Re: [OMPI users] Fortran support on Windows Open-MPI

[Damien]

I ended up using the SVN Trunk from today, everything is working fine on 
that.


Damien

On 10/05/2010 2:33 PM, Shiqing Fan wrote:

Hi Damien,

That's a known problem. see this ticket 
https://svn.open-mpi.org/trac/ompi/ticket/2404 . It will be applied 
into 1.5 branch very soon. But if you apply the patch by yourself, it 
should also work.


Thanks,
Shiqing

Re: [OMPI users] Fortran support on Windows Open-MPI

[Damien]

Ah.  So it is.  I'll try to remember to look there first.

Damien

On 10/05/2010 2:33 PM, Shiqing Fan wrote:

Hi Damien,

That's a known problem. see this ticket 
https://svn.open-mpi.org/trac/ompi/ticket/2404 . It will be applied 
into 1.5 branch very soon. But if you apply the patch by yourself, it 
should also work.


Thanks,
Shiqing

Re: [OMPI users] Fortran support on Windows Open-MPI

[Shiqing Fan]

Hi Damien,

That's a known problem. see this ticket 
https://svn.open-mpi.org/trac/ompi/ticket/2404 . It will be applied into 
1.5 branch very soon. But if you apply the patch by yourself, it should 
also work.


Thanks,
Shiqing


On 2010-5-10 10:08 PM, Damien wrote:
Interesting.  If I add the Fortran compiler as a new entry through the 
GUI, CMake wipes it.  If I use the option to specify the compiler 
paths manually on Configure, I can add the Fortran compiler in that 
way and it works.


Then there's a compiler error.  In 
orte\mca\odls\process\odls_process_module.c, right at the top, there's


static bool odls_process_child_died( pid_t pid, unsigned int timeout,
 int* exit_status )
{
int error;
HANDLE handle = OpenProcess( PROCESS_TERMINATE | SYNCHRONIZE, FALSE,
 (DWORD)pid );
if( 0 == child->pid || INVALID_HANDLE_VALUE == handle ) {
error = GetLastError();
/* Let's suppose that the process dissapear ... by now */
return true;
}
CloseHandle(handle);
/* The child didn't die, so return false */
return false;
}

This line "0 == child->pid" causes a compiler error that tanks the 
build, because child doesn't exist in that scope.  Should that just be 
"0 == pid", seeing as pid is the argument passed to the function 
anyway?  The build seems fine with this fix.


Finally, there's an installation error on mpi_portable_platform.h.  
That file isn't generated as part of the build, and the installation 
command is around line 150 of ompi/CMakeLists.txt.  If you comment out 
the installation of that file the installation works correctly.


I used the 1.5a1r23092 snapshot for this.

Now to make sure it works...

Damien

On 10/05/2010 4:50 AM, Shiqing Fan wrote:



Hi,

Normally, that means a wrong path or incompatible compiler version, 
e.g. 32 bit vs 64 bit.



Shiqing

On 2010-5-7 6:54 PM, Damien wrote:
nd 2.8.1.  In the CMake GUI, I checked the OMPI_WANT_F77_BINDINGS 
option, and added a FilePath for CMAKE_Fortran_COMPILER of 
C:/Program Files (x86)/Intel/Compiler/11.1/065/bin/ia32/ifort.exe.  
When I re-run the Configure, CMake wipes the CMAKE_Fortran_COMPILER 
variable and complains about a missing Fortran compiler.  Any 
suggestions? 






--
--
Shiqing Fan  http://www.hlrs.de/people/fan
High Performance Computing   Tel.: +49 711 685 87234
  Center Stuttgart (HLRS)Fax.: +49 711 685 65832
Address:Allmandring 30   email: f...@hlrs.de
70569 Stuttgart

Re: [OMPI users] Fortran support on Windows Open-MPI

[Damien]

Interesting.  If I add the Fortran compiler as a new entry through the 
GUI, CMake wipes it.  If I use the option to specify the compiler paths 
manually on Configure, I can add the Fortran compiler in that way and it 
works.


Then there's a compiler error.  In 
orte\mca\odls\process\odls_process_module.c, right at the top, there's


static bool odls_process_child_died( pid_t pid, unsigned int timeout,
 int* exit_status )
{
int error;
HANDLE handle = OpenProcess( PROCESS_TERMINATE | SYNCHRONIZE, FALSE,
 (DWORD)pid );
if( 0 == child->pid || INVALID_HANDLE_VALUE == handle ) {
error = GetLastError();
/* Let's suppose that the process dissapear ... by now */
return true;
}
CloseHandle(handle);
/* The child didn't die, so return false */
return false;
}

This line "0 == child->pid" causes a compiler error that tanks the 
build, because child doesn't exist in that scope.  Should that just be 
"0 == pid", seeing as pid is the argument passed to the function 
anyway?  The build seems fine with this fix.


Finally, there's an installation error on mpi_portable_platform.h.  That 
file isn't generated as part of the build, and the installation command 
is around line 150 of ompi/CMakeLists.txt.  If you comment out the 
installation of that file the installation works correctly.


I used the 1.5a1r23092 snapshot for this.

Now to make sure it works...

Damien

On 10/05/2010 4:50 AM, Shiqing Fan wrote:



Hi,

Normally, that means a wrong path or incompatible compiler version, 
e.g. 32 bit vs 64 bit.



Shiqing

On 2010-5-7 6:54 PM, Damien wrote:
nd 2.8.1.  In the CMake GUI, I checked the OMPI_WANT_F77_BINDINGS 
option, and added a FilePath for CMAKE_Fortran_COMPILER of C:/Program 
Files (x86)/Intel/Compiler/11.1/065/bin/ia32/ifort.exe.  When I 
re-run the Configure, CMake wipes the CMAKE_Fortran_COMPILER variable 
and complains about a missing Fortran compiler.  Any suggestions? 

Re: [OMPI users] PGI problems

[Prentice Bisbal]

Dave Love wrote:
> NEWS says that problems with PGI 10 were fixed in 1.4.1, but PGI 10
> won't configure 1.4.2 for me:
> 
>   configure: WARNING: Your compiler does not support offsetof macro
>   configure: error: Configure: Cannot continue
>   # pgcc -V
>   
>   pgcc 10.1-0 64-bit target on x86-64 Linux -tp k8-64e 
>   Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
>   Copyright 2000-2010, STMicroelectronics, Inc.  All Rights Reserved.
> 
> Actually I get the same result using PGI 8, so I guess this is something
> different from Ticket #2129.
> 
> Does anyone have a fix, workaround, or diagnosis before I try to find
> one and make a bug report?

Dave,

I compiled 1.4.1 with PGI 9.0-3 a couple of months ago, and I just
compiled 1.4.2 with PGI 10.4:

$ pgcc -V

pgcc 10.4-0 64-bit target on x86-64 Linux -tp shanghai-64
Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
Copyright 2000-2010, STMicroelectronics, Inc.  All Rights Reserved.

Here's the configure command I used for the 1.4.2/10.4 build:

./configure CC=pgcc CXX=pgCC F77=pgf77 FC=pgf90 LDFLAGS="-L/usr/lib64"
--prefix=/usr/local/openmpi-1.4.2/pgi-10.4/x86_64 --disable-ipv6
--with-sge --with-openib --enable-static --with-libnuma=/usr | tee
configure.log 2>&1


Since I was successful compiled 1.4.1 with PGI 9 and 1.4.2 with PGI
10.4, I suspect the problem is local to you. Can you go through your
environment and make sure you don't have any settings that are incorrect
for this build that the configure script is picking up, like an
incorrect CPPFLAGS, LDFLAGS, or something like that?

I didn't see your exact configure command. If you're not already doing
so, I'd make sure you explicitly list the CC, CXX, FC and F77 variables,
including the full path to them if necessary to remove ambiguity about
what compiler you're really using.

-- 
Prentice Bisbal
Linux Software Support Specialist/System Administrator
School of Natural Sciences
Institute for Advanced Study
Princeton, NJ

Re: [OMPI users] Dynamic libraries in OpenMPI

[Prentice Bisbal]

Are you runing thee jobs through a queuing system like PBS, Torque, or SGE?

Prentice

Miguel Ángel Vázquez wrote:
> Hello Prentice,
> 
> Thank you for your advice but that doesn't solve the problem.
> 
> The non-login bash updates properly the $LD_LIBRARY_PATH value.
> 
> Any other idea?
> 
> Thanks,
> 
> Miguel
> 
> 2010/5/7 Prentice Bisbal mailto:prent...@ias.edu>>
> 
> 
> 
> Miguel Ángel Vázquez wrote:
> > Dear all,
> >
> > I am trying to run a C++ program which uses dynamic libraries
> under mpi.
> >
> > The compilation command looks like:
> >
> >  mpiCC `pkg-config --cflags itpp`  -o montecarlo  montecarlo.cpp
> > `pkg-config --libs itpp`
> >
> > And it works if I executed it in one machine:
> >
> > mpirun -np 2 -H localhost montecarlo
> >
> > I tested this both in the "master node" and in the "compute nodes" and
> > it works. However, when I try to run it with two different machines:
> >
> > mpirun -np 2 -H localhost,hpcnode1 montecarlo
> >
> > The program claims that it can't find the shared libraries:
> >
> > montecarlo: error while loading shared libraries: libitpp.so.6: cannot
> > open shared object file: No such file or directory
> >
> > The LD_LIBRARY_PATH is set properly at every machine, any idea
> where the
> > problem is? I attached you the config.log and the result of the
> omp-info
> > --all
> >
> > Thank you in advance,
> >
> > Miguel
> 
> Miguel,
> 
> Shells behave differently depending on whether it is an interactive
> login shell or a non-interactive shell. For example, the bash shell uses
> .bash_profile in case, but .bashrc in the other. Check the documentation
> for your shell and see what files it uses in each case, and make sure
> the non-login config file has the necessary settings for your MPI jobs.
>  It sounds like your login shell environment is okay, but your non-login
> environment isn't setup correctly. This is a common problem.
> 
> I use bash, and to keep it simple, my .bash_profile is just a symbolic
> link to .bashrc. That way, both shell types have the same environment.
> This isn't always a good idea, but in my case it's fine.
> 
> --
> Prentice

Re: [OMPI users] 'readv failed: Connection timed out' issue

[Guanyinzhu]

Did "--mca mpi_preconnect_all 1" work?



I also face this problem "readv failed: connection time out" in the production 
environment, and our engineer has reproduced this scenario at 20 nodes with 
gigabye ethernet and limit one ethernet speed to 2MB/s, then a MPI_Isend && 
MPI_Recv ring that means each node call MPI_Isend send data to the next node 
and then call MPI_Recv recv data from the prior with large size for many 
cycles, then we get the following error log:

[btl_tcp_frag.c:216:mca_btl_tcp_frag_recv] mca_btl_tcp_frag_recv: readv  
failed: Connection timed out (110)



our environment:

Open MPI version 1.3.1,  using btl tcp component.



I thought it might because the network fd was set nonblocking, and the 
nonblocking call of connect() might be error and the epoll_wait() was wake up 
by the error but treat it as success and call 
mca_btl_tcp_endpoint_recv_handler(), the nonblocking readv() call on a failed 
connected fd, so it return -1, and set the errorno to 110 which means 
connection timed out.


> From: ljdu...@scinet.utoronto.ca
> Date: Tue, 20 Apr 2010 09:24:17 -0400
> To: us...@open-mpi.org
> Subject: Re: [OMPI users] 'readv failed: Connection timed out' issue
> 
> On 2010-04-20, at 9:18AM, Terry Dontje wrote:
> 
> > Hi Jonathan,
> > 
> > Do you know what the top level function is or communication pattern? Is it 
> > some type of collective or a pattern that has a many to one. 
> 
> Ah, should have mentioned. The best-characterized code that we're seeing this 
> with is an absolutely standard (logically) regular grid hydrodynamics code, 
> only does nearest neighbour communication for exchanging guardcells; the Wait 
> in this case is, I think, just a matter of overlapping communication with 
> computation of the inner zones. There are things like allreduces in there, as 
> well, for setting timesteps, but the communication pattern is overall 
> extremely regular and well-behaved.
> 
> > What might be happening is that since OMPI uses a lazy connections by 
> > default if all processes are trying to establish communications to the same 
> > process you might run into the below.
> > 
> > You might want to see if setting "--mca mpi_preconnect_all 1" helps any. 
> > But beware this will cause your startup to increase. However, this might 
> > give us insight as to whether the problem is flooding a single rank with 
> > connect requests.
> 
> I'm certainly willing to try it.
> 
> - Jonathan
> 
> -- 
> Jonathan Dursi 
> 
> 
> 
> 
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

_
一张照片的自白――Windows Live照片的可爱视频介绍
http://windowslivesky.spaces.live.com/blog/cns!5892B6048E2498BD!889.entry

[OMPI users] sunstudio patch needed

[Dave Love]

For the benefit of anyone else trying to build with it on x86_64
GNU/Linux (or, presumably, i386):  Sunstudio 12, update 1 loops while
compiling 1.4.2's btl_sm.c with configure's default flags.  Sun patch
141859-04 fixes that.

[OMPI users] openmpi + share points

[Christophe Peyret]

Hello,

I am building a cluster with 6 Apple xserve running OSX Server 10.6 :

node1.cluster
node2.cluster
node3.cluster
node4.cluster
node5.cluster
node6.cluster

I've intalled openmpi in directory /opt/openmpi-1.4.2 of node1 then I made a 
share point of /opt -> /Network/opt and define variables

export MPI_HOME=/Network/opt/openmpi-1.4.2
export OPAL_PREFIX=/Network/opt/openmpi-1.4.2

I can access to openmpi from all nodes. However, I still face a problem when I 
launch a computation 

 mpirun --prefix /Network/opt/openmpi-1.4.2 -n 4 -hostfile ~peyret/hostfile  
space64 -f Test/cfm56_hp_Rigid/cfm56_hp_Rigid.def -fast

is returns me the error message :

[node2.cluster:09163] mca: base: component_find: unable to open 
/Network/opt/openmpi-1.4.2/lib/openmpi/mca_odls_default: file not found 
(ignored)
[node4.cluster:08867] mca: base: component_find: unable to open 
/Network/opt/openmpi-1.4.2/lib/openmpi/mca_odls_default: file not found 
(ignored)
[node3.cluster:08880] mca: base: component_find: unable to open 
/Network/opt/openmpi-1.4.2/lib/openmpi/mca_odls_default: file not found 
(ignored)

any idea ?

Christophe

Re: [OMPI users] Dynamic libraries in OpenMPI

[Miguel Ángel Vázquez]

Ok, thank you, I'll contact my sysadmin.

2010/5/10 Ralph Castain 

> Doesn't that indicate precisely what Prentice said? ssh isn't picking up
> your remote .bashrc file and executing it.
>
> Try just doing "mpirun -n 1 -H hpcnode1 printenv" and see if you get the
> envars you expect from you .bashrc. If not, talk to your sysadmin about how
> to fix the problem - could be a system config issue, permissions on your
> .bashrc (typical source of this kind of trouble), etc.
>
>
> On May 10, 2010, at 6:15 AM, Miguel Ángel Vázquez wrote:
>
> Version: OMPI 1.3.3
>
> Shell: bash
>
> I already fixed the problem with a shell script like
> #!/bin/sh
> export LD_LIBRARY_PATH= ...
> ./montecarlo
>
> But, it seems that openmpi look neither bash_profile not .bashrc.
>
> Thank you,
>
> Miguel
>
> 2010/5/10 Ralph Castain 
>
>> What version of OMPI? What shell?
>>
>> On May 10, 2010, at 2:05 AM, Miguel Ángel Vázquez wrote:
>>
>> Hello Prentice,
>>
>> Thank you for your advice but that doesn't solve the problem.
>>
>> The non-login bash updates properly the $LD_LIBRARY_PATH value.
>>
>> Any other idea?
>>
>> Thanks,
>>
>> Miguel
>>
>> 2010/5/7 Prentice Bisbal 
>>
>>>
>>>
>>> Miguel Ángel Vázquez wrote:
>>> > Dear all,
>>> >
>>> > I am trying to run a C++ program which uses dynamic libraries under
>>> mpi.
>>> >
>>> > The compilation command looks like:
>>> >
>>> >  mpiCC `pkg-config --cflags itpp`  -o montecarlo  montecarlo.cpp
>>> > `pkg-config --libs itpp`
>>> >
>>> > And it works if I executed it in one machine:
>>> >
>>> > mpirun -np 2 -H localhost montecarlo
>>> >
>>> > I tested this both in the "master node" and in the "compute nodes" and
>>> > it works. However, when I try to run it with two different machines:
>>> >
>>> > mpirun -np 2 -H localhost,hpcnode1 montecarlo
>>> >
>>> > The program claims that it can't find the shared libraries:
>>> >
>>> > montecarlo: error while loading shared libraries: libitpp.so.6: cannot
>>> > open shared object file: No such file or directory
>>> >
>>> > The LD_LIBRARY_PATH is set properly at every machine, any idea where
>>> the
>>> > problem is? I attached you the config.log and the result of the
>>> omp-info
>>> > --all
>>> >
>>> > Thank you in advance,
>>> >
>>> > Miguel
>>>
>>> Miguel,
>>>
>>> Shells behave differently depending on whether it is an interactive
>>> login shell or a non-interactive shell. For example, the bash shell uses
>>> .bash_profile in case, but .bashrc in the other. Check the documentation
>>> for your shell and see what files it uses in each case, and make sure
>>> the non-login config file has the necessary settings for your MPI jobs.
>>>  It sounds like your login shell environment is okay, but your non-login
>>> environment isn't setup correctly. This is a common problem.
>>>
>>> I use bash, and to keep it simple, my .bash_profile is just a symbolic
>>> link to .bashrc. That way, both shell types have the same environment.
>>> This isn't always a good idea, but in my case it's fine.
>>>
>>> --
>>> Prentice
>>> ___
>>> 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
>>
>
> ___
> 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] Questions about binding processes

[Terry Dontje]

NGUYEN Laurent wrote:
Ok, thank you for your answer. I think this rankfile feature is very 
interesting to run some jobs like MPMD jobs or hybrid jobs 
(multithreaded or GPU for examples).


Regards,

Point taken.  The basic premise Jeff and I are working on is to see if 
we could come up with a set of options that can cover most cases of job 
layouts.  I am thinking jobs that are fairly uniform in layout (which I 
believe hybrid jobs can be) are easily supported.  In the case of MPMD 
jobs I imagine one can conjure up a non-uniform layout that would be 
difficult, if not impossible, to define with some options.


As I said before I don't believe rankfiles will be flushed anytime soon 
and they may never be because of non-uniform layout jobs.


--
Oracle
Terry D. Dontje | Principal Software Engineer
Developer Tools Engineering | +1.650.633.7054
Oracle * - Performance Technologies*
95 Network Drive, Burlington, MA 01803
Email terry.don...@oracle.com 

Re: [OMPI users] Dynamic libraries in OpenMPI

[Ralph Castain]

Doesn't that indicate precisely what Prentice said? ssh isn't picking up your 
remote .bashrc file and executing it.

Try just doing "mpirun -n 1 -H hpcnode1 printenv" and see if you get the envars 
you expect from you .bashrc. If not, talk to your sysadmin about how to fix the 
problem - could be a system config issue, permissions on your .bashrc (typical 
source of this kind of trouble), etc.


On May 10, 2010, at 6:15 AM, Miguel Ángel Vázquez wrote:

> Version: OMPI 1.3.3
> 
> Shell: bash
> 
> I already fixed the problem with a shell script like
> #!/bin/sh
> export LD_LIBRARY_PATH= ...
> ./montecarlo
> 
> But, it seems that openmpi look neither bash_profile not .bashrc.
> 
> Thank you,
> 
> Miguel
> 
> 2010/5/10 Ralph Castain 
> What version of OMPI? What shell?
> 
> On May 10, 2010, at 2:05 AM, Miguel Ángel Vázquez wrote:
> 
>> Hello Prentice,
>> 
>> Thank you for your advice but that doesn't solve the problem.
>> 
>> The non-login bash updates properly the $LD_LIBRARY_PATH value.
>> 
>> Any other idea?
>> 
>> Thanks,
>> 
>> Miguel
>> 
>> 2010/5/7 Prentice Bisbal 
>> 
>> 
>> Miguel Ángel Vázquez wrote:
>> > Dear all,
>> >
>> > I am trying to run a C++ program which uses dynamic libraries under mpi.
>> >
>> > The compilation command looks like:
>> >
>> >  mpiCC `pkg-config --cflags itpp`  -o montecarlo  montecarlo.cpp
>> > `pkg-config --libs itpp`
>> >
>> > And it works if I executed it in one machine:
>> >
>> > mpirun -np 2 -H localhost montecarlo
>> >
>> > I tested this both in the "master node" and in the "compute nodes" and
>> > it works. However, when I try to run it with two different machines:
>> >
>> > mpirun -np 2 -H localhost,hpcnode1 montecarlo
>> >
>> > The program claims that it can't find the shared libraries:
>> >
>> > montecarlo: error while loading shared libraries: libitpp.so.6: cannot
>> > open shared object file: No such file or directory
>> >
>> > The LD_LIBRARY_PATH is set properly at every machine, any idea where the
>> > problem is? I attached you the config.log and the result of the omp-info
>> > --all
>> >
>> > Thank you in advance,
>> >
>> > Miguel
>> 
>> Miguel,
>> 
>> Shells behave differently depending on whether it is an interactive
>> login shell or a non-interactive shell. For example, the bash shell uses
>> .bash_profile in case, but .bashrc in the other. Check the documentation
>> for your shell and see what files it uses in each case, and make sure
>> the non-login config file has the necessary settings for your MPI jobs.
>>  It sounds like your login shell environment is okay, but your non-login
>> environment isn't setup correctly. This is a common problem.
>> 
>> I use bash, and to keep it simple, my .bash_profile is just a symbolic
>> link to .bashrc. That way, both shell types have the same environment.
>> This isn't always a good idea, but in my case it's fine.
>> 
>> --
>> Prentice
>> ___
>> 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
> 
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users

Re: [OMPI users] Dynamic libraries in OpenMPI

[Miguel Ángel Vázquez]

Version: OMPI 1.3.3

Shell: bash

I already fixed the problem with a shell script like
#!/bin/sh
export LD_LIBRARY_PATH= ...
./montecarlo

But, it seems that openmpi look neither bash_profile not .bashrc.

Thank you,

Miguel

2010/5/10 Ralph Castain 

> What version of OMPI? What shell?
>
> On May 10, 2010, at 2:05 AM, Miguel Ángel Vázquez wrote:
>
> Hello Prentice,
>
> Thank you for your advice but that doesn't solve the problem.
>
> The non-login bash updates properly the $LD_LIBRARY_PATH value.
>
> Any other idea?
>
> Thanks,
>
> Miguel
>
> 2010/5/7 Prentice Bisbal 
>
>>
>>
>> Miguel Ángel Vázquez wrote:
>> > Dear all,
>> >
>> > I am trying to run a C++ program which uses dynamic libraries under mpi.
>> >
>> > The compilation command looks like:
>> >
>> >  mpiCC `pkg-config --cflags itpp`  -o montecarlo  montecarlo.cpp
>> > `pkg-config --libs itpp`
>> >
>> > And it works if I executed it in one machine:
>> >
>> > mpirun -np 2 -H localhost montecarlo
>> >
>> > I tested this both in the "master node" and in the "compute nodes" and
>> > it works. However, when I try to run it with two different machines:
>> >
>> > mpirun -np 2 -H localhost,hpcnode1 montecarlo
>> >
>> > The program claims that it can't find the shared libraries:
>> >
>> > montecarlo: error while loading shared libraries: libitpp.so.6: cannot
>> > open shared object file: No such file or directory
>> >
>> > The LD_LIBRARY_PATH is set properly at every machine, any idea where the
>> > problem is? I attached you the config.log and the result of the omp-info
>> > --all
>> >
>> > Thank you in advance,
>> >
>> > Miguel
>>
>> Miguel,
>>
>> Shells behave differently depending on whether it is an interactive
>> login shell or a non-interactive shell. For example, the bash shell uses
>> .bash_profile in case, but .bashrc in the other. Check the documentation
>> for your shell and see what files it uses in each case, and make sure
>> the non-login config file has the necessary settings for your MPI jobs.
>>  It sounds like your login shell environment is okay, but your non-login
>> environment isn't setup correctly. This is a common problem.
>>
>> I use bash, and to keep it simple, my .bash_profile is just a symbolic
>> link to .bashrc. That way, both shell types have the same environment.
>> This isn't always a good idea, but in my case it's fine.
>>
>> --
>> Prentice
>> ___
>> 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] Dynamic libraries in OpenMPI

[Ralph Castain]

What version of OMPI? What shell?

On May 10, 2010, at 2:05 AM, Miguel Ángel Vázquez wrote:

> Hello Prentice,
> 
> Thank you for your advice but that doesn't solve the problem.
> 
> The non-login bash updates properly the $LD_LIBRARY_PATH value.
> 
> Any other idea?
> 
> Thanks,
> 
> Miguel
> 
> 2010/5/7 Prentice Bisbal 
> 
> 
> Miguel Ángel Vázquez wrote:
> > Dear all,
> >
> > I am trying to run a C++ program which uses dynamic libraries under mpi.
> >
> > The compilation command looks like:
> >
> >  mpiCC `pkg-config --cflags itpp`  -o montecarlo  montecarlo.cpp
> > `pkg-config --libs itpp`
> >
> > And it works if I executed it in one machine:
> >
> > mpirun -np 2 -H localhost montecarlo
> >
> > I tested this both in the "master node" and in the "compute nodes" and
> > it works. However, when I try to run it with two different machines:
> >
> > mpirun -np 2 -H localhost,hpcnode1 montecarlo
> >
> > The program claims that it can't find the shared libraries:
> >
> > montecarlo: error while loading shared libraries: libitpp.so.6: cannot
> > open shared object file: No such file or directory
> >
> > The LD_LIBRARY_PATH is set properly at every machine, any idea where the
> > problem is? I attached you the config.log and the result of the omp-info
> > --all
> >
> > Thank you in advance,
> >
> > Miguel
> 
> Miguel,
> 
> Shells behave differently depending on whether it is an interactive
> login shell or a non-interactive shell. For example, the bash shell uses
> .bash_profile in case, but .bashrc in the other. Check the documentation
> for your shell and see what files it uses in each case, and make sure
> the non-login config file has the necessary settings for your MPI jobs.
>  It sounds like your login shell environment is okay, but your non-login
> environment isn't setup correctly. This is a common problem.
> 
> I use bash, and to keep it simple, my .bash_profile is just a symbolic
> link to .bashrc. That way, both shell types have the same environment.
> This isn't always a good idea, but in my case it's fine.
> 
> --
> Prentice
> ___
> 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

[OMPI users] PGI problems

[Dave Love]

NEWS says that problems with PGI 10 were fixed in 1.4.1, but PGI 10
won't configure 1.4.2 for me:

  configure: WARNING: Your compiler does not support offsetof macro
  configure: error: Configure: Cannot continue
  # pgcc -V

  pgcc 10.1-0 64-bit target on x86-64 Linux -tp k8-64e 
  Copyright 1989-2000, The Portland Group, Inc.  All Rights Reserved.
  Copyright 2000-2010, STMicroelectronics, Inc.  All Rights Reserved.

Actually I get the same result using PGI 8, so I guess this is something
different from Ticket #2129.

Does anyone have a fix, workaround, or diagnosis before I try to find
one and make a bug report?

Re: [OMPI users] Questions about binding processes

[NGUYEN Laurent]

Ok, thank you for your answer. I think this rankfile feature is very  
interesting to run some jobs like MPMD jobs or hybrid jobs  
(multithreaded or GPU for examples).


Regards,

--
--
NGUYEN Laurent

HPC Engineer
CS:SI

email: laurent.ngu...@c-s.fr

web: http://www.c-s.fr

CS:SI
22 avenue Galilée
92350  Le Plessis Robinson



Terry Dontje  a écrit :


NGUYEN Laurent wrote:

Hello,

I'm trying to understand the difference between theses two options:

" --mca mpi_paffinity_alone 1 "
and
" --bind-to-core "

To me, it's the same thing (may be paffinity have maffinity in  
addition) but the purpose af theses options is to bind MPI process  
to processors. Which is the best to obtain performances?


They are essentially the same thing.  The history is that  
mpi_paffinity_alone came first.  Then a group of us decided that we  
wanted to be able to do more than just core binding (like  
bind-to-socket and eventually others) so we decided a more  
descriptive name made sense.  I would suggest sticking with  
--bind-to-core just so thinks look clear in your mpirun command.   
That and the possibility that one day mpi_paffinity_alone is  
deprecated.
I have another question about processes bindings: I use rankfiles  
to have a precise binding of my process on processor or socket (it  
useful for hybrid computing like pthread or OpenMP). I read you  
don't want to maintain this feature: how can I substitute it?
IMO, I say we do support it and will until we find a suitable  
replacement (there is a proposal that Jeff and I have bounced around  
to each other intermittently but have not brought it to the  
community).   There have been discussion about lack of testing of  
rankfiles and other binding related items making it hard for some to  
feel comfortable about putting code back that may have side negative  
side affects.  But I don't equate that to mean we will not support  
or take bug reports on the rankfile feature.


--
Oracle
Terry D. Dontje | Principal Software Engineer
Developer Tools Engineering | +1.650.633.7054
Oracle * - Performance Technologies*
95 Network Drive, Burlington, MA 01803
Email terry.don...@oracle.com 







This message was sent using IMP, the Internet Messaging Program.

Re: [OMPI users] Fortran support on Windows Open-MPI

[Shiqing Fan]

Hi,

Normally, that means a wrong path or incompatible compiler version, e.g. 
32 bit vs 64 bit.



Shiqing

On 2010-5-7 6:54 PM, Damien wrote:
nd 2.8.1.  In the CMake GUI, I checked the OMPI_WANT_F77_BINDINGS 
option, and added a FilePath for CMAKE_Fortran_COMPILER of C:/Program 
Files (x86)/Intel/Compiler/11.1/065/bin/ia32/ifort.exe.  When I re-run 
the Configure, CMake wipes the CMAKE_Fortran_COMPILER variable and 
complains about a missing Fortran compiler.  Any suggestions? 



--
--
Shiqing Fan  http://www.hlrs.de/people/fan
High Performance Computing   Tel.: +49 711 685 87234
  Center Stuttgart (HLRS)Fax.: +49 711 685 65832
Address:Allmandring 30   email: f...@hlrs.de
70569 Stuttgart

Re: [OMPI users] Questions about binding processes

[Terry Dontje]

NGUYEN Laurent wrote:

Hello,

I'm trying to understand the difference between theses two options:

" --mca mpi_paffinity_alone 1 "
and
" --bind-to-core "

To me, it's the same thing (may be paffinity have maffinity in 
addition) but the purpose af theses options is to bind MPI process to 
processors. Which is the best to obtain performances?


They are essentially the same thing.  The history is that 
mpi_paffinity_alone came first.  Then a group of us decided that we 
wanted to be able to do more than just core binding (like bind-to-socket 
and eventually others) so we decided a more descriptive name made 
sense.  I would suggest sticking with --bind-to-core just so thinks look 
clear in your mpirun command.  That and the possibility that one day 
mpi_paffinity_alone is deprecated.
I have another question about processes bindings: I use rankfiles to 
have a precise binding of my process on processor or socket (it useful 
for hybrid computing like pthread or OpenMP). I read you don't want to 
maintain this feature: how can I substitute it?
IMO, I say we do support it and will until we find a suitable 
replacement (there is a proposal that Jeff and I have bounced around to 
each other intermittently but have not brought it to the community).   
There have been discussion about lack of testing of rankfiles and other 
binding related items making it hard for some to feel comfortable about 
putting code back that may have side negative side affects.  But I don't 
equate that to mean we will not support or take bug reports on the 
rankfile feature.


--
Oracle
Terry D. Dontje | Principal Software Engineer
Developer Tools Engineering | +1.650.633.7054
Oracle * - Performance Technologies*
95 Network Drive, Burlington, MA 01803
Email terry.don...@oracle.com 

[OMPI users] Questions about binding processes

[NGUYEN Laurent]

Hello,

I'm trying to understand the difference between theses two options:

" --mca mpi_paffinity_alone 1 "
and
" --bind-to-core "

To me, it's the same thing (may be paffinity have maffinity in  
addition) but the purpose af theses options is to bind MPI process to  
processors. Which is the best to obtain performances?


I have another question about processes bindings: I use rankfiles to  
have a precise binding of my process on processor or socket (it useful  
for hybrid computing like pthread or OpenMP). I read you don't want to  
maintain this feature: how can I substitute it?


Thank you for your answers.


Best Regards,

--
NGUYEN Laurent

HPC Enginner
CS:SI

email: laurent.ngu...@c-s.fr

web: http://www.c-s.fr

CS:SI
22 avenue Galilée
92350  Le Plessis Robinson







This message was sent using IMP, the Internet Messaging Program.

Re: [OMPI users] Dynamic libraries in OpenMPI

[Miguel Ángel Vázquez]

Hello Prentice,

Thank you for your advice but that doesn't solve the problem.

The non-login bash updates properly the $LD_LIBRARY_PATH value.

Any other idea?

Thanks,

Miguel

2010/5/7 Prentice Bisbal 

>
>
> Miguel Ángel Vázquez wrote:
> > Dear all,
> >
> > I am trying to run a C++ program which uses dynamic libraries under mpi.
> >
> > The compilation command looks like:
> >
> >  mpiCC `pkg-config --cflags itpp`  -o montecarlo  montecarlo.cpp
> > `pkg-config --libs itpp`
> >
> > And it works if I executed it in one machine:
> >
> > mpirun -np 2 -H localhost montecarlo
> >
> > I tested this both in the "master node" and in the "compute nodes" and
> > it works. However, when I try to run it with two different machines:
> >
> > mpirun -np 2 -H localhost,hpcnode1 montecarlo
> >
> > The program claims that it can't find the shared libraries:
> >
> > montecarlo: error while loading shared libraries: libitpp.so.6: cannot
> > open shared object file: No such file or directory
> >
> > The LD_LIBRARY_PATH is set properly at every machine, any idea where the
> > problem is? I attached you the config.log and the result of the omp-info
> > --all
> >
> > Thank you in advance,
> >
> > Miguel
>
> Miguel,
>
> Shells behave differently depending on whether it is an interactive
> login shell or a non-interactive shell. For example, the bash shell uses
> .bash_profile in case, but .bashrc in the other. Check the documentation
> for your shell and see what files it uses in each case, and make sure
> the non-login config file has the necessary settings for your MPI jobs.
>  It sounds like your login shell environment is okay, but your non-login
> environment isn't setup correctly. This is a common problem.
>
> I use bash, and to keep it simple, my .bash_profile is just a symbolic
> link to .bashrc. That way, both shell types have the same environment.
> This isn't always a good idea, but in my case it's fine.
>
> --
> Prentice
> ___
> users mailing list
> us...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/users
>

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

[Tim Prince]

On 5/9/2010 8:45 PM, Terry Frankcombe wrote:
   

I don't know what Jeff meant by that, but we haven't seen a feasible way
of disabling HT without rebooting and using the BIOS options.
 

According to this page:
http://dag.wieers.com/blog/is-hyper-threading-enabled-on-a-linux-system
in RHEL5/CentOS-5 it's easy to switch it on and off on the fly.
___
   
That's the same as Jeff explained.  It requires root privilege, and 
affects all users.


--
Tim  Prince