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Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
From: Gus Correa (gus_at_[hidden])
Date: 2009-05-04 21:49:10


Hi Ralph and Geffroy

I've been following this thread with a lot of interest.
Setting processor affinity and pin the processes to cores
was next on my "TODO" list, and I just started it.

I tried to use three different versions of rankfile,
with OpenMPI 1.3.1 on a dual-socket quad-core
Opteron machine.
In all cases I've got errors similar to Geoffroy's.

The mpiexec command line is:

${MPIEXEC} \
         -prefix ${PREFIX} \
         -np ${NP} \
        -rf my_rankfile \
         -mca btl openib,sm,self \
        -mca mpi_leave_pinned 0 \
        -mca paffinity_base_verbose 5 \
         xhpl

I use Torque, and I generate the rankfile programatically based
on the $PBS_NODEFILE.

Here are three rank files I used:

#1 rankfile (trying to associate slot=physical_id:core_id from
/proc/cpuinfo)
[gus_at_monk hpl]$ more my_rankfile
rank 0=node24 slot=0:0
rank 1=node24 slot=0:1
rank 2=node24 slot=0:2
rank 3=node24 slot=0:3
rank 4=node24 slot=1:0
rank 5=node24 slot=1:1
rank 6=node24 slot=1:2
rank 7=node24 slot=1:3

#2 rankfile (trying to associaate slot=processor from /proc/cpuinfo)
[gus_at_monk hpl]$ more my_rankfile
rank 0=node24 slot=0
rank 1=node24 slot=1
rank 2=node24 slot=2
rank 3=node24 slot=3
rank 4=node24 slot=4
rank 5=node24 slot=5
rank 6=node24 slot=6
rank 7=node24 slot=7

#3 rankfile (Similar to #1 but with "p" that the FAQs say stands for
"physical")
[gus_at_monk hpl]$ more my_rankfile
rank 0=node24 slot=p0:0
rank 1=node24 slot=p0:1
rank 2=node24 slot=p0:2
rank 3=node24 slot=p0:3
rank 4=node24 slot=p1:0
rank 5=node24 slot=p1:1
rank 6=node24 slot=p1:2
rank 7=node24 slot=p1:3

***

In all cases I get this error (just like Geoffroy):

******

Rankfile claimed host node24 that was not allocated or oversubscribed
it's slots
:

--------------------------------------------------------------------------
[node24.cluster:23762] [[59468,0],0] ORTE_ERROR_LOG: Bad parameter in
file ../..
/../../../orte/mca/rmaps/rank_file/rmaps_rank_file.c at line 108
[node24.cluster:23762] [[59468,0],0] ORTE_ERROR_LOG: Bad parameter in
file ../..
/../../orte/mca/rmaps/base/rmaps_base_map_job.c at line 87
[node24.cluster:23762] [[59468,0],0] ORTE_ERROR_LOG: Bad parameter in
file ../..
/../../orte/mca/plm/base/plm_base_launch_support.c at line 77
[node24.cluster:23762] [[59468,0],0] ORTE_ERROR_LOG: Bad parameter in
file ../..
/../../../orte/mca/plm/tm/plm_tm_module.c at line 167
--------------------------------------------------------------------------
A daemon (pid unknown) died unexpectedly on signal 1 while attempting to
launch so we are aborting.

********

I confess I am a bit confused about the nomenclature.

What do you call CPU in the rankfile context?
How about slot, core, and socket?

Linux keeps information about these items in /proc/cpuinfo,
in /sys/devices/system/cpu,
and in /sys/devices/system/nodes.
However, the nomenclature is different from OpenMPI.

How can one use that information to build a correct rankfile?
I read the mpiexec man page and the FAQs but I am still confused.

Questions:
1) In the rankfile notation slot=cpu_num, is cpu-num the same as
"processor" in /proc/cpuinfo, or is it the same as "physical id" in
/proc/cpuinfo?

2) In the rankfile notation slot=socket_num:core_num, is socket_num the
same as "physical id" in /proc/cpuinfo, or something else?

3) Is core_num in the rankfile notation the same as "core id" or the
same as "processor" in /proc/cpuinfo?
Or is it yet another thing?

Geoffroy sent the /proc/cpuinfo of his
Intel dual-socket dual-core machine.
I enclose the one from my AMD dual-socket quad-core below.
The architectures (non-NUMA vs. NUMA) are different and so are the
numbering schemes:

Geoffrey's numbers go like this (each column match a single core):
processor---0-1-2-3
physical-id-0-3-0-3 (alternating physical IDs)
core--------0-0-1-1

Whereas my numbers go like this:
processor---0-1-2-3-4-5-6-7
physical-id-0-0-0-0-1-1-1-1 (physical IDs don't alternate)
core--------0-1-2-3-0-1-2-3

So, first I think a clarification about the nomenclature would
really help us build meaningful rankfiles.
I suggest to relate the names in rankfile to those in /proc/cpuinfo,
if possible (or to /sys/devices/system/cpu or /sys/devices/system/nodes).
(Other OSs may use different names though.)
The tables above show that things can get confusing to the user,
if the connection between the two is not made.

Second, as Ralph pointed out, there may be a bug to fix as well.

****

It would be great to have the rankfile functionality working.
However, the good news is that just setting processor affinity
works fine.
This is OK for now, since I am using the whole node.
The mpirun command line I used is :

${MPIEXEC} \
         -prefix ${PREFIX} \
         -np ${NP} \
        -mca mpi_paffinity_alone 1 \
         -mca btl openib,sm,self \
        -mca mpi_leave_pinned 0 \
        -mca paffinity_base_verbose 5 \
         xhpl

Thank you,
Gus Correa

################

$ cat /proc/cpuinfo
processor : 0
vendor_id : AuthenticAMD
cpu family : 16
model : 4
model name : Quad-Core AMD Opteron(tm) Processor 2376
stepping : 2
cpu MHz : 800.000
cache size : 512 KB
physical id : 0
siblings : 4
core id : 0
cpu cores : 4
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc pni cx16 popcnt lahf_lm
cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse
3dnowprefetch osvw
bogomips : 4625.83
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor : 1
vendor_id : AuthenticAMD
cpu family : 16
model : 4
model name : Quad-Core AMD Opteron(tm) Processor 2376
stepping : 2
cpu MHz : 800.000
cache size : 512 KB
physical id : 0
siblings : 4
core id : 1
cpu cores : 4
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc pni cx16 popcnt lahf_lm
cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse
3dnowprefetch osvw
bogomips : 4623.16
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor : 2
vendor_id : AuthenticAMD
cpu family : 16
model : 4
model name : Quad-Core AMD Opteron(tm) Processor 2376
stepping : 2
cpu MHz : 800.000
cache size : 512 KB
physical id : 0
siblings : 4
core id : 2
cpu cores : 4
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc pni cx16 popcnt lahf_lm
cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse
3dnowprefetch osvw
bogomips : 4623.16
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor : 3
vendor_id : AuthenticAMD
cpu family : 16
model : 4
model name : Quad-Core AMD Opteron(tm) Processor 2376
stepping : 2
cpu MHz : 800.000
cache size : 512 KB
physical id : 0
siblings : 4
core id : 3
cpu cores : 4
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc pni cx16 popcnt lahf_lm
cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse
3dnowprefetch osvw
bogomips : 4622.82
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor : 4
vendor_id : AuthenticAMD
cpu family : 16
model : 4
model name : Quad-Core AMD Opteron(tm) Processor 2376
stepping : 2
cpu MHz : 800.000
cache size : 512 KB
physical id : 1
siblings : 4
core id : 0
cpu cores : 4
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc pni cx16 popcnt lahf_lm
cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse
3dnowprefetch osvw
bogomips : 4623.15
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor : 5
vendor_id : AuthenticAMD
cpu family : 16
model : 4
model name : Quad-Core AMD Opteron(tm) Processor 2376
stepping : 2
cpu MHz : 800.000
cache size : 512 KB
physical id : 1
siblings : 4
core id : 1
cpu cores : 4
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc pni cx16 popcnt lahf_lm
cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse
3dnowprefetch osvw
bogomips : 4623.16
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor : 6
vendor_id : AuthenticAMD
cpu family : 16
model : 4
model name : Quad-Core AMD Opteron(tm) Processor 2376
stepping : 2
cpu MHz : 800.000
cache size : 512 KB
physical id : 1
siblings : 4
core id : 2
cpu cores : 4
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc pni cx16 popcnt lahf_lm
cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse
3dnowprefetch osvw
bogomips : 4622.83
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

processor : 7
vendor_id : AuthenticAMD
cpu family : 16
model : 4
model name : Quad-Core AMD Opteron(tm) Processor 2376
stepping : 2
cpu MHz : 800.000
cache size : 512 KB
physical id : 1
siblings : 4
core id : 3
cpu cores : 4
fpu : yes
fpu_exception : yes
cpuid level : 5
wp : yes
flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov
pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt
pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc pni cx16 popcnt lahf_lm
cmp_legacy svm extapic cr8_legacy altmovcr8 abm sse4a misalignsse
3dnowprefetch osvw
bogomips : 4623.16
TLB size : 1024 4K pages
clflush size : 64
cache_alignment : 64
address sizes : 48 bits physical, 48 bits virtual
power management: ts ttp tm stc 100mhzsteps hwpstate [8]

Geoffroy Pignot wrote:
> Hi Ralph
>
> Thanks for your extra tests. Before leaving , I just pointed out a
> problem coming from running plpa across different rh distribs (<=>
> different Linux kernels). Indeed, I configure and compile openmpi on
> rhel4 , then I run on rhel5. I think my problem comes from this
> approximation. I'll do few more tests tomorrow morning (France) and keep
> you inform.
>
> Regards
>
> Geoffroy
>
>
>
>
>
>
>
>
>
>
> Message: 2
> Date: Mon, 4 May 2009 13:34:40 -0600
> From: Ralph Castain <rhc_at_[hidden] <mailto:rhc_at_[hidden]>>
> Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
> To: Open MPI Users <users_at_[hidden] <mailto:users_at_[hidden]>>
> Message-ID:
> <71d2d8cc0905041234m76eb5a9dx57a773997779db73_at_[hidden]
> <mailto:71d2d8cc0905041234m76eb5a9dx57a773997779db73_at_[hidden]>>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Hmmm...I'm afraid I can't replicate the problem. All seems to be working
> just fine on the RHEL systems available to me. The procs indeed bind
> to the
> specified processors in every case.
>
> rhc_at_odin ~/trunk]$ cat rankfile
> rank 0=odin001 slot=0
> rank 1=odin002 slot=1
>
> [rhc_at_odin mpi]$ mpirun -rf ../../../rankfile -n 2
> --leave-session-attached
> -mca paffinity_base_verbose 5 ./mpi_spin
> [odin001.cs.indiana.edu:09297 <http://odin001.cs.indiana.edu:09297>
> <http://odin001.cs.indiana.edu:9297/>]
> paffinity slot assignment: slot_list == 0
> [odin001.cs.indiana.edu:09297 <http://odin001.cs.indiana.edu:09297>
> <http://odin001.cs.indiana.edu:9297/>]
> paffinity slot assignment: rank 0 runs on cpu #0 (#0)
> [odin002.cs.indiana.edu:13566 <http://odin002.cs.indiana.edu:13566>]
> paffinity slot assignment: slot_list == 1
> [odin002.cs.indiana.edu:13566 <http://odin002.cs.indiana.edu:13566>]
> paffinity slot assignment: rank 1 runs on cpu
> #1 (#1)
>
> Suspended
> [rhc_at_odin mpi]$ ssh odin001
> [rhc_at_odin001 ~]$ ps axo stat,user,psr,pid,pcpu,comm | grep rhc
> S rhc 0 9296 0.0 orted
> RLl rhc 0 9297 100 mpi_spin
>
> [rhc_at_odin mpi]$ ssh odin002
> [rhc_at_odin002 ~]$ ps axo stat,user,psr,pid,pcpu,comm | grep rhc
> S rhc 0 13562 0.0 orted
> RLl rhc 1 13566 102 mpi_spin
>
>
> Not sure where to go from here...perhaps someone else can spot the
> problem?
> Ralph
>
>
> On Mon, May 4, 2009 at 8:28 AM, Ralph Castain <rhc_at_[hidden]
> <mailto:rhc_at_[hidden]>> wrote:
>
> > 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] <mailto: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] <mailto:rhc_at_[hidden]>>
> >>> Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
> >>> To: Open MPI Users <users_at_[hidden] <mailto:users_at_[hidden]>>
> >>> Message-ID: <D01D7B16-4B47-46F3-AD41-D1A90B2E4927_at_[hidden]
> <mailto: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]
> <mailto: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] <mailto:rhc_at_[hidden]>>
> >>> > Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
> >>> > To: Open MPI Users <users_at_[hidden]
> <mailto:users_at_[hidden]>>
> >>> > Message-ID:
> >>> >
> <71d2d8cc0904300545v61a42fe1k50086d2704d0f7e6_at_[hidden]
> <mailto: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] <mailto:rhc_at_[hidden]>>
> >>> > Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
> >>> > To: Open MPI Users <users_at_[hidden]
> <mailto:users_at_[hidden]>>
> >>> > Message-ID: <F6290ADA-A196-43F0-A853-CBCB802D8D9C_at_[hidden]
> <mailto: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]
> <mailto:lenny.verkhovsky_at_[hidden]>>
> >>> > > Subject: Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??
> >>> > > To: Open MPI Users <users_at_[hidden]
> <mailto:users_at_[hidden]>>
> >>> > > Message-ID:
> >>> > >
> <453d39990904120826t2e1d1d33l7bb1fe3de65b5361_at_[hidden]
> <mailto: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]
> <mailto: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] <mailto:users_at_[hidden]>
> >>> > > http://www.open-mpi.org/mailman/listinfo.cgi/users
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> >>> > End of users Digest, Vol 1202, Issue 2
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