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Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
From: Lenny Verkhovsky (lenny.verkhovsky_at_[hidden])
Date: 2009-04-20 09:50:29


Me too, sorry, it definately seems like a bug. Somewere in the code probably
undefined variable.
I just never tested this code with such "bizzare" command line :)

Lenny.

On Mon, Apr 20, 2009 at 4:08 PM, Geoffroy Pignot <geopignot_at_[hidden]>wrote:

> Thanks,
>
> I am not in a hurry but it would be nice if I could benefit from this
> feature in the next release.
> Regards
>
> Geoffroy
>
>
>
> 2009/4/20 <users-request_at_[hidden]>
>
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>>
>> 1. Re: 1.3.1 -rf rankfile behaviour ?? (Ralph Castain)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 20 Apr 2009 05:59:52 -0600
>> From: Ralph Castain <rhc_at_[hidden]>
>> Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
>> To: Open MPI Users <users_at_[hidden]>
>> Message-ID: <6378A8C1-1763-4A1C-ABCA-C6FCC36054E6_at_[hidden]>
>>
>> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
>> DelSp="yes"
>>
>> Honestly haven't had time to look at it yet - hopefully in the next
>> couple of days...
>>
>> Sorry for delay
>>
>>
>> On Apr 20, 2009, at 2:58 AM, Geoffroy Pignot wrote:
>>
>> > Do you have any news about this bug.
>> > Thanks
>> >
>> > Geoffroy
>> >
>> >
>> > Message: 1
>> > Date: Tue, 14 Apr 2009 07:57:44 -0600
>> > From: Ralph Castain <rhc_at_[hidden]>
>> > Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
>> > To: Open MPI Users <users_at_[hidden]>
>> > Message-ID: <BEB90473-0747-43BF-A1E9-6FA4E77778D7_at_[hidden]>
>> > Content-Type: text/plain; charset="us-ascii"; Format="flowed";
>> > DelSp="yes"
>> >
>> > Ah now, I didn't say it -worked-, did I? :-)
>> >
>> > Clearly a bug exists in the program. I'll try to take a look at it (if
>> > Lenny doesn't get to it first), but it won't be until later in the
>> > week.
>> >
>> > On Apr 14, 2009, at 7:18 AM, Geoffroy Pignot wrote:
>> >
>> > > I agree with you Ralph , and that 's what I expect from openmpi but
>> > > my second example shows that it's not working
>> > >
>> > > cat hostfile.0
>> > > r011n002 slots=4
>> > > r011n003 slots=4
>> > >
>> > > cat rankfile.0
>> > > rank 0=r011n002 slot=0
>> > > rank 1=r011n003 slot=1
>> > >
>> > > mpirun --hostfile hostfile.0 -rf rankfile.0 -n 1 hostname : -n 1
>> > > hostname
>> > > ### CRASHED
>> > >
>> > > > > Error, invalid rank (1) in the rankfile (rankfile.0)
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > [r011n002:25129] [[63976,0],0] ORTE_ERROR_LOG: Bad parameter in
>> > > file
>> > > > > rmaps_rank_file.c at line 404
>> > > > > [r011n002:25129] [[63976,0],0] ORTE_ERROR_LOG: Bad parameter in
>> > > file
>> > > > > base/rmaps_base_map_job.c at line 87
>> > > > > [r011n002:25129] [[63976,0],0] ORTE_ERROR_LOG: Bad parameter in
>> > > file
>> > > > > base/plm_base_launch_support.c at line 77
>> > > > > [r011n002:25129] [[63976,0],0] ORTE_ERROR_LOG: Bad parameter in
>> > > file
>> > > > > plm_rsh_module.c at line 985
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > A daemon (pid unknown) died unexpectedly on signal 1 while
>> > > > attempting to
>> > > > > launch so we are aborting.
>> > > > >
>> > > > > There may be more information reported by the environment (see
>> > > > above).
>> > > > >
>> > > > > This may be because the daemon was unable to find all the needed
>> > > > shared
>> > > > > libraries on the remote node. You may set your LD_LIBRARY_PATH
>> > to
>> > > > have the
>> > > > > location of the shared libraries on the remote nodes and this
>> > will
>> > > > > automatically be forwarded to the remote nodes.
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > orterun noticed that the job aborted, but has no info as to the
>> > > > process
>> > > > > that caused that situation.
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > orterun: clean termination accomplished
>> > >
>> > >
>> > >
>> > > Message: 4
>> > > Date: Tue, 14 Apr 2009 06:55:58 -0600
>> > > From: Ralph Castain <rhc_at_[hidden]>
>> > > Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
>> > > To: Open MPI Users <users_at_[hidden]>
>> > > Message-ID: <F6290ADA-A196-43F0-A853-CBCB802D8D9C_at_[hidden]>
>> > > Content-Type: text/plain; charset="us-ascii"; Format="flowed";
>> > > DelSp="yes"
>> > >
>> > > The rankfile cuts across the entire job - it isn't applied on an
>> > > app_context basis. So the ranks in your rankfile must correspond to
>> > > the eventual rank of each process in the cmd line.
>> > >
>> > > Unfortunately, that means you have to count ranks. In your case, you
>> > > only have four, so that makes life easier. Your rankfile would look
>> > > something like this:
>> > >
>> > > rank 0=r001n001 slot=0
>> > > rank 1=r001n002 slot=1
>> > > rank 2=r001n001 slot=1
>> > > rank 3=r001n002 slot=2
>> > >
>> > > HTH
>> > > Ralph
>> > >
>> > > On Apr 14, 2009, at 12:19 AM, Geoffroy Pignot wrote:
>> > >
>> > > > Hi,
>> > > >
>> > > > I agree that my examples are not very clear. What I want to do
>> > is to
>> > > > launch a multiexes application (masters-slaves) and benefit from
>> > the
>> > > > processor affinity.
>> > > > Could you show me how to convert this command , using -rf option
>> > > > (whatever the affinity is)
>> > > >
>> > > > mpirun -n 1 -host r001n001 master.x options1 : -n 1 -host
>> > r001n002
>> > > > master.x options2 : -n 1 -host r001n001 slave.x options3 : -n 1 -
>> > > > host r001n002 slave.x options4
>> > > >
>> > > > Thanks for your help
>> > > >
>> > > > Geoffroy
>> > > >
>> > > >
>> > > >
>> > > >
>> > > >
>> > > > Message: 2
>> > > > Date: Sun, 12 Apr 2009 18:26:35 +0300
>> > > > From: Lenny Verkhovsky <lenny.verkhovsky_at_[hidden]>
>> > > > Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
>> > > > To: Open MPI Users <users_at_[hidden]>
>> > > > Message-ID:
>> > > > <453d39990904120826t2e1d1d33l7bb1fe3de65b5361_at_[hidden]
>> > >
>> > > > Content-Type: text/plain; charset="iso-8859-1"
>> > > >
>> > > > Hi,
>> > > >
>> > > > The first "crash" is OK, since your rankfile has ranks 0 and 1
>> > > > defined,
>> > > > while n=1, which means only rank 0 is present and can be
>> > allocated.
>> > > >
>> > > > NP must be >= the largest rank in rankfile.
>> > > >
>> > > > What exactly are you trying to do ?
>> > > >
>> > > > I tried to recreate your seqv but all I got was
>> > > >
>> > > > ~/work/svn/ompi/trunk/build_x86-64/install/bin/mpirun --hostfile
>> > > > hostfile.0
>> > > > -rf rankfile.0 -n 1 hostname : -rf rankfile.1 -n 1 hostname
>> > > > [witch19:30798] mca: base: component_find: paffinity
>> > > > "mca_paffinity_linux"
>> > > > uses an MCA interface that is not recognized (component MCA
>> > > v1.0.0 !=
>> > > > supported MCA v2.0.0) -- ignored
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > 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_carto_base_select failed
>> > > > --> Returned value -13 instead of OPAL_SUCCESS
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > [witch19:30798] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in
>> > > file
>> > > > ../../orte/runtime/orte_init.c at line 78
>> > > > [witch19:30798] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in
>> > > file
>> > > > ../../orte/orted/orted_main.c at line 344
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > A daemon (pid 11629) died unexpectedly with status 243 while
>> > > > attempting
>> > > > to launch so we are aborting.
>> > > >
>> > > > There may be more information reported by the environment (see
>> > > above).
>> > > >
>> > > > This may be because the daemon was unable to find all the needed
>> > > > shared
>> > > > libraries on the remote node. You may set your LD_LIBRARY_PATH to
>> > > > have the
>> > > > location of the shared libraries on the remote nodes and this will
>> > > > automatically be forwarded to the remote nodes.
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > mpirun noticed that the job aborted, but has no info as to the
>> > > process
>> > > > that caused that situation.
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > mpirun: clean termination accomplished
>> > > >
>> > > >
>> > > > Lenny.
>> > > >
>> > > >
>> > > > On 4/10/09, Geoffroy Pignot <geopignot_at_[hidden]> wrote:
>> > > > >
>> > > > > Hi ,
>> > > > >
>> > > > > I am currently testing the process affinity capabilities of
>> > > > openmpi and I
>> > > > > would like to know if the rankfile behaviour I will describe
>> > below
>> > > > is normal
>> > > > > or not ?
>> > > > >
>> > > > > cat hostfile.0
>> > > > > r011n002 slots=4
>> > > > > r011n003 slots=4
>> > > > >
>> > > > > cat rankfile.0
>> > > > > rank 0=r011n002 slot=0
>> > > > > rank 1=r011n003 slot=1
>> > > > >
>> > > > >
>> > > > >
>> > > >
>> > >
>> >
>> ##################################################################################
>> > > > >
>> > > > > mpirun --hostfile hostfile.0 -rf rankfile.0 -n 2 hostname ###
>> > OK
>> > > > > r011n002
>> > > > > r011n003
>> > > > >
>> > > > >
>> > > > >
>> > > >
>> > >
>> >
>> ##################################################################################
>> > > > > but
>> > > > > mpirun --hostfile hostfile.0 -rf rankfile.0 -n 1 hostname : -n 1
>> > > > hostname
>> > > > > ### CRASHED
>> > > > > *
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > Error, invalid rank (1) in the rankfile (rankfile.0)
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > [r011n002:25129] [[63976,0],0] ORTE_ERROR_LOG: Bad parameter in
>> > > file
>> > > > > rmaps_rank_file.c at line 404
>> > > > > [r011n002:25129] [[63976,0],0] ORTE_ERROR_LOG: Bad parameter in
>> > > file
>> > > > > base/rmaps_base_map_job.c at line 87
>> > > > > [r011n002:25129] [[63976,0],0] ORTE_ERROR_LOG: Bad parameter in
>> > > file
>> > > > > base/plm_base_launch_support.c at line 77
>> > > > > [r011n002:25129] [[63976,0],0] ORTE_ERROR_LOG: Bad parameter in
>> > > file
>> > > > > plm_rsh_module.c at line 985
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > A daemon (pid unknown) died unexpectedly on signal 1 while
>> > > > attempting to
>> > > > > launch so we are aborting.
>> > > > >
>> > > > > There may be more information reported by the environment (see
>> > > > above).
>> > > > >
>> > > > > This may be because the daemon was unable to find all the needed
>> > > > shared
>> > > > > libraries on the remote node. You may set your LD_LIBRARY_PATH
>> > to
>> > > > have the
>> > > > > location of the shared libraries on the remote nodes and this
>> > will
>> > > > > automatically be forwarded to the remote nodes.
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > orterun noticed that the job aborted, but has no info as to the
>> > > > process
>> > > > > that caused that situation.
>> > > > >
>> > > >
>> > >
>> >
>> --------------------------------------------------------------------------
>> > > > > orterun: clean termination accomplished
>> > > > > *
>> > > > > It seems that the rankfile option is not propagted to the second
>> > > > command
>> > > > > line ; there is no global understanding of the ranking inside a
>> > > > mpirun
>> > > > > command.
>> > > > >
>> > > > >
>> > > > >
>> > > >
>> > >
>> >
>> ##################################################################################
>> > > > >
>> > > > > Assuming that , I tried to provide a rankfile to each command
>> > > line:
>> > > > >
>> > > > > cat rankfile.0
>> > > > > rank 0=r011n002 slot=0
>> > > > >
>> > > > > cat rankfile.1
>> > > > > rank 0=r011n003 slot=1
>> > > > >
>> > > > > mpirun --hostfile hostfile.0 -rf rankfile.0 -n 1 hostname : -rf
>> > > > rankfile.1
>> > > > > -n 1 hostname ### CRASHED
>> > > > > *[r011n002:28778] *** Process received signal ***
>> > > > > [r011n002:28778] Signal: Segmentation fault (11)
>> > > > > [r011n002:28778] Signal code: Address not mapped (1)
>> > > > > [r011n002:28778] Failing at address: 0x34
>> > > > > [r011n002:28778] [ 0] [0xffffe600]
>> > > > > [r011n002:28778] [ 1]
>> > > > > /tmp/HALMPI/openmpi-1.3.1/lib/libopen-rte.so.
>> > > > 0(orte_odls_base_default_get_add_procs_data+0x55d)
>> > > > > [0x5557decd]
>> > > > > [r011n002:28778] [ 2]
>> > > > > /tmp/HALMPI/openmpi-1.3.1/lib/libopen-rte.so.
>> > > > 0(orte_plm_base_launch_apps+0x117)
>> > > > > [0x555842a7]
>> > > > > [r011n002:28778] [ 3] /tmp/HALMPI/openmpi-1.3.1/lib/openmpi/
>> > > > mca_plm_rsh.so
>> > > > > [0x556098c0]
>> > > > > [r011n002:28778] [ 4] /tmp/HALMPI/openmpi-1.3.1/bin/orterun
>> > > > [0x804aa27]
>> > > > > [r011n002:28778] [ 5] /tmp/HALMPI/openmpi-1.3.1/bin/orterun
>> > > > [0x804a022]
>> > > > > [r011n002:28778] [ 6] /lib/libc.so.6(__libc_start_main+0xdc)
>> > > > [0x9f1dec]
>> > > > > [r011n002:28778] [ 7] /tmp/HALMPI/openmpi-1.3.1/bin/orterun
>> > > > [0x8049f71]
>> > > > > [r011n002:28778] *** End of error message ***
>> > > > > Segmentation fault (core dumped)*
>> > > > >
>> > > > >
>> > > > >
>> > > > > I hope that I've found a bug because it would be very important
>> > > > for me to
>> > > > > have this kind of capabiliy .
>> > > > > Launch a multiexe mpirun command line and be able to bind my
>> > exes
>> > > > and
>> > > > > sockets together.
>> > > > >
>> > > > > Thanks in advance for your help
>> > > > >
>> > > > > Geoffroy
>> > > > _______________________________________________
>> > > > users mailing list
>> > > > users_at_[hidden]
>> > > > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> > >
>> > > -------------- next part --------------
>> > > HTML attachment scrubbed and removed
>> > >
>> > > ------------------------------
>> > >
>> > > _______________________________________________
>> > > users mailing list
>> > > users_at_[hidden]
>> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> > >
>> > > End of users Digest, Vol 1202, Issue 2
>> > > **************************************
>> > >
>> > > _______________________________________________
>> > > users mailing list
>> > > users_at_[hidden]
>> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
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>> > -------------- next part --------------
>> > HTML attachment scrubbed and removed
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>> > ------------------------------
>> >
>> > Message: 2
>> > Date: Tue, 14 Apr 2009 10:30:58 -0400
>> > From: Prentice Bisbal <prentice_at_[hidden]>
>> > Subject: Re: [OMPI users] PGI Fortran pthread support
>> > To: Open MPI Users <users_at_[hidden]>
>> > Message-ID: <49E49E22.9040502_at_[hidden]>
>> > Content-Type: text/plain; charset=ISO-8859-1
>> >
>> > Orion,
>> >
>> > I have no trouble getting thread support during configure with PGI
>> > 8.0-3
>> >
>> > Are there any other compilers in your path before the PGI compilers?
>> > Even if the PGI compilers come first, try specifying the PGI compilers
>> > explicitly with these environment variables (bash syntax shown):
>> >
>> > export CC=pgcc
>> > export CXX=pgCC
>> > export F77=pgf77
>> > export FC=pgf90
>> >
>> > also check the value of CPPFLAGS and LDFLAGS, and make sure they are
>> > correct for your PGI compilers.
>> >
>> > --
>> > Prentice
>> >
>> > Orion Poplawski wrote:
>> > > Seeing the following building openmpi 1.3.1 on CentOS 5.3 with PGI
>> > pgf90
>> > > 8.0-5 fortran compiler:
>> > >
>> > > checking if C compiler and POSIX threads work with -Kthread... no
>> > > checking if C compiler and POSIX threads work with -kthread... no
>> > > checking if C compiler and POSIX threads work with -pthread... yes
>> > > checking if C++ compiler and POSIX threads work with -Kthread... no
>> > > checking if C++ compiler and POSIX threads work with -kthread... no
>> > > checking if C++ compiler and POSIX threads work with -pthread... yes
>> > > checking if F77 compiler and POSIX threads work with -Kthread... no
>> > > checking if F77 compiler and POSIX threads work with -kthread... no
>> > > checking if F77 compiler and POSIX threads work with -pthread... no
>> > > checking if F77 compiler and POSIX threads work with -pthreads... no
>> > > checking if F77 compiler and POSIX threads work with -mt... no
>> > > checking if F77 compiler and POSIX threads work with -mthreads... no
>> > > checking if F77 compiler and POSIX threads work with -lpthreads...
>> > no
>> > > checking if F77 compiler and POSIX threads work with -llthread... no
>> > > checking if F77 compiler and POSIX threads work with -lpthread... no
>> > > checking for PTHREAD_MUTEX_ERRORCHECK_NP... yes
>> > > checking for PTHREAD_MUTEX_ERRORCHECK... yes
>> > > checking for working POSIX threads package... no
>> > > checking if C compiler and Solaris threads work... no
>> > > checking if C++ compiler and Solaris threads work... no
>> > > checking if F77 compiler and Solaris threads work... no
>> > > checking for working Solaris threads package... no
>> > > checking for type of thread support... none found
>> > >
>> >
>> >
>> >
>> > ------------------------------
>> >
>> > _______________________________________________
>> > users mailing list
>> > users_at_[hidden]
>> > http://www.open-mpi.org/mailman/listinfo.cgi/users
>> >
>> > End of users Digest, Vol 1202, Issue 4
>> > **************************************
>> >
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>>
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>
>
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