Re: [OMPI users] Open-mpi running issue and bug

[Ralph Castain]

If you are building from a tarball, you don't need nor want to run autogen. All 
you want to do is run ./configure.

If you attempt to run autogen, you'll have to install all the required tools - 
including an appropriate libtool. Unless you are adding a component to OMPI, 
you're better off not doing so.


On Jan 3, 2013, at 7:19 PM, Edge Edge  wrote:

> Hi,
> 
> When I issue the following command as shown in the info listed 
> (http://www.open-mpi.org/community/help/):
> [home@edge openmpi-1.6.3]$mpirun --bynode --hostfile my_hostfile.txt 
> --tag-output ompi_info -v ompi full --parsable 
> [home@edge openmpi-1.6.3]$ 
> --
> It looks like opal_init failed for some reason; your parallel process is
> likely to abort.  There are many reasons that a parallel process can
> fail during opal_init; some of which are due to configuration or
> environment problems.  This failure appears to be an internal failure;
> here's some additional information (which may only be relevant to an
> Open MPI developer):
> 
>   opal_shmem_base_select failed
>   --> Returned value -1 instead of OPAL_SUCCESS
> --
> [home@edge:77658] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file 
> runtime/orte_init.c at line 79
> [home@edge:77658] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file orterun.c 
> at line 694
> 
> I was downloading "openmpi-1.6.3".
> If I issue the following command in order to install openmpi-1.6.3.
> It gives me the following log info after I issue, ./autogen.sh
> log file:
> *** Running GNU tools
> [Running] autom4te --language=m4sh ompi_get_version.m4sh -o 
> ompi_get_version.sh
> [Running] libtoolize --automake --copy --ltdl
> 
> -
> It seems that the execution of "libtoolize --automake --copy --ltdl" has 
> failed.  See above for
> the specific error message that caused it to abort.
> -
> 
> error log file:
> configure.in:2125: installing `confdb/config.guess'
> configure.in:2125: installing `confdb/config.sub'
> configure.in:210: installing `confdb/install-sh'
> configure.in:210: installing `confdb/missing'
> adio/ad_bgl/Makefile.am: installing `confdb/depcomp'
> configure.in:96: installing `config/compile'
> configure.in:34: installing `config/config.guess'
> configure.in:34: installing `config/config.sub'
> configure.in:8: installing `config/install-sh'
> configure.in:8: installing `config/missing'
> rfg/Makefile.am: installing `config/depcomp'
> configure.in:10: installing `config/config.guess'
> configure.in:10: installing `config/config.sub'
> configure.in:11: installing `config/install-sh'
> configure.in:11: installing `config/missing'
> otfauxlib/Makefile.am: installing `config/depcomp'
> libtoolize: `COPYING.LIB' not found in `/usr/share/libtool/libltdl'
> 
> Thanks and looking forward to hear from you.
> 
> best regards
> Edge
> 
> From: Jeff Squyres (jsquyres) 
> To: Open MPI Users  
> Cc: Edge Edge  
> Sent: Sunday, December 30, 2012 2:07 AM
> Subject: Re: [OMPI users] Open-mpi running issue and bug
> 
> Please sent all the info listed here:
> 
> http://www.open-mpi.org/community/help/
> 
> 
> On Dec 28, 2012, at 11:42 AM, Ralph Castain 
> wrote:
> 
> > What version of OMPI are you using? How was it configured?
> > 
> > 
> > On Dec 28, 2012, at 2:16 AM, Edge Edge  wrote:
> > 
> >> Hi,
> >> 
> >> Currently I was trying to run mpirun to improve the performance of my 
> >> running.
> >> However it keeps on showing the following bug:
> >> 
> >> --
> >> It looks like opal_init failed for some reason; your parallel process is
> >> likely to abort.  There are many reasons that a parallel process can
> >> fail during opal_init; some of which are due to configuration or
> >> environment problems.  This failure appears to be an internal failure;
> >> here's some additional information (which may only be relevant to an
> >> Open MPI developer):
> >> 
> >>  opal_shmem_base_select failed
> >>  --> Returned value -1 instead of OPAL_SUCCESS
> >> --
> >> [home:07059] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file 
> >> runtime/orte_init.c at line 79
> >> [home:07059] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file orterun.c 
> >> at line 694
> >> make: *** [sample-1.fa] Error 255
> >> 
> >> Can I know how to solve this bug?
> >> I got try to google around but I still fail to find related answer.
> >> 
> >> Below is the spec of my server:
> >> Linux home 2.6.32-71.el6.x86_64 #1 SMP Wed Sep 1 01:33:01 EDT 2010 x86_64 
> >> x86_64 x86_64 GNU/Linux
> >> 
> >> 

[hwloc-users] "-lnuma" missing from pkg-config information?

[Erik Schnetter]

I just installed hwloc 1.6 on a Linux Red Hat system. libnuma is required
for linking -- I receive linker errors if I omit -lnuma, and I see that
-lnuma is listed in libhwloc.la under "dependency_libs". However,
pkgconfig/hwloc.pc does not mention libnuma. It does mention libpci, though.

Does this sound like an error when hwloc.pc is generated, or am I
misunderstanding how pkg-config works? If you give me a pointer, I'd be
happy to try an provide a patch.

-erik


-- 
Erik Schnetter 
http://www.perimeterinstitute.ca/personal/eschnetter/

Re: [OMPI users] Open-mpi running issue and bug

[Edge Edge]

Hi,

When I issue the following command as shown in the info listed 
(http://www.open-mpi.org/community/help/):
[home@edge openmpi-1.6.3]$mpirun --bynode --hostfile my_hostfile.txt 
--tag-output ompi_info -v ompi full --parsable 
[home@edge openmpi-1.6.3]$ 
--

It looks like opal_init failed for some reason; your parallel process is
likely to abort.  There are many reasons that a parallel process can
fail during opal_init; some of which are due to configuration or
environment problems.  This failure appears to be an internal failure;
here's some additional information (which may only be relevant to an
Open MPI developer):

  opal_shmem_base_select failed
  --> Returned value -1 instead of OPAL_SUCCESS
--
[home@edge:77658] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file 
runtime/orte_init.c at line 79
[home@edge:77658] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file orterun.c 
at line 694

I was downloading "openmpi-1.6.3".
If I issue the following command in order to install openmpi-1.6.3.
It gives me the following log info after I issue, ./autogen.sh
log file:
*** Running GNU tools
[Running] autom4te --language=m4sh ompi_get_version.m4sh -o ompi_get_version.sh
[Running] libtoolize --automake --copy --ltdl

-
It seems that the execution of "libtoolize --automake --copy --ltdl" has 
failed.  See above for
the specific error message that caused it to abort.
-


error log file:
configure.in:2125: installing `confdb/config.guess'
configure.in:2125: installing `confdb/config.sub'
configure.in:210: installing `confdb/install-sh'
configure.in:210: installing `confdb/missing'
adio/ad_bgl/Makefile.am: installing `confdb/depcomp'
configure.in:96: installing `config/compile'
configure.in:34: installing `config/config.guess'
configure.in:34: installing `config/config.sub'
configure.in:8: installing `config/install-sh'
configure.in:8: installing `config/missing'
rfg/Makefile.am: installing `config/depcomp'
configure.in:10: installing `config/config.guess'
configure.in:10: installing `config/config.sub'
configure.in:11: installing `config/install-sh'
configure.in:11: installing `config/missing'
otfauxlib/Makefile.am: installing `config/depcomp'
libtoolize: `COPYING.LIB' not found in `/usr/share/libtool/libltdl'

Thanks and looking forward to hear from you.

best regards
Edge



 From: Jeff Squyres (jsquyres) 
To: Open MPI Users  
Cc: Edge Edge  
Sent: Sunday, December 30, 2012 2:07 AM
Subject: Re: [OMPI users] Open-mpi running issue and bug
 
Please sent all the info listed here:

    http://www.open-mpi.org/community/help/


On Dec 28, 2012, at 11:42 AM, Ralph Castain 
wrote:

> What version of OMPI are you using? How was it configured?
> 
> 
> On Dec 28, 2012, at 2:16 AM, Edge Edge  wrote:
> 
>> Hi,
>> 
>> Currently I was trying to run mpirun to improve the performance of my 
>> running.
>> However it keeps on showing the following bug:
>> 
>> --
>> It looks like opal_init failed for some reason; your parallel process is
>> likely to abort.  There are many reasons that a parallel process can
>> fail during opal_init; some of which are due to configuration or
>> environment problems.  This failure appears to be an internal failure;
>> here's some additional information (which may only be relevant to an
>> Open MPI developer):
>> 
>>   opal_shmem_base_select failed
>>   --> Returned value -1 instead of OPAL_SUCCESS
>> --
>> [home:07059] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file 
>> runtime/orte_init.c at line 79
>> [home:07059] [[INVALID],INVALID] ORTE_ERROR_LOG: Error in file orterun.c at 
>> line 694
>> make: *** [sample-1.fa] Error 255
>> 
>> Can I know how to solve this bug?
>> I got try to google around but I still fail to find related answer.
>> 
>> Below is the spec of my server:
>> Linux home 2.6.32-71.el6.x86_64 #1 SMP Wed Sep 1 01:33:01 EDT 2010 x86_64 
>> x86_64 x86_64 GNU/Linux
>> 
>> Hope it is useful for you in order to solve the bug.
>> 
>> Thanks.
>> 
>> 
>> best regards
>> Edge
>> 
>> 
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

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

[Chuck Yahoo]

It's nice to see that this mail list has a lot of activity !

Thanks for the tips, I haven't used modules in quite a few years, having been 
spoiled by Java ;-)

Takes me back to the good old days, spending 10x more time configuring than 
coding !

Chuck

On Jan 3, 2013, at 1:05 PM, Ralph Castain  wrote:

> FWIW: I test it regularly on Mountain Lion, without problem. We know that 
> some of the bindings aren't quite right, particularly on some of the 
> collectives, but send/recv is fine
> 
> 
> On Jan 3, 2013, at 10:09 AM, "Beatty, Daniel D CIV NAVAIR, 474300D" 
>  wrote:
> 
>> Greetings Chuck, 
>> I tend to agree with Doug.  It hope to be able to test soon OpenMPI under 
>> Lion/Mountain Lion.  If someone has already done so, especially with Java, 
>> that could be quite handy.
>> 
>> V/R,
>> 
>> Daniel Beatty, Ph.D.
>> Computer Scientist, Detonation Sciences Branch
>> Code 474300D
>> 1 Administration Circle M/S 1109
>> China Lake, CA 93555
>> daniel.bea...@navy.mil
>> (LandLine) (760)939-7097 
>> (iPhone) (806)438-6620
>> 
>>  
>> 
>> 
>> On 1/3/13 9:49 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  wrote:
>> 
>> 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, 2013, at 9:22 AM, Chuck Mosher wrote:
>> 
>> Hi,
>> 
>> I've been trying to get a working version of the MPI java bindings on Mac 
>> OSX (10.6.8 with Java 1.6.0_37).
>> 
>> I ran into a number of issues along the way that I thought I would record 
>> here for others who might be foolish enough to try the same ;-)
>> 
>> The issues I had to spend time with were:
>> 
>> 1. Installing a C compiler that can run from the command line
>> 2. Finding and installing an appropriate Java JDK for my OS version
>> 3. Building and installing OpenMPI for the first time on a Mac
>> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed 
>> already on my Mac
>> 5. Figuring out syntax for using the mpirun command line to run java
>> 6. Odd behavior when trying to use "localhost" or the output from `hostname` 
>> on the command line or in a hostfile
>> 
>> Resolution for each of these in order:
>> 
>> 1. Installing a C compiler for the command line
>> Found a good resource here:
>> http://www.macobserver.com/tmo/article/install_the_command_line_c_compilers_in_os_x_lion
>>  
>> 
>>  
>> The solution is to install XCode, then enable command line compilers from 
>> the XCode console.
>> 
>> 2. Finding and installing an appropriate Java JDK for my OS version
>> Used this resource to eventually figure out what to do:
>> http://www.wikihow.com/Install-the-JDK-(Java-Development-Kit)-on-Mac-OS-X 
>>  
>> It didn't exactly match my setup, but had enough clues.
>> The solution is to first find your java version (java -version, 1.6.0_37 in 
>> my case) and then match that version number to the Apple Java update version 
>> (11 in my case). 
>> The key document is:
>> http://developer.apple.com/library/mac/#technotes/tn2002/tn2110.html
>> Which is a table relating java version numbers to the appropriate "Java for 
>> Mac OS X xx.x Update xx".
>> Once you know the update number, you can download the JDK installer from
>> https://developer.apple.com/downloads/index.action
>> where you of course have to have an Apple developer ID to access.
>> Enter "java" in the search bar on the left and find the matching java 
>> update, and you're good to go.
>> 
>> 3. Building and installing OpenMPI for the first time on a Mac
>> After the usual false starts with a new installation on a new OS, I managed 
>> to get a working build of openmpi-1.7rc5 with Java bindings.
>> I could only find the java bindings in the 1.7 pre-release.
>> I used the defaults as much as possible. 
>> 
>> After downloading from:
>> http://www.open-mpi.org/software/ompi/v1.7/
>> and unarchiving to Downloads, open a Terminal window.
>> 
>> cd Downloads/openmpi-1.7rc5
>> ./configure --enable-java --prefix=/usr/local
>> make all
>> sudo make install
>> 
>> Verify that you can run the commands and examples:
>> 
>> chuck-> /usr/local/bin/mpirun -version
>> mpirun (Open MPI) 1.7rc5
>> 
>> chuck-> cd examples
>> chuck-> make
>> chuck-> /usr/local/bin/mpirun -np 2 hello_c
>> Hello, world, I am 0 of 2, (Open MPI v1.7rc5, package: Open MPI 
>> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
>> Hello, world, I am 1 of 2, (Open MPI v1.7rc5, 

[hwloc-users] Single hwloc.h header files that work on linux and windows

[Rolf vandeVaart]

I have an application is supposed to work with both windows and linux.  To that 
end, I downloaded hwloc, configured and then included the hwloc header files in 
my application.  I dynamically load the libhwloc.so library and map the 
functions I need.  If libhwloc.so is not there, then I can still run but give a 
warning.  However, I have run into a problem.  hwloc.h includes a whole bunch 
of other headers, one of which is config.h.  And config.h is specific to how 
the library was configured.  Therefore, when I attempt to compile my 
application on windows, I get an error about missing pthread.h file.  This is 
probably one of many differences.

Is there a special hwloc.h and supporting headers that is system independent so 
I can include them and build on both windows and linux?  Or do I need to have 
two different sets of header files, one for linux and one for windows?   
Perhaps I just need a config.h for windows and one for linux and select them at 
build time.

Rolf

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

[Ralph Castain]

FWIW: I test it regularly on Mountain Lion, without problem. We know that some 
of the bindings aren't quite right, particularly on some of the collectives, 
but send/recv is fine


On Jan 3, 2013, at 10:09 AM, "Beatty, Daniel D CIV NAVAIR, 474300D" 
 wrote:

> Greetings Chuck, 
> I tend to agree with Doug.  It hope to be able to test soon OpenMPI under 
> Lion/Mountain Lion.  If someone has already done so, especially with Java, 
> that could be quite handy.
> 
> V/R,
> 
> Daniel Beatty, Ph.D.
> Computer Scientist, Detonation Sciences Branch
> Code 474300D
> 1 Administration Circle M/S 1109
> China Lake, CA 93555
> daniel.bea...@navy.mil
> (LandLine) (760)939-7097 
> (iPhone) (806)438-6620
> 
>  
> 
> 
> On 1/3/13 9:49 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  wrote:
> 
> 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, 2013, at 9:22 AM, Chuck Mosher wrote:
> 
> Hi,
> 
> I've been trying to get a working version of the MPI java bindings on Mac OSX 
> (10.6.8 with Java 1.6.0_37).
> 
> I ran into a number of issues along the way that I thought I would record 
> here for others who might be foolish enough to try the same ;-)
> 
> The issues I had to spend time with were:
> 
> 1. Installing a C compiler that can run from the command line
> 2. Finding and installing an appropriate Java JDK for my OS version
> 3. Building and installing OpenMPI for the first time on a Mac
> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed 
> already on my Mac
> 5. Figuring out syntax for using the mpirun command line to run java
> 6. Odd behavior when trying to use "localhost" or the output from `hostname` 
> on the command line or in a hostfile
> 
> Resolution for each of these in order:
> 
> 1. Installing a C compiler for the command line
> Found a good resource here:
> http://www.macobserver.com/tmo/article/install_the_command_line_c_compilers_in_os_x_lion
>  
> 
>  
> The solution is to install XCode, then enable command line compilers from the 
> XCode console.
> 
> 2. Finding and installing an appropriate Java JDK for my OS version
> Used this resource to eventually figure out what to do:
> http://www.wikihow.com/Install-the-JDK-(Java-Development-Kit)-on-Mac-OS-X 
>  
> It didn't exactly match my setup, but had enough clues.
> The solution is to first find your java version (java -version, 1.6.0_37 in 
> my case) and then match that version number to the Apple Java update version 
> (11 in my case). 
> The key document is:
> http://developer.apple.com/library/mac/#technotes/tn2002/tn2110.html
> Which is a table relating java version numbers to the appropriate "Java for 
> Mac OS X xx.x Update xx".
> Once you know the update number, you can download the JDK installer from
> https://developer.apple.com/downloads/index.action
> where you of course have to have an Apple developer ID to access.
> Enter "java" in the search bar on the left and find the matching java update, 
> and you're good to go.
> 
> 3. Building and installing OpenMPI for the first time on a Mac
> After the usual false starts with a new installation on a new OS, I managed 
> to get a working build of openmpi-1.7rc5 with Java bindings.
> I could only find the java bindings in the 1.7 pre-release.
> I used the defaults as much as possible. 
> 
> After downloading from:
> http://www.open-mpi.org/software/ompi/v1.7/
> and unarchiving to Downloads, open a Terminal window.
> 
> cd Downloads/openmpi-1.7rc5
> ./configure --enable-java --prefix=/usr/local
> make all
> sudo make install
> 
> Verify that you can run the commands and examples:
> 
> chuck-> /usr/local/bin/mpirun -version
> mpirun (Open MPI) 1.7rc5
> 
> chuck-> cd examples
> chuck-> make
> chuck-> /usr/local/bin/mpirun -np 2 hello_c
> Hello, world, I am 0 of 2, (Open MPI v1.7rc5, package: Open MPI 
> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
> Hello, world, I am 1 of 2, (Open MPI v1.7rc5, package: Open MPI 
> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
> 
> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed 
> already on my Mac
> OpenMPI Version 1.2.8 was already installed for my OS in /usr/bin
> So, if you accidentally type:
> 
> chuck-> mpirun -np 2 hello_c
> --
> A requested component was not found, or was unable 

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

[Beatty, Daniel D CIV NAVAIR, 474300D]

Greetings Chuck, 
I tend to agree with Doug.  It hope to be able to test soon OpenMPI under
Lion/Mountain Lion.  If someone has already done so, especially with Java,
that could be quite handy.

V/R,

Daniel Beatty, Ph.D.
Computer Scientist, Detonation Sciences Branch
Code 474300D
1 Administration Circle M/S 1109
China Lake, CA 93555
daniel.bea...@navy.mil
(LandLine) (760)939-7097
(iPhone) (806)438-6620




On 1/3/13 9:49 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  wrote:
> 
>> 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, 2013, at 9:22 AM, Chuck Mosher wrote:
>> 
>>> Hi,
>>> 
>>> I've been trying to get a working version of the MPI java bindings on Mac
>>> OSX (10.6.8 with Java 1.6.0_37).
>>> 
>>> I ran into a number of issues along the way that I thought I would record
>>> here for others who might be foolish enough to try the same ;-)
>>> 
>>> The issues I had to spend time with were:
>>> 
>>> 1. Installing a C compiler that can run from the command line
>>> 2. Finding and installing an appropriate Java JDK for my OS version
>>> 3. Building and installing OpenMPI for the first time on a Mac
>>> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed
>>> already on my Mac
>>> 5. Figuring out syntax for using the mpirun command line to run java
>>> 6. Odd behavior when trying to use "localhost" or the output from `hostname`
>>> on the command line or in a hostfile
>>> 
>>> Resolution for each of these in order:
>>> 
>>> 1. Installing a C compiler for the command line
>>> Found a good resource here:
>>> http://www.macobserver.com/tmo/article/install_the_command_line_c_compilers_
>>> in_os_x_lion 
>>> >> _in_os_x_lion> 
>>> The solution is to install XCode, then enable command line compilers from
>>> the XCode console.
>>> 
>>> 2. Finding and installing an appropriate Java JDK for my OS version
>>> Used this resource to eventually figure out what to do:
>>> http://www.wikihow.com/Install-the-JDK-(Java-Development-Kit)-on-Mac-OS-X
>>> 
>>> It didn't exactly match my setup, but had enough clues.
>>> The solution is to first find your java version (java -version, 1.6.0_37 in
>>> my case) and then match that version number to the Apple Java update version
>>> (11 in my case).
>>> The key document is:
>>> http://developer.apple.com/library/mac/#technotes/tn2002/tn2110.html
>>> Which is a table relating java version numbers to the appropriate "Java for
>>> Mac OS X xx.x Update xx".
>>> Once you know the update number, you can download the JDK installer from
>>> https://developer.apple.com/downloads/index.action
>>> where you of course have to have an Apple developer ID to access.
>>> Enter "java" in the search bar on the left and find the matching java
>>> update, and you're good to go.
>>> 
>>> 3. Building and installing OpenMPI for the first time on a Mac
>>> After the usual false starts with a new installation on a new OS, I managed
>>> to get a working build of openmpi-1.7rc5 with Java bindings.
>>> I could only find the java bindings in the 1.7 pre-release.
>>> I used the defaults as much as possible.
>>> 
>>> After downloading from:
>>> http://www.open-mpi.org/software/ompi/v1.7/
>>> and unarchiving to Downloads, open a Terminal window.
>>> 
>>> cd Downloads/openmpi-1.7rc5
>>> ./configure --enable-java --prefix=/usr/local
>>> make all
>>> sudo make install
>>> 
>>> Verify that you can run the commands and examples:
>>> 
>>> chuck-> /usr/local/bin/mpirun -version
>>> mpirun (Open MPI) 1.7rc5
>>> 
>>> chuck-> cd examples
>>> chuck-> make
>>> chuck-> /usr/local/bin/mpirun -np 2 hello_c
>>> Hello, world, I am 0 of 2, (Open MPI v1.7rc5, package: Open MPI
>>> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
>>> Hello, world, I am 1 of 2, (Open MPI v1.7rc5, package: Open MPI
>>> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
>>> 
>>> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed
>>> already on my Mac
>>> OpenMPI Version 1.2.8 was already installed for my OS in /usr/bin
>>> So, if you accidentally type:
>>> 
>>> chuck-> mpirun -np 2 hello_c
>>> --
>>> A requested component was not found, or was unable to be opened
>>> ...
>>> 
>>> you picked up the wrong "mpirun" and you will get a bunch of error output
>>> complaining about sockets or mis-matched shared library 

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

[Doug Reeder]

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  wrote:
> 
>> 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, 2013, at 9:22 AM, Chuck Mosher wrote:
>> 
>>> ___
>>> users mailing list
>>> us...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> 
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

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

[Ralph Castain]

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  wrote:

> 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, 2013, at 9:22 AM, Chuck Mosher wrote:
> 
>> Hi,
>> 
>> I've been trying to get a working version of the MPI java bindings on Mac 
>> OSX (10.6.8 with Java 1.6.0_37).
>> 
>> I ran into a number of issues along the way that I thought I would record 
>> here for others who might be foolish enough to try the same ;-)
>> 
>> The issues I had to spend time with were:
>> 
>> 1. Installing a C compiler that can run from the command line
>> 2. Finding and installing an appropriate Java JDK for my OS version
>> 3. Building and installing OpenMPI for the first time on a Mac
>> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed 
>> already on my Mac
>> 5. Figuring out syntax for using the mpirun command line to run java
>> 6. Odd behavior when trying to use "localhost" or the output from `hostname` 
>> on the command line or in a hostfile
>> 
>> Resolution for each of these in order:
>> 
>> 1. Installing a C compiler for the command line
>> Found a good resource here:
>> http://www.macobserver.com/tmo/article/install_the_command_line_c_compilers_in_os_x_lion
>> The solution is to install XCode, then enable command line compilers from 
>> the XCode console.
>> 
>> 2. Finding and installing an appropriate Java JDK for my OS version
>> Used this resource to eventually figure out what to do:
>> http://www.wikihow.com/Install-the-JDK-(Java-Development-Kit)-on-Mac-OS-X
>> It didn't exactly match my setup, but had enough clues.
>> The solution is to first find your java version (java -version, 1.6.0_37 in 
>> my case) and then match that version number to the Apple Java update version 
>> (11 in my case). 
>> The key document is:
>> http://developer.apple.com/library/mac/#technotes/tn2002/tn2110.html
>> Which is a table relating java version numbers to the appropriate "Java for 
>> Mac OS X xx.x Update xx".
>> Once you know the update number, you can download the JDK installer from
>> https://developer.apple.com/downloads/index.action
>> where you of course have to have an Apple developer ID to access.
>> Enter "java" in the search bar on the left and find the matching java 
>> update, and you're good to go.
>> 
>> 3. Building and installing OpenMPI for the first time on a Mac
>> After the usual false starts with a new installation on a new OS, I managed 
>> to get a working build of openmpi-1.7rc5 with Java bindings.
>> I could only find the java bindings in the 1.7 pre-release.
>> I used the defaults as much as possible. 
>> 
>> After downloading from:
>> http://www.open-mpi.org/software/ompi/v1.7/
>> and unarchiving to Downloads, open a Terminal window.
>> 
>> cd Downloads/openmpi-1.7rc5
>> ./configure --enable-java --prefix=/usr/local
>> make all
>> sudo make install
>> 
>> Verify that you can run the commands and examples:
>> 
>> chuck-> /usr/local/bin/mpirun -version
>> mpirun (Open MPI) 1.7rc5
>> 
>> chuck-> cd examples
>> chuck-> make
>> chuck-> /usr/local/bin/mpirun -np 2 hello_c
>> Hello, world, I am 0 of 2, (Open MPI v1.7rc5, package: Open MPI 
>> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
>> Hello, world, I am 1 of 2, (Open MPI v1.7rc5, package: Open MPI 
>> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
>> 
>> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed 
>> already on my Mac
>> OpenMPI Version 1.2.8 was already installed for my OS in /usr/bin
>> So, if you accidentally type:
>> 
>> chuck-> mpirun -np 2 hello_c
>> --
>> A requested component was not found, or was unable to be opened
>> ...
>> 
>> you picked up the wrong "mpirun" and you will get a bunch of error output 
>> complaining about sockets or mis-matched shared library versions.
>> 
>> I dealt with this moving the existing OpenMPI related commands to a 
>> subdirectory, and then created symbolic links from /usr/local/bin to 
>> /usr/bin for the commands I needed.
>> 
>> 5. Figuring out syntax for using the mpirun command line to run java
>> First be sure you can run Java
>> 
>> chuck-> /usr/bin/java -version
>> java version "1.6.0_37"
>> Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)
>> Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)
>> 
>> Then be sure you can run your java class from the command line as well. To 
>> figure this out I created a couple of simple java files in a temp directory:
>> 
>> chuck-> cd ~/tmp
>> chuck-> mkdir classes
>> chuck -> cat HelloWorld.java
>> 

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

[Doug Reeder]

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, 2013, at 9:22 AM, Chuck Mosher wrote:

> Hi,
> 
> I've been trying to get a working version of the MPI java bindings on Mac OSX 
> (10.6.8 with Java 1.6.0_37).
> 
> I ran into a number of issues along the way that I thought I would record 
> here for others who might be foolish enough to try the same ;-)
> 
> The issues I had to spend time with were:
> 
> 1. Installing a C compiler that can run from the command line
> 2. Finding and installing an appropriate Java JDK for my OS version
> 3. Building and installing OpenMPI for the first time on a Mac
> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed 
> already on my Mac
> 5. Figuring out syntax for using the mpirun command line to run java
> 6. Odd behavior when trying to use "localhost" or the output from `hostname` 
> on the command line or in a hostfile
> 
> Resolution for each of these in order:
> 
> 1. Installing a C compiler for the command line
> Found a good resource here:
> http://www.macobserver.com/tmo/article/install_the_command_line_c_compilers_in_os_x_lion
> The solution is to install XCode, then enable command line compilers from the 
> XCode console.
> 
> 2. Finding and installing an appropriate Java JDK for my OS version
> Used this resource to eventually figure out what to do:
> http://www.wikihow.com/Install-the-JDK-(Java-Development-Kit)-on-Mac-OS-X
> It didn't exactly match my setup, but had enough clues.
> The solution is to first find your java version (java -version, 1.6.0_37 in 
> my case) and then match that version number to the Apple Java update version 
> (11 in my case). 
> The key document is:
> http://developer.apple.com/library/mac/#technotes/tn2002/tn2110.html
> Which is a table relating java version numbers to the appropriate "Java for 
> Mac OS X xx.x Update xx".
> Once you know the update number, you can download the JDK installer from
> https://developer.apple.com/downloads/index.action
> where you of course have to have an Apple developer ID to access.
> Enter "java" in the search bar on the left and find the matching java update, 
> and you're good to go.
> 
> 3. Building and installing OpenMPI for the first time on a Mac
> After the usual false starts with a new installation on a new OS, I managed 
> to get a working build of openmpi-1.7rc5 with Java bindings.
> I could only find the java bindings in the 1.7 pre-release.
> I used the defaults as much as possible. 
> 
> After downloading from:
> http://www.open-mpi.org/software/ompi/v1.7/
> and unarchiving to Downloads, open a Terminal window.
> 
> cd Downloads/openmpi-1.7rc5
> ./configure --enable-java --prefix=/usr/local
> make all
> sudo make install
> 
> Verify that you can run the commands and examples:
> 
> chuck-> /usr/local/bin/mpirun -version
> mpirun (Open MPI) 1.7rc5
> 
> chuck-> cd examples
> chuck-> make
> chuck-> /usr/local/bin/mpirun -np 2 hello_c
> Hello, world, I am 0 of 2, (Open MPI v1.7rc5, package: Open MPI 
> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
> Hello, world, I am 1 of 2, (Open MPI v1.7rc5, package: Open MPI 
> chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
> 
> 4. Conflicts with the existing OpenMPI version 1.2.8 that was installed 
> already on my Mac
> OpenMPI Version 1.2.8 was already installed for my OS in /usr/bin
> So, if you accidentally type:
> 
> chuck-> mpirun -np 2 hello_c
> --
> A requested component was not found, or was unable to be opened
> ...
> 
> you picked up the wrong "mpirun" and you will get a bunch of error output 
> complaining about sockets or mis-matched shared library versions.
> 
> I dealt with this moving the existing OpenMPI related commands to a 
> subdirectory, and then created symbolic links from /usr/local/bin to /usr/bin 
> for the commands I needed.
> 
> 5. Figuring out syntax for using the mpirun command line to run java
> First be sure you can run Java
> 
> chuck-> /usr/bin/java -version
> java version "1.6.0_37"
> Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)
> Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)
> 
> Then be sure you can run your java class from the command line as well. To 
> figure this out I created a couple of simple java files in a temp directory:
> 
> chuck-> cd ~/tmp
> chuck-> mkdir classes
> chuck -> cat HelloWorld.java
> 
> public class HelloWorld {
>   public static void main(String[] args) {
> System.out.println("Hello World, from Java !");
>   }
> }
> 
> chuck-> javac -d classes HelloWorld.java
> chuck-> java -cp ./classes HelloWorld
> 
> Hello World, from Java !
> 
> No sense going further 

[OMPI users] MPI Java Bindings on Mac OSX

[Chuck Mosher]

Hi,

I've been trying to get a working version of the MPI java bindings on Mac OSX 
(10.6.8 with Java 1.6.0_37).

I ran into a number of issues along the way that I thought I would record here 
for others who might be foolish enough to try the same ;-)

The issues I had to spend time with were:

1. Installing a C compiler that can run from the command line2. Finding and 
installing an appropriate Java JDK for my OS version
3. Building and installing OpenMPI for the first time on a Mac
4. Conflicts with the existing OpenMPI version 1.2.8 that was installed already 
on my Mac
5. Figuring out syntax for using the mpirun command line to run java
6. Odd behavior when trying to use "localhost" or the output from `hostname` on 
the command line or in a hostfile

Resolution for each of these in order:

1. Installing a C compiler for the command line
Found a good resource here:
http://www.macobserver.com/tmo/article/install_the_command_line_c_compilers_in_os_x_lion

The solution is to install XCode, then enable command line compilers from the 
XCode console.

2. Finding and installing an appropriate Java JDK for my OS version

Used this resource to eventually figure out what to do:
http://www.wikihow.com/Install-the-JDK-(Java-Development-Kit)-on-Mac-OS-X

It didn't exactly match my setup, but had enough clues.
The solution is to first find your java version (java -version, 1.6.0_37 in my 
case) and then match that version number to the Apple Java update version (11 
in my case). 
The key document is:
http://developer.apple.com/library/mac/#technotes/tn2002/tn2110.html

Which is a table relating java version numbers to the appropriate "Java for Mac 
OS X xx.x Update xx".
Once you know the update number, you can download the JDK installer from
https://developer.apple.com/downloads/index.action

where you of course have to have an Apple developer ID to access.
Enter "java" in the search bar on the left and find the matching java update, 
and you're good to go.

3. Building and installing OpenMPI for the first time on a Mac

After the usual false starts with a new installation on a new OS, I managed to 
get a working build of openmpi-1.7rc5 with Java bindings.
I could only find the java bindings in the 1.7 pre-release.
I used the defaults as much as possible. 

After downloading from:
http://www.open-mpi.org/software/ompi/v1.7/

and unarchiving to Downloads, open a Terminal window.

cd Downloads/openmpi-1.7rc5
./configure --enable-java --prefix=/usr/local
make all
sudo make install

Verify that you can run the commands and examples:

chuck-> /usr/local/bin/mpirun -version
mpirun (Open MPI) 1.7rc5

chuck-> cd examples
chuck-> make
chuck-> /usr/local/bin/mpirun -np 2 hello_c
Hello, world, I am 0 of 2, (Open MPI v1.7rc5, package: Open MPI 
chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)
Hello, world, I am 1 of 2, (Open MPI v1.7rc5, package: Open MPI 
chuck@chucks-iMac.local Distribution, ident: 1.7rc5, Oct 30, 2012, 111)

4. Conflicts with the existing OpenMPI version 1.2.8 that was installed already 
on my Mac

OpenMPI Version 1.2.8 was already installed for my OS in /usr/bin
So, if you accidentally type:

chuck-> mpirun -np 2 hello_c
--
A requested component was not found, or was unable to be opened
...

you picked up the wrong "mpirun" and you will get a bunch of error output 
complaining about sockets or mis-matched shared library versions.

I dealt with this moving the existing OpenMPI related commands to a 
subdirectory, and then created symbolic links from /usr/local/bin to /usr/bin 
for the commands I needed.

5. Figuring out syntax for using the mpirun command line to run java

First be sure you can run Java

chuck-> /usr/bin/java -version
java version "1.6.0_37"
Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)

Then be sure you can run your java class from the command line as well. To 
figure this out I created a couple of simple java files in a temp directory:

chuck-> cd ~/tmp
chuck-> mkdir classes
chuck -> cat HelloWorld.java

public class HelloWorld {
  public static void main(String[] args) {
    System.out.println("Hello World, from Java !");
  }
}

chuck-> javac -d classes HelloWorld.java
chuck-> java -cp ./classes HelloWorld

Hello World, from Java !

No sense going further until you can get the code above to run.
If you have that working, then you can try the MPI version of HelloWorld:

chuck-> cat HelloWorldMPI.java

import mpi.*;
class HelloWorldMPI {
  public static void main(String[] args) throws MPIException {
    MPI.Init(args);
    System.out.println("Hello world from rank " + 
      MPI.COMM_WORLD.Rank() + " of " +
      MPI.COMM_WORLD.Size() );
    MPI.Finalize();
  }
}

chuck-> /usr/local/bin/mpijavac -d classes HelloWorldMPI.java

/usr/local/bin/mpirun -np 2 /usr/bin/java -cp ./classes HelloWorldMPI

Hello world 

Re: [OMPI users] grpcomm component hier gone...

[Ake Sandgren]

On Thu, 2013-01-03 at 07:14 -0800, Ralph Castain wrote:
> > Well, it isn't :-)
> > configure says:
> > --- MCA component grpcomm:pmi (m4 configuration macro)
> > checking for MCA component grpcomm:pmi compile mode... dso
> > checking if user requested PMI support... no
> > checking if MCA component grpcomm:pmi can compile... no
> 
> Ah - that is the problem. You need to configure 
> --with-pmi=

Ahh thanks. Was assuming i needed something like that.

> > Not sure what you mean here. slurm's pmi module is available (and Intel
> > MPI can use it if i point it to it).
> 
> Yeah, we need to be pointed to it just like Intel.

Doh :-(

> > 
> > Anyway, I think that if there is code that tries to use the hier
> > component it shouldn't have been removed.
> 
> Agreed - it looks like something picked up an unintended change. Just trying 
> to help you work with it as I don't know when a 1.6.4 will occur.

I pulled the 1.6.1 hier component and reran autogen so i have it working
but it's good to know what's to be expected in later releases.

Re: [OMPI users] mpirun - All Nodes Filled

[Chuck Mosher]

Ralph,

Thanks for the response !

If I substitute the output from `hostname` (Chucks-iMac.local) I get the same 
behavior, but using `hostname -s` (Chucks-iMac) all is well.
So, to summarize:

Fails:
mpirun -host localhost -np 1 java -version
mpirun -host `hostname` -np 1 java -version

Succeeds:
mpirun -host `hostname -s` -np 1 java -version

At least I have a fix for now !

Best regards,
Chuck Mosher



 From: Ralph Castain 
To: Chuck Mosher ; Open MPI Users  
Sent: Thursday, January 3, 2013 9:02 AM
Subject: Re: [OMPI users] mpirun - All Nodes Filled
 

Hmmm...I would say there is a bug in 1.7 then! It isn't recognizing the word 
"localhost" as being your local host. I'll take a look at it.

Thanks!


On Jan 3, 2013, at 6:53 AM, Chuck Mosher  wrote:

Simple question for today !
>
>
>I am working on converting a public domain code suite 
>(http://www.JavaSeis.org) to use openmpi rather than mpiJava.
>So far, all has gone well, other than the usual issues with getting all the 
>paths and variables straightened out.
>For automation purposes, I would like to be able to specify everything from 
>the command line, rather than using files.
>
>
>Why does this command work:
>
>
>chuck-> /usr/local/bin/mpirun -np 1 /usr/bin/java -version
>java version "1.6.0_37"
>Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)
>Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)
>
>
>But this one does not:
>
>
>chuck-> /usr/local/bin/mpirun -np 1  -host localhost /usr/bin/java -version
>--
>All nodes which are allocated for this job are already filled.
>--
>
>
>Nor does this one:
>
>
>chuck-> cat hostfile
>localhost slots=2
>
>
>chuck->/usr/local/bin/mpirun -np 1 -hostfile hostfile /usr/bin/java -cp . 
>-version
>--
>All nodes which are allocated for this job are already filled.
>--
>
>
>
>
>For reference:
>
>
>chuck-> /usr/local/bin/mpirun -version
>mpirun (Open MPI) 1.7rc5
>
>
>Report bugs to http://www.open-mpi.org/community/help/
>
>
>chuck-> uname -a
>Darwin iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 PDT 
>2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
>
>
>My build was done with "configure --enable-mpi-java --prefix=/usr/local".
>
>
>Thanks for any insight !
>
>
>Chuck Mosher
>chuckmos...@javaseis.org
>
>___
>users mailing list
>us...@open-mpi.org
>http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] grpcomm component hier gone...

[Ralph Castain]

On Jan 3, 2013, at 7:07 AM, Ake Sandgren  wrote:

> On Thu, 2013-01-03 at 07:00 -0800, Ralph Castain wrote:
>> On Jan 3, 2013, at 6:52 AM, Ake Sandgren  wrote:
>> 
>>> On Thu, 2013-01-03 at 06:18 -0800, Ralph Castain wrote:
 On Jan 3, 2013, at 3:01 AM, Ake Sandgren  wrote:
 
> On Thu, 2013-01-03 at 11:54 +0100, Ake Sandgren wrote:
>> On Thu, 2013-01-03 at 11:15 +0100, Ake Sandgren wrote:
>>> Hi!
>>> 
>>> The grpcomm component hier seems to have vanished between 1.6.1 and
>>> 1.6.3.
>>> Why?
>>> It seems that the version of slurm we are using (not the latest at the
>>> moment) is using it for startup.
 
 It should be using PMI if you are directly launching processes via srun, 
 and should not be using hier any more.
>>> 
>>> Shouldn't the grpcomm pmi component be turned on by default then, if it
>>> is needed?
>> 
>> It should be
> 
> Well, it isn't :-)
> configure says:
> --- MCA component grpcomm:pmi (m4 configuration macro)
> checking for MCA component grpcomm:pmi compile mode... dso
> checking if user requested PMI support... no
> checking if MCA component grpcomm:pmi can compile... no

Ah - that is the problem. You need to configure 
--with-pmi=

> 
>>> So what is the real problem here?
>> 
>> Do you have PMI installed and running on your system? I think that is the 
>> source of the trouble - if PMI isn't running, then this will fail.
> 
> Not sure what you mean here. slurm's pmi module is available (and Intel
> MPI can use it if i point it to it).

Yeah, we need to be pointed to it just like Intel.

> 
> Anyway, I think that if there is code that tries to use the hier
> component it shouldn't have been removed.

Agreed - it looks like something picked up an unintended change. Just trying to 
help you work with it as I don't know when a 1.6.4 will occur.


> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] grpcomm component hier gone...

[Ake Sandgren]

On Thu, 2013-01-03 at 07:00 -0800, Ralph Castain wrote:
> On Jan 3, 2013, at 6:52 AM, Ake Sandgren  wrote:
> 
> > On Thu, 2013-01-03 at 06:18 -0800, Ralph Castain wrote:
> >> On Jan 3, 2013, at 3:01 AM, Ake Sandgren  wrote:
> >> 
> >>> On Thu, 2013-01-03 at 11:54 +0100, Ake Sandgren wrote:
>  On Thu, 2013-01-03 at 11:15 +0100, Ake Sandgren wrote:
> > Hi!
> > 
> > The grpcomm component hier seems to have vanished between 1.6.1 and
> > 1.6.3.
> > Why?
> > It seems that the version of slurm we are using (not the latest at the
> > moment) is using it for startup.
> >> 
> >> It should be using PMI if you are directly launching processes via srun, 
> >> and should not be using hier any more.
> > 
> > Shouldn't the grpcomm pmi component be turned on by default then, if it
> > is needed?
> 
> It should be

Well, it isn't :-)
configure says:
--- MCA component grpcomm:pmi (m4 configuration macro)
checking for MCA component grpcomm:pmi compile mode... dso
checking if user requested PMI support... no
checking if MCA component grpcomm:pmi can compile... no

> > So what is the real problem here?
> 
> Do you have PMI installed and running on your system? I think that is the 
> source of the trouble - if PMI isn't running, then this will fail.

Not sure what you mean here. slurm's pmi module is available (and Intel
MPI can use it if i point it to it).

Anyway, I think that if there is code that tries to use the hier
component it shouldn't have been removed.

Re: [OMPI users] mpirun - All Nodes Filled

[Ralph Castain]

Hmmm...I would say there is a bug in 1.7 then! It isn't recognizing the word 
"localhost" as being your local host. I'll take a look at it.

Thanks!

On Jan 3, 2013, at 6:53 AM, Chuck Mosher  wrote:

> Simple question for today !
> 
> I am working on converting a public domain code suite 
> (http://www.JavaSeis.org) to use openmpi rather than mpiJava.
> So far, all has gone well, other than the usual issues with getting all the 
> paths and variables straightened out.
> For automation purposes, I would like to be able to specify everything from 
> the command line, rather than using files.
> 
> Why does this command work:
> 
> chuck-> /usr/local/bin/mpirun -np 1 /usr/bin/java -version
> java version "1.6.0_37"
> Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)
> Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)
> 
> But this one does not:
> 
> chuck-> /usr/local/bin/mpirun -np 1  -host localhost /usr/bin/java -version
> --
> All nodes which are allocated for this job are already filled.
> --
> 
> Nor does this one:
> 
> chuck-> cat hostfile
> localhost slots=2
> 
> chuck->/usr/local/bin/mpirun -np 1 -hostfile hostfile /usr/bin/java -cp . 
> -version
> --
> All nodes which are allocated for this job are already filled.
> --
> 
> 
> For reference:
> 
> chuck-> /usr/local/bin/mpirun -version
> mpirun (Open MPI) 1.7rc5
> 
> Report bugs to http://www.open-mpi.org/community/help/
> 
> chuck-> uname -a
> Darwin iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 
> PDT 2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64
> 
> My build was done with "configure --enable-mpi-java --prefix=/usr/local".
> 
> Thanks for any insight !
> 
> Chuck Mosher
> chuckmos...@javaseis.org
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] grpcomm component hier gone...

[Ralph Castain]

On Jan 3, 2013, at 6:52 AM, Ake Sandgren  wrote:

> On Thu, 2013-01-03 at 06:18 -0800, Ralph Castain wrote:
>> On Jan 3, 2013, at 3:01 AM, Ake Sandgren  wrote:
>> 
>>> On Thu, 2013-01-03 at 11:54 +0100, Ake Sandgren wrote:
 On Thu, 2013-01-03 at 11:15 +0100, Ake Sandgren wrote:
> Hi!
> 
> The grpcomm component hier seems to have vanished between 1.6.1 and
> 1.6.3.
> Why?
> It seems that the version of slurm we are using (not the latest at the
> moment) is using it for startup.
>> 
>> It should be using PMI if you are directly launching processes via srun, and 
>> should not be using hier any more.
> 
> Shouldn't the grpcomm pmi component be turned on by default then, if it
> is needed?

It should be

> 
> 
 
 Hmm it seems it is the ess_slurmd_module.c that is using grpcomm=hier.
>> 
>> Yes - that is the *only* scenario (a direct launch of procs via srun) that 
>> should use hier
> 
> What i have in my submit file is:
> #SBATCH -n x
> 
> srun some-mpi-binary
> 
> This fails since hier is missing.
> 
> The reason one wants to use srun and not mpirun is getting slurms cgroup
> containement.
> 
>>> 
>>> orte/mca/plm/base/plm_base_rsh_support.c also tries to use the hier
>>> grpcomm
>> 
>> Something is very wrong if that is true. How was this configured, and how 
>> are you starting this job?
> 
> Not sure if it actually tries to use hier at runtime, i just noticed
> that it had a setenv OMPI_MCA_grpcomm=hier in the code.
> 
> So what is the real problem here?

Do you have PMI installed and running on your system? I think that is the 
source of the trouble - if PMI isn't running, then this will fail.


> 
> configure line is:
> ./configure --enable-orterun-prefix-by-default --enable-cxx-exceptions
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

[OMPI users] mpirun - All Nodes Filled

[Chuck Mosher]

Simple question for today !

I am working on converting a public domain code suite (http://www.JavaSeis.org) 
to use openmpi rather than mpiJava.
So far, all has gone well, other than the usual issues with getting all the 
paths and variables straightened out.
For automation purposes, I would like to be able to specify everything from the 
command line, rather than using files.

Why does this command work:

chuck-> /usr/local/bin/mpirun -np 1 /usr/bin/java -version
java version "1.6.0_37"
Java(TM) SE Runtime Environment (build 1.6.0_37-b06-434-10M3909)
Java HotSpot(TM) 64-Bit Server VM (build 20.12-b01-434, mixed mode)

But this one does not:

chuck-> /usr/local/bin/mpirun -np 1  -host localhost /usr/bin/java -version
--
All nodes which are allocated for this job are already filled.
--

Nor does this one:

chuck-> cat hostfile
localhost slots=2

chuck->/usr/local/bin/mpirun -np 1 -hostfile hostfile /usr/bin/java -cp . 
-version
--
All nodes which are allocated for this job are already filled.
--


For reference:

chuck-> /usr/local/bin/mpirun -version
mpirun (Open MPI) 1.7rc5

Report bugs to http://www.open-mpi.org/community/help/

chuck-> uname -a
Darwin iMac.local 10.8.0 Darwin Kernel Version 10.8.0: Tue Jun  7 16:32:41 PDT 
2011; root:xnu-1504.15.3~1/RELEASE_X86_64 x86_64

My build was done with "configure --enable-mpi-java --prefix=/usr/local".

Thanks for any insight !

Chuck Mosher
chuckmos...@javaseis.org

Re: [OMPI users] grpcomm component hier gone...

[Ake Sandgren]

On Thu, 2013-01-03 at 06:18 -0800, Ralph Castain wrote:
> On Jan 3, 2013, at 3:01 AM, Ake Sandgren  wrote:
> 
> > On Thu, 2013-01-03 at 11:54 +0100, Ake Sandgren wrote:
> >> On Thu, 2013-01-03 at 11:15 +0100, Ake Sandgren wrote:
> >>> Hi!
> >>> 
> >>> The grpcomm component hier seems to have vanished between 1.6.1 and
> >>> 1.6.3.
> >>> Why?
> >>> It seems that the version of slurm we are using (not the latest at the
> >>> moment) is using it for startup.
> 
> It should be using PMI if you are directly launching processes via srun, and 
> should not be using hier any more.

Shouldn't the grpcomm pmi component be turned on by default then, if it
is needed?

> >>> 
> >> 
> >> Hmm it seems it is the ess_slurmd_module.c that is using grpcomm=hier.
> 
> Yes - that is the *only* scenario (a direct launch of procs via srun) that 
> should use hier

What i have in my submit file is:
#SBATCH -n x

srun some-mpi-binary

This fails since hier is missing.

The reason one wants to use srun and not mpirun is getting slurms cgroup
containement.

> > 
> > orte/mca/plm/base/plm_base_rsh_support.c also tries to use the hier
> > grpcomm
> 
> Something is very wrong if that is true. How was this configured, and how are 
> you starting this job?

Not sure if it actually tries to use hier at runtime, i just noticed
that it had a setenv OMPI_MCA_grpcomm=hier in the code.

So what is the real problem here?

configure line is:
./configure --enable-orterun-prefix-by-default --enable-cxx-exceptions

Re: [OMPI users] grpcomm component hier gone...

[Ralph Castain]

On Jan 3, 2013, at 3:01 AM, Ake Sandgren  wrote:

> On Thu, 2013-01-03 at 11:54 +0100, Ake Sandgren wrote:
>> On Thu, 2013-01-03 at 11:15 +0100, Ake Sandgren wrote:
>>> Hi!
>>> 
>>> The grpcomm component hier seems to have vanished between 1.6.1 and
>>> 1.6.3.
>>> Why?
>>> It seems that the version of slurm we are using (not the latest at the
>>> moment) is using it for startup.

It should be using PMI if you are directly launching processes via srun, and 
should not be using hier any more.

>>> 
>> 
>> Hmm it seems it is the ess_slurmd_module.c that is using grpcomm=hier.

Yes - that is the *only* scenario (a direct launch of procs via srun) that 
should use hier

> 
> orte/mca/plm/base/plm_base_rsh_support.c also tries to use the hier
> grpcomm

Something is very wrong if that is true. How was this configured, and how are 
you starting this job?


> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] grpcomm component hier gone...

[Ake Sandgren]

On Thu, 2013-01-03 at 11:54 +0100, Ake Sandgren wrote:
> On Thu, 2013-01-03 at 11:15 +0100, Ake Sandgren wrote:
> > Hi!
> > 
> > The grpcomm component hier seems to have vanished between 1.6.1 and
> > 1.6.3.
> > Why?
> > It seems that the version of slurm we are using (not the latest at the
> > moment) is using it for startup.
> > 
> 
> Hmm it seems it is the ess_slurmd_module.c that is using grpcomm=hier.

orte/mca/plm/base/plm_base_rsh_support.c also tries to use the hier
grpcomm

Re: [OMPI users] grpcomm component hier gone...

[Ake Sandgren]

On Thu, 2013-01-03 at 11:15 +0100, Ake Sandgren wrote:
> Hi!
> 
> The grpcomm component hier seems to have vanished between 1.6.1 and
> 1.6.3.
> Why?
> It seems that the version of slurm we are using (not the latest at the
> moment) is using it for startup.
> 

Hmm it seems it is the ess_slurmd_module.c that is using grpcomm=hier.

Please fix :-)

[OMPI users] grpcomm component hier gone...

[Ake Sandgren]

Hi!

The grpcomm component hier seems to have vanished between 1.6.1 and
1.6.3.
Why?
It seems that the version of slurm we are using (not the latest at the
moment) is using it for startup.

-- 
Ake Sandgren, HPC2N, Umea University, S-90187 Umea, Sweden
Internet: a...@hpc2n.umu.se   Phone: +46 90 7866134 Fax: +46 90 7866126
Mobile: +46 70 7716134 WWW: http://www.hpc2n.umu.se

[OMPI users] Help: OpenMPI Compilation in Raspberry Pi

[Lee Eric]

Hi,

I am going to compile OpenMPI 1.6.3 in Raspberry Pi and encounter following
errors.

make[2]: Entering directory `/root/openmpi-1.6.3/opal'
  CC class/opal_bitmap.lo
  CC class/opal_free_list.lo
  CC class/opal_hash_table.lo
  CC class/opal_list.lo
  CC class/opal_object.lo
/tmp/ccniCtj0.s: Assembler messages:
/tmp/ccniCtj0.s:83: Error: selected processor does not support ARM mode
`ldrex r3,[r1]'
/tmp/ccniCtj0.s:86: Error: selected processor does not support ARM mode
`strex r4,r0,[r1]'
make[2]: *** [class/opal_object.lo] Error 1
make[2]: Leaving directory `/root/openmpi-1.6.3/opal'
make[1]: *** [all-recursive] Error 1
make[1]: Leaving directory `/root/openmpi-1.6.3/opal'
make: *** [all-recursive] Error 1

Can anyone have any idea to fix that issue?

I'm using Fedora 17 rootfs and kernel version is "Linux fedora-arm 3.6.11+
#1 PREEMPT Wed Jan 2 15:14:23 CST 2013 armv6l armv6l armv6l GNU/Linux".

Thanks.

Eric Lee