Re: [OMPI users] lammps MD code fails with Open MPI 1.3

[Jeff Pummill]

It's probably not the same issue as this is one of the very few codes 
that I maintain which is C++ and not fortran :-(


It behaved similarly on another system when I built it against a new 
version (1.0??) of MVAPICH. I had to roll back a version from that as well.


I may contact the lammps people and see if they know what's going on as 
well.



Jeff F. Pummill
Senior Linux Cluster Administrator
TeraGrid Campus Champion - UofA
University of Arkansas
Fayetteville, Arkansas 72701
(479) 575 - 4590
http://hpc.uark.edu

"In theory, there is no difference between theory and
practice. But in practice, there is!" /-- anonymous/


Jeff Squyres wrote:
Actually, there was a big Fortran bug that crept in after 1.3 that was 
just fixed on the trunk last night.  If you're using Fortran 
applications with some compilers (e.g., Intel), the 1.3.1 nightly 
snapshots may have hung in some cases.  The problem should be fixed in 
tonight's 1.3.1 nightly snapshot.



On Feb 20, 2009, at 12:46 AM, Nysal Jan wrote:


It could be the same bug reported here
http://www.open-mpi.org/community/lists/users/2009/02/8010.php

Can you try a recent snapshot of 1.3.1
(http://www.open-mpi.org/nightly/v1.3/) to verify if this has been fixed

--Nysal

On Thu, 2009-02-19 at 16:09 -0600, Jeff Pummill wrote:

I built a fresh version of lammps v29Jan09 against Open MPI 1.3 which
in turn was built with Gnu compilers v4.2.4 on an Ubuntu 8.04 x86_64
box. This Open MPI build was able to generate usable binaries such as
XHPL and NPB, but the lammps binary it generated was not usable.

I tried it with a couple of different versions of the lammps source,
but to no avail. No errors during the builds and a binary was created,
but when executing the job it quickly exits with no messages other
than:

jpummil@stealth:~$ mpirun -np 4 -hostfile
hosts /home/jpummil/lmp_Stealth-OMPI < in.testbench_small
LAMMPS (22 Jan 2008)

Interestingly, I downloaded Open MPI 1.2.8, built it with the same
configure options I had used with 1.3, and it worked.

I'm getting by fine with 1.2.8. I just wanted to file a possible bug
report on 1.3 and see if others have seen this behavior.

Cheers!

--
Jeff F. Pummill
Senior Linux Cluster Administrator
TeraGrid Campus Champion - UofA
University of Arkansas


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[OMPI users] lammps MD code fails with Open MPI 1.3

[Jeff Pummill]

I built a fresh version of lammps v29Jan09 against Open MPI 1.3 which in 
turn was built with Gnu compilers v4.2.4 on an Ubuntu 8.04 x86_64 box. 
This Open MPI build was able to generate usable binaries such as XHPL 
and NPB, but the lammps binary it generated was not usable.


I tried it with a couple of different versions of the lammps source, but 
to no avail. No errors during the builds and a binary was created, but 
when executing the job it quickly exits with no messages other than:


jpummil@stealth:~$ mpirun -np 4 -hostfile hosts 
/home/jpummil/lmp_Stealth-OMPI < in.testbench_small

LAMMPS (22 Jan 2008)

Interestingly, I downloaded Open MPI 1.2.8, built it with the same 
configure options I had used with 1.3, and it worked.


I'm getting by fine with 1.2.8. I just wanted to file a possible bug 
report on 1.3 and see if others have seen this behavior.


Cheers!

--
Jeff F. Pummill
Senior Linux Cluster Administrator
TeraGrid Campus Champion - UofA
University of Arkansas
//

Re: [OMPI users] MPI-2 Supported on Open MPI 1.2.5?

[Jeff Pummill]

Haha, yeah we found out about that one when trying to run Linpack with 
threaded BLAS implementations.


On the MPI-2 note, anyone running MATLAB and the parallel toolkit under 
Open MPI? They are unreasonably obscure about what MPI they need 
although I do believe they need MPI-2 functions.


If it will work with Open MPI, and is not a nightmare to set up, I may 
try it as some of my users would be elated. If there are excessive 
problems, I may opt for SciLab which is supposed to be an "equivalent" 
and open source.



Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
Fayetteville, Arkansas 72701
(479) 575 - 4590
http://hpc.uark.edu

"In theory, there is no difference between theory and
practice. But in practice, there is!" /-- anonymous/


Brian Budge wrote:
One small (or to some, not so small) note is that full multi-threading 
with OpenMPI is very unlikely to work with infiniband right now.


  Brian

On Mon, Mar 10, 2008 at 6:24 AM, Michael <mk...@ieee.org 
<mailto:mk...@ieee.org>> wrote:


Quick answer, till you get a complete answer, Yes, OpenMPI has long
supported most of the MPI-2 features.

Michael

On Mar 7, 2008, at 7:44 AM, Jeff Pummill wrote:
> Just a quick question...
>
> Does Open MPI 1.2.5 support most or all of the MPI-2 directives and
> features?
>
> I have a user who specified MVAPICH2 as he needs some features like
> extra task spawning, but I am trying to standardize on Open MPI
> compiled against Infiniband for my primary software stack.
>
> Thanks!
>
> --
> Jeff F. Pummill
> Senior Linux Cluster Administrator
> University of Arkansas

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[OMPI users] MPI-2 Supported on Open MPI 1.2.5?

[Jeff Pummill]

Just a quick question...

Does Open MPI 1.2.5 support most or all of the MPI-2 directives and 
features?


I have a user who specified MVAPICH2 as he needs some features like 
extra task spawning, but I am trying to standardize on Open MPI compiled 
against Infiniband for my primary software stack.


Thanks!

--
Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
//

Re: [OMPI users] openMPI on 64 bit SUSE 10.2 OS

[Jeff Pummill]

Is it possible that this could be a problem with /usr/lib64 as opposed 
to /usr/lib?


Just a thought...

Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
//


Hsieh, Pei-Ying (MED US) wrote:

Hi, Edgar and Galen,

Thanks for the quick reply!

What puzzles me is that, on 32 bit OpenSUSE, I was able to compile elmer
solver without any issue using the same script.  I am planning to use
HYPRE library, but, configure file indicated that it cannot find hypre
either which is another puzzle to me.  I will look into this further.

Best,

pei 


-Original Message-
From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On
Behalf Of Edgar Gabriel
Sent: Tuesday, February 12, 2008 4:28 PM
To: Open MPI Users
Subject: Re: [OMPI users] openMPI on 64 bit SUSE 10.2 OS

I doubt that this has to do anything with the platform. We are running 
here Open MPI on a 64bit architecture using SuSe 10.2  since quite a 
while successfully. However, you configure log is indicating, the 
parpack could not be found, so you might have to change the CFLAGS and 
LDFLAGS in order for you configure script to find the according library.


Hsieh, Pei-Ying (MED US) wrote:
  

configure: error: The MPI version needs parpack. Disabling MPI.
peiying@saturn:~/elmer/elmer-5.4.0/fem-5.4.0>   



Thanks
Edgar
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Re: [OMPI users] flash2.5 with openmpi

[Jeff Pummill]

I'm guessing he means the ASC FLASH code which simulates star explosions...

Brock?


Jeff F. Pummill
University of Arkansas
//


Doug Reeder wrote:

Brock,

Do you mean flash memory, like a USB memory stick. What kid of file  
system is on the memory. Is there some filesystem limit you are  
bumping into.


Doug Reeder
On Jan 25, 2008, at 8:38 AM, Brock Palen wrote:

  

Is anyone using flash with openMPI?  we are here, but when ever it
tries to write its second checkpoint file it segfaults once it gets
to 2.2GB always in the same location.

Debugging is a pain as it takes 3 days to get to that point.  Just
wondering if anyone else has seen this same behavior.


Brock Palen
Center for Advanced Computing
bro...@umich.edu
(734)936-1985


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Re: [OMPI users] Tracing the library using gdb and xterm

[Jeff Pummill]

Krishna,

When you log in to the remote system, use ssh -X or ssh -Y which will 
export the xterm back thru the ssh connection.


Jeff Pummill
University of Arkansas


Krishna Chaitanya wrote:

Hi,
   I have been tracing the interactions between the PERUSE 
and MPI library,on one machine. I have been using gdb along with xterm 
to have two windows open at the same time as I step through the code. 
I wish to get a better glimpse of the working of the point to point 
calls, by launching the job on two machines and by tracing the flow in 
a similar manner. This is where I stand as of now :


mpirun --prefix /usr/local -hostfile machines  -np 2 xterm -e gdb 
peruse_ex1

xterm Xt error: Can't open display:
xterm:  DISPLAY is not set

   I tried using the display option for xterm and setting 
the value as 0.0, that was not of much help.
   If someone can guide me as to where the DISPLAY 
parameter has to be set to allow the remote machine to open the xterm 
window, it will be of great help.


Thanks,
Krishna
  



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In the middle of difficulty, lies opportunity


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Re: [OMPI users] "Hostfile" on Multicore Node?

[Jeff Pummill]

So, it appears that for a machine of this type (dual quad core cpu's), 
this approach would be correct for my tests...


[jpummill@n1 bin]$ more my-hosts
n1 slots=8 max_slots=8

and subsequently, launch two jobs in this configuration...
/home/jpummill/openmpi-1.2.2/bin/mpirun --hostfile my-hosts -np 4 
--byslot ./cg.C.4


It appears that this does avoid oversubscribing any particular core as I 
am not exceeding my core count by running just the two jobs requiring 4 
cores each.


Thanks,

Jeff Pummill





George Bosilca wrote:
The cleaner way to define such an environment is by using the 
max-slots and/or slots options in the hostfile. Here is a FAQ entry 
about how Open MPI deal with these options 
(http://www.open-mpi.org/faq/?category=running#mpirun-scheduling).


  george.


On Oct 26, 2007, at 10:52 AM, Jeff Pummill wrote:

I am doing some testing on a variety of 8-core nodes in which I just 
want to execute a couple of executables and have them distributed to 
the available cores without overlapping. Typically, this would be 
done with a parameter like -machinefile machines, but I have no idea 
what names to put into the machines file as this is a single node 
with two quad core cpu's. As I am launching the jobs sans scheduler, 
I need to specify what cores to run on I would think to keep from 
overscheduling some cores while others receive nothing to do at all.


Simple suggestions? Maybe Open MPI takes care of this detail for me?

Thanks!

Jeff Pummill
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[OMPI users] "Hostfile" on Multicore Node?

[Jeff Pummill]

I am doing some testing on a variety of 8-core nodes in which I just 
want to execute a couple of executables and have them distributed to the 
available cores without overlapping. Typically, this would be done with 
a parameter like /-machinefile machines/, but I have no idea what names 
to put into the /machines/ file as this is a single node with two quad 
core cpu's. As I am launching the jobs sans scheduler, I need to specify 
what cores to run on I would think to keep from overscheduling some 
cores while others receive nothing to do at all.


Simple suggestions? Maybe Open MPI takes care of this detail for me?

Thanks!

Jeff Pummill

Re: [OMPI users] SLURM vs. Torque?

[Jeff Pummill]

SLURM was really easy to build and install, plus it's a project of LLNL 
and I love stuff that the Nat'l Labs architect.


The SLURM message board is also very active and quick to respond to 
questions and problems.



Jeff F. Pummill



Bill Johnstone wrote:

Hello All.

We are starting to need resource/scheduling management for our small
cluster, and I was wondering if any of you could provide comments on
what you think about Torque vs. SLURM?  On the basis of the appearance
of active development as well as the documentation, SLURM seems to be
superior, but can anyone shed light on how they compare in use?

I realize the truth in the stock answer of "it depends on what you
need/want," but as of yet we are not experienced enough with this kind
of thing to have a set of firm requirements.  At this point, we can
probably adapt our workflow/usage a little bit to accomodate the way
the resource manager works.  And of course we'll be using OpenMPI with
whatever resource manager we go with.

Anyway, enough from me -- I'm looking to hear other's experiences and
viewpoints.

Thanks for any input!

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Re: [OMPI users] OpenMPI Documentation?

[Jeff Pummill]

Jeff,

Count us in at the UofA. My initial impressions of Open MPI are very 
good and I would be open to contributing to this effort as time allows.


Thanks!

Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
Fayetteville, Arkansas 72701
(479) 575 - 4590
http://hpc.uark.edu

"A supercomputer is a device for turning compute-bound
problems into I/O-bound problems." -Seymour Cray


Jeff Squyres wrote:
So there are at least a few people who are interested in this effort  
(keep chiming in if you are interested so that we can get a tally of  
who would like to be involved).


What kind of resources / organization would be useful for this  
group?  Indiana University graciously hosts all of Open MPI's  
electronic resources (Subversion, web site, bug tracking, DNS,  
mailing lists, ...) and I certainly can't speak for them, but if we  
ask nicely, I'd be willing to bet that they would add some hosting  
services for a documentation project (if such additional resources  
would be helpful, of course).


I would also be happy to host a teleconference if talking about all  
this start/admin stuff for an hour would save 1-2 weeks worth of  
detailed e-mails.


-

The only current documentation we have is:

- the web FAQ
- the README in the tarball

What is conspicuously missing is a nice PDF and/or HTML tarball with  
comprehensive documentation.  But I think that FAQ/README also fit  
into the general category of documentation, so it might make sense to  
put all 3 of these items under the control of one group.  The obvious  
rationale here is that all three could stay in tighter sync if  
there's one group monitoring all 3.


One point worth mentioning: Open MPI is all about community  
consensus, but "s/he who implements usually wins".  :-)  So if we get  
an active group working on documentation, the FAQ could be totally re- 
done if the group so decides (for example).


All this being said, the OMPI developers *have* talked about  
documentation a bit over time.  Here's some of the points from prior  
discussions, in no particular order:


- It highly desirable to have documentation that can be output in  
multiple different forms (PDF, HTML, ...whatever).  If possible, the  
docs should be shipped in distribution tarballs and hosted on the  
OMPI web site.


- LAM/MPI had two great docs: one for installation LAM/MPI and one  
for using LAM/MPI.  These might be good example documents for what  
Open MPI might want to do (see http://www.lam-mpi.org/using/docs/),  
regardless of the back-end technology used to generate the docs.   
Source LaTeX for these guides are available if it would be helpful (I  
wrote most of them).


- It would be most helpful if the documentation is written in a tool  
that has free editors, preferably cross-platform and available in  
multiple POSIX-like environments (Solaris, Linux, OS X).  MS Office  
was explicitly rejected because of its requirement for Windows/OS X  
(other Office clones were not really discussed).  LaTeX was discussed  
but wasn't favored due to the steep learning curve and general lack  
of experience with it outside of academia.


- First documentation should be aimed towards users.  Developer  
documentation might follow.


- Once upon a time, we developers started to use doxygen for  
documentation, but it has proven to be lousy for book-like entities  
(IONSHO).  Doxygen is decent for code documentation, but not documents.


- A few recent discussions about documentation came to the conclusion  
that Docbook (www.docbook.org) looked promising, but we didn't get  
deep into details / investigating the feasibility.  One obvious Big  
Project using Docbook is Subversion (see http://svnbook.red- 
bean.com/).  Docbook-produced HTML and PDF seem to look both pretty  
and functional.


- It would also be nice if sub-distributions of Open MPI could take  
the documentation and -- in some defined automated fashion -- be able  
to do the following:
 - insert their own "chapters" or "sections" that are specific to  
that sub-distribution (e.g., Sun ClusterTools have some Solaris- 
specific stuff, OFED have some OpenFabrics-specific stuff, etc.)
 - remove/"turn off" specific sections of documentation (e.g.,  
OFED would likely not include any documentation about Myricom  
networks [and vice versa])
This would go a long ways towards being able to keep the community  
documentation in sync with docs included in targeted/vendor OMPI  
releases.


- The OMPI web site is almost entirely written in PHP and is mirrored  
around the world.  It would be *strongly* preferred if the web-site  
hosting of the docs is fully mirror-able (because assumedly docs are  
one of the things that users would want to browse the most).  Hence,  
requiring a new kind of server other than HTML/PHP would require  
very, very strong rationale.  :-)


- The technology of choice for displaying on the web site is PHP.   
But that still leaves open a wide variety 

[OMPI users] MVAPI Options on Job Submission

[Jeff Pummill]

I have successfully compiled Open MPI 1.2.3 against Intel 8.1 compiler 
suite and old (3 years) mvapi stack using the following configure:


configure --prefix=/nfsutil/openmpi-1.2.3 
--with-mvapi=/usr/local/topspin/ CC=icc CXX=icpc F77=ifort FC=ifort


Do I need to assign any particular flags to the command line submission 
to ensure that it is using the IB network instead of the TCP? Or 
possibly disable the Gig-E with ^tcp to see if it still runs successfully?


I just want to be sure that Open MPI is actually USING the IB network 
and mvapi.


Thanks!

Jeff Pummill

[OMPI users] Building OMPI with dated tools & libs

[Jeff Pummill]

Good morning all,

I have been very impressed so far with OpenMPI on one of our smaller 
clusters running Gnu compilers and Gig-E interconnects, so I am 
considering a build on our large cluster. The potential problem is that 
the compilers are Intel 8.1 versions and the Infiniband is supported by 
three year old Topspin (now Cisco) drivers and libraries. Basically, 
this is a cluster that runs a very heavy workload using MVAPICH, thus we 
have adopted the "if it ain't broke, don't fix it" methodology...thus 
all of the drivers, libraries, and compilers are approximately 3 years old.


Would it be reasonable to expect OpenMPI 1.2.3 to build and run in such 
an environment?


Thanks!

Jeff Pummill
University of Arkansas

Re: [OMPI users] OpenMPI / SLURM Job Issues

[Jeff Pummill]

Hey Jeff,

Finally got my test nodes back and was looking at the info you sent. On 
the SLURM page, it states the following:


*Open MPI* <http://www.open-mpi.org/> relies upon SLURM to allocate 
resources for the job and then mpirun to initiate the tasks. When using 
salloc command, mpirun's -nolocal option is recommended. For example:


$ salloc -n4 sh# allocates 4 processors and spawns shell for job

mpirun -np 4 -nolocal a.out
exit  # exits shell spawned by initial salloc command


You are saying that I need to use the slurm salloc, then pass SLURM a 
script? Or could I just add it all into the script? Fro eaample:


#!/bin/sh
salloc -n4
mpirun my_mpi_application

Then, run with srun -b myscript.sh


Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
Fayetteville, Arkansas 72701
(479) 575 - 4590
http://hpc.uark.edu

"A supercomputer is a device for turning compute-bound
problems into I/O-bound problems." -Seymour Cray


Jeff Squyres wrote:
Ick; I'm surprised that we don't have this info on the FAQ.  I'll try  
to rectify that shortly.


How are you launching your jobs through SLURM?  OMPI currently does  
not support the "srun -n X my_mpi_application" model for launching  
MPI jobs.  You must either use the -A option to srun (i.e., get an  
interactive SLURM allocation) or use the -b option (submit a script  
that runs on the first node in the allocation).  Your script can be  
quite short:


#!/bin/sh
mpirun my_mpi_application

Note that OMPI will automatically figure out how many cpu's are in  
your SLURM allocation, so you don't need to specify "-np X".  Hence,  
you can run the same script without modification no matter how many  
cpus/nodes you get from SLURM.


It's on the long-term plan to get "srun -n X my_mpi_application"  
model to work; it just hasn't bubbled up high enough in the priority  
stack yet... :-\



On Jun 20, 2007, at 1:59 PM, Jeff Pummill wrote:

  
Just started working with OpenMPI / SLURM combo this morning. I can  
successfully launch this job from the command line and it runs to  
completion, but when launching from SLURM they hang.


They appear to just sit with no load apparent on the compute nodes  
even though SLURM indicates they are running...


[jpummil@trillion ~]$ sinfo -l
Wed Jun 20 12:32:29 2007
PARTITION AVAIL  TIMELIMIT   JOB_SIZE ROOT SHARE GROUPS   
NODES   STATE NODELIST
debug*   up   infinite 1-infinite   nonoall   
8   allocated compute-1-[1-8]
debug*   up   infinite 1-infinite   nonoall   
1idle compute-1-0


[jpummil@trillion ~]$ squeue -l
Wed Jun 20 12:32:20 2007
  JOBID PARTITION NAME USERSTATE   TIME TIMELIMIT   
NODES NODELIST(REASON)
 79 debug   mpirun  jpummil  RUNNING   5:27  
UNLIMITED  2 compute-1-[1-2]
 78 debug   mpirun  jpummil  RUNNING   5:58  
UNLIMITED  2 compute-1-[3-4]
 77 debug   mpirun  jpummil  RUNNING   7:00  
UNLIMITED  2 compute-1-[5-6]
 74 debug   mpirun  jpummil  RUNNING  11:39  
UNLIMITED  2 compute-1-[7-8]


Are there any known issues of this nature involving OpenMPI and SLURM?

Thanks!

Jeff F. Pummill

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Re: [OMPI users] f90 support not built with gfortran?

[Jeff Pummill]

Thanks guys!

Setting F77=gfortran did the trick.


Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
Fayetteville, Arkansas 72701
(479) 575 - 4590
http://hpc.uark.edu

"A supercomputer is a device for turning compute-bound
problems into I/O-bound problems." -Seymour Cray


Jeff Squyres wrote:

On Jun 12, 2007, at 5:56 AM, Terry Frankcombe wrote:

  

I downloaded and configured v1.2.2 this morning on an Opteron cluster
using the following configure directives...

./configure --prefix=/share/apps CC=gcc CXX=g++ F77=g77 FC=gfortran
CFLAGS=-m64 CXXFLAGS=-m64 FFLAGS=-m64 FCFLAGS=-m64
  

What does config.log say?  (Look for 'Fortran 90'.)  config.log should
be your first port of call when trying to debug build problems in any
"configure"-d project.



Exactly.  OMPI's configure probably determined that it should not  
build the F90 bindings, so it didn't (hence, mpif90 is non- 
functional).  If I had to guess, it's because you specified both g77  
and gfortran.  When using gfortran, you should probably use it for  
both F77 and FC.  That will likely fix your problem.


If it doesn't, please see this web page for more details on getting  
help:


 http://www.open-mpi.org/community/help/

Consider this a compile-time problem (because OMPI decided not to  
build the F90 bindings) and send all the information listed.  Thanks!


  

[OMPI users] f90 support not built with gfortran?

[Jeff Pummill]

Greetings all,

I downloaded and configured v1.2.2 this morning on an Opteron cluster 
using the following configure directives...


./configure --prefix=/share/apps CC=gcc CXX=g++ F77=g77 FC=gfortran 
CFLAGS=-m64 CXXFLAGS=-m64 FFLAGS=-m64 FCFLAGS=-m64


Compilation seemed to go OK and there IS an mpif90 option in 
/bin..but it gives me the following error when I try to compile my 
source file:


/share/apps/bin/mpif90 -c -I/share/apps/include -O3 ft.f
Unfortunately, this installation of Open MPI was not compiled with
Fortran 90 support.  As such, the mpif90 compiler is non-functional.

I am certain that gfortran is installed and working correctly as I 
tested compilation of a small piece of serial code with it.


Something I am doing wrong?

--
Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
Fayetteville, Arkansas 72701

Re: [OMPI users] Library Definitions

[Jeff Pummill]

Glad to contribute Victor!

I am running on a home workstation that uses an AMD 3800 cpu attached to 
2 gigs of ram.
My timings for FT were 175 secs with one core and 110 on two cores with 
-O3 and -mtune=amd64 as tuning options.


Brock, Terry and Jeff are all exactly correct in their comments 
regarding benchmarks. There are simply too many variables to contend 
with. In addition, one and two core runs on a single workstation 
probably isn't the best evaluation of OpenMPI. As you expand to more 
devices and generate bigger problems (HPL or HPCC for example), a better 
overall picture will emerge.



Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas



victor marian wrote:

  Thank you everybody for the advices.
  I ran the NAS benchmark class B and it runs in 181
seconds on one core and in 90 seconds on two cores, so
it scales almost perfectly.
  What were your timings, Jeff, and what processor do
you exactly have?
  Mine is a Pentium D at 2.8GHz.

 Victor


--- Jeff Pummill <jpum...@uark.edu> wrote:

  

Victor,

Build the FT benchmark and build it as a class B
problem. This will run 
in the 1-2 minute range instead of 2-4 seconds the
CG class A benchmark 
does.



Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas



Terry Frankcombe wrote:


Hi Victor

I'd suggest 3 seconds of CPU time is far, far to
  

small a problem to do


scaling tests with.  Even with only 2 CPUs, I
  

wouldn't go below 100


times that.


On Mon, 2007-06-11 at 01:10 -0700, victor marian
  

wrote:

  
  

Hi Jeff

I ran the NAS Parallel Bechmark and it gives for


me


-bash%/export/home/vmarian/fortran/benchmarks/NPB3.2/NPB3.2-MPI/bin$
  

mpirun -np 1 cg.A.1



--
  

[0,1,0]: uDAPL on host SERVSOLARIS was unable to


find


any NICs.
Another transport will be used instead, although


this


may result in
lower performance.



--
  

 NAS Parallel Benchmarks 3.2 -- CG Benchmark

 Size:  14000
 Iterations:15
 Number of active processes: 1
 Number of nonzeroes per row:   11
 Eigenvalue shift: .200E+02
 Benchmark completed
 VERIFICATION SUCCESSFUL
 Zeta is  0.171302350540E+02
 Error is 0.512264003323E-13


 CG Benchmark Completed.
 Class   =A
 Size=14000
 Iterations  =   15
 Time in seconds = 3.02
 Total processes =1
 Compiled procs  =1
 Mop/s total =   495.93
 Mop/s/process   =   495.93
 Operation type  =   floating point
 Verification=   SUCCESSFUL
 Version =  3.2
 Compile date=  11 Jun 2007





-bash%/export/home/vmarian/fortran/benchmarks/NPB3.2/NPB3.2-MPI/bin$
  

mpirun -np 2 cg.A.2



--
  

[0,1,0]: uDAPL on host SERVSOLARIS was unable to


find


any NICs.
Another transport will be used instead, although


this


may result in
lower performance.



--
  
--
  

[0,1,1]: uDAPL on host SERVSOLARIS was unable to


find


any NICs.
Another transport will be used instead, although


this


may result in
lower performance.



--
  

 NAS Parallel Benchmarks 3.2 -- CG Benchmark

 Size:  14000
 Iterations:15
 Number of active processes: 2
 Number of nonzeroes per row:   11
 Eigenvalue shift: .200E+02

 Benchmark completed
 VERIFICATION SUCCESSFUL
 Zeta is  0.171302350540E+02
 Error is 0.522633719989E-13


 CG Benchmark Completed.
 Class   =A
 Size=14000
 Iterations  =   15
 Time in seconds = 2.47
 Total processes =2
 Compiled procs  =2
 Mop/s total =   606.32
 Mop/s/process   =   303.16
 Operation type  =   floating point
 Verification=   SUCCESSFUL
 Version =  3.2
 Compile date=  11 Jun 2007


You can remark that the scalling is not so


good


like yours. Maibe I am having comunications


problems


between processors.
   You can also remark that I am faster on one


process


concared to your processor.

   

Re: [OMPI users] Library Definitions

[Jeff Pummill]

Victor,

Build the FT benchmark and build it as a class B problem. This will run 
in the 1-2 minute range instead of 2-4 seconds the CG class A benchmark 
does.



Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas



Terry Frankcombe wrote:

Hi Victor

I'd suggest 3 seconds of CPU time is far, far to small a problem to do
scaling tests with.  Even with only 2 CPUs, I wouldn't go below 100
times that.


On Mon, 2007-06-11 at 01:10 -0700, victor marian wrote:
  

Hi Jeff

I ran the NAS Parallel Bechmark and it gives for me
-bash%/export/home/vmarian/fortran/benchmarks/NPB3.2/NPB3.2-MPI/bin$
mpirun -np 1 cg.A.1
--
[0,1,0]: uDAPL on host SERVSOLARIS was unable to find
any NICs.
Another transport will be used instead, although this
may result in
lower performance.
--
 NAS Parallel Benchmarks 3.2 -- CG Benchmark

 Size:  14000
 Iterations:15
 Number of active processes: 1
 Number of nonzeroes per row:   11
 Eigenvalue shift: .200E+02
 Benchmark completed
 VERIFICATION SUCCESSFUL
 Zeta is  0.171302350540E+02
 Error is 0.512264003323E-13


 CG Benchmark Completed.
 Class   =A
 Size=14000
 Iterations  =   15
 Time in seconds = 3.02
 Total processes =1
 Compiled procs  =1
 Mop/s total =   495.93
 Mop/s/process   =   495.93
 Operation type  =   floating point
 Verification=   SUCCESSFUL
 Version =  3.2
 Compile date=  11 Jun 2007


-bash%/export/home/vmarian/fortran/benchmarks/NPB3.2/NPB3.2-MPI/bin$
mpirun -np 2 cg.A.2
--
[0,1,0]: uDAPL on host SERVSOLARIS was unable to find
any NICs.
Another transport will be used instead, although this
may result in
lower performance.
--
--
[0,1,1]: uDAPL on host SERVSOLARIS was unable to find
any NICs.
Another transport will be used instead, although this
may result in
lower performance.
--


 NAS Parallel Benchmarks 3.2 -- CG Benchmark

 Size:  14000
 Iterations:15
 Number of active processes: 2
 Number of nonzeroes per row:   11
 Eigenvalue shift: .200E+02

 Benchmark completed
 VERIFICATION SUCCESSFUL
 Zeta is  0.171302350540E+02
 Error is 0.522633719989E-13


 CG Benchmark Completed.
 Class   =A
 Size=14000
 Iterations  =   15
 Time in seconds = 2.47
 Total processes =2
 Compiled procs  =2
 Mop/s total =   606.32
 Mop/s/process   =   303.16
 Operation type  =   floating point
 Verification=   SUCCESSFUL
 Version =  3.2
 Compile date=  11 Jun 2007


You can remark that the scalling is not so good
like yours. Maibe I am having comunications problems
between processors.
   You can also remark that I am faster on one process
concared to your processor.

   Victor





--- Jeff Pummill <jpum...@uark.edu> wrote:



Perfect! Thanks Jeff!

The NAS Parallel Benchmark on a dual core AMD
machine now returns this...
[jpummil@localhost bin]$ mpirun -np 1 cg.A.1
NAS Parallel Benchmarks 3.2 -- CG Benchmark
CG Benchmark Completed.
 Class   =A
 Size=14000
 Iterations  =   15
 Time in seconds = 4.75
 Total processes =1
 Compiled procs  =1
 Mop/s total =   315.32

...and...

[jpummil@localhost bin]$ mpirun -np 2 cg.A.2
NAS Parallel Benchmarks 3.2 -- CG Benchmark
 CG Benchmark Completed.
 Class   =A
 Size=14000
 Iterations  =   15
 Time in seconds = 2.48
 Total processes =2
 Compiled procs  =2
 Mop/s total =   604.46

Not quite linear, but one must account for all of
the OS traffic that 
one core or the other must deal with.



Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
Fayetteville, Arkansas 72701
(479) 575 - 4590
http://hpc.uark.edu

"A supercomputer is a device for turning
compute-bound
problems into I/O-bound problems." -Seymour Cray


Jeff Squyres wro

Re: [OMPI users] Problem running MPI on a dual-core pentium D

[Jeff Pummill]

Hey Victor!

I just ran the old classic cpi.c just to verify that OpenMPI was 
working. Now I need to grab some actual benchmarking code.  I may try 
the NAS Parallel Benchmarks from here...


http://www.nas.nasa.gov/Resources/Software/npb.html

They were pretty easy to build and run under mpich. I can't imagine it'd 
be any different on OpenMPI.



Jeff F. Pummill



victor marian wrote:

  I can't turn it off right now to look in BIOS (the
computer is not at home), but I think the Pentium D
which is dual-core doesn't support hyper-threading. 
  The program I made relies on an MPI library (it is

not a benchmarking program). I think you are right,
maibe I should run a benchmarking program first to see
what happens. If you have a benchmarking program I
would gladly test it. 
   What is the best way to debug OpenMPI programs?

Until now I ran prism which is part of the
SunClusterTools.

  Victor

--- Jeff Pummill <jpum...@uark.edu> wrote:

  

Victor,

Just on a hunch, look in your BIOS to see if
Hyperthreading is turned 
on. If so, turn it off. We have seen some unusual
behavior on some of 
our machines unless this is disabled.


I am interested in your progress as I have just
begun working with 
OpenMPI as well. I have used mpich for quite some
time, but felt 
compelled to get some experience with OpenMPI as
well. I just installed 
it this weekend on an AMD dual-core machine with 2
gigs of ram. Maybe I 
will try and replicate your experiment if you can
direct me to what 
program you are benchmarking.


Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
Fayetteville, Arkansas 72701
(479) 575 - 4590
http://hpc.uark.edu

victor marian wrote:


The problem is that my executable file runs on the
Pentium D in 80 seconds on two cores and in 25
  

seconds


on one core.
And on another Sun SMP machine with 20 processors
  

it


runs perfectly (the problem is perfectly
  

scallable).


  Victor Marian
  Laboratory of Machine Elements and Tribology
  University Politehnica of Bucharest
  Romania


--- Brock Palen <bro...@umich.edu> wrote:

  
  

It means that your OMPI was compiled to support
uDAPL  (a type of  
infinibad network)  but that your computer does


not

have such a card  
installed.  Because you dont it will fall back to
ethernet.  But  
because you are just running on a single machine.

You will use the  
fastest form of communication using shared

memory. 

so you can ignore  
that message.  Unless in the future you add a


uDAPL

powered network  
and you still get that message then you need to

worry.

Brock Palen
Center for Advanced Computing
bro...@umich.edu
(734)936-1985


On Jun 10, 2007, at 9:18 AM, victor marian wrote:




Hello,

I have a Pentium D computer with Solaris 10
  
  

installed.



I installed OpenMPI, succesfully compiled my
  
  

Fortran



program, but when giving
mpirun -np 2 progexe
I receive
[0,1,0]: uDAPL on host SERVSOLARIS was unable to
  
  

find



any NICs.
Another transport will be used instead, although
  
  

this



may result in
lower performance.

I am a begginer in MPI and don't know what it
  
  

means.



What
 should I do to solve the problem?
Thank you.







  
  

__
  
  
  

__
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their life, your  



story. Play Sims Stories at Yahoo! Games.
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Games.

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Re: [OMPI users] Problem running MPI on a dual-core pentium D

[Jeff Pummill]

Victor,

Just on a hunch, look in your BIOS to see if Hyperthreading is turned 
on. If so, turn it off. We have seen some unusual behavior on some of 
our machines unless this is disabled.


I am interested in your progress as I have just begun working with 
OpenMPI as well. I have used mpich for quite some time, but felt 
compelled to get some experience with OpenMPI as well. I just installed 
it this weekend on an AMD dual-core machine with 2 gigs of ram. Maybe I 
will try and replicate your experiment if you can direct me to what 
program you are benchmarking.


Jeff F. Pummill
Senior Linux Cluster Administrator
University of Arkansas
Fayetteville, Arkansas 72701
(479) 575 - 4590
http://hpc.uark.edu

victor marian wrote:

The problem is that my executable file runs on the
Pentium D in 80 seconds on two cores and in 25 seconds
on one core.
And on another Sun SMP machine with 20 processors it
runs perfectly (the problem is perfectly scallable).

  Victor Marian
  Laboratory of Machine Elements and Tribology
  University Politehnica of Bucharest
  Romania


--- Brock Palen  wrote:

  

It means that your OMPI was compiled to support
uDAPL  (a type of  
infinibad network)  but that your computer does not
have such a card  
installed.  Because you dont it will fall back to
ethernet.  But  
because you are just running on a single machine. 
You will use the  
fastest form of communication using shared memory. 
so you can ignore  
that message.  Unless in the future you add a uDAPL
powered network  
and you still get that message then you need to

worry.

Brock Palen
Center for Advanced Computing
bro...@umich.edu
(734)936-1985


On Jun 10, 2007, at 9:18 AM, victor marian wrote:



Hello,

I have a Pentium D computer with Solaris 10
  

installed.


I installed OpenMPI, succesfully compiled my
  

Fortran


program, but when giving
mpirun -np 2 progexe
I receive
[0,1,0]: uDAPL on host SERVSOLARIS was unable to
  

find


any NICs.
Another transport will be used instead, although
  

this


may result in
lower performance.

I am a begginer in MPI and don't know what it
  

means.


What
 should I do to solve the problem?
Thank you.







  

__
  

__
Moody friends. Drama queens. Your life? Nope! -
  
their life, your  


story. Play Sims Stories at Yahoo! Games.
http://sims.yahoo.com/
___
users mailing list
us...@open-mpi.org
http://www.open-mpi.org/mailman/listinfo.cgi/users


  

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