date:20091008

Re: [OMPI users] Making RPM from source that respects --prefix

2009-10-08 Thread Jeff Squyres


On Oct 7, 2009, at 9:36 PM, Bill Johnstone wrote:

Thank you for your responses.  Based on the information you both  
provided, I was able to get buildrpm to make the OMPI RPM the way I  
wanted.  I ended up having to define _prefix , _mandir , and  
_infodir .




Ah, yes -- _mandir and _infodir.  Sorry; I should have mentioned  
those, but I always forget that some distros don't automatically put  
those dirs under _prefix.  Sigh.


Additionally, I found I had to use --define "shell_scripts_basename  
mpivars" because without that, when I tried to use mpi-selector, mpi- 
selector did not find the installation since it specifically seems  
to look for the shell scripts as mpivars.{sh,csh} rather than  
mpivars-1.3.3.{sh,csh} as the .spec file builds.  I think the .spec  
file should be changed to match what mpi-selector expects.




The intent of putting the version string at the end of the shell  
script names was to allow them to co-exist with other Open MPI  
installs in the same tree.  In hindsight, that seems a little silly,  
because the scripts are installed in bindir -- where you can clearly  
only have 1 Open MPI installed at a time.  I'll fix.


Jeff, it might also be really useful to have a .spec build option to  
allow the RPM to register itself as the system default.  I hand- 
modified the .spec file to do this.  Please let me know if I should  
register a feature request somewhere more formally.




Sure, that sounds reasonable.  What --define option did you add for  
it?  Something like --define "mpi_selector_default 1" that causes -- 
system to be added to the mpi-selector command lines in %post and  
%preun?


--
Jeff Squyres
jsquy...@cisco.com

[OMPI users] Compilation problems of OpenMPI 1.3.3 with Snow Leopard

2009-10-08 Thread Hakime Seddik

Following my previous post regarding the problems that i am having to  
compile OpenMPI 1.3.3 on Snow Leopard, here are some observations:


- OpenMPI 1.2.9 compiles fine on Snow Leopard. Staring with OpenMPI  
1.3, the compilation fails with the error message described in my   
previous post. Note that OpenMPI 1.3 was compiling fine on Mac OS 10.5  
Leopard.


- OpenMPI 1.3.3 compiled fine on a system running Mac OS 10.4.11 Tiger.

Best regards,

Hakime Seddik
Glacier and Ice Sheet Research Group
Tel:+81-(0)90-6263-4074
email: hak...@pop.lowtem.hokudai.ac.jp

Institute of Low Temperature Science
Hokkaido University, Kita-19, Nishi-8, Kita-ku
Sapporo 060-0819. Japan

Re: [OMPI users] MPI_Comm_accept()/connect() errors

2009-10-08 Thread Blesson Varghese

The PATH variable contains
/home/hx019035/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/
bin:/usr/games:/usr/local/maui/bin/:

/home/hx019035/bin contains the local installation of OMPI 1.3.3



The LD_LIBRARY_PATH variable contains /home/hx019035/lib:



These variables are being set in the .profile file on the hpcc00 node. 



Would there be a change anywhere else?





From: Ralph Castain [mailto:rhc.open...@gmail.com] On Behalf Of Ralph
Castain
Sent: 07 October 2009 13:32
To: Blesson Varghese
Subject: Re: [OMPI users] MPI_Comm_accept()/connect() errors



Yes, it does. But the error message indicates a 1.2 version is running on
hpcc00.



On Oct 7, 2009, at 5:46 AM, Blesson Varghese wrote:



Just a quick question. Would mpirun -version give me the version of the
mpirun being executed? I am getting the result of that as 1.3.3.



From: Ralph Castain [mailto:rhc.open...@gmail.com] On Behalf Of Ralph
Castain
Sent: 07 October 2009 11:58
To: Blesson Varghese
Subject: Re: [OMPI users] MPI_Comm_accept()/connect() errors



Hate to tell you this, but your output clearly indicates you are NOT running
1.3.3 - that is an output from a 1.2.x version of OMPI.



Check you path and ld_library_path - you're still picking up the 1.2.5
version somewhere.





On Oct 7, 2009, at 4:05 AM, Blesson Varghese wrote:





Hi,



Please refer to the emails below.



I have made an upgrade to Open MPI 1.3.3 as suggested. The necessary
environment variables have all been set. Attaching the output of ompi_info
-all. However, the errors continue to persist.



[hpcc00:31864] [0,0,0] ORTE_ERROR_LOG: Not found in file dss/dss_unpack.c at
line 209

[hpcc00:31864] [0,0,0] ORTE_ERROR_LOG: Not found in file
communicator/comm_dyn.c at line 186

[hpcc00:31864] *** An error occurred in MPI_Comm_connect

[hpcc00:31864] *** on communicator MPI_COMM_WORLD

[hpcc00:31864] *** MPI_ERR_INTERN: internal error

[hpcc00:31864] *** MPI_ERRORS_ARE_FATAL (goodbye)





The server program is as follows:



#include 

#include 

#include 



int main( int argc, char **argv )

{

  MPI_Comm client;

  MPI_Status status;

  char port_name[MPI_MAX_PORT_NAME];

  int buf;

  int size, again;

  MPI_Info portInfo;



  MPI_Init( ,  );



  MPI_Comm_size(MPI_COMM_WORLD, );



  MPI_Open_port(MPI_INFO_NULL, port_name);



  printf("server available at %s\n",port_name);



  MPI_Comm_accept(port_name, MPI_INFO_NULL, 0, MPI_COMM_WORLD, 
);

  MPI_Recv(, 1, MPI_INT, MPI_ANY_SOURCE, MPI_ANY_TAG, client,
 );

  MPI_Comm_disconnect(  );

}



The client program is as follows:



#include 

#include 

#include 

#include 



int main( int argc, char **argv )

{

MPI_Comm server;

int buf = 8;

char port_name[MPI_MAX_PORT_NAME];

MPI_Info portInfo;



MPI_Init( ,  );



strcpy(port_name, "0.0.0:2000"); //The port name is hardcoded since
0.0.0:2000 is generated by the server program

MPI_Comm_connect(port_name, MPI_INFO_NULL, 0, MPI_COMM_WORLD,  );



MPI_Send(, 1, MPI_INT, 0, 1, server );



MPI_Comm_disconnect(  );

MPI_Finalize();

return 0;

}



Would you please advise?



Regards,

Blesson.





-Original Message-
From: Blesson Varghese [mailto:hx019...@reading.ac.uk] 
Sent: 03 October 2009 12:20
To: 'Jeff Squyres'
Subject: RE: [OMPI users] MPI_Comm_accept()/connect() errors



Thank you. I shall try the upgrade very soon.



-Original Message-

From: Jeff Squyres [mailto:jsquy...@cisco.com]

Sent: 03 October 2009 12:18

To: Blesson Varghese

Subject: Re: [OMPI users] MPI_Comm_accept()/connect() errors



On Oct 3, 2009, at 7:14 AM, Blesson Varghese wrote:



> Thanks for your reply Jeff. Since, it is a teaching cluster of the

> University,  I am quite unsure if I would be able to upgrade it very 

> soon.

> 

> Do you reckon that the error is due to the Open MPI version?

> 



You can always install your own version of Open MPI under your $HOME 

or somesuch -- there is no requirement that Open MPI is installed by 

root in a central location.



That being said, you might want to check with your administrator to 

ensure that this is ok with local policies -- see if they did any 

special setup for Open MPI, etc.



But yes, we made a bunch of COMM_SPAWN improvements since the 1.2 

series.



--

Jeff Squyres

jsquy...@cisco.com





From: Blesson Varghese [mailto:hx019...@reading.ac.uk] 
Sent: 01 October 2009 12:01
To: 'Open MPI Users'; 'Ralph Castain'
Subject: RE: [OMPI users] MPI_Comm_accept()/connect() errors



The following is the information regarding the error. I am running Open MPI
1.2.5 on Ubuntu 4.2.4, kernel version 2.6.24



I ran the server program as mpirun -np 1 server. This program gave me the
output port as 0.1.0:2000. I used this port name value as the command line
argument for the client program: mpirun -np 1 client 0.1.1:2000.



- The output of the "ompi_info --all" is attached with the email

- PATH

[OMPI users] Re : Re : Yet another stdin problem

2009-10-08 Thread Kilou Zelabia



Thanks a lot !  will try this solution.

Best regards.
Zellabia. S



De : Roman Cheplyaka 
À : Open MPI Users 
Envoyé le : Mer 7 Octobre 2009, 17 h 42 min 58 s
Objet : Re: [OMPI users] Re : Yet another stdin problem

As a slight modification, you can write a wrapper script

#!/bin/sh
my_exe < inputs.txt

and pass it to mpirun.

2009/10/7 Kilou Zelabia :
> Ok thanks!
> That's a solution but i was wondering if there could exist a more elegant
> one ? means without any modification at the source level
>
> 
> De : Roman Cheplyaka 
> À : Open MPI Users 
> Envoyé le : Mer 7 Octobre 2009, 17 h 06 min 55 s
> Objet : Re: [OMPI users] Yet another stdin problem
>
> Why not modify your program to read inputs.txt instead of stdin?
>
> 2009/10/7 Kilou Zelabia :
>> Dear all,
>>
>> I'm trying to lunch an MPI program using the command
>>
>> mpirun -np 64 my_exe < inputs.txt
>>
>> inputs.txt actually contains the entries that  are read by all processes
>> however it seems that openmpi redirect the stdin only to the processes
>> with
>> rank 0. with leads to a segmentation fault on the other processes.
>> The option "-stdin rank" doesn't help since i need all processes read the
>> inputs.txt file.
>>
>> I'v tested with openmpi 1.3 and 1.2 whitout success.
>>
>> Thanks in advance for you help.
>>
>> Zellabia. S
>>
>>
>>
>>
>> ___
>> users mailing list
>> us...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>>
>
>
>
> --
> Roman I. Cheplyaka
>
> ___
> 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
>



-- 
Roman I. Cheplyaka

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

[OMPI users] Compilation problems of OpenMPI 1.3.3 with Snow Leopard

2009-10-08 Thread Hakime Seddik


Hi,

I am having problems to compile the latest release of OpenMPI on Snow  
Leopard (Mac OS 10.6). I have installed the latest gfortran compiler  
(which can be found here: http://hpc.sourceforge.net/) and when trying  
to compile OpenMPI 1.3.3, i get some linking issues:


Making all in tools/wrappers
depbase=`echo opal_wrapper.o | sed 's|[^/]*$|.deps/&|;s|\.o$||'`;\
	gcc "-DEXEEXT=\"\"" -I. -I../../../opal/include -I../../../orte/ 
include -I../../../ompi/include -I../../../opal/mca/paffinity/linux/ 
plpa/src/libplpa   -I../../..  -D_REENTRANT  -DNDEBUG -O5 -ftree- 
vectorize -finline-functions -fno-strict-aliasing  -fvisibility=hidden  
-MT opal_wrapper.o -MD -MP -MF $depbase.Tpo -c -o opal_wrapper.o  
opal_wrapper.c &&\

mv -f $depbase.Tpo $depbase.Po
cc1: note: -ftree-vectorize enables strict aliasing.  -fno-strict- 
aliasing is ignored when Auto Vectorization is used.
/bin/sh ../../../libtool --tag=CC   --mode=link gcc  -DNDEBUG -O5 - 
ftree-vectorize -finline-functions -fno-strict-aliasing  - 
fvisibility=hidden  -export-dynamic   -o opal_wrapper  
opal_wrapper.o ../../../opal/libopen-pal.la -lutil
libtool: link: gcc -DNDEBUG -O5 -ftree-vectorize -finline-functions - 
fno-strict-aliasing -fvisibility=hidden -o .libs/opal_wrapper  
opal_wrapper.o  ../../../opal/.libs/libopen-pal.dylib -lutil

Undefined symbols:
  "_opal_few", referenced from:
  _main in opal_wrapper.o
  "_opal_os_path", referenced from:
  _add_extra_includes in opal_wrapper.o
  _main in opal_wrapper.o
  "_opal_argv_insert", referenced from:
  _options_data_expand in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  "_opal_argv_count", referenced from:
  _add_extra_includes in opal_wrapper.o
  _options_data_expand in opal_wrapper.o
  _find_options_index in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  "_opal_basename", referenced from:
  _main in opal_wrapper.o
  "_opal_install_dirs_expand", referenced from:
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  "_opal_argv_append_nosize", referenced from:
  _add_extra_includes in opal_wrapper.o
  _main in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  "_opal_argv_split", referenced from:
  _add_extra_includes in opal_wrapper.o
  _options_data_expand in opal_wrapper.o
  _load_env_data_argv in opal_wrapper.o
  _main in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  "_opal_argv_delete", referenced from:
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  "_opal_argv_free", referenced from:
  _options_data_expand in opal_wrapper.o
  _load_env_data_argv in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _data_callback in opal_wrapper.o
  _data_callback in opal_wrapper.o
  "_opal_argv_copy", referenced from:
  _main in opal_wrapper.o
  "_opal_finalize_util", referenced from:
  _main in opal_wrapper.o
  "_opal_show_help", referenced from:
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  "_opal_util_keyval_parse", referenced from:
  _main in opal_wrapper.o
  "_opal_install_dirs", referenced from:
  _main in opal_wrapper.o
  "_opal_init_util", referenced from:
  _main in opal_wrapper.o
  "_opal_path_findv", referenced from:
  _main in opal_wrapper.o
  "_opal_strerror", referenced from:
  _main in opal_wrapper.o
  "_opal_argv_join", referenced from:
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
  _main in opal_wrapper.o
ld: symbol(s) not found
collect2: ld returned 1 exit status
make[2]: *** [opal_wrapper] Error 1
make[1]: *** [all-recursive] Error 1
make: *** [all-recursive] Error 1


The same problem appears when trying to compile OpenMPI 1.3.2.

Did someone have the same problem?

Re: [OMPI users] Making RPM from source that respects --prefix

[OMPI users] Compilation problems of OpenMPI 1.3.3 with Snow Leopard

Re: [OMPI users] MPI_Comm_accept()/connect() errors

[OMPI users] Re : Re : Yet another stdin problem

[OMPI users] Compilation problems of OpenMPI 1.3.3 with Snow Leopard

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