[OMPI users] Rebuild RPM for CentOS 7.1

2015-10-31 Thread Oliver 
hi all

I am trying to rebuild 1.10 RPM from the src rpm on Cent OS 7. The build
process went fine without problem. Whiling trying to install the rpm, I
encountered the following error:


Examining openmpi-1.10.0-1.x86_64.rpm: openmpi-1.10.0-1.x86_64
Marking openmpi-1.10.0-1.x86_64.rpm to be installed
Resolving Dependencies
--> Running transaction check
---> Package openmpi.x86_64 0:1.10.0-1 will be installed
--> Finished Dependency Resolution

...

Transaction check error:
  file /usr/bin from install of openmpi-1.10.0-1.x86_64 conflicts with file
from package filesystem-3.2-18.el7.x86_64
  file /usr/lib64 from install of openmpi-1.10.0-1.x86_64 conflicts with
file from package filesystem-3.2-18.el7.x86_64

what am I missing, is there a fix?

TIA

-- 
Oliver

Re: [OMPI users] Unable to compile for libnumactl and libnumactl-devel

2015-10-31 Thread Fabian Wein 

> Am 30.10.2015 um 21:45 schrieb Jeff Squyres (jsquyres) :
> 
> Oh, that's an interesting idea: perhaps the "bind to numa" is failing -- but 
> perhaps "bind to socket" would work.
> 
> Can you try:
> 
> /opt/openmpi-1.10.0-gcc/bin/mpiexec -bind-to numa -n 4 hostname
> /opt/openmpi-1.10.0-gcc/bin/mpiexec -bind-to socket -n 4 hostname
> 
Both report the same error. Interestingly -bind-to-socket works but it does not 
bring me the performance I expect for the petsc benchmark.

I have a second ubuntu 14.4 system (two old quad core xenons) and build ompi 
there. If it works there I can try to move the binaries.

Secondly I will try intel-mpi.

Thanks for your help and efforts!


/opt/petsc-3.6.2$ /opt/openmpi-1.10.0-gcc/bin/mpiexec -bind-to-socket -n 4 
hostname
--
The following command line option and corresponding MCA parameter have
been deprecated and replaced as follows:

  Command line option:
Deprecated:  --bind-to-socket
Replacement: --bind-to socket

  Equivalent MCA parameter:
Deprecated:  hwloc_base_bind_to_socket
Replacement: hwloc_base_binding_policy=socket

The deprecated forms *will* disappear in a future version of Open MPI.
Please update to the new syntax.
--
leo
leo
leo
leo






> 
> 
> 
>> On Oct 30, 2015, at 12:02 PM, Fabian Wein  wrote:
>> 
>> On 10/30/2015 02:48 PM, Dave Love wrote:
>>> Fabian Wein  writes:
>>> 
 Is this a valid test?
 
 
 /opt/openmpi-1.10.0-gcc/bin/mpiexec -n 4 hostname
 leo
 leo
 leo
 leo
>>> 
>>> So, unless you turned off the default binding -- to socket? check the
>>> mpirun man page -- it worked, but the "numa" level failed.  I don't know
>>> if that level has to exist, and there have been bugs in that area
>>> before.  Running lstopo might be useful, and checking that you're
>>> picking up the right hwloc dynamic library.
>> 
>> Sorry, I don't understand. Where is hwloc dynamically linked? I made now 
>> sure I
>> have only one type of libhwloc.so and libnuma.so on the system (there were 
>> versions
>> of an older date). Is a a way to check the lib if it has the feature?
>> 
>> mpiexec only links libnuma which was actually the old version and is now the 
>> one I
>> build from the numactl source by myself.
>> 
>> ldd /opt/openmpi-1.10.0-gcc/bin/mpiexec
>>  linux-vdso.so.1 =>  (0x7dbaa000)
>>  libopen-rte.so.12 => /opt/openmpi-1.10.0-gcc/lib/libopen-rte.so.12 
>> (0x7fbfdae58000)
>>  libopen-pal.so.13 => /opt/openmpi-1.10.0-gcc/lib/libopen-pal.so.13 
>> (0x7fbfdab78000)
>>  libpthread.so.0 => /lib/x86_64-linux-gnu/libpthread.so.0 
>> (0x7fbfda958000)
>>  libc.so.6 => /lib/x86_64-linux-gnu/libc.so.6 (0x7fbfda59)
>>  libnuma.so.1 => /usr/lib/x86_64-linux-gnu/libnuma.so.1 
>> (0x7fbfda38)
>>  libdl.so.2 => /lib/x86_64-linux-gnu/libdl.so.2 (0x7fbfda178000)
>>  librt.so.1 => /lib/x86_64-linux-gnu/librt.so.1 (0x7fbfd9f7)
>>  libutil.so.1 => /lib/x86_64-linux-gnu/libutil.so.1 (0x7fbfd9d68000)
>>  /lib64/ld-linux-x86-64.so.2 (0x7fbfdb0d8000)
>> 
>>> 
>>> What happens if you try to bind to sockets, assuming you don't want to
>>> bind to cores?  [I don't understand why the default isn't to cores when
>>> you have only one process per core.]
>> 
>> bind-to cpu and socket bring the same error as bind-to numa.
>> 
>> 
>> 
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> 
> 
> -- 
> Jeff Squyres
> jsquy...@cisco.com
> For corporate legal information go to: 
> http://www.cisco.com/web/about/doing_business/legal/cri/
> 
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Re: [OMPI users] Relative indexing error in OpenMPI 1.8.7

2015-10-31 Thread Ralph Castain 
Sorry for delayed response. This was indeed a bug, and I have repaired it on 
the master. I’ll file a request to have it moved over to the upcoming 2.0 
release.

I’m afraid it missed the deadline for 1.10.1, and there are no current plans 
for a 1.10.2. Likewise, we have stopped supporting the 1.8 series.

Sorry for the inconvenience.
Ralph


> On Oct 8, 2015, at 10:32 PM, waku2005  wrote:
> 
> Dear OpenMPI users
> 
> Relative indexing error occurs in my CentOS small cluster.
> What and where should I check ?
> 
> Environment:
> - 4node GbE cluster (CentOS 6.7)
> - OpenMPI 1.8.7 (builded usin system compiler, gcc version 4.4.7 20120313 and 
> installed /usr/local/openmpi-1.8.7) 
> - use ssh without password authentification (using RSA key) 
> 
> This is "myhosts" file:
> --
> ensis10 slots=4
> ensis12 slots=6
> ensis13 slots=6
> ensis14 slots=6
> --  
> 
> Command line and error messgae: 
> $ mpirun --hostfile ./myhosts -np 4 -host +n2 hostname
> --
> A relative host was specified, but no prior allocation has been made.
> Thus, there is no way to determine the proper host to be used.
> 
> -host: +n2
> 
> Please see the orte_hosts man page for further information.
> --
> 
> # In case of direct hostname specification, it works fine such as:
> # [@ensis10] $ mpirun --hostfile ./myhosts -np 4 -host ensis12 hostname
> # ensis12
> # ensis12
> # ensis12
> # ensis12
> #
> 
> Thanks in advance
> 
> 
> -- 
> 
> S.Wakashima  (waku2...@gmail.com )
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