Re: [OMPI users] difference between OpenMPI - intel MPI -- how to understand where\why

2016-02-16 Thread Eugene Loh
Which one is producing correct (or at least reasonable) results? Are both results correct? Do you have ways of assessing correctness of your results? On February 16, 2016 at 5:19:16 AM, Diego Avesani (diego.aves...@gmail.com) wrote: Dear all, I have written an fortran-MPI code.

Re: [OMPI users] OpenMPI Profiling

2016-01-07 Thread Eugene Loh
I don't know specifically what you want to do, but there is a FAQ section on profiling and tracing. http://www.open-mpi.org/faq/?category=perftools On 12/31/2015 9:03 AM, anil maurya wrote: I have compiled HPL using OpenMPI and GotoBLAS. I want to do profiling and tracing. I have compiled

Re: [OMPI users] now 1.9 [was: I have still a problem withrankfiles in openmpi-1.6.4rc3]

2013-02-10 Thread Eugene Loh
On 2/10/2013 1:14 AM, Siegmar Gross wrote: I don't think the problem is related to Solaris. I think it's also on Linux. E.g., I can reproduce the problem with 1.9a1r28035 on Linux using GCC compilers. Siegmar: can you confirm this is a problem also on Linux? E.g., with OMPI 1.9, on one of

Re: [OMPI users] now 1.9 [was: I have still a problem with rankfiles in openmpi-1.6.4rc3]

2013-02-09 Thread Eugene Loh
On 02/09/13 00:32, Ralph Castain wrote: On Feb 6, 2013, at 2:59 PM, Eugene Loh <eugene@oracle.com> wrote: On 02/06/13 04:29, Siegmar Gross wrote: thank you very much for your answer. I have compiled your program and get different behaviours for openmpi-1.6.4rc3 and openmpi-1.9. I

Re: [hwloc-users] hwloc-bind --get on Solaris for binding to a single core

2013-02-07 Thread Eugene Loh
On 02/06/13 02:03, Samuel Thibault wrote: Eugene Loh, le Wed 06 Feb 2013 07:50:02 +0100, a écrit : How about adding a check upon entry to hwloc_solaris_get_sth_cpubind(): if processor_bind() shows binding, report this and be done. If not, then continue on with the lgroup logic that's already

Re: [OMPI users] I have still a problem with rankfiles in openmpi-1.6.4rc3

2013-02-07 Thread Eugene Loh
On 02/07/13 01:05, Siegmar Gross wrote: thank you very much for your patch. I have applied the patch to openmpi-1.6.4rc4. Open MPI: 1.6.4rc4r28022 : [B .][. .] (slot list 0:0) : [. B][. .] (slot list 0:1) : [B B][. .] (slot list 0:0-1) : [. .][B .] (slot list 1:0) : [. .][. B] (slot list 1:1)

[OMPI users] now 1.9 [was: I have still a problem with rankfiles in openmpi-1.6.4rc3]

2013-02-06 Thread Eugene Loh
On 02/06/13 04:29, Siegmar Gross wrote: thank you very much for your answer. I have compiled your program and get different behaviours for openmpi-1.6.4rc3 and openmpi-1.9. I get the following output for openmpi-1.9 (different outputs !!!). sunpc1 rankfiles 104 mpirun --report-bindings

Re: [OMPI users] I have still a problem with rankfiles in openmpi-1.6.4rc3

2013-02-06 Thread Eugene Loh
On 02/06/13 04:29, Siegmar Gross wrote: Hi thank you very much for your answer. I have compiled your program and get different behaviours for openmpi-1.6.4rc3 and openmpi-1.9. Yes, something else seems to be going on for 1.9. For 1.6, try the attached patch. It works for me, but my machines

[hwloc-users] hwloc-bind --get on Solaris for binding to a single core

2013-02-06 Thread Eugene Loh
This is on a Solaris 11 system with hwloc 1.6.1: % lstopo-no-graphics Machine (4095MB) + NUMANode L#0 (P#0 4095MB) + Socket L#0 Core L#0 + PU L#0 (P#0) Core L#1 + PU L#1 (P#1) Core L#2 + PU L#2 (P#2) Core L#3 + PU L#3 (P#3) % hwloc-bind socket:0.pu:1 hwloc-bind --get 0x000f I assume

Re: [OMPI users] I have still a problem with rankfiles in openmpi-1.6.4rc3

2013-02-05 Thread Eugene Loh
On 02/05/13 13:20, Eugene Loh wrote: On 02/05/13 00:30, Siegmar Gross wrote: now I can use all our machines once more. I have a problem on Solaris 10 x86_64, because the mapping of processes doesn't correspond to the rankfile. A few comments. First of all, the heterogeneous environment had

Re: [OMPI users] I have still a problem with rankfiles in openmpi-1.6.4rc3

2013-02-05 Thread Eugene Loh
On 02/05/13 00:30, Siegmar Gross wrote: now I can use all our machines once more. I have a problem on Solaris 10 x86_64, because the mapping of processes doesn't correspond to the rankfile. I removed the output from "hostfile" and wrapped around long lines. tyr rankfiles 114 cat rf_ex_sunpc #

Re: [OMPI users] MPI_Recv operation time

2012-11-05 Thread Eugene Loh
On 11/5/2012 1:07 AM, huydanlin wrote: Hi, My objective is I want to calculate the time perform by MPI_Send & MPI_Recv . In case MPI_Send, i can put the timer before the MPI_Send and after its. like this " t1=MPI_Wtime(), MPI_Send t2= MPI_Wtime tsend= t2 -t1; it mean when the message

Re: [OMPI users] segmentation fault with openmpi-1.6.2

2012-09-10 Thread Eugene Loh
On 09/10/12 11:37, Ralph Castain wrote: On Sep 10, 2012, at 8:12 AM, Aleksey Senin wrote: On 10/09/2012 15:41, Siegmar Gross wrote: Hi, I have built openmpi-1.6.2rc1 and get the following error. tyr small_prog 123 mpicc -showme cc

Re: [OMPI users] Regarding the execution time calculation

2012-05-05 Thread Eugene Loh
MPI_Wtime() returns the elapsed time since some arbitrary time in the past. It is a measure of "wallclock" time, not of CPU time or anything. On 5/4/2012 3:08 PM, Jingcha Joba wrote: Lets say I have a code like this start = MPI_Wtime() stop = MPI_Wtime(); What happens when right after

Re: [OMPI users] MPI_Testsome with incount=0, NULL array_of_indices and array_of_statuses causes MPI_ERR_ARG

2012-03-15 Thread Eugene Loh
On 03/13/12 13:25, Jeffrey Squyres wrote: On Mar 9, 2012, at 5:17 PM, Jeremiah Willcock wrote: On Open MPI 1.5.1, when I call MPI_Testsome with incount=0 and the two output arrays NULL, I get an argument error (MPI_ERR_ARG). Is this the intended behavior? If incount=0, no requests can

Re: [OMPI users] parallelising ADI

2012-03-06 Thread Eugene Loh
Parallelize in distributed-memory fashion or is multi-threaded good enough? Anyhow, you should be able to find many resources with an Internet search. This particular mailing list is more for users of OMPI, a particular MPI implementation. One approach would be to distribute only one axis,

Re: [OMPI users] Mpirun: How to print STDOUT of just one process?

2012-02-01 Thread Eugene Loh
On 2/1/2012 7:59 AM, Frank wrote: When running mpirun -n 2 the STDOUT streams of both processes are combined and are displayed by the shell. In such an interleaved format its hard to tell what line comes from which node. As far as this part goes, there is also "mpirun --tag-output". Check

Re: [OMPI users] Openmpi performance issue

2011-12-27 Thread Eugene Loh
If I remember correctly, both Intel MPI and MVAPICH2 bind processes by default. OMPI does not. There are many cases where the "bind by default" behavior gives better default performance. (There are also cases where it can give catastrophically worse performance.) Anyhow, it seems possible

Re: [OMPI users] Process Migration

2011-11-10 Thread Eugene Loh
On 11/10/2011 5:19 AM, Jeff Squyres wrote: On Nov 10, 2011, at 8:11 AM, Mudassar Majeed wrote: Thank you for your reply. I am implementing a load balancing function for MPI, that will balance the computation load and the communication both at a time. So my algorithm assumes that all the cores

Re: [OMPI users] EXTERNAL: Re: How to set up state-less node /tmp for OpenMPI usage

2011-11-03 Thread Eugene Loh
thing like --mca ^sm? -Original Message- From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Eugene Loh Sent: Thursday, November 03, 2011 12:54 PM To: us...@open-mpi.org Subject: Re: [OMPI users] EXTERNAL: Re: How to set up state-less node /tmp for OpenMPI

Re: [OMPI users] EXTERNAL: Re: How to set up state-less node /tmp for OpenMPI usage

2011-11-03 Thread Eugene Loh
I've not been following closely. Why must one use shared-memory communications? How about using other BTLs in a "loopback" fashion?

Re: [OMPI users] Application in a cluster

2011-10-19 Thread Eugene Loh
Maybe someone else on this list has a better idea what you're trying to do, but I'll attempt to answer your question. MPI is basically a set of library calls that can be used for processes to communicate with one another. Of course, a program need not have any MPI calls in it, but if you

Re: [OMPI users] Proper way to redirect GUI

2011-10-02 Thread Eugene Loh
Often you set the environment variable DISPLAY to any display you like. Export environment variables with "mpirun -x DISPLAY". On 10/2/2011 5:32 AM, Xin Tong wrote: I am launch a program with a GUI interface, How do i redirect the GUI to the machine i issued mpirun on ?

Re: [OMPI users] MPIRUN + Environtment Variable

2011-09-30 Thread Eugene Loh
On 09/29/11 20:54, Xin Tong wrote: I need to set up some environment variables before I run my application ( appA ). I am currently using mpirun -np 1 -host socrates (socrates is another machine) appA. Before appA runs, it expects some environment variables to be set up. How do i do that ? %

Re: [OMPI users] EXTERNAL: Re: How could OpenMPI (or MVAPICH) affect floating-point results?

2011-09-20 Thread Eugene Loh
I've not been following closely. How do you know you're using the identical compilation flags? Are you saying you specify the same flags to "mpicc" (or whatever) or are you confirming that the back-end compiler is seeing the same flags? The MPI compiler wrapper (mpicc, et al.) can add

Re: [OMPI users] custom sparse collective non-reproducible deadlock, MPI_Sendrecv, MPI_Isend/MPI_Irecv or MPI_Send/MPI_Recv question

2011-09-19 Thread Eugene Loh
On 9/18/2011 9:12 AM, Evghenii Gaburov wrote: Hi All, Update to the original posting: METHOD4 also resulted in a deadlock on system HPC2 after 5h of run with 32 MPI tasks; also, "const int scale=1;" was missing in the code snippet posted above. --Evghenii Message: 2 Date: Sun, 18 Sep

Re: [OMPI users] RE : MPI hangs on multiple nodes

2011-09-19 Thread Eugene Loh
Should be fine. Once MPI_Send returns, it should be safe to reuse the buffer. In fact, the return of the call is the only way you have of checking that the message has left the user's send buffer. The case you're worried about is probably MPI_Isend, where you have to check completion with

Re: [OMPI users] Problem with MPI_Wtime()

2011-09-15 Thread Eugene Loh
On 9/15/2011 5:51 AM, Ghislain Lartigue wrote: start_0 = MPI_Wtime() start_1 = MPI_Wtime() call foo() end_1 = MPI_Wtime() write(*,*) "timer1 = ",end1-start1 start_2 = MPI_Wtime() call bar() end_2 = MPI_Wtime() write(*,*) "timer2 = ",end2-start2 end_0 = MPI_Wtime() write(*,*) "timer0 =

Re: [OMPI users] Problem with MPI_BARRIER

2011-09-09 Thread Eugene Loh
On 9/8/2011 11:47 AM, Ghislain Lartigue wrote: I guess you're perfectly right! I will try to test it tomorrow by putting a call system("wait(X)) befor the barrier! What does "wait(X)" mean? Anyhow, here is how I see your computation: A) The first barrier simply synchronizes the processes.

Re: [OMPI users] Problem with MPI_BARRIER

2011-09-08 Thread Eugene Loh
endif enddo The first call to the barrier works perfectly fine, but the second one gives the strange behavior... Ghislain. Le 8 sept. 2011 à 16:53, Eugene Loh a écrit : On 9/8/2011 7:42 AM, Ghislain Lartigue wrote: I will check that, but as I said in first email, this strange beha

Re: [OMPI users] Problem with MPI_BARRIER

2011-09-08 Thread Eugene Loh
On 9/8/2011 7:42 AM, Ghislain Lartigue wrote: I will check that, but as I said in first email, this strange behaviour happens only in one place in my code. Is the strange behavior on the first time, or much later on? (You seem to imply later on, but I thought I'd ask.) I agree the behavior

Re: [OMPI users] Problem with MPI_BARRIER

2011-09-08 Thread Eugene Loh
I agree sentimentally with Ghislain. The time spent in a barrier should conceptually be some wait time, which can be very long (possibly on the order of milliseconds or even seconds), and the time to execute the barrier operations, which should essentially be "instantaneous" on some time

Re: [OMPI users] High CPU usage with yield_when_idle =1 on CFS

2011-09-01 Thread Eugene Loh
On 8/31/2011 11:48 PM, Randolph Pullen wrote: I recall a discussion some time ago about yield, the Completely F%’d Scheduler (CFS) and OpenMPI. My system is currently suffering from massive CPU use while busy waiting. This gets worse as I try to bump up user concurrency. Yup. I am running

Re: [OMPI users] poll taking too long in open-mpi

2011-08-26 Thread Eugene Loh
On 8/23/2011 1:24 PM, Dick Kachuma wrote: I have used gprof to profile a program that uses openmpi. The result shows that the code spends a long time in poll (37% on 8 cores, 50% on 16 and 85% on 32). I was wondering if there is anything I can do to reduce the time spent in poll. In serial

Re: [OMPI users] Documentation of MPI Implementation

2011-08-23 Thread Eugene Loh
On 8/23/2011 12:32 AM, Hoang-Vu Dang wrote: Dear all, Where could I find a detailed documentation about algorithms that has been using in Open MPI ? For example, I would like to answer following questions: how MPI_Algather operation is done? what is the complexity in term of the number of

Re: [OMPI users] Urgent Question regarding, MPI_ANY_SOURCE.

2011-07-15 Thread Eugene Loh
I'm going to echo what you've already heard here: it is impossible for a process to receive a message that was sent to a different process. A sender must specify a unique destination. No process other than the destination process will see that message. In what you write below, why do you

Re: [OMPI users] OpenMPI vs Intel Efficiency question

2011-07-12 Thread Eugene Loh
On 7/12/2011 4:45 PM, Mohan, Ashwin wrote: I noticed that the exact same code took 50% more time to run on OpenMPI than Intel. It would be good to know if that extra time is spent inside MPI calls or not. There is a discussion of how you might do this here:

Re: [OMPI users] openmpi (1.2.8 or above) and Intel composer XE 2011 (aka 12.0)

2011-05-27 Thread Eugene Loh
On 5/27/2011 4:32 AM, Jeff Squyres wrote: On May 27, 2011, at 4:30 AM, Robert Horton wrote: To be clear, if you explicitly list which BTLs to use, OMPI will only (try to) use exactly those and no others. It might be worth putting the sm btl in the FAQ:

Re: [OMPI users] configure: mpi-threads disabled by default

2011-05-04 Thread Eugene Loh
Depending on what version you use, the option has been renamed --enable-mpi-thread-multiple. Anyhow, there is widespread concern whether the support is robust. The support is known to be limited and the performance poor. On 5/4/2011 9:14 AM, Mark Dixon wrote: I've been asked about

Re: [OMPI users] --enable-progress-threads broken in 1.5.3?

2011-04-28 Thread Eugene Loh
CMR 2728 did this. I think the changes are in 1.5.4. On 4/28/2011 5:00 AM, Jeff Squyres wrote: It is quite likely that --enable-progress-threads is broken. I think it's even disabled in 1.4.x; I wonder if we should do the same in 1.5.x...

Re: [OMPI users] Problem with setting up openmpi-1.4.3

2011-04-13 Thread Eugene Loh
amosl...@gmail.com wrote: Hi, I am embarrassed! I submitted a note to the users on setting up openmpi-1.4.3 using SUSE-11.3 under Linux and received several replies. I wanted to transfer them but they disappeared for no apparent reason. I hope that those that sent me messages

Re: [OMPI users] mpi problems,

2011-04-06 Thread Eugene Loh
Nehemiah Dacres wrote: also, I'm not sure if I'm reading the results right. According to the last run, did using the sun compilers (update 1 )  result in higher performance with sunct? On Wed, Apr 6, 2011 at 11:38 AM, Nehemiah Dacres wrote: this first test was run as

Re: [OMPI users] Shared Memory Performance Problem.

2011-03-30 Thread Eugene Loh
Michele Marena wrote: I've launched my app with mpiP both when two processes are on different node and when two processes are on the same node. The process 0 is the manager (gathers the results only), processes 1 and 2 are  workers (compute). This is the case processes 1 and 2

Re: [OMPI users] Is there an mca parameter equivalent to -bind-to-core?

2011-03-23 Thread Eugene Loh
Gus Correa wrote: Ralph Castain wrote: On Mar 21, 2011, at 9:27 PM, Eugene Loh wrote: Gustavo Correa wrote: Dear OpenMPI Pros Is there an MCA parameter that would do the same as the mpiexec switch '-bind-to-core'? I.e., something that I could set up not in the mpiexec command line

Re: [OMPI users] Is there an mca parameter equivalent to -bind-to-core?

2011-03-22 Thread Eugene Loh
Gustavo Correa wrote: Dear OpenMPI Pros Is there an MCA parameter that would do the same as the mpiexec switch '-bind-to-core'? I.e., something that I could set up not in the mpiexec command line, but for the whole cluster, or for an user, etc. In the past I used '-mca mpi

Re: [OMPI users] multi-threaded programming

2011-03-08 Thread Eugene Loh
.  That should cover your case.  See the man page for MPI_Init_thread().  My question should not have anything to do with your case. On Tue, Mar 8, 2011 at 12:34 PM, Eugene Loh <eugene@oracle.com> wrote: Let's say you have multi-threaded MPI processes, you request MPI_THREAD_MU

[OMPI users] multi-threaded programming

2011-03-08 Thread Eugene Loh
Let's say you have multi-threaded MPI processes, you request MPI_THREAD_MULTIPLE and get MPI_THREAD_MULTIPLE, and you use the self,sm,tcp BTLs (which have some degree of threading support). Is it okay to have an [MPI_Isend|MPI_Irecv] on one thread be completed by an MPI_Wait on another

Re: [OMPI users] using MPI through Qt

2011-03-01 Thread Eugene Loh
Eye RCS 51 wrote: Hi, In an effort to make a Qt gui using MPI, I have the following: 1. Gui started in master node. 2. In Gui, through a pushbutton, a global variable x is assigned some value; let say, x=1000; 3. I want this value to be know to all nodes. So I used broadcast in the

Re: [OMPI users] What's wrong with this code?

2011-02-23 Thread Eugene Loh
Prentice Bisbal wrote: Jeff Squyres wrote: Can you put together a small example that shows the problem... Jeff, Thanks for requesting that. As I was looking at the oringinal code to write a small test program, I found the source of the error. Doesn't it aways work that way.

Re: [OMPI users] Calculate time spent on non blocking communication?

2011-02-03 Thread Eugene Loh
brak Qamar wrote: As asked the reason of such calculation of non blocking communication, the main reason is that I want to look into the program as how much it percent time is consumed on communication alone, computation alone and the intersection of both. On Thu, Feb 3, 2011 at 5:08 AM, Eugene Lo

Re: [OMPI users] Calculate time spent on non blocking communication?

2011-02-02 Thread Eugene Loh
Correa wrote: However, OpenMPI may give this info, with non-MPI (hence non-portable) functions, I'd guess. From: Eugene Loh <eugene@oracle.com> Anyhow, the Peruse instrumentation in OMPI might help.

Re: [OMPI users] Calculate time spent on non blocking communication?

2011-02-02 Thread Eugene Loh
cation. From: Eugene Loh <eugene@oracle.com> You probably have to start by defining what you mean by "the time it took for the communication".  Anyhow, the Peruse instrumentation in OMPI might help. Again, you should probably start by thinking more precisely about what time you

Re: [OMPI users] Calculate time spent on non blocking communication?

2011-02-01 Thread Eugene Loh
Bibrak Qamar wrote: Hello All, I am using non-blocking send and receive, and i want to calculate the time it took for the communication. Is there any method or a way to do this using openmpi. You probably have to start by defining what you mean by "the time it took for the communication".

Re: [OMPI users] maximising bandwidth

2011-01-31 Thread Eugene Loh
David Zhang wrote: Blocking send/recv, as the name suggest, stop processing your master and slave code until the data is received on the slave side. Just to clarify... If you use point-to-point send and receive calls, you can make the block/nonblock decision independently on the send and

Re: [OMPI users] Running OpenMPI on SGI Altix with 4096 cores : very poor performance

2011-01-07 Thread Eugene Loh
Gilbert Grosdidier wrote: Any other suggestion ? Can any more information be extracted from profiling?  Here is where I think things left off: Eugene Loh wrote: Gilbert Grosdidier wrote: #     [time]   [calls]    <%mpi>  <%wall> #

Re: [OMPI users] mpirun --nice 10 prog ??

2011-01-07 Thread Eugene Loh
David Mathog wrote: Ralph Castain wrote: Afraid not - though you could alias your program name to be "nice --10 prog" Is there an OMPI wish list? If so, can we please add to it "a method to tell mpirun what nice values to use when it starts programs on nodes"?

Re: [OMPI users] Running OpenMPI on SGI Altix with 4096 cores: very poor performance

2010-12-22 Thread Eugene Loh
rformance problem you're looking for? Le 22/12/2010 18:50, Eugene Loh a écrit : Can you isolate a bit more where the time is being spent?  The performance effect you're describing appears to be drastic.  Have you profiled the code?  Some choices of tools can be found in the FAQ http://www.open

Re: [OMPI users] Open MPI vs IBM MPI performance help

2010-12-22 Thread Eugene Loh
I'm curious if that resolved the issue. David Singleton wrote: http://www.open-mpi.org/faq/?category=running#oversubscribing On 12/03/2010 06:25 AM, Price, Brian M (N-KCI) wrote: Additional testing seems to show that the problem is related to barriers and how often they poll to determine

Re: [OMPI users] difference between single and double precision

2010-12-16 Thread Eugene Loh
Jeff Squyres wrote: On Dec 16, 2010, at 5:14 AM, Mathieu Gontier wrote: We have lead some tests and the option btl_sm_eager_limit has a positive consequence on the performance. Eugene, thank you for your links. Good! Just be aware of the tradeoff you're making: space for

Re: [OMPI users] MPI_Bcast vs. per worker MPI_Send?

2010-12-14 Thread Eugene Loh
David Mathog wrote: For the receive I do not see how to use a collective. Each worker sends back a data structure, and the structures are of of varying size. This is almost always the case in Bioinformatics, where what is usually coming back from each worker is a count M of the number of

Re: [OMPI users] curious behavior during wait for broadcast: 100% cpu

2010-12-14 Thread Eugene Loh
David Mathog wrote: Is there a tool in openmpi that will reveal how much "spin time" the processes are using? I don't know what sort of answer is helpful for you, but I'll describe one option. With Oracle Message Passing Toolkit (formerly Sun ClusterTools, anyhow, an OMPI distribution

Re: [OMPI users] MPI_Bcast vs. per worker MPI_Send?

2010-12-13 Thread Eugene Loh
David Mathog wrote: Is there a rule of thumb for when it is best to contact N workers with MPI_Bcast vs. when it is best to use a loop which cycles N times and moves the same information with MPI_Send to one worker at a time? The rule of thumb is to use a collective whenever you can. The

Re: [OMPI users] How to check if Send was made or not before performing a recv

2010-12-12 Thread Eugene Loh
of defining MPI calls. On Sat, Dec 11, 2010 at 10:28 AM, Eugene Loh <eugene@oracle.com> wrote: Alaukik Aggarwal wrote: I am using Open MPI 1.4.3. I have to perform a receive operation from processes that are sending data. It might happen that some of the processes don't sen

Re: [OMPI users] How to check if Send was made or not before performing a recv

2010-12-11 Thread Eugene Loh
Alaukik Aggarwal wrote: Hi, I am using Open MPI 1.4.3. I have to perform a receive operation from processes that are sending data. It might happen that some of the processes don't send data (might have completed in-fact). So, how do I perform check on which processes to receive data from and

Re: [OMPI users] Guaranteed run rank 0 on a given machine?

2010-12-10 Thread Eugene Loh
David Mathog wrote: Also, in my limited testing --host and -hostfile seem to be mutually exclusive. No. You can use both together. Indeed, the mpirun man page even has examples of this (though personally, I don't see having a use for this). I think the idea was you might use a hostfile to

Re: [OMPI users] Method for worker to determine its "rank" on a single machine?

2010-12-10 Thread Eugene Loh
Terry Dontje wrote: On 12/10/2010 09:19 AM, Richard Treumann wrote: It seems to me the MPI_Get_processor_name description is too ambiguous to make this 100% portable.  I assume most MPI implementations simply use the hostname so all processes on the same host will return the same

Re: [OMPI users] curious behavior during wait for broadcast: 100% cpu

2010-12-08 Thread Eugene Loh
Ralph Castain wrote: I know we have said this many times - OMPI made a design decision to poll hard while waiting for messages to arrive to minimize latency. If you want to decrease cpu usage, you can use the yield_when_idle option (it will cost you some latency, though) - see ompi_info

Re: [OMPI users] difference between single and double precision

2010-12-06 Thread Eugene Loh
Mathieu Gontier wrote: Nevertheless, one can observed some differences between MPICH and OpenMPI from 25% to 100% depending on the options we are using into our software. Tests are lead on a single SGI node on 6 or 12 processes, and thus, I am focused on the sm option. Is it possible to

Re: [OMPI users] difference between single and double precision

2010-12-05 Thread Eugene Loh
Mathieu Gontier wrote: Dear OpenMPI users I am dealing with an arithmetic problem. In fact, I have two variants of my code: one in single precision, one in double precision. When I compare the two executable built with MPICH, one can observed an expected difference of performance:

Re: [OMPI users] Calling MPI_Test() too many times results in a time spike

2010-11-30 Thread Eugene Loh
Ioannis Papadopoulos wrote: Has anyone observed similar behaviour? Is it something that I'll have to deal with it in my code or does it indeed qualify as an issue to be looked into? I would say this is NOT an issue that merits much attention. There are too many potential performance

Re: [OMPI users] mpool_sm_max_size disappeared ?

2010-11-29 Thread Eugene Loh
Gilbert Grosdidier wrote: I found this parameter mpool_sm_max_size in this post: http://www.open-mpi.org/community/lists/devel/2008/11/4883.php But I was unable to spot it back into the 'ompi_info -all' output for v 1.4.3. Is it still existing ? No.  If not,

Re: [OMPI users] tool for measuring the ping with accuracy

2010-11-23 Thread Eugene Loh
George Markomanolis wrote: Dear Eugene, Thanks a lot for the answer you were right for the eager mode. I have one more question. I am looking for an official tool to measure the ping time, just sending a message of 1 byte or more and measure the duration of the MPI_Send command on the rank

Re: [OMPI users] Making MPI_Send to behave as blocking for all the sizes of the messages

2010-11-18 Thread Eugene Loh
Try lowering the eager threshold more gradually... e.g., 4K, 2K, 1K, 512, etc. -- and watch what happens. I think you will see what you expect, except once you get too small then the value is ignored entirely. So, the setting just won't work at the extreme value (0) you want. Maybe the

Re: [OMPI users] Open MPI data transfer error

2010-11-05 Thread Eugene Loh
Debugging is not a straightforward task. Even posting the code doesn't necessarily help (since no one may be motivated to help or they can't reproduce the problem or...). You'll just have to try different things and see what works for you. Another option is to trace the MPI calls. If a

Re: [OMPI users] Need Help for understand heat equation 2D mpi solving version

2010-10-29 Thread Eugene Loh
christophe petit wrote: i am still trying to understand the parallelized version of the heat equation 2D solving that we saw at school. I am confused between the shift of the values near to the bounds done by the "updateBound" routine  and the main loop (at line 161 in main code)  which

Re: [OMPI users] Using hostfile with default hostfile

2010-10-27 Thread Eugene Loh
jody wrote: Where is the option 'default-hostfile' described? Try "mpirun --help". Not everything makes it to the man page. Heck, not everything is documented! It does not appear in mpirun's man page (for v. 1.4.2) and i couldn't find anything like that with googling. On Wed, Oct 27,

Re: [OMPI users] try to understand heat equation 2D mpi version

2010-10-22 Thread Eugene Loh
christophe petit wrote: i'm studying the parallelized version of a solving 2D heat equation code in order to understand cartesian topology and the famous "MPI_CART_SHIFT". Here's my problem at this part of the code :

Re: [OMPI users] Question about MPI_Barrier

2010-10-21 Thread Eugene Loh
the second sentence. Thanks a lot. On Thu, Oct 21, 2010 at 9:58 AM, Eugene Loh <eugene@oracle.com> wrote: Jeff Squyres wrote: MPI::COMM_WORLD.Barrier(); if(rank == master) t1 = clock(); "code A"; MPI::COMM_WORLD.Barrier(); if(rank == master) t2 = clock();

Re: [OMPI users] Question about MPI_Barrier

2010-10-21 Thread Eugene Loh
Jeff Squyres wrote: Ah. The original code snipit you sent was: MPI::COMM_WORLD.Barrier(); if(rank == master) t1 = clock(); "code A"; MPI::COMM_WORLD.Barrier(); if(rank == master) t2 = clock(); "code B"; Remember that the time that individual processes exit barrier is not guaranteed to be

Re: [OMPI users] busy wait in MPI_Recv

2010-10-19 Thread Eugene Loh
Brian Budge wrote: Hi all - I just ran a small test to find out the overhead of an MPI_Recv call when no communication is occurring. It seems quite high. I noticed during my google excursions that openmpi does busy waiting. I also noticed that the option to -mca mpi_yield_when_idle seems

Re: [OMPI users] How to time data transfers?

2010-10-13 Thread Eugene Loh
Ed Peddycoart wrote: I need to do some performance tests on my mpi app.  I simply want to determine how long it takes for my sends from one process to be received by another process.  Here is the code I used as my example for non-blocking send/receive...  if( myrank == 0 ) {   

Re: [OMPI users] OpenMPI and glut

2010-10-08 Thread Eugene Loh
Ed Peddycoart wrote: After searching some more and reading some FAQs on the opmi website,  I see sugestions on how to make a remote app use the local display to render, but that isn't what I need... Let me revise or clarify my question:    I have an app which will run on 5

Re: [OMPI users] Pros and cons of --enable-heterogeneous

2010-10-07 Thread Eugene Loh
David Ronis wrote: Ralph, thanks for the reply. If I build with enable-heterogeneous and then decide to run on a homogeneous set of nodes, does the additional "overhead" go away or become completely negligible; i.e., if no conversion is necessary. I'm no expert, but I think the overhead

Re: [OMPI users] Bad performance when scattering big size of data?

2010-10-04 Thread Eugene Loh
Storm Zhang wrote: Here is what I meant: the results of 500 procs in fact shows it with 272-304(<500) real cores, the program's running time is good, which is almost five times 100 procs' time. So it can be handled very well. Therefore I guess OpenMPI or Rocks OS does make use of

Re: [OMPI users] Shared memory

2010-09-24 Thread Eugene Loh
It seems to me there are two extremes. One is that you replicate the data for each process.  This has the disadvantage of consuming lots of memory "unnecessarily." Another extreme is that shared data is distributed over all processes.  This has the disadvantage of making at least some of the

Re: [OMPI users] latency #2

2010-09-13 Thread Eugene Loh
Georges Markomanolis wrote: Dear all, Hi again, after using MPI_Ssend seems to be what I was looking for but I would like to know more about MPI_Send. For example sending 1 byte with MPI_Send it takes 8.69 microsec but with MPI_Ssend it takes 152.9 microsec. I understand the difference

Re: [OMPI users] computing the latency with OpenMpi

2010-09-13 Thread Eugene Loh
Georges Markomanolis wrote: I have some questions about the duration of the communication with MPI_Send and MPI_Recv. I am using either SkaMPI either my implementation to measure the pingpong (MPI_Send and MPI_Recv) time between two nodes for 1 byte and more. The timing of the pingpong is

Re: [OMPI users] MPI_Reduce performance

2010-09-10 Thread Eugene Loh
Richard Treumann wrote: Hi Ashley I understand the problem with descriptor flooding can be serious in an application with unidirectional data dependancy. Perhaps we have a different perception of how common that is. Ashley speculated it was a "significant minority."  I don't

Re: [OMPI users] MPI_Reduce performance

2010-09-09 Thread Eugene Loh
Alex A. Granovsky wrote: Isn't in evident from the theory of random processes and probability theory that in the limit of infinitely large cluster and parallel process, the probability of deadlocks with current implementation is unfortunately quite a finite quantity and in

Re: [OMPI users] MPI_Reduce performance

2010-09-09 Thread Eugene Loh
Gus Correa wrote: More often than not some components lag behind (regardless of how much you tune the number of processors assigned to each component), slowing down the whole scheme. The coupler must sit and wait for that late component, the other components must sit and wait for the coupler,

Re: [OMPI users] is there a way to bring to light _all_ configure options in a ready installation?

2010-08-24 Thread Eugene Loh
Terry Dontje wrote: Jeff Squyres wrote: You should be able to run "./configure --help" and see a lengthy help message that includes all the command line options to configure. Is that what you're looking for? No, he wants to know what configure options were used with some

Re: [OMPI users] problem with .bashrc stetting of openmpi

2010-08-16 Thread Eugene Loh
sun...@chem.iitb.ac.in wrote: sun...@chem.iitb.ac.in wrote: Dear Open-mpi users, I installed openmpi-1.4.1 in my user area and then set the path for openmpi in the .bashrc file as follow. However, am still getting following error message whenever am starting the

Re: [OMPI users] Hyper-thread architecture effect on MPI jobs

2010-08-11 Thread Eugene Loh
The way MPI processes are being assigned to hardware threads is perhaps neither controlled nor optimal.  On the HT nodes, two processes may end up sharing the same core, with poorer performance. Try submitting your job like this % cat myrankfile1 rank  0=os223 slot=0 rank  1=os221 slot=0

Re: [OMPI users] OpenMPI providing rank?

2010-08-04 Thread Eugene Loh
Eugene Loh wrote: Yves Caniou wrote: Le Wednesday 28 July 2010 15:05:28, vous avez écrit : I am confused. I thought all you wanted to do is report out the binding of the process - yes? Are you trying to set the affinity bindings yourself? If the latter, then your

Re: [OMPI users] Hybrid OpenMPI / OpenMP run pins OpenMP threads to a single core

2010-08-04 Thread Eugene Loh
David Akin wrote: All, I'm trying to get the OpenMP portion of the code below to run multicore on a couple of 8 core nodes. I was gone last week and am trying to catch up on e-mail. This thread was a little intriguing. I agree with Ralph and Terry: *) OMPI should not be binding by

Re: [OMPI users] execuation time is not stable with 2 processes

2010-08-04 Thread Eugene Loh
Tad Lake wrote: I run it : mpirun -np 2 --host node2 ./a.out But the result of time is not stable with difference of 100 times. For example, the max value of time can be 3000, meanwhile the min is 100. Again, know what results to expect. Is 3000 a reasonable time and 100 too fast? Or, is

Re: [OMPI users] execuation time is not stable with 2 processes

2010-08-04 Thread Eugene Loh
Mark Potts wrote: Hi, I'd opt for the fact that tv0 is given value only on rank 0 and tv1 is only given value on rank 1. Kind of hard to get a diff betwn the two on either rank with that setup. You need to determine the tv0 and tv1 on both ranks. I don't understand this.

Re: [OMPI users] Fortran MPI Struct with Allocatable Array

2010-08-02 Thread Eugene Loh
I can't give you a complete answer, but I think this is less an MPI question and more of a Fortran question.  The question is if you have a Fortran derived type, one of whose components is a POINTER, what does the data structure look like in linear memory?  I could imagine the answer is

Re: [OMPI users] OpenMPI providing rank?

2010-08-01 Thread Eugene Loh
Yves Caniou wrote: Le Wednesday 28 July 2010 15:05:28, vous avez écrit : I am confused. I thought all you wanted to do is report out the binding of the process - yes? Are you trying to set the affinity bindings yourself? If the latter, then your script doesn't do anything that

Re: [OMPI users] Help on the big picture..

2010-07-30 Thread Eugene Loh
Two comments interwoven below... Cristobal Navarro wrote: i was not aware that openMPI internally uses shared memory in case two proceses reside on the same node, which is perfect. The ways OMP uses shared memory and Open MPI (or most other MPI implementations) uses shared memory are very

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