we print (note that ltdl is
| referring to the fact that a dependent library is not found).
I buy that explanation any day, but what is funny is that the
btl = ^openib
does suppress the warning on some of my systems (all running 1.2.4) but not
others (also running 1.
I've been scratching my head over this:
lnx01:/usr/lib> orterun -n 2 --mca btl ^openib ~/c++/tests/mpitest
[lnx01:14417] mca: base: component_find: unable to open btl openib: file not
found (ignored)
[lnx01:14418] mca: base: component_find: unable to open btl openib: file not
found (ignored)
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 o
Brian,
On 12 October 2007 at 13:55, Brian Granger wrote:
| > My guess is that Rmpi is dynamically loading libmpi.so, but not
| > specifying the RTLD_GLOBAL flag. This means that libmpi.so is not
| > available to the components the way it should be, and all goes
| > downhill from there. It only
ont.
Actually, looked like you didn't CC him.
Hth, Dirk
|
| Thanks
|
| Brian
|
| On 10/10/07, Brian Barrett wrote:
| > On Oct 10, 2007, at 1:27 PM, Dirk Eddelbuettel wrote:
| > > | Does this happen for all MPI programs (potentially only those that
| > > | use the MPI-2 one-
Brian,
Man you're good! :)
On 10 October 2007 at 13:49, Brian Barrett wrote:
| On Oct 10, 2007, at 1:27 PM, Dirk Eddelbuettel wrote:
| > | Does this happen for all MPI programs (potentially only those that
| > | use the MPI-2 one-sided stuff), or just your R environment?
| >
|
Jeff,
Thanks for the reply. I have gotten much closer, and it looks like all
wounds were self-inflicted. More below.
On 9 October 2007 at 22:01, Jeff Squyres wrote:
| On Oct 9, 2007, at 3:50 PM, Dirk Eddelbuettel wrote:
|
| > edd@ron:~$ orterun -n 2 --mca mca_component_show_load_errors
On 9 October 2007 at 08:08, Jeff Squyres wrote:
| On Oct 7, 2007, at 12:53 AM, Dirk Eddelbuettel wrote:
|
| > | Not that I can tell. What else could I test? The build-logs
| > don't reveal
| > | anything fishy -- all pt2pt occurrences look fine. The build itself
| > | pr
w what to try next.
Dirk
| Brian
|
| On 10/6/07, Dirk Eddelbuettel wrote:
| >
| > On 6 October 2007 at 09:36, Dirk Eddelbuettel wrote:
| > |
| > | On 5 October 2007 at 21:31, Brian Barrett wrote:
| > | | On Oct 5, 2007, at 8:48 PM, Dirk Eddelbuettel wrote:
| > | |
| > | | &g
On 6 October 2007 at 09:36, Dirk Eddelbuettel wrote:
|
| On 5 October 2007 at 21:31, Brian Barrett wrote:
| | On Oct 5, 2007, at 8:48 PM, Dirk Eddelbuettel wrote:
| |
| | > With the (Debian package of the) current 1.2.4 release, I am seeing
| | > a lot of
| | >
| | >
On 5 October 2007 at 21:31, Brian Barrett wrote:
| On Oct 5, 2007, at 8:48 PM, Dirk Eddelbuettel wrote:
|
| > With the (Debian package of the) current 1.2.4 release, I am seeing
| > a lot of
| >
| > mca: base: component_find: unable to open osc pt2pt: file not
| >
Hi all,
With the (Debian package of the) current 1.2.4 release, I am seeing a lot of
mca: base: component_find: unable to open osc pt2pt: file not found (ignored)
that I'd like to suppress.
For these Debian packages, we added a (commented-out by default) entry to
suppress the Infiniband no
On 26 September 2007 at 13:37, Francesco Pietra wrote:
| Are any detailed directions for upgrading (for common guys, not experts, I
| mean)? My 1.2.3 version on Debian Linux amd64 runs perfectly.
How about
sudo apt-get update; sudo apt-get dist-upgrade
provided you point to Debian unsta
On 18 July 2007 at 19:14, Dirk Eddelbuettel wrote:
|
| Hi Tim,
|
| Thanks for the follow-up
|
| On 18 July 2007 at 17:22, Tim Prins wrote:
| |
| | > Yes, this helps tremendously. I installed rsh, and now it pretty much
| | > works.
| | Glad this worked out for you.
| |
| | >
| |
Hi Tim,
Thanks for the follow-up
On 18 July 2007 at 17:22, Tim Prins wrote:
|
| > Yes, this helps tremendously. I installed rsh, and now it pretty much
| > works.
| Glad this worked out for you.
|
| >
| > The one missing detail is that I can't seem to get the stdout/stderr
| > output. For ex
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