[OMPI users] cartofile

I feel like I should know, but what's a cartofile? I guess you supply "topological" information about a host, but I can't tell how this information is used by, say, mpirun.

Re: [OMPI users] Messages getting lost during transmission (?)

Dennis Luxen wrote: In MPI, you must complete every MPI_Isend by MPI_Wait on the request handle (or a variant like MPI_Waitall or MPI_Test that returns TRUE). An un-completed MPI_Isend leaves resources tied up. Good point, but that doesn't seem to help. I augmented each MPI_Isend with a MPI

Re: [OMPI users] Help!

guosong wrote: I am new to open MPI I am not, but I'm not real familiar with thread-safe MPI programming.  Still, I saw no other replies to your question, so I'll make an attempt to answer. MPI does not guarantee thread safety.  E.g., see http://www.mpi-forum.org/docs/mpi-20-html/node162.h

Re: [OMPI users] Job distribution on many-core NUMA system

A. Austen wrote: On Fri, 28 Aug 2009 10:16 -0700, "Eugene Loh" wrote: Big topic and actually the subject of much recent discussion. Here are a few comments: 1) "Optimally" depends on what you're doing. A big issue is making sure each MPI pr

Re: [OMPI users] Job distribution on many-core NUMA system

Big topic and actually the subject of much recent discussion. Here are a few comments: 1) "Optimally" depends on what you're doing. A big issue is making sure each MPI process gets as much memory bandwidth (and cache and other shared resources) as possible. This would argue that processes

Re: [OMPI users] Anyscientific application heavily using MPI_Barrier?

Richard Treumann wrote: Guess I should have kept quiet a bit longer. As I recall we had already seen a counter example to Jeff's stronger statement and that motivated my narrower one. If there are no wildcard receives - every MPI_Barrier call is semantica

Re: [OMPI users] Anyscientific application heavily using MPI_Barrier?

Jeff Squyres wrote: On Aug 24, 2009, at 1:03 PM, Eugene Loh wrote: E.g., let's say P0 and P1 each send a message to P2, both using the same tag and communicator. Let's say P2 does two receives on that communicator and tag, using a wildcard source. So, the messages could be r

Re: [OMPI users] Any scientific application heavily using MPI_Barrier?

Going back to this thread from earlier this calendar year... Ganesh wrote: Hi Dick, Jeff paraphrased an unnamed source as suggesting that: "any MPI program that relies on a barrier for correctness is an incorrect MPI application." . That is probably too strong. How about thi

Re: [OMPI users] MPI loop problem

Julia He wrote: does the problem show up even if you turn MPI off? My answer: Yes and No. Yes, when I used ifort compiler. But the problem did not show up when I used gfortran, which was much slower. Okay.  So, if this is not an MPI problem, as m

Re: [OMPI users] MPI loop problem

Is the problem independent of the the number of MPI processes?  (You suggest this is the case.) If so, does this problem show up even with np=1 (a single MPI process)? If so, does the problem show up even if you turn MPI off? If so, the problem would seem to be unrelated to the MPI implement

Re: [OMPI users] Help: How to accomplish processors affinity

Lee Amy wrote: I build a Kerrighed Clusters Like Lenny, I'm not familiar with such clusters, but... with 4 nodes so they look like a big SMP machine. every node has 1 processor with dingle core. 1) Dose MPI programs could be running on such kinds of machine? If yes, could anyone show me som

Re: [OMPI users] rank file error: Rankfile claimed...

jody wrote: But can you explain what the meaning of the max-slots entry is? I checked the FAQs http://www.open-mpi.org/faq/?category=running#simple-spmd-run http://www.open-mpi.org/faq/?category=running#mpirun-scheduling but i couldn't find any explanation. (furthermore, in the FAQ it says "ma

Re: [OMPI users] programming qsn??

amjad ali wrote: Please tell me that if have multiple such ISEND-RECV squrntially for sending receiving data then DO we need to declare separate status(MPI_STATUS_SIZE) with for example status1, status2, ; or a single declaration of it will work for all?? First of all, it really is good

Re: [OMPI users] programming qsn??

amjad ali wrote: I am parallelizing a CFD 2D code in FORTRAN+OPENMPI. Suppose that the grid (all triangles) is partitioned among 8 processes using METIS. Each process has different number of neighboring processes. Suppose each process has n elements/faces whose data it need

Re: [OMPI users] strange IMB runs

I was away on vacation for two weeks and therefore missed most of this thread, but I'm quite interested. Michael Di Domenico wrote: >I'm not sure I understand what's actually happened here. I'm running >IMB on an HP superdome, just comparing the PingPong benchmark > >HP-MPI v2.3 >Max ~ 700-800

Re: [OMPI users] Hooks for Collective's sync/transfer activity?

Manfred Muecke wrote: I would like to understand in more detail how much time some collective communication calls really spend waiting for the last process to enter. I know this can be done by logging entry times for each process, but I wonder if there is a better and more efficient way. "Bette

Re: [OMPI users] Receiving an unknown number of messages

Shaun Jackman wrote: 2 calls MPI_Test. No message is waiting, so 2 decides to send. 2 sends to 0 and does not block (0 has one MPI_Irecv posted) 3 calls MPI_Test. No message is waiting, so 3 decides to send. 3 sends to 1 and does not block (1 has one MPI_Irecv posted) 0 calls MPI_Test. No messag

Re: [OMPI users] Receiving an unknown number of messages

Shaun Jackman wrote: Eugene Loh wrote: Shaun Jackman wrote: For my MPI application, each process reads a file and for each line sends a message (MPI_Send) to one of the other processes determined by the contents of that line. Each process posts a single MPI_Irecv and uses

Re: [OMPI users] Profiling performance by forcing transport choice.

Nifty Tom Mitchell wrote: On Thu, Jun 25, 2009 at 08:37:21PM -0400, Jeff Squyres wrote: Subject: Re: [OMPI users] 50%performance reduction due to OpenMPI v 1.3.2forcing allMPI traffic over Ethernet instead of using Infiniband While the previous thread on "performance r

Re: [OMPI users] Receiving an unknown number of messages

Shaun Jackman wrote: For my MPI application, each process reads a file and for each line sends a message (MPI_Send) to one of the other processes determined by the contents of that line. Each process posts a single MPI_Irecv and uses MPI_Request_get_status to test for a received message. If a

Re: [OMPI users] OpenMPI vs Intel MPI

Lenny Verkhovsky wrote: 2.   if you are using Open MPI 1.3 you dont have to use mpi_leave_pinned 1 , since it's a default value And if you're using "-mca btl self,sm" on a single node, I think mpi_leave_pinned is immaterial (since it's for openib). On Thu, Jul 2, 2009 at 4:47 PM, Swamy K

Re: [OMPI users] OpenMPI vs Intel MPI

Swamy Kandadai wrote: Jeff: I'm not Jeff, but... Linpack has different characteristics at different problem sizes. At small problem sizes, any number of different overheads could be the problem. At large problem sizes, one should approach the peak floating-point performance of the machin

Re: [OMPI users] Compile problems with 1.3.2

it depends... On Mon, Jun 29, 2009 at 2:28 PM, Eugene Loh wrote: Open MPI *does* have VampirTrace in it... Okay, yeah. You'd want to build OMPI with VT, but then need to find a tool to read the data. I thought I had sent e-mail out on this subject before, but cannot find it. Ot

Re: [OMPI users] Compile problems with 1.3.2

Jim Kusznir wrote: Ok, trying now. This does bring up a question I've been meaning to ask. I need to find a way to analyze the efficiency of parallel jobs, and the only way I've known about in the past is through vampire. I do not have the software license presently (and last I looked, it was

Re: [OMPI users] Bug in 1.3.2?: sm btl and isend is serializes

George Bosilca wrote: MPI does not impose any global order on the messages. The only requirement is that between two peers on the same communicator the messages (or at least the part required for the matching) is delivered in order. This make both execution traces you sent with your origin

Re: [OMPI users] Bug in 1.3.2?: sm btl and isend is serializes

Mark Bolstad wrote: I have a small test code that I've managed to duplicate the results from a larger code. In essence, using the sm btl with ISend, I wind up with the communication being completely serialized, i.e., all the calls from process 1 complete, then all from 2, ... I need to do so

Re: [OMPI users] Bug in 1.3.2?: sm btl and isend is serializes

Mark Bolstad wrote: I'll post the test code if requested (this email is already long) Yipes, how long is the test code? Short enough to send, yes? Please send.

Re: [OMPI users] top question

tsi...@coas.oregonstate.edu wrote: Thanks for the explanation. I am using GigEth + Open MPI and the buffered MPI_BSend. I had already noticed that top behaved differently on another cluster with Infinibandb + MPICH. So the only option to find out how much time each process is waiting arou

Re: [OMPI users] mpi trace visualization

Roman Martonak wrote: I would like to profile the MPI code using the vampir trace integrated in openmpi-1.3.2. In order to visualize the trace files, apart from commercial vampir, is there some free viewer for the OTF files ? I'm rusty on this stuff. If you go to http://www.paratools.com/ot

Re: [OMPI users] Performance testing software?

HPL can "stress test" the MPI, but it is typically relatively insensitive to MPI performance. The usual use produces a measure of the peak floating-point performance of the system. A broader set of system performance measurements are found in the HPCC (HPC Challenge) tests, which include HPL.

Re: [OMPI users] "An error occurred in MPI_Recv" with more than 2 CPU

vasilis wrote: The original issue, still reflected by the subject heading of this e-mail, was that a message overran its receive buffer. That was fixed by using tags to distinguish different kinds of messages (res, jacob, row, and col). I thought the next problem was the small (10^-

Re: [OMPI users] "An error occurred in MPI_Recv" with more than 2 CPU

vasilis wrote: On Wednesday 27 of May 2009 8:35:49 pm Eugene Loh wrote: At the level of this particular e-mail thread, the issue seems to me to be different. Results are added together in some arbitrary order and there are variations on order of 10^-10. This is not an issue of

Re: [OMPI users] "An error occurred in MPI_Recv" with more than 2 CPU

George Bosilca wrote: This is a problem of numerical stability, and there is no solution for such a problem in MPI. Usually, preconditioning the input matrix improve the numerical stability. At the level of this particular e-mail thread, the issue seems to me to be different. Results are

Re: [OMPI users] "An error occurred in MPI_Recv" with more than 2 CPU

vasilis wrote: Rank 0 accumulates all the res_cpu values into a single array, res. It starts with its own res_cpu and then adds all other processes. When np=2, that means the order is prescribed. When np>2, the order is no longer prescribed and some floating-point rounding variations

Re: [OMPI users] "An error occurred in MPI_Recv" with more than 2 CPU

vasilis wrote: Thank you Eugene for your suggestion. I used different tags for each variable, and now I do not get this error. The problem now is that I am getting a different solution when I use more than 2 CPUs. I checked the matrices and I found that they differ by a very small amount of

Re: [OMPI users] MPI_COMM_WORLD Error

mtcreekm...@broncs.utpa.edu wrote: I and new to OpenMPI and  have looked for this, but not getting anywhere. I got an example program off this site: The compute PI in Fortran example.  http://www.mcs.anl.gov/research/projects/mpi/usingmpi/examples/simplempi/main

Re: [OMPI users] "An error occurred in MPI_Recv" with more than 2 CPU

vasilis wrote: Dear openMpi users, I am trying to develop a code that runs in parallel mode with openMPI (1.3.2 version). The code is written in Fortran 90, and I am running on a cluster If I use 2 CPU the program runs fine, but for a larger number of CPUs I get the following error: [com

Re: [OMPI users] MPI processes hang when using OpenMPI 1.3.2 and Gcc-4.4.0

Simone Pellegrini wrote: sorry for the delay but I did some additional experiments to found out whether the problem was openmpi or gcc! The program just hangs... and never terminates! I am running on a SMP machine with 32 cores, actually it is a Sun Fire X4600 X2. (8 quad-core Barcelona AMD

Re: [OMPI users] OpenMPI deadlocks and race conditions ?

François PELLEGRINI wrote: users-requ...@open-mpi.org wrote: Date: Thu, 14 May 2009 17:06:07 -0700 From: Eugene Loh Subject: Re: [OMPI users] OpenMPI deadlocks and race conditions ? To: Open MPI Users Fran?ois PELLEGRINI wrote: I sometimes run into deadlocks in

Re: [OMPI users] OpenMPI deadlocks and race conditions ?

François PELLEGRINI wrote: I sometimes run into deadlocks in OpenMPI (1.3.3a1r21206), when running my MPI+threaded PT-Scotch software. So, are there multiple threads per process that perform message-passing operations? Other comments below. Luckily, the case is very small, with 4 procs onl

Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??

Eugene Loh wrote: Put more strongly, the "correct" (subjective term) way for an MPI implementation to bind processes is upon process creation and waiting until MPI_Init is "wrong". This point of view has nothing to do with asking the MPI implementation to support binding

Re: [OMPI users] 1.3.1 -rf rankfile behaviour ??

Ralph Castain wrote: On May 5, 2009, at 3:37 AM, Geoffroy Pignot wrote: The result is : everything works fine with MPI executables : logical !!! What I was trying to do , was to run non MPI exes thanks to mpirun. There , openmpi is not able to bind these processes to a particular CPU. My

Re: [OMPI users] MPI processes hang when using OpenMPI 1.3.2 and Gcc-4.4.0

? *) How large is N? Eugene Loh wrote: Simone Pellegrini wrote: Dear all, I have successfully compiled and installed openmpi 1.3.2 on a 8 socket quad-core machine from Sun. I have used both Gcc-4.4 and Gcc-4.3.3 during the compilation phase but when I try to run simple MPI programs proce

Re: [OMPI users] MPI processes hang when using OpenMPI 1.3.2 and Gcc-4.4.0

I'm responsible for some sm changes in 1.3.2, so I can try looking at this. Some questions below: Simone Pellegrini wrote: Dear all, I have successfully compiled and installed openmpi 1.3.2 on a 8 socket quad-core machine from Sun. I have used both Gcc-4.4 and Gcc-4.3.3 during the compilat

Re: [OMPI users] sharing memory between processes

Barnabas Debreczeni wrote: I am using PGAPack as a GA library, and it uses MPI to parallelize optimization runs. This is how I got to Open MPI. Let me see if I understand the underlying premise. You want to parallelize, but there are some large shared tables. There are many different para

Re: [OMPI users] MPI_Bcast from OpenMPI

Second cluster is almost the same features with the previous one From: Eugene Loh To: Open MPI Users Sent: Friday, April 24, 2009 1:26:14 AM Subject: Re: [OMPI users] MPI_Bcast from OpenMPI So, the remaining mystery is the 6x or so spike at 128 Mbyte.  Dunno.  How important is it to resolve that mystery?

Re: [OMPI users] MPI_Bcast from OpenMPI

Okay.  So, going back to Jeff's second surprise, we have 256 Mbyte/2.5 sec = 100 Mbyte/sec = 1 Gbit/sec (sloppy math).  So, without getting into details of what we're measuring/reporting here, there doesn't on the face of it appear to be anything wrong with the baseline performance.  Jeff was r

Re: [OMPI users] Open-MPI and gprof

jody wrote: If i get vprof or one of the other tools running, i'll write something up - perhaps the profiling subject would be worthy for a FAQ entry... Yes, perhaps. Note that there really are lots of options out there. Spend a few minutes googling. There are tools, surveys of tools, et

Re: [OMPI users] SHARED Memory----------------

shan axida wrote: It have read that FAQ. Terrific.  If you want to offer feedback for its improvement, that feedback would be welcome. Does it mean shared memory communication is used when send messages  between the processes in same node in default? Yes. No need an

Re: [OMPI users] SHARED Memory----------------

memory among processes which are runing in a node? From: Eugene Loh To: Open MPI Users Sent: Thursday, April 23, 2009 1:20:05 PM Subject: Re: [OMPI users] SHARED Memory Just to clarify (since "send to self" strikes me as confusing

Re: [OMPI users] SHARED Memory----------------

Just to clarify (since "send to self" strikes me as confusing)... If you're talking about using shared memory for point-to-point MPI message passing, OMPI typically uses it automatically between two processes on the same node.  It is *not* used for a process sending to itself.  There is a well

Re: [OMPI users] Problem with running openMPI program

Ankush Kaul wrote: @gus we are not able to make hpl sucessfully. i think it has to do something with blas i cannot find blas tar file on the net, i found rpm but de installation steps is with tar file. First of all, this mail list is for Open MPI issues. On this list are people who are

Re: [OMPI users] Problem with running openMPI program

Ankush Kaul wrote: @Eugene they are ok but we wanted something better, which would more clearly show de diff in using a single pc and the cluster. Another option is the NAS Parallel Benchmarks.  They are older, but well known, self-verifying, report performance, and relatively small and acce

Re: [OMPI users] Open-MPI and gprof

jody wrote: Hi I wanted to profile my application using gprof, and proceeded like when profiling a normal application: - compile everything with option -pg - run application - call gprof This returns a normal-looking output, but i don't know whether this is the data for node 0 only or accumulate

Re: [OMPI users] Problem with running openMPI program

Ankush Kaul wrote: let me describe what i want to do. i had taken linux clustering as my final year engineering project as i m really iintrested in 0networking. to tell de truth our college does not have any professor with knowledge of clustering. the aim of our project was just to make a

Re: [OMPI users] Debugging memory use of Open MPI

Shaun Jackman wrote: Eugene Loh wrote: What's the rest? I said the shared-memory area is much smaller, but I was confused about which OMPI release I was using. So, the shared-memory area was 128 Mbyte and it was getting mapped in once for each process, and so it was counted doubly.

Re: [OMPI users] Debugging memory use of Open MPI

Eugene Loh wrote: Shaun Jackman wrote: What's the purpose of the 400 MB that MPI_Init has allocated? It's for... um, I don't know. Let's see... About a third of it appears to be vt_open() -> VTThrd_open() -> VTGen_open which I'm guessing is due to the Vam

Re: [OMPI users] Debugging memory use of Open MPI

Shaun Jackman wrote: Wow. Thanks, Eugene. I definitely have to look into the Sun HPC ClusterTools. It looks as though it could be very informative. Great. And, I didn't mean to slight TotalView. I'm just not familiar with it. What's the purpose of the 400 MB that MPI_Init has allocated?

Re: [OMPI users] Debugging memory use of Open MPI

Shaun Jackman wrote: Eugene Loh wrote: On the other hand, I assume the memory imbalance we're talking about is rather severe. Much more than 2500 bytes to be noticeable, I would think. Is that really the situation you're imagining? The memory imbalance is drastic. I'm ex

Re: [OMPI users] Debugging memory use of Open MPI

On Apr 14, 2009, at 12:02 PM, Shaun Jackman wrote: Assuming the problem is congestion and that messages are backing up, ... I'd check this assumption first before going too far down that path. You might be able to instrument your code to spit out sends and receives. VampirTrace (and PERU

Re: [OMPI users] Debugging memory use of Open MPI

Shaun Jackman wrote: Eugene Loh wrote: At 2500 bytes, all messages will presumably be sent "eagerly" -- without waiting for the receiver to indicate that it's ready to receive that particular message. This would suggest congestion, if any, is on the receiver side. Some kin

Re: [OMPI users] Problem with running openMPI program

Ankush Kaul wrote: Finally, after mentioning the hostfiles the cluster is working fine. We downloaded few benchmarking softwares but i would like to know if there is any GUI based benchmarking software so that its easier to demonstrate the working of our cluster while displaying our cluster.

Re: [OMPI users] Debugging memory use of Open MPI

Shaun Jackman wrote: Eugene Loh wrote: I'm no expert, but I think it's something like this: 1) If the messages are short, they're sent over to the receiver. If the receiver does not expect them (no MPI_Irecv posted), it buffers them up. 2) If the messages are long, only

Re: [OMPI users] Debugging memory use of Open MPI

Shaun Jackman wrote: When running my Open MPI application, I'm seeing three processors that are using five times as much memory as the others when they should all use the same amount of memory. To start the debugging process, I would like to know if it's my application or the Open MPI library

Re: [OMPI users] Factor of 10 loss in performance with 1.3.x

Steve Kargl wrote: I can rebuild 1.2.9 and 1.3.1. Is there any particular configure options that I should enable/disable? I hope someone else will chime in here, because I'm somewhat out of ideas. All I'm saying is that 10-usec latencies on sm with 1.3.0 or 1.3.1 are out of line with what o

Re: [OMPI users] Factor of 10 loss in performance with 1.3.x

Iain Bason wrote: But maybe Steve should try 1.3.2 instead? Does that have your improvements in it? 1.3.2 has the single-queue implementation and automatic sizing of the sm mmap file, both intended to fix problems at large np. At np=2, you shouldn't expect to see much difference. And th

Re: [OMPI users] Factor of 10 loss in performance with 1.3.x

Iain Bason wrote: There are a bunch changes in the shared memory module between 1.2.9 and 1.3.1. One significant change is the introduction of the "sendi" internal interface. I believe George Bosilca did the initial implementation. This is just a wild guess, but maybe there is somethin

Re: [OMPI users] Factor of 10 loss in performance with 1.3.x

Steve Kargl wrote: I recently upgraded OpenMPI from 1.2.9 to 1.3 and then 1.3.1. One of my colleagues reported a dramatic drop in performance with one of his applications. My investigation shows a factor of 10 drop in communication over the memory bus. I've placed a figure that iilustrates the

Re: [OMPI users] Open MPI 2009 released

Ah. George, you should have thought about that. I understand your eagerness to share this exciting news, but perhaps an April-1st announcement detracted from the seriousness of this grand development. Here's another desirable MPI feature. People talk about "error detection/correction". We

Re: [OMPI users] Bogus memcpy or bogus valgrind record

Jeff Squyres wrote: On Mar 28, 2009, at 5:31 AM, François PELLEGRINI wrote: MPI_Comm_size (MPI_COMM_WORLD, &procglbnbr); MPI_Comm_rank (MPI_COMM_WORLD, &proclocnum); dataloctab = malloc (2 * (procglbnbr + 1) * sizeof (int)); dataglbtab = dataloctab + 2; Why +2? Shouldn't it be +pr

Re: [OMPI users] Collective operations and synchronization

Shaun Jackman wrote: On Tue, 2009-03-24 at 07:03 -0800, Eugene Loh wrote: I'm not sure I understand this suggestion, so I'll say it the way I understand it. Would it be possible for each process to send an "all done" message to each of its neighbors? Conversely, each

Re: [OMPI users] MPI Blocking Routines and Memory Leaks

Simon Köstlin wrote: I'm new to MPI and I've got a question about blocking routines like the Send-, Wait-Function and so on. I wrote a parallel program that uses the blocking Send and the Nonblocking Isend function. Now my question: If I'm sending something with the blocking Send function it

Re: [OMPI users] Collective operations and synchronization

Ashley Pittman wrote: On 23 Mar 2009, at 23:36, Shaun Jackman wrote: loop { MPI_Ibsend (for every edge of every leaf node) MPI_barrier MPI_Iprobe/MPI_Recv (until no messages pending) MPI_Allreduce (number of nodes removed) } until (no nodes removed by any node) Previously, I attempted to use

Re: [OMPI users] Collective operations and synchronization

Shaun Jackman wrote: I've just read in the Open MPI documentation [1] That's the MPI spec, actually. that collective operations, such as MPI_Allreduce, may synchronize, but do not necessarily synchronize. My algorithm requires a collective operation and synchronization; is there a better (m

Re: [OMPI users] valgrind complaint in openmpi 1.3 (mca_mpool_sm_alloc)

Åke Sandgren wrote: Hi! Valgrind seems to think that there is an use of uninitialized value in mca_mpool_sm_alloc, i.e. the if(mpool_sm->mem_node >= 0) { Backtracking that i found that mem_node is not set during initializing in mca_mpool_sm_init. The resources parameter is never used and the mp

Re: [OMPI users] Any scientific application heavilyusing MPI_Barrier?

Jeff Squyres wrote: If you're exchanging data at the end of an iteration, then you effectively have a synchronization anyway -- no need for an extra barrier synchronization. Ralph Castain wrote: Ummmnot to put gasoline on the fire, but...if the data exchange is blocking, why do you n

Re: [OMPI users] Memory leak in my code

Mark Allan wrote: Dear all, With this simple code I find I am getting a memory leak when I run on 2 processors.  Can anyone advise why? I'm fairly new to MPI (have only done very simple things in the past).  I'm trying to do a non-blocking send

Re: [OMPI users] MPI_Gatherv and 0 size?

I think the question is about passing NULL as a buffer pointer. E.g., MPI_Send(NULL, 0, mytype,dst, tag,comm); vs MPI_Send(&dummy,0,mytype,dst,tag,comm); George Bosilca wrote: The only restriction the MPI standard impose on the sendcounts and recvcounts arrays is that the values be non-neg

Re: [OMPI users] v1.3: mca_common_sm_mmap_init error

Prentice Bisbal wrote: Jeff Squyres wrote: On Feb 2, 2009, at 4:48 PM, Prentice Bisbal wrote No. I was running just a simple "Hello, world" program to test v1.3 when these errors occured. And as soon as I reverted to 1.2.8, the errors disappeared. FW

Re: [OMPI users] Asynchronous behaviour of MPI Collectives

Jeff Squyres wrote: As you have notes, MPI_Barrier is the *only* collective operation that MPI guarantees to have any synchronization properties (and it's a fairly weak guarantee at that; no process will exit the barrier until every process has entered the barrier -- but there's no guarantee

Re: [OMPI users] openMPI, transfer data from multiple sources to one destination

Jack Bryan wrote: I need to transfer data from multiple sources to one destination. The requirement is: (1) The sources and destination nodes may work asynchronously.   (2) Each source node generates data package in their own paces.     And, there may be many packages to send. Whenever,

Re: [OMPI users] sending message to the source(0) from other processors

Win Than Aung wrote: thanks for your reply jeff so i tried following #include #include int main(int argc, char **argv) {  int np, me, sbuf = -1, rbuf = -2,mbuf=1000; int data[2];  MPI_Init(&argc,&argv);  MPI_Comm_size(MPI_COMM_WORLD,&np);  MPI_Comm_rank(MPI_COMM

Re: [OMPI users] sending message to the source(0) from other processors

Win Than Aung wrote: MPI_Recv() << is it possible to receive the message sent from other sources? I tried MPI_ANY_SOURCE in place of source but it doesn't work out Yes of course. Can you send a short example of what doesn't work? The example should presumably be less than about 20 line

Re: [OMPI users] trouble using --mca mpi_yield_when_idle 1

Jeff Squyres wrote: On Dec 12, 2008, at 11:46 AM, Eugene Loh wrote: FWIW, I've run into the need for this a few times due to HPCC tests on large (>100 MPI procs) nodes or multicore systems. HPCC (among other things) looks at the performance of a single process while all ot

Re: [OMPI users] trouble using --mca mpi_yield_when_idle 1

Jeff Squyres wrote: FWIW, Open MPI does have on its long-term roadmap to have "blocking" progress -- meaning that it'll (probably) spin aggressively for a while and if nothing "interesting" is happening, it'll go into a blocking mode and let the process block in some kind of OS call. Alth

Re: [OMPI users] trouble using --mca mpi_yield_when_idle 1

douglas.gupt...@dal.ca wrote: Proceeding from that, it seems that "mpi_recv" is implemented as "poll forever until the message comes" and NOT as "sleep until the message comes" I had assumed, until now, that mpi_recv would be implemented as the second. It isn't a binary situatio

Re: [OMPI users] trouble using --mca mpi_yield_when_idle 1

Jens wrote: Hi Terry, I would like to run a paraview-server all time on our cluster (even though it is not in use 24h) - but this would simply result in some kind of "heating-thread". Even though it has (in theory) no impact on the node performace (which is part of a grid-engine), it would sim

Re: [OMPI users] trouble using --mca mpi_yield_when_idle 1

Douglas Guptill wrote: Hi: I am using openmpi-1.2.8 to run a 2 processor job on an Intel Quad-core cpu. Opsys is Debian etch. I am reaonably sure that, most of the time, one process is waiting for results from the other. The code is fortran 90, and uses mpi_send and mpi_recv. Yet "gnome-sys

Re: [OMPI users] Progress of the asynchronous messages

vladimir marjanovic wrote: In order to overlap communication and computation I don't want to use MPI_Wait. Right.  One thing to keep in mind is that there are two ways of overlapping communication and computation.  One is you start a send (MPI_Isend), you do a bunch of computation

Re: [OMPI users] Progress of the asynchronous messages

vladimir marjanovic wrote: I am new user of Open MPI, I've used MPICH before. There is performance bug with the following scenario: proc_B:  MPI_Isend(...,proc_A,..,&request)                 do{   sleep(1);      MPI_Test(..,&flag,&request);   

Re: [OMPI users] Equivalent .h files

Benjamin Lamptey wrote: Hello, I am new at using open-mpi and will like to know something basic. What is the equivalent of the "mpif.h" in open-mpi which is normally "included" at the beginning of mpi codes (fortran in this case). I shall appreciate that for cpp as well. For Fortran:

Re: [OMPI users] MPI_SUM and MPI_REAL16 with MPI_ALLREDUCE in fortran90

I think the KINDs are compiler dependent. For Sun Studio Fortran, REAL*16 and REAL(16) are the same thing. For Intel, maybe it's different. I don't know. Try running this program: double precision xDP real(16) x16 real*16 xSTAR16 write(6,*) kind(xDP), kind(x16), kind(xSTAR16), kind(1.0_16)

Re: [OMPI users] Performance: MPICH2 vs OpenMPI

Sangamesh B wrote: I reinstalled all softwares with -O3 optimization. Following are the performance numbers for a 4 process job on a single node: MPICH2: 26 m 54 s OpenMPI: 24 m 39 s I'm not sure I'm following. OMPI is faster here, but is that a result of MPICH2 slowing down? The or

Re: [OMPI users] Performance: MPICH2 vs OpenMPI

Brian Dobbins wrote: On Thu, Oct 9, 2008 at 10:13 AM, Jeff Squyres wrote: On Oct 9, 2008, at 8:06 AM, Sangamesh B wrote: OpenMPI : 120m 6s MPICH2 :  67m 44s That seems to indicate that something else is going on -- with -np 1, there

Re: [OMPI users] Performance: MPICH2 vs OpenMPI

Eugene Loh wrote: Sangamesh B wrote: The job is run on 2 nodes - 8 cores. OpenMPI - 25 m 39 s. MPICH2 - 15 m 53 s. I don't understand MPICH very well, but it seemed as though some of the flags used in building MPICH are supposed to be added in automatically to the mpicc/etc com

Re: [OMPI users] Performance: MPICH2 vs OpenMPI

Sangamesh B wrote: I wanted to switch from mpich2/mvapich2 to OpenMPI, as OpenMPI supports both ethernet and infiniband. Before doing that I tested an application 'GROMACS' to compare the performance of MPICH2 & OpenMPI. Both have been compiled with GNU compilers. After this benchmark, I cam

Re: [OMPI users] Odd MPI_Bcast behavior

I guess this must depend on what BTL you're using.  If I run all processes on the same node, I get the behavior you expect.  So, are you running processes on the same node, or different nodes and, if different, via TCP or IB? Gregory D Abram wrote: I have a little program which initializes,

Re: [OMPI users] MPI_sendrecv = MPI_Send+ MPI_RECV ?

Aurélien Bouteiller wrote: You can't assume that MPI_Send does buffering. Yes, but I think this is what Eric meant by misinterpreting Enrico's problem. The communication pattern is to send a message, which is received remotely. There is remote computation, and then data is sent back. No

Re: [OMPI users] Warnings in Ubuntu Hardy

Dirk Eddelbuettel wrote: On 6 September 2008 at 22:13, Davi Vercillo C. Garcia () wrote: | I'm trying to execute some programs in my notebook (Ubuntu 8.04) using | OpenMPI, and I always get a warning message like: | | libibverbs: Fatal: couldn't read uverbs ABI version. | -

Re: [OMPI users] CPU burning in Wait state

Jeff Squyres wrote: OMPI currently polls for message passing progress. While you're in MPI_BCAST, it's quite possible/ likely that OMPI will poll hard until the BCAST is done. It is possible that a future version of OMPI will use a hybrid polling+non- polling approach for progress, such th

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