date:20121206

[OMPI devel] how to compile codes in orte/test/system

2012-12-06 Thread Cao, Jimmy

Hi folks

Anyone can tell me how to compile codes in orte/test/system? There is a 
Makefile under the directory.  When I try to compile these test case with that 
Makefile, I got the following errors.
It seems  the header file of hwloc and libevent is missing.

=
ortecc -gsigusr_trap.c   -o sigusr_trap
In file included from 
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc142.h:20,
 from /usr/local/include/openmpi/opal/mca/hwloc/hwloc.h:148,
 from /usr/local/include/openmpi/orte/util/proc_info.h:44,
 from sigusr_trap.c:13:
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:49:34: 
error:

/autogen/config.h: No such file or directory
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:58:26: 
error: hwloc/rename.h: No such file or directory
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:64:26: 
error: hwloc/bitmap.h: No such file or directory
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:65:26: 
error: hwloc/cpuset.h: No such file or directory
In file included from 
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc142.h:20,
 from /usr/local/include/openmpi/opal/mca/hwloc/hwloc.h:148,
 from /usr/local/include/openmpi/orte/util/proc_info.h:44,
 from sigusr_trap.c:13:
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:81: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘unsigned’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:128: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘hwloc_cpuset_t’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:130: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before 
‘hwloc_const_cpuset_t’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:145: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘hwloc_nodeset_t’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:148: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before 
‘hwloc_const_nodeset_t’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:292: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
In file included from 
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc142.h:20,
 from /usr/local/include/openmpi/opal/mca/hwloc/hwloc.h:148,
 from /usr/local/include/openmpi/orte/util/proc_info.h:44,
 from sigusr_trap.c:13:
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:310: 
error: expected specifier-qualifier-list before ‘hwloc_uint64_t’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:370: 
error: expected specifier-qualifier-list before ‘hwloc_cpuset_t’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:476: 
error: expected specifier-qualifier-list before ‘hwloc_uint64_t’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:570: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:584: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:590: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘void’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:603: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘void’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:639: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:649: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:658: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:726: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:742: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:768: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:794: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:817: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
/usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:840: 
error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__

Re: [OMPI devel] how to compile codes in orte/test/system

2012-12-06 Thread Ralph Castain

Hi Jimmy

You need to configure --with-devel-headers to install the necessary headers.
Ralph



On Wed, Dec 5, 2012 at 11:58 PM, Cao, Jimmy  wrote:

> Hi folks
>
> Anyone can tell me how to compile codes in orte/test/system? There is a
> Makefile under the directory.  When I try to compile these test case with
> that Makefile, I got the following errors.
> It seems  the header file of hwloc and libevent is missing.
>
> =
> ortecc -gsigusr_trap.c   -o sigusr_trap
> In file included from
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc142.h:20,
>  from
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc.h:148,
>  from /usr/local/include/openmpi/orte/util/proc_info.h:44,
>  from sigusr_trap.c:13:
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:49:34:
> error:
>
> /autogen/config.h: No such file or directory
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:58:26:
> error: hwloc/rename.h: No such file or directory
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:64:26:
> error: hwloc/bitmap.h: No such file or directory
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:65:26:
> error: hwloc/cpuset.h: No such file or directory
> In file included from
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc142.h:20,
>  from
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc.h:148,
>  from /usr/local/include/openmpi/orte/util/proc_info.h:44,
>  from sigusr_trap.c:13:
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:81:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘unsigned’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:128:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before
> ‘hwloc_cpuset_t’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:130:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before
> ‘hwloc_const_cpuset_t’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:145:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before
> ‘hwloc_nodeset_t’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:148:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before
> ‘hwloc_const_nodeset_t’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:292:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> In file included from
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc142.h:20,
>  from
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc.h:148,
>  from /usr/local/include/openmpi/orte/util/proc_info.h:44,
>  from sigusr_trap.c:13:
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:310:
> error: expected specifier-qualifier-list before ‘hwloc_uint64_t’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:370:
> error: expected specifier-qualifier-list before ‘hwloc_cpuset_t’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:476:
> error: expected specifier-qualifier-list before ‘hwloc_uint64_t’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:570:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:584:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:590:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘void’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:603:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘void’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:639:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:649:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:658:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:726:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:742:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:768:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before ‘int’
> /usr/local/include/openmpi/opal/mca/hwloc/hwloc142/hwloc/include/hwloc.h:794:
> error: expected ‘=’, ‘,’, ‘;’, ‘asm’ or ‘__attribute__’ before

Re: [OMPI devel] CRIU checkpoint support in Open-MPI?

2012-12-06 Thread George Bosilca

Samuel,

Yes, all contributions are welcomed. It should be almost trivial to write a new 
backend in Open MPI to support what the kernel developers will agree to add as 
C/R capabilities. A good starting point to look at are the existing modules in 
opal/mca/crs.

  george.


On Dec 6, 2012, at 03:56 , Christopher Samuel  wrote:

> -BEGIN PGP SIGNED MESSAGE-
> Hash: SHA1
> 
> Hi folks,
> 
> I don't know if people have seen that the Linux kernel community is
> following its own different checkpoint/restart path to those currently
> supported by OMPI, namely that of the OpenVZ developers
> "checkpoint/restore in user space" project (CRIU).
> 
> You can read more about its current state here:
> 
> https://lwn.net/Articles/525675/
> 
> The CRIU website is here:
> 
> http://criu.org/
> 
> CRIU will also be up for discussion at LCA2013 in Canberra this year
> (though I won't be there):
> 
> http://linux.conf.au/schedule/30116/view_talk?day=thursday
> 
> Is there interest from OMPI in supporting this, given it looks like
> it's quite likely to make it into the mainline kernel?
> 
> Or is better to wait for it to be merged, and then take a look?
> 
> All the best,
> Chris
> - -- 
> Christopher SamuelSenior Systems Administrator
> VLSCI - Victorian Life Sciences Computation Initiative
> Email: sam...@unimelb.edu.au Phone: +61 (0)3 903 55545
> http://www.vlsci.org.au/  http://twitter.com/vlsci
> 
> -BEGIN PGP SIGNATURE-
> Version: GnuPG v1.4.11 (GNU/Linux)
> Comment: Using GnuPG with undefined - http://www.enigmail.net/
> 
> iEYEARECAAYFAlDACXYACgkQO2KABBYQAh8LIQCfagfyZNzK3KVKb+W0etJV4tyL
> AxwAn0z6q7TVNcOTom0tmvy7brfFf4QV
> =SLvF
> -END PGP SIGNATURE-
> ___
> devel mailing list
> de...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/devel

Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk: ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/ml opal/util/keyval orte/mca/rmaps/rank_file

2012-12-06 Thread Hjelm, Nathan T

Done. We now clean up correctly in new flex while having support for old flex.

-Nathan

On Monday, December 03, 2012 6:36 PM, devel-boun...@open-mpi.org 
[devel-boun...@open-mpi.org] on behalf of George Bosilca [bosi...@icl.utk.edu] 
wrote:
> To: Open MPI Developers
> Subject: Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk:
> ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/ml
> opal/util/keyval orte/mca/rmaps/rank_file
> 
> Cool, I'm looking forward. Meanwhile I'll go back and use the 1.6, which 
> hopefully compiles.
> 
>   Thanks,
> george.
> 
> 
> On Dec 4, 2012, at 02:34 , "Hjelm, Nathan T"  wrote:
> 
>> Sorry about that. We are working on a fix that both supports flex 2.5.4 
>> (*#*&@ redhat) and cleans up the lex state correctly in modern flex. It 
>> should be done in the next day or so.
>>
>> -Nathan
>>
>> On Monday, December 03, 2012 6:28 PM, devel-boun...@open-mpi.org 
>> [devel-boun...@open-mpi.org] on behalf of George Bosilca 
>> [bosi...@icl.utk.edu] wrote:
>>> To: de...@open-mpi.org
>>> Subject: Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk:
>>> ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/mlopal/util/keyval 
>>> orte/mca/rmaps/rank_file
>>>
>>> I remember there were some discussions about lex (or flex) and their 
>>> version, but I don't remember the specifics. Whatever the outcome was, 
>>> we're back at having a problem there, more specifically a missing reference 
>>> (opal_util_keyval_yylex_destroy) which seems to indicate the issue was not 
>>> fixed.
>>>
>>>  george.
>>>
>>>
>>>
>>>
>>> On Nov 9, 2012, at 23:00 , svn-commit-mai...@open-mpi.org wrote:
>>>
 Author: hjelmn (Nathan Hjelm)
 Date: 2012-11-09 17:00:27 EST (Fri, 09 Nov 2012)
 New Revision: 27580
 URL: https://svn.open-mpi.org/trac/ompi/changeset/27580

 Log:
 add prototypes for lex destroy functions

 Text files modified:
  trunk/ompi/mca/btl/openib/btl_openib_lex.h   | 1 +
  trunk/ompi/mca/btl/wv/btl_wv_lex.h   | 1 +
  trunk/ompi/mca/coll/ml/coll_ml_lex.h | 1 +
  trunk/opal/util/keyval/keyval_lex.h  | 1 +
  trunk/orte/mca/rmaps/rank_file/rmaps_rank_file.h | 2 ++
  5 files changed, 6 insertions(+), 0 deletions(-)
>>>
>>> ___
>>> devel mailing list
>>> de...@open-mpi.org
>>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
>>
>> ___
>> devel mailing list
>> de...@open-mpi.org
>> http://www.open-mpi.org/mailman/listinfo.cgi/devel
> 
> 
> ___
> devel mailing list
> de...@open-mpi.org
> http://www.open-mpi.org/mailman/listinfo.cgi/devel

Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk: ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/ml opal/util/keyval orte/mca/rmaps/rank_file

2012-12-06 Thread Paul Hargrove

Nathan,

What does this mean with respect to "clean up" and old flex?
Have you simply conceded that old flex will leak memory?

-Paul

On Thu, Dec 6, 2012 at 4:16 PM, Hjelm, Nathan T  wrote:

> Done. We now clean up correctly in new flex while having support for old
> flex.
>
> -Nathan

-- 
Paul H. Hargrove  phhargr...@lbl.gov
Future Technologies Group
Computer and Data Sciences Department Tel: +1-510-495-2352
Lawrence Berkeley National Laboratory Fax: +1-510-486-6900

Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk: ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/ml opal/util/keyval orte/mca/rmaps/rank_file

2012-12-06 Thread Hjelm, Nathan T

Well, I *think* the destroy functions I added to the .l files for the old flex 
case will clean up everything correctly. What I mean is we will correctly clean 
up  when using new flex (valgrind clean). We still recommend using new flex 
(2.5.33 or newer recommended) but we will continue to support old flex because 
of Redhat's decision to include old flex in RHEL 5.

-Nathan

From: devel-boun...@open-mpi.org [devel-boun...@open-mpi.org] on behalf of Paul 
Hargrove [phhargr...@lbl.gov]
Sent: Thursday, December 06, 2012 5:20 PM
To: Open MPI Developers
Subject: Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk: 
ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/ml opal/util/keyval 
orte/mca/rmaps/rank_file

Nathan,

What does this mean with respect to "clean up" and old flex?
Have you simply conceded that old flex will leak memory?

-Paul

On Thu, Dec 6, 2012 at 4:16 PM, Hjelm, Nathan T 
mailto:hje...@lanl.gov>> wrote:
Done. We now clean up correctly in new flex while having support for old flex.

-Nathan

--
Paul H. Hargrove  
phhargr...@lbl.gov
Future Technologies Group
Computer and Data Sciences Department Tel: +1-510-495-2352
Lawrence Berkeley National Laboratory Fax: +1-510-486-6900

[OMPI devel] how to compile codes in orte/test/system

Re: [OMPI devel] how to compile codes in orte/test/system

Re: [OMPI devel] CRIU checkpoint support in Open-MPI?

Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk: ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/ml opal/util/keyval orte/mca/rmaps/rank_file

Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk: ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/ml opal/util/keyval orte/mca/rmaps/rank_file

Re: [OMPI devel] [OMPI svn] svn:open-mpi r27580 - in trunk: ompi/mca/btl/openib ompi/mca/btl/wv ompi/mca/coll/ml opal/util/keyval orte/mca/rmaps/rank_file

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