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Subject: Re: [OMPI users] How do I compile OpenMPI in Xcode 3.1
From: Vicente Puig (vpuibor_at_[hidden])
Date: 2009-05-04 19:26:15


But it doesn't work well.
For example, I am trying to debug a program, "floyd" in this case, and when
I make a breakpoint:

No line 26 in file "../../../gcc-4.2-20060805/libgfortran/fmain.c".

I am getting disappointed and frustrated that I can not work well with
openmpi in my Mac. There should be a was to make it run in Xcode, uff...

2009/5/4 Jeff Squyres <jsquyres_at_[hidden]>

> I get those as well. I believe that they are (annoying but) harmless -- an
> artifact of how the freeware gcc/gofrtran that I use was built.
>
>
>
> On May 4, 2009, at 1:47 PM, Vicente Puig wrote:
>
> Maybe I had to open a new thread, but if you have any idea why I receive
>> it when I use gdb for debugging an openmpi program:
>>
>> warning: Could not find object file
>> "/Users/admin/build/i386-apple-darwin9.0.0/libgcc/_umoddi3_s.o" - no debug
>> information available for
>> "../../../gcc-4.3-20071026/libgcc/../gcc/libgcc2.c".
>>
>>
>> warning: Could not find object file
>> "/Users/admin/build/i386-apple-darwin9.0.0/libgcc/_udiv_w_sdiv_s.o" - no
>> debug information available for
>> "../../../gcc-4.3-20071026/libgcc/../gcc/libgcc2.c".
>>
>>
>> warning: Could not find object file
>> "/Users/admin/build/i386-apple-darwin9.0.0/libgcc/_udivmoddi4_s.o" - no
>> debug information available for
>> "../../../gcc-4.3-20071026/libgcc/../gcc/libgcc2.c".
>>
>>
>> warning: Could not find object file
>> "/Users/admin/build/i386-apple-darwin9.0.0/libgcc/unwind-dw2_s.o" - no debug
>> information available for
>> "../../../gcc-4.3-20071026/libgcc/../gcc/unwind-dw2.c".
>>
>>
>> warning: Could not find object file
>> "/Users/admin/build/i386-apple-darwin9.0.0/libgcc/unwind-dw2-fde-darwin_s.o"
>> - no debug information available for
>> "../../../gcc-4.3-20071026/libgcc/../gcc/unwind-dw2-fde-darwin.c".
>>
>>
>> warning: Could not find object file
>> "/Users/admin/build/i386-apple-darwin9.0.0/libgcc/unwind-c_s.o" - no debug
>> information available for
>> "../../../gcc-4.3-20071026/libgcc/../gcc/unwind-c.c".
>> .......
>>
>>
>>
>> There is no 'admin' so I don't know why it happen. It works well with a C
>> program.
>>
>> Any idea??.
>>
>> Thanks.
>>
>>
>> Vincent
>>
>>
>>
>>
>>
>> 2009/5/4 Vicente Puig <vpuibor_at_[hidden]>
>> I can run openmpi perfectly with command line, but I wanted a graphic
>> interface for debugging because I was having problems.
>>
>> Thanks anyway.
>>
>> Vincent
>>
>> 2009/5/4 Warner Yuen <wyuen_at_[hidden]>
>>
>> Admittedly, I don't use Xcode to build Open MPI either.
>>
>> You can just compile Open MPI from the command line and install everything
>> in /usr/local/. Make sure that gfortran is set in your path and you should
>> just be able to do a './configure --prefix=/usr/local'
>>
>> After the installation, just make sure that your path is set correctly
>> when you go to use the newly installed Open MPI. If you don't set your path,
>> it will always default to using the version of OpenMPI that ships with
>> Leopard.
>>
>>
>> Warner Yuen
>> Scientific Computing
>> Consulting Engineer
>> Apple, Inc.
>> email: wyuen_at_[hidden]
>> Tel: 408.718.2859
>>
>>
>>
>>
>> On May 4, 2009, at 9:13 AM, users-request_at_[hidden] wrote:
>>
>> Send users mailing list submissions to
>> users_at_[hidden]
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> or, via email, send a message with subject or body 'help' to
>> users-request_at_[hidden]
>>
>> You can reach the person managing the list at
>> users-owner_at_[hidden]
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of users digest..."
>>
>>
>> Today's Topics:
>>
>> 1. Re: How do I compile OpenMPI in Xcode 3.1 (Vicente Puig)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 4 May 2009 18:13:45 +0200
>> From: Vicente Puig <vpuibor_at_[hidden]>
>> Subject: Re: [OMPI users] How do I compile OpenMPI in Xcode 3.1
>> To: Open MPI Users <users_at_[hidden]>
>> Message-ID:
>> <3e9a21680905040913u3f36d3c9rdcd3413bfdcd0c9_at_[hidden]>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> If I can not make it work with Xcode, which one could I use?, which one
>> do
>> you use to compile and debug OpenMPI?.
>> Thanks
>>
>> Vincent
>>
>>
>> 2009/5/4 Jeff Squyres <jsquyres_at_[hidden]>
>>
>> Open MPI comes pre-installed in Leopard; as Warner noted, since Leopard
>> doesn't ship with a Fortran compiler, the Open MPI that Apple ships has
>> non-functional mpif77 and mpif90 wrapper compilers.
>>
>> So the Open MPI that you installed manually will use your Fortran
>> compilers, and therefore will have functional mpif77 and mpif90 wrapper
>> compilers. Hence, you probably need to be sure to use the "right" wrapper
>> compilers. It looks like you specified the full path specified to
>> ExecPath,
>> so I'm not sure why Xcode wouldn't work with that (like I mentioned, I
>> unfortunately don't use Xcode myself, so I don't know why that wouldn't
>> work).
>>
>>
>>
>>
>> On May 4, 2009, at 11:53 AM, Vicente wrote:
>>
>> Yes, I already have gfortran compiler on /usr/local/bin, the same path
>> as my mpif90 compiler. But I've seen when I use the mpif90 on /usr/bin
>> and on /Developer/usr/bin says it:
>>
>> "Unfortunately, this installation of Open MPI was not compiled with
>> Fortran 90 support. As such, the mpif90 compiler is non-functional."
>>
>>
>> That should be the problem, I will have to change the path to use the
>> gfortran I have installed.
>> How could I do it? (Sorry, I am beginner)
>>
>> Thanks.
>>
>>
>> El 04/05/2009, a las 17:38, Warner Yuen escribi?:
>>
>> Have you installed a Fortran compiler? Mac OS X's developer tools do
>> not come with a Fortran compiler, so you'll need to install one if
>> you haven't already done so. I routinely use the Intel IFORT
>> compilers with success. However, I hear many good things about the
>> gfortran compilers on Mac OS X, you can't beat the price of gfortran!
>>
>>
>> Warner Yuen
>> Scientific Computing
>> Consulting Engineer
>> Apple, Inc.
>> email: wyuen_at_[hidden]
>> Tel: 408.718.2859
>>
>>
>>
>>
>> On May 4, 2009, at 7:28 AM, users-request_at_[hidden] wrote:
>>
>> Send users mailing list submissions to
>> users_at_[hidden]
>>
>> To subscribe or unsubscribe via the World Wide Web, visit
>> http://www.open-mpi.org/mailman/listinfo.cgi/users
>> or, via email, send a message with subject or body 'help' to
>> users-request_at_[hidden]
>>
>> You can reach the person managing the list at
>> users-owner_at_[hidden]
>>
>> When replying, please edit your Subject line so it is more specific
>> than "Re: Contents of users digest..."
>>
>>
>> Today's Topics:
>>
>> 1. How do I compile OpenMPI in Xcode 3.1 (Vicente)
>> 2. Re: 1.3.1 -rf rankfile behaviour ?? (Ralph Castain)
>>
>>
>> ----------------------------------------------------------------------
>>
>> Message: 1
>> Date: Mon, 4 May 2009 16:12:44 +0200
>> From: Vicente <vpuibor_at_[hidden]>
>> Subject: [OMPI users] How do I compile OpenMPI in Xcode 3.1
>> To: users_at_[hidden]
>> Message-ID: <1C2C0085-940F-43BB-910F-975871AE2F09_at_[hidden]>
>> Content-Type: text/plain; charset="windows-1252"; Format="flowed";
>> DelSp="yes"
>>
>> Hi, I've seen the FAQ "How do I use Open MPI wrapper compilers in
>> Xcode", but it's only for MPICC. I am using MPIF90, so I did the
>> same,
>> but changing MPICC for MPIF90, and also the path, but it did not
>> work.
>>
>> Building target ?fortran? of project ?fortran? with configuration
>> ?Debug?
>>
>>
>> Checking Dependencies
>> Invalid value 'MPIF90' for GCC_VERSION
>>
>>
>> The file "MPIF90.cpcompspec" looks like this:
>>
>> 1 /**
>> 2 Xcode Coompiler Specification for MPIF90
>> 3
>> 4 */
>> 5
>> 6 { Type = Compiler;
>> 7 Identifier = com.apple.compilers.mpif90;
>> 8 BasedOn = com.apple.compilers.gcc.4_0;
>> 9 Name = "MPIF90";
>> 10 Version = "Default";
>> 11 Description = "MPI GNU C/C++ Compiler 4.0";
>> 12 ExecPath = "/usr/local/bin/mpif90"; // This gets
>> converted to the g++ variant automatically
>> 13 PrecompStyle = pch;
>> 14 }
>>
>> and is located in "/Developer/Library/Xcode/Plug-ins"
>>
>> and when I do mpif90 -v on terminal it works well:
>>
>> Using built-in specs.
>> Target: i386-apple-darwin8.10.1
>> Configured with: /tmp/gfortran-20090321/ibin/../gcc/configure --
>> prefix=/usr/local/gfortran --enable-languages=c,fortran --with-gmp=/
>> tmp/gfortran-20090321/gfortran_libs --enable-bootstrap
>> Thread model: posix
>> gcc version 4.4.0 20090321 (experimental) [trunk revision 144983]
>> (GCC)
>>
>>
>> Any idea??
>>
>> Thanks.
>>
>> Vincent
>> -------------- next part --------------
>> HTML attachment scrubbed and removed
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 4 May 2009 08:28:26 -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:
>> <71d2d8cc0905040728h2002f4d7s4c49219eee29e86f_at_[hidden]>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> Unfortunately, I didn't write any of that code - I was just fixing
>> the
>> mapper so it would properly map the procs. From what I can tell,
>> the proper
>> things are happening there.
>>
>> I'll have to dig into the code that specifically deals with parsing
>> the
>> results to bind the processes. Afraid that will take awhile longer
>> - pretty
>> dark in that hole.
>>
>>
>> On Mon, May 4, 2009 at 8:04 AM, Geoffroy Pignot
>> <geopignot_at_[hidden]> wrote:
>>
>> Hi,
>>
>> So, there are no more crashes with my "crazy" mpirun command. But
>> the
>> paffinity feature seems to be broken. Indeed I am not able to pin my
>> processes.
>>
>> Simple test with a program using your plpa library :
>>
>> r011n006% cat hostf
>> r011n006 slots=4
>>
>> r011n006% cat rankf
>> rank 0=r011n006 slot=0 ----> bind to CPU 0 , exact ?
>>
>> r011n006% /tmp/HALMPI/openmpi-1.4a/bin/mpirun --hostfile hostf --
>> rankfile
>> rankf --wdir /tmp -n 1 a.out
>> PLPA Number of processors online: 4
>> PLPA Number of processor sockets: 2
>> PLPA Socket 0 (ID 0): 2 cores
>> PLPA Socket 1 (ID 3): 2 cores
>>
>> Ctrl+Z
>> r011n006%bg
>>
>> r011n006% ps axo stat,user,psr,pid,pcpu,comm | grep gpignot
>> R+ gpignot 3 9271 97.8 a.out
>>
>> In fact whatever the slot number I put in my rankfile , a.out
>> always runs
>> on the CPU 3. I was looking for it on CPU 0 accordind to my
>> cpuinfo file
>> (see below)
>> The result is the same if I try another syntax (rank 0=r011n006
>> slot=0:0
>> bind to socket 0 - core 0 , exact ? )
>>
>> Thanks in advance
>>
>> Geoffroy
>>
>> PS: I run on rhel5
>>
>> r011n006% uname -a
>> Linux r011n006 2.6.18-92.1.1NOMAP32.el5 #1 SMP Sat Mar 15 01:46:39
>> CDT 2008
>> x86_64 x86_64 x86_64 GNU/Linux
>>
>> My configure is :
>> ./configure --prefix=/tmp/openmpi-1.4a --libdir='${exec_prefix}/
>> lib64'
>> --disable-dlopen --disable-mpi-cxx --enable-heterogeneous
>>
>>
>> r011n006% cat /proc/cpuinfo
>> processor : 0
>> vendor_id : GenuineIntel
>> cpu family : 6
>> model : 15
>> model name : Intel(R) Xeon(R) CPU 5150 @ 2.66GHz
>> stepping : 6
>> cpu MHz : 2660.007
>> cache size : 4096 KB
>> physical id : 0
>> siblings : 2
>> core id : 0
>> cpu cores : 2
>> fpu : yes
>> fpu_exception : yes
>> cpuid level : 10
>> wp : yes
>> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr
>> pge mca
>> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall
>> nx lm
>> constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm
>> bogomips : 5323.68
>> clflush size : 64
>> cache_alignment : 64
>> address sizes : 36 bits physical, 48 bits virtual
>> power management:
>>
>> processor : 1
>> vendor_id : GenuineIntel
>> cpu family : 6
>> model : 15
>> model name : Intel(R) Xeon(R) CPU 5150 @ 2.66GHz
>> stepping : 6
>> cpu MHz : 2660.007
>> cache size : 4096 KB
>> physical id : 3
>> siblings : 2
>> core id : 0
>> cpu cores : 2
>> fpu : yes
>> fpu_exception : yes
>> cpuid level : 10
>> wp : yes
>> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr
>> pge mca
>> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall
>> nx lm
>> constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm
>> bogomips : 5320.03
>> clflush size : 64
>> cache_alignment : 64
>> address sizes : 36 bits physical, 48 bits virtual
>> power management:
>>
>> processor : 2
>> vendor_id : GenuineIntel
>> cpu family : 6
>> model : 15
>> model name : Intel(R) Xeon(R) CPU 5150 @ 2.66GHz
>> stepping : 6
>> cpu MHz : 2660.007
>> cache size : 4096 KB
>> physical id : 0
>> siblings : 2
>> core id : 1
>> cpu cores : 2
>> fpu : yes
>> fpu_exception : yes
>> cpuid level : 10
>> wp : yes
>> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr
>> pge mca
>> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall
>> nx lm
>> constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm
>> bogomips : 5319.39
>> clflush size : 64
>> cache_alignment : 64
>> address sizes : 36 bits physical, 48 bits virtual
>> power management:
>>
>> processor : 3
>> vendor_id : GenuineIntel
>> cpu family : 6
>> model : 15
>> model name : Intel(R) Xeon(R) CPU 5150 @ 2.66GHz
>> stepping : 6
>> cpu MHz : 2660.007
>> cache size : 4096 KB
>> physical id : 3
>> siblings : 2
>> core id : 1
>> cpu cores : 2
>> fpu : yes
>> fpu_exception : yes
>> cpuid level : 10
>> wp : yes
>> flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr
>> pge mca
>> cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall
>> nx lm
>> constant_tsc pni monitor ds_cpl vmx est tm2 cx16 xtpr lahf_lm
>> bogomips : 5320.03
>> clflush size : 64
>> cache_alignment : 64
>> address sizes : 36 bits physical, 48 bits virtual
>> power management:
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Mon, 4 May 2009 04:45:57 -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: <D01D7B16-4B47-46F3-AD41-D1A90B2E4927_at_[hidden]>
>>
>> Content-Type: text/plain; charset="us-ascii"; Format="flowed";
>> DelSp="yes"
>>
>> My apologies - I wasn't clear enough. You need a tarball from
>> r21111
>> or greater...such as:
>>
>> http://www.open-mpi.org/nightly/trunk/openmpi-1.4a1r21142.tar.gz
>>
>> HTH
>> Ralph
>>
>>
>> On May 4, 2009, at 2:14 AM, Geoffroy Pignot wrote:
>>
>> Hi ,
>>
>> I got the openmpi-1.4a1r21095.tar.gz tarball, but unfortunately my
>> command doesn't work
>>
>> cat rankf:
>> rank 0=node1 slot=*
>> rank 1=node2 slot=*
>>
>> cat hostf:
>> node1 slots=2
>> node2 slots=2
>>
>> mpirun --rankfile rankf --hostfile hostf --host node1 -n 1
>> hostname : --host node2 -n 1 hostname
>>
>> Error, invalid rank (1) in the rankfile (rankf)
>>
>>
>>
>> --------------------------------------------------------------------------
>> [r011n006:28986] [[45541,0],0] ORTE_ERROR_LOG: Bad parameter in
>> file
>> rmaps_rank_file.c at line 403
>> [r011n006:28986] [[45541,0],0] ORTE_ERROR_LOG: Bad parameter in
>> file
>> base/rmaps_base_map_job.c at line 86
>> [r011n006:28986] [[45541,0],0] ORTE_ERROR_LOG: Bad parameter in
>> file
>> base/plm_base_launch_support.c at line 86
>> [r011n006:28986] [[45541,0],0] ORTE_ERROR_LOG: Bad parameter in
>> file
>> plm_rsh_module.c at line 1016
>>
>>
>> Ralph, could you tell me if my command syntax is correct or
>> not ? if
>> not, give me the expected one ?
>>
>> Regards
>>
>> Geoffroy
>>
>>
>>
>>
>> 2009/4/30 Geoffroy Pignot <geopignot_at_[hidden]>
>> Immediately Sir !!! :)
>>
>> Thanks again Ralph
>>
>> Geoffroy
>>
>>
>>
>>
>>
>> ------------------------------
>>
>> Message: 2
>> Date: Thu, 30 Apr 2009 06:45:39 -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:
>> <71d2d8cc0904300545v61a42fe1k50086d2704d0f7e6_at_[hidden]>
>> Content-Type: text/plain; charset="iso-8859-1"
>>
>> I believe this is fixed now in our development trunk - you can
>> download any
>> tarball starting from last night and give it a try, if you like.
>> Any
>> feedback would be appreciated.
>>
>> Ralph
>>
>>
>> On Apr 14, 2009, at 7:57 AM, Ralph Castain wrote:
>>
>> 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
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>> Jeff Squyres
>> Cisco Systems
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>
>
> --
> Jeff Squyres
> Cisco Systems
>
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