Re: [OMPI users] MPI Java Bindings on Mac OSX

Ralph, The source is available at http://modules.sourceforge.net/ Doug On Jan 3, 2013, at 10:49 AM, Ralph Castain wrote: > Hi Doug > > What modules software do you use on the Mac? Would be nice to know :-) > > > On Jan 3, 2013, at 8:34 AM, Doug Reeder <d...@c

Re: [OMPI users] MPI Java Bindings on Mac OSX

Chuck, In step 4 you might want to consider the following --prefix=/usr/local/openmpi-1.7rc5 and use the modules software to select which version of openmpi to use. I have to have multiple versions of openmpi available on my macs and this approach has worked well for me. Doug Reeder On Jan 3

Re: [OMPI users] regarding the problem occurred while running an mpi programs

That is well documented as a BAD idea. On Apr 25, 2012, at 8:23 AM, seshendra seshu wrote: > Hi > Yes i run in root. > > On Wed, Apr 25, 2012 at 4:20 PM, tyler.bal...@huskers.unl.edu > wrote: > Seshendra, > > Do you always run in root? If not your root bash

Re: [OMPI users] heterogenous cluster

Jody, With the gnu compilers the -m32 flag works. With other compilire's the same or other flag should work. Doug Reeder On Feb 1, 2011, at 11:46 PM, jody wrote: > Thanks for your reply. > > If i try your suggestion, every process fails with the following message: > > *

Re: [OMPI users] How closely tied is a specific release of OpenMPI to the host operating system and other system software?

they automatically get the correct version of openmpi. Doug Reeder On Feb 1, 2011, at 2:02 PM, Jeffrey A Cummings wrote: > I use OpenMPI on a variety of platforms: stand-alone servers running Solaris > on sparc boxes and Linux (mostly CentOS) on AMD/Intel boxes, also Linux > (again CentOS)

Re: [OMPI users] Mac Ifort and gfortran together

Hello, You may me bumping into conflicts between the apple supplied ompi and your mpi. I use modules to force my mpi to the front of the PATH and DYLD_LIBRARY_PATH variables. Doug Reeder On Dec 15, 2010, at 5:22 PM, Jeff Squyres wrote: > Sorry for the ginormous delay in replying here; I bl

Re: [OMPI users] Bad performance when scattering big size of data?

rom a hyperthreading expert, preferably form intel. Doug Reeder On Oct 4, 2010, at 9:53 AM, Storm Zhang wrote: > We have 64 compute nodes which are dual qual-core and hyperthreaded CPUs. So > we have 1024 compute units shown in the ROCKS 5.3 system. I'm trying to > scatter an array fro

Re: [OMPI users] Building OpenMPI 10.4 with PGI fortran 10.8 and gcc

Axel, Should the argument be -ipthread? Doug Reeder On Sep 14, 2010, at 12:17 PM, Axel Schweiger wrote: > Trying to build a hybrid OpenMPI with PGI fortran and gcc to support WRF model > The problem appears to be due to a -pthread switch passed to pgfortran. > > > > libtoo

Re: [OMPI users] Configuring with torque: error and patch

John, I haven't done a build with torque lately, but I think you need to have a -ltorque argument in the load step. Doug Reeder On May 30, 2010, at 9:13 AM, John Cary wrote: Upon configuring and building openmpi on a system with torque, I repeatedly got build errors of the sort, /bin/sh

Re: [OMPI users] Building 1.4.x on mac snow leopard with intel compilers

Mike, Are you sure that you are getting the openmpi that you built and not the one supplied w/ OS X. I use modules to make sure that I am getting the openmpi version I build instead of the OS X suppleid version. Doug Reeder On May 23, 2010, at 10:45 AM, Glass, Micheal W wrote: I’m having

Re: [OMPI users] How do I run OpenMPI safely on a Nehalem standalone machine?

welcome input/insight from an intel hardware engineer. I make sure that I don't ask for more processors than there are physical cores and that seems to work. Doug Reeder On May 4, 2010, at 7:06 PM, Gus Correa wrote: Hi Ralph Thank you so much for your help. You are right, paffinity is turned

Re: [OMPI users] openmpi 1.4.1 and xgrid

Cristobal, It may be a 10.6 vs 10.5 difference. In the configure --help output it looks like --with-xgrid=no should turn off the default behavior of building with support for xgrid. Doug Reeder On Apr 30, 2010, at 3:28 PM, Cristobal Navarro wrote: this is strange, because some weeks ago i

Re: [OMPI users] openmpi 1.4.1 and xgrid

Alan, I haven't tried to build 1.4.x on os x 10.6.x yet, but it sounds like the configure script has become too clever by half. Is there a configure argument to force no xgrid (e.g., --with-xgrid=no or -- enable-xgrid=no). Doug Reeder On Apr 30, 2010, at 3:12 PM, Alan wrote: Hi guys

Re: [OMPI users] openmpi 1.4.1 and xgrid

Alan, Are you sure that the ompi_info and mpirun that you are using are the 1.4.1 versions and not the apple supplied versions. I use modules to help ensure that I am using the openmpi that I built and not the apple supplied versions. Doug Reeder On Apr 30, 2010, at 12:14 PM, Alan wrote

Re: [OMPI users] configure script fails

Christoph, It looks like you need to add -L/usr/local/lib to the fortran and f90 flags, either on the configure input or in the environment variables, so that the loader can find libgfortran. Doug On Jan 13, 2010, at 4:09 PM, von Tycowicz, Christoph wrote: Hi, when running the configure

Re: [OMPI users] OpenMPI on OS X - file is not of required architecture

Andreas, Have you checked that ifort is creating 64 bit objects. If I remember correctly with 10.1 the default was to create 32 bit objects. Doug Reeder On Sep 11, 2009, at 3:25 PM, Andreas Haselbacher wrote: On Fri, Sep 11, 2009 at 5:10 PM, Jeff Squyres <jsquy...@cisco.com>

Re: [OMPI users] ompi_info segmentation fault with Snow Leopard

Marcus, What version of openmpi ships with 10.6. Are you making sure that you are getting the includes and libraries for 1.3.3 and not the native apple version of openmpi. Doug Reeder On Sep 1, 2009, at 4:31 PM, Marcus Herrmann wrote: Hi, I am trying to install openmpi 1.3.3 under OSX

Re: [OMPI users] Configuration problem or network problem?

Lin, Try -np 16 and not running on the head node. Doug Reeder On Jul 6, 2009, at 7:08 PM, Zou, Lin (GE, Research, Consultant) wrote: Hi all, The system I use is a PS3 cluster, with 16 PS3s and a PowerPC as a headnode, they are connected by a high speed switch. There are point

Re: [OMPI users] Compiling Open MPI with PGI compilers in 32-bit mode

Ethan, It looks likesome of the object files that you are trying to link to the malloc.o and malloc-stats.o were compiled as 64 bit objects. Are you using the 32 bit compiler flag for the compile step as well as the link step. Doug Reeder On Mar 20, 2009, at 10:49 AM, Ethan Mallove wrote

Re: [OMPI users] 1.3 and --preload-files and --preload-binary

Josh, It sounds like . is not in your path. That would prevent mpirun from seeing the binary in the current directory. Doug Reeder On Jan 22, 2009, at 10:48 AM, Josh Hursey wrote: As a followup. I can confirm that --preload-files is not working as it should. I was able to use --preload

Re: [OMPI users] FW: Re: [MTT users] Is the stock MPI that comes with OSX leopard broken with xgrid?

I believe that the openmpi that comes with leopard doesn't support xgrid. If you type ompi_info|grep xgrid you get nothing. I'm not sure what apple was thinking. Doug Reeder On Dec 17, 2008, at 6:30 AM, Ethan Mallove wrote: Hi John, I'm forwarding your question to the Open MPI users list

Re: [OMPI users] OpenMPI runtime-specific environment variable?

Brian, I'm not sure I understand the problem. The ale3d program from LLNL operates exactly as you describe and it can be built with mpich, lam, or openmpi. Doug Reeder On Oct 21, 2008, at 3:08 PM, Adams, Brian M wrote: -Original Message- From: users-boun...@open-mpi.org

Re: [OMPI users] OpenMPI runtime-specific environment variable?

Brian, In your code branch for the parallel run you could set an environment or internal variable when you call mpi_init. Can you parse the command line (arg 0) and figure out if you are running parallel or serial. Doug Reeder On Oct 20, 2008, at 3:40 PM, Adams, Brian M wrote: I work

Re: [OMPI users] Passing LD_LIBRARY_PATH to orted

In torque/pbs using the #PBS -V command pushes the environment variables out to the nodes. I don't know if that is what was happening with slurm. Doug Reeder On Oct 14, 2008, at 12:33 PM, Ralph Castain wrote: I -think- there is...at least here, it does seem to behave that way on our

Re: [OMPI users] OMPI link error with petsc 2.3.3

Yann, It looks like somehow the libmpi and libmpi_f90 have different values for the variable mpi_fortran_status_ignore. It sounds like a configure problem. You might check the mpi include files to see if you can see where the different values are coming from. Doug Reeder On Oct 7, 2008

Re: [OMPI users] segfault issue - possible bug in openmpi

Shafagh, I missed the dependence on the number of processors. Apparently there is some thread support. Doug On Oct 4, 2008, at 5:29 PM, Shafagh Jafer wrote: Doug Reeder, Daniel is saying that the problem only occurs in openmpi when running more than 16 processes. So could that still

Re: [OMPI users] segfault issue - possible bug in openmpi

Daniel, Are you using threads. I don't think the opempi-1.2.x work with threads. Doug Reeder On Oct 3, 2008, at 2:30 PM, Daniel Hansen wrote: Oh, by the way, here is the segfault: [m4b-1-8:11481] *** Process received signal *** [m4b-1-8:11481] Signal: Segmentation fault (11) [m4b-1-8:11481

Re: [OMPI users] 1.2.2 to 1.2.7 differences.

the target:< --- On Wed, 10/1/08, Doug Reeder <d...@rain.org> wrote: From: Doug Reeder <d...@rain.org> Subject: Re: [OMPI users] 1.2.2 to 1.2.7 differences. To: "Open MPI Users" <us...@open-mpi.org> Date: Wednesday, October 1, 2008, 8:58 PM Shafagh, You should be able

Re: [OMPI users] 1.2.2 to 1.2.7 differences.

probably want to upgrade to gcc 3.x.x or 4.x.x and use module for that also). Doug Reeder On Oct 1, 2008, at 8:11 PM, Shafagh Jafer wrote: On our cluster we have RedHat Linux 7.3 Professional, and on the cluster specification it says the following: -The cluster should be able to run the follwoing

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:

Re: [OMPI users] compile openmpi with a gcc that is not default gcc??

Shafagh, You could put the full paths to the 3.4.4 compiler in the configure arguments. See configure -help. Doug Reeder On Sep 27, 2008, at 3:21 PM, Shafagh Jafer wrote: I have a simple question: My default gcc is 2.95.3, so I installed a newer version in my own home directory, it's gcc

Re: [OMPI users] Configure and Build ok, but mpi module not recognized?

Jeff, I think that unless make all depends on make clean and make clean depends on Makefile, you have to manually run make clean and/or manually delete the module files. Doug Reeder On Sep 22, 2008, at 3:16 PM, Jeff Squyres wrote: On Sep 22, 2008, at 6:08 PM, Brian Harker wrote: Here's

Re: [OMPI users] Configure and Build ok, but mpi module not recognized?

Brian, Try doing a make clean before doing the build with your new make file (from the new configure process). It looks like you are getting the leftover module files from the old makefile/compilers. Doug reeder On Sep 22, 2008, at 2:52 PM, Brian Harker wrote: Ok, here's something funny

Re: [OMPI users] How to get started?

Yes, I run it on my dual core apple notebook. Doug Reeder On Aug 15, 2008, at 9:58 AM, Anugraha Sankaranarayanan wrote: >>Are you talking about single notebook or multiple? Doesn't make sense to just have it single machine - unless you're building codes that gonna go into a cluster.

Re: [OMPI users] mpirun on 8-way node with rsh

the number of processors you requested from torque. It will communicate with torque to find out which ones to use. Doug Reeder On Aug 3, 2008, at 10:45 AM, Pete Schmitt wrote: I use the following: mpirun -machinefile machine.file -np 8 ./mpi- program and the machine file has the following

Re: [OMPI users] getting fortran90 to compile

Zachary, I believe you need to ad F90=/usr/bin/gfortran-4.2 (or something similar) to the configure arguments, FC= just gets f77 support. Doug Reeder On Jul 13, 2008, at 8:58 AM, zach wrote: I installed openmpi like ./configure --prefix= FC=/usr/bin/gfortran-4.2 make all install When i

Re: [OMPI users] gfortran bindings apparently not built on mac os leopard

variable. Doug Reeder On Jun 16, 2008, at 9:25 AM, Weirs, V Gregory wrote: I am having trouble building mpif77/mpif90 with gfortran on Mac OS 10.5. Or maybe just running. The configure, make all, and make install seemed to go just fine, finding my gfortran and apparently using

Re: [OMPI users] Different CC for orte and opmi?

to push the intel libraries out to the nodes or worry about the LD_LIBRARY_PATH. Doug Reeder On Jun 10, 2008, at 4:28 AM, Ashley Pittman wrote: Sorry, I'll try and fill in the background. I'm attempting to package openmpi for a number of customers we have, whenever possible on our clusters

Re: [OMPI users] Different CC for orte and opmi?

that orted is using. Doug Reeder On Jun 9, 2008, at 12:54 PM, Ashley Pittman wrote: Putting to side any religious views I might have about static linking how would that help in this case? It appears to be orted itself that fails to link, I'm assuming that the application would actually run

Re: [OMPI users] Different CC for orte and opmi?

Ashley, It could work but I think you would be better off to try and statically link the intel libraries. Doug Reeder On Jun 9, 2008, at 4:34 AM, Ashley Pittman wrote: Is there a way to use a different compiler for the orte component and the shared library component when using openmpi

Re: [OMPI users] Open MPI instructional videos

Jeff, I believe that with quicktime-pro you can export the videos in several formats. Doug Reeder On Jun 3, 2008, at 1:48 PM, Jeff Squyres wrote: On May 30, 2008, at 9:55 AM, Andreas Schäfer wrote: I've never really dig into Open MPI's guts, not because I wasn't interested, but mainly

Re: [OMPI users] openmpi 32-bit g++ compilation issue

I don't know if this is something you can control in the configure step for open-mpi. Doug Reeder On May 19, 2008, at 2:48 PM, Arif Ali wrote: Hi, OS: SLES10 SP1 OFED: 1.3 openmpi: 1.2 1.2.5 1.2.6 compilers: gcc g++ gfortran I am creating a 32-bit build of openmpi on an Infiniband cluster

Re: [OMPI users] Install BLACS and ScaLAPACK on Leopard

Linwei, Did you build the liblapack.a file, it is of the wrong architecture. Doug Reeder On May 7, 2008, at 2:58 PM, Linwei Wang wrote: Hi, Doug I've checked the makefiles and make sure that flag -m64 is used for all the compiling but the error still exists.. Linwei On May 7, 2008, at 5

Re: [OMPI users] Install BLACS and ScaLAPACK on Leopard

Linwei, It looks like you are getting a mix of 32 and 64 bit code (hence the 'file is not of required architecture' error). Are you using the command line flag -m64 for some parts of the build and not for others. You need to use either -m32 or -m64 for all the builds. Doug Reeder On May

Re: [OMPI users] Install BLACS and ScaLAPACK on Leopard

programs then using -funderscoring should help. Doug Reeder On May 5, 2008, at 11:21 AM, Linwei Wang wrote: Dear Reeder, I've tried add gfortran flag "-fno-underscoring", but the same errors persist... Is that possible because that I have both g77 and gfortran in my computer? Best,

Re: [OMPI users] Install BLACS and ScaLAPACK on Leopard

in a different directory than the apple version ( use -- prefix in the openmpi configure command). You will also need to remove the apple version or rename the openmpi include and library files so that the linker can find your new, fortran supporting version. Doug Reeder On May 1, 2008, at 8

Re: [OMPI users] trouble building on a macbook

Robert, Did you mean to install openmpi-1.2.6 in /usr. That is where the apple supplied openmpi-1.2.3 in is installed. That doesn't appear to be the problem causing your make install error. Were there any warnings or errors when you ran make. Doug Reeder On Apr 27, 2008, at 1:11 PM

Re: [OMPI users] install intel mac with Laopard

Jeff, I think that error message is a good compromise and addresses the most common problems that cause it to be written. Doug Reeder On Apr 25, 2008, at 4:08 AM, Jeff Squyres wrote: Sorry, I should have been more specific: how about

Re: [OMPI users] install intel mac with Laopard

e. On Apr 24, 2008, at 11:57 AM, Doug Reeder wrote: Jeff, For the specific problem of the gcc compiler creating i386 objects and ifort creating x86_64 objects, in the config.log file it says configure:26935: ifort -o conftest conftest.f conftest_c.o >&% ld: warning in conftest_c.o, file i

Re: [OMPI users] install intel mac with Laopard

the real problem. Right now the information is in the config.log file but it doesn't jump out at you. Doug Reeder On Apr 24, 2008, at 8:40 AM, Jeff Squyres wrote: On Apr 24, 2008, at 11:07 AM, Doug Reeder wrote: Make sure that your compilers are all creaqting code for the same architectur

Re: [OMPI users] Problems with program-execution with OpenMPI: Orted: command not found

Stephan, A couple things to try Put -np 2 after -hostfile /home/stephan/mpd.hosts put the command you want to run after -np 2 Good luck, Doug Reeder On Apr 21, 2008, at 11:56 PM, gildo@gmx.de wrote: Dear all, I wanted to compare MPICH and OpenMPI. MPICH works fine. So I installed

Re: [OMPI users] remote host not accessible

it be? Should I configure open-MPI about this mount point? Can't it work without mounting? I think it should work since the processes are locally run via SSH on remote machines. D. Doug Reeder skrev: Danesh, Do they all have access to the sam file system/physical hard drive. You will probably need

Re: [OMPI users] remote host not accessible

Danesh, Do they all have access to the sam file system/physical hard drive. You will probably need to NFS mount the filesystem on master on the other two systems. Doug Reeder On Apr 1, 2008, at 1:46 PM, Danesh Daroui wrote: Hi all, I have installed Open-MPI on three machine which runs

Re: [OMPI users] ScaLapack and BLACS on Leopard

from gfortran or g95. Looking at the cost of adding processors with g95/gfortran to get the same throughput as with ifort you recover the $549 compiler cost real quickly. Doug Reeder On Mar 6, 2008, at 9:20 AM, Gregory John Orris wrote: Sorry for the long delay in response. Let's get back

Re: [OMPI users] -prefix option to mpirun.

Ashley, Could you define an alias for mpirun that includes -prefix and the necessary argument. Doug Reeder On Mar 4, 2008, at 6:28 AM, Ashley Pittman wrote: Hello, I work for medium sized UK based ISV and am packaging open-mpi so that is can be made available as an option to our users

Re: [OMPI users] shared libraly problem with openmpi-1.2.3 and opensuse10.2

/lib64 in your LD_LIBRARY_PATH otherwise put /usr/lib in your LD_LIBRARY_PATH. Doug Reeder On Feb 19, 2008, at 10:00 PM, yoshi.plala wrote: Dear sirs I am a beginer with openmpi-1.2.3 (and opensuse10.2). But, I have some experience with mpich-1.2 and FreeBSD5.4. I am struggling with them

Re: [OMPI users] flash2.5 with openmpi

Brock, Do you mean flash memory, like a USB memory stick. What kid of file system is on the memory. Is there some filesystem limit you are bumping into. Doug Reeder On Jan 25, 2008, at 8:38 AM, Brock Palen wrote: Is anyone using flash with openMPI? we are here, but when ever it tries

Re: [OMPI users] Tracing the library using gdb and xterm

Krishna, Would it work to launch the gdb/ddd process separately on the remote machine and then attaching to the mpi running jobfrom within gdb/ddd. Something like ssh -X [hostname|ip address] [ddd|gdb] Doug Reeder On Jan 3, 2008, at 8:32 AM, Jeff Squyres wrote: Per my previous mail

Re: [OMPI users] Tracing the library using gdb and xterm

Krishna, Review the ssh and sshd man pages. When using ssh -X it takes care of defining the DISPLAY and sending the X11 images to your screen. Defining DISPLY directly generally won't work (that is how you do it with rlogin but not with ssh). Doug Reeder On Jan 3, 2008, at 1:54 AM

Re: [OMPI users] Tracing the library using gdb and xterm

Krishna, If you are using ssh to connect to the second machine you need to be sure that ssh X11 forwarding is enabled and you may need to have mpi use ssh -X or ssh -Y to connect to the second machine. That is how the DISPLAY gets set using ssh. Doug Reeder On Jan 1, 2008, at 8:11 AM

[OMPI users] compiler warnings in openmpi-1.2.5rc2

Hello, The attachment contains a short explanation of a compiler warning using the gcc-4.3.0 compilers from hpc-sourceforge on os x 10.5.1. The warning doesn't occur when using the apple gcc-4.0.1 compilers. This was on a mac /x86 machine. Doug Reeder openmpi.wrn Description: Binary