[OMPI users] Rank specific argument to mpirun

into different communicators and this pattern breaks that logic. Is there an alternative approach to doing this? Thank you, Saliya -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center Indiana Universi

Re: [OMPI users] Rank specific argument to mpirun

e:- $OMPI_*) > to its ranks. So I believe you may use $OMPI_COMM_WORLD_LOCAL_RANK to > specifically filter out parameters within the script. > > Regards > Udayanga Wickramasinghe > Research Assistant > School of Informatics and Computing | CREST > Indiana University, Bloomingt

Re: [OMPI users] Rank specific argument to mpirun

nvironment variables (ie:- $OMPI_*) > to its ranks. So I believe you may use $OMPI_COMM_WORLD_LOCAL_RANK to > specifically filter out parameters within the script. > > Regards > Udayanga Wickramasinghe > Research Assistant > School of Informatics and Computing | CREST > Indiana University, Bloomington

Re: [OMPI users] Rank specific argument to mpirun

I tested and the number of ranks in world comm is correct. I couldn't find the bug that causes the program to produce erroneous answers when this scheme is used, though. On Fri, Jul 29, 2016 at 3:38 PM, Saliya Ekanayake wrote: > Thank you, that's good to know. > > Yes, tes

Re: [OMPI users] OpenMPI + Hadoop

rplus/Greenplum_RalphCastain-1up.pdf, but wonder if there's some detailed steps on getting a simple MR program running with OpenMPI. Thank you, Saliya On Mon, Feb 24, 2014 at 1:22 PM, Saliya Ekanayake wrote: > Thank you Ralph. I'll get back to you if I run into issues. > > > On Mo

[OMPI users] How to replace --cpus-per-proc by --map-by

t 0]]: [B/B/B/B][./././.]* *[i52:31765] MCW rank 1 bound to socket 0[core 0[hwt 0]], socket 0[core 1[hwt 0]], socket 0[core 2[hwt 0]], socket 0[core 3[hwt 0]]: [B/B/B/B][./././.]* Is there a better way without using -cpus-per-proc as suggested to get the same effect? Thank you, Saliya -- Saliya

Re: [OMPI users] How to replace --cpus-per-proc by --map-by

> > [i52:31765] MCW rank 1 bound to socket 0[core 0[hwt 0]], socket 0[core 1 > [hwt 0]], socket 0[core 2[hwt 0]], socket 0[core 3[hwt 0]]: > [B/B/B/B][./././.] > > > > > > Is there a better way without using -cpus-per-pr

Re: [OMPI users] How to replace --cpus-per-proc by --map-by

ore 3[hwt 0]]: > > [B/B/B/B][./././.] > > > [i52:31765] MCW rank 1 bound to socket 0[core 0[hwt 0]], socket 0[core > 1 > > [hwt 0]], socket 0[core 2[hwt 0]], socket 0[core 3[hwt 0]]: > > [B/B/B/B][./././.] > > > > > > > > >

[OMPI users] Contributing Examples for Java Binding

ons plus kmeans clustering and matrix multiplication. If possible I'd like to contribute these to OpenMPI and wonder what's your input on this. Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

Re: [OMPI users] Contributing Examples for Java Binding

; Thanks! > Ralph > > On Apr 3, 2014, at 1:44 PM, Saliya Ekanayake wrote: > > Hi, > > I've been working on some applications in our group where I've been using > OpenMPI Java binding. Over the course of this work, I've accumulated > several samples that I w

Re: [OMPI users] Contributing Examples for Java Binding

faq/?category=java). > > > On Apr 3, 2014, at 7:09 PM, Saliya Ekanayake wrote: > > > Great. I will cleanup and send you a tarball. > > > > Thank you > > Saliya > > > > On Apr 3, 2014 5:51 PM, "Ralph Castain" wrote: > > We'd be happ

[OMPI users] Optimal mapping/binding when threads are used?

to speed up these Tx*1*xN cases? Also, I expected B to perform better than A as threads could utilize all 8 cores, but it wasn't the case. Thank you, Saliya [image: Inline image 1] -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

Re: [OMPI users] Optimal mapping/binding when threads are used?

ry, and so messaging will run slower - > and you want the ranks that share a node to be the ones that most > frequently communicate to each other, if you can identify them. > > HTH > Ralph > > On Apr 10, 2014, at 5:59 PM, Saliya Ekanayake wrote: > > Hi, > > I am eval

Re: [OMPI users] Optimal mapping/binding when threads are used?

Just an update. Yes, binding to all is as same as binding to none. I was mistaken by my memory :) On Fri, Apr 11, 2014 at 1:22 AM, Saliya Ekanayake wrote: > Thank you Ralph for the details and it's a good point you mentioned on > mapping by node vs socket. We have another program

[OMPI users] OpenMPI with Gemini Interconnect

f you could give some suggestions on how to build OpenMPI with Gemini support. [1] https://www.open-mpi.org/papers/cug-2012/cug_2012_open_mpi_for_cray_xe_xk.pdf Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com http://saliya.org

Re: [OMPI users] OpenMPI with Gemini Interconnect

luster. Unfortunately, due to a Cray bug, case 80503, that has > not yet worked. > Ray > > > On 4/16/2014 4:44 PM, Saliya Ekanayake wrote: > > Hi, > > We have a Cray XE6/XK7 supercomputer (BigRed II) and I was trying to get > OpenMPI Java b

Re: [OMPI users] OpenMPI with Gemini Interconnect

http://saliya.org > > > > ___ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > _______ > > users mailing list

Re: [OMPI users] SIGSEGV for Java program in openmpi-1.8.2rc2 on Solaris 10

rs mailing list > > us...@open-mpi.org > > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > > Link to this post: > http://www.open-mpi.org/community/lists/users/2014/07/24870.php > > > -- > Jeff Squyres > jsquy...@cisco.com > For corporate legal information go to: > http://www.cisco.com/web/about/doing_business/legal/cri/ > > ___ > users mailing list > us...@open-mpi.org > Subscription: http://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2014/07/24874.php > -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

[OMPI users] Best way to communicate a 2d array with Java binding

n and send it I guess 2 would internally do the copying to a buffer and use it, so suggesting 1. is the best option. Is this the case or is there a better way to do this? Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com http://saliya.org

Re: [OMPI users] Best way to communicate a 2d array with Java binding

Thank you Oscar for the detailed information, but I'm still wondering how would the copying in 2 would be different than what's done here with copying to a buffer. On Fri, Aug 22, 2014 at 2:17 PM, Oscar Vega-Gisbert wrote: > El 22/08/14 17:10, Saliya Ekanayake escribió: > >

Re: [OMPI users] Best way to communicate a 2d array with Java binding

s for copying? Thank you, Saliya On Fri, Aug 22, 2014 at 3:24 PM, Oscar Vega-Gisbert wrote: > El 22/08/14 20:44, Saliya Ekanayake escribió: > > Thank you Oscar for the detailed information, but I'm still wondering how >> would the copying in 2 would be different t

Re: [OMPI users] Best way to communicate a 2d array with Java binding

Yes, these are all MPI_DOUBLE On Fri, Aug 22, 2014 at 3:38 PM, Rob Latham wrote: > > > On 08/22/2014 10:10 AM, Saliya Ekanayake wrote: > >> Hi, >> >> I've a quick question about the usage of Java binding. >> >> Say there's a 2 dimensional d

Re: [OMPI users] Best way to communicate a 2d array with Java binding

Please find inline comments. On Fri, Aug 22, 2014 at 3:45 PM, Rob Latham wrote: > > > On 08/22/2014 02:40 PM, Saliya Ekanayake wrote: > >> Yes, these are all MPI_DOUBLE >> > > well, yeah, but since you are talking about copying into a "direct buffer"

[OMPI users] What could cause a segfault in OpenMPI?

. The ompi_info is attached. 2. cd to examples directory and mpicc hello_c.c 3. mpirun -np 2 ./a.out 4. Error text is attached. Please let me know if you need more info. Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliy

Re: [OMPI users] What could cause a segfault in OpenMPI?

iya, > > Would you mind trying to reproduce the problem using the latest 1.8 > release - 1.8.3? > > Thanks, > > Howard > > > 2014-11-04 11:10 GMT-07:00 Saliya Ekanayake : > >> Hi, >> >> I am using OpenMPI 1.8.1 in a Linux cluster that we recently se

Re: [OMPI users] What could cause a segfault in OpenMPI?

p/ > > > > On Nov 4, 2014, at 1:10 PM, Saliya Ekanayake wrote: > > > Hi, > > > > I am using OpenMPI 1.8.1 in a Linux cluster that we recently setup. It > builds fine, but when I try to run even the simplest hello.c program it'll > cause a segfault. Any

Re: [OMPI users] What could cause a segfault in OpenMPI?

Hi Jeff, You are probably busy, but just checking if you had a chance to look at this. Thanks, Saliya On Thu, Nov 6, 2014 at 9:19 AM, Saliya Ekanayake wrote: > Hi Jeff, > > I've attached a tar file with information. > > Thank you, > Saliya > > On Tue, Nov 4,

Re: [OMPI users] What could cause a segfault in OpenMPI?

dditional information to give a clue as to what is happening. :-( > > > > On Nov 9, 2014, at 11:43 AM, Saliya Ekanayake wrote: > > > Hi Jeff, > > > > You are probably busy, but just checking if you had a chance to look at > this. > > > > Thanks, >

[OMPI users] Accessing Process Affinity within MPI Program

Hi, Is it possible to get information on the process affinity that's set in mpirun command within the MPI program? For example I'd like to know the number of cores that a given rank is bound to. Thank you -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Infor

[OMPI users] Question on Mapping and Binding

k you, Saliya -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center Indiana University, Bloomington Cell 812-391-4914 http://saliya.org

Re: [OMPI users] Question on Mapping and Binding

ou specified - I believe by default > we bind to socket when mapping by socket. If you want them bound to core, > you might need to add —bind-to core. > > I can take a look at it - I *thought* we had reset that to bind-to core > when PE=N was specified, but maybe that got lost. &

Re: [OMPI users] Question on Mapping and Binding

Thank you and one last question. Is it possible to avoid a core and instruct OMPI to use only the other cores? On Mon, Dec 22, 2014 at 2:08 PM, Ralph Castain wrote: > > On Dec 22, 2014, at 10:45 AM, Saliya Ekanayake wrote: > > Hi Ralph, > > Yes the report bindings show the

Re: [OMPI users] What could cause a segfault in OpenMPI?

_object_t *) (&m->cm_recv_msg_queue))->obj_magic_id' failed. Thank you, Saliya On Mon, Nov 10, 2014 at 10:01 AM, Saliya Ekanayake wrote: > Thank you Jeff, I'll try this and let you know. > > Saliya > On Nov 10, 2014 6:42 AM, "Jeff Squyres (jsquyres)" > wr

Re: [OMPI users] OMPI users] What could cause a segfault in OpenMPI?

btl_openib_connect_udcm.c:736: udcm_module_finalize: > Assertion `((0xdeafbeedULL << 32) + 0xdeafbeedULL) == ((opal_object_t *) > (&m->cm_recv_msg_queue))->obj_magic_id' failed. > > Thank you, > Saliya > > On Mon, Nov 10, 2014 at 10:01 AM, Saliya Ekanayake > w

Re: [OMPI users] OMPI users] What could cause a segfault in OpenMPI?

What I heard from the administrator is that, "The tests that work are the simple utilities ib_read_lat and ib_read_bw that measures latency and bandwith between two nodes. They are part of the "perftest" repo package." On Dec 28, 2014 10:20 AM, "Saliya Ekanayake&qu

Re: [OMPI users] OMPI users] What could cause a segfault in OpenMPI?

the ibv_ud_pingpong test - that will exercise > the portion of the system under discussion. > > > On Dec 28, 2014, at 2:31 PM, Saliya Ekanayake wrote: > > What I heard from the administrator is that, > > "The tests that work are the simple utilities ib_read_lat and ib_read_bw >

Re: [OMPI users] OMPI users] What could cause a segfault in OpenMPI?

the test worked, but you are still encountering an error > when executing an MPI job? Or are you saying things now work? > > > On Dec 28, 2014, at 5:58 PM, Saliya Ekanayake wrote: > > Thank you Ralph. This produced the warning on memory limits similar to [1] > and setting ul

Re: [OMPI users] Accessing Process Affinity within MPI Program

nfigure Open MPI with > --enable-mpi-ext=affinity or --enable-mpi-ext=all). See: > > http://www.open-mpi.org/doc/v1.8/man3/OMPI_Affinity_str.3.php > > > > On Dec 21, 2014, at 1:57 AM, Saliya Ekanayake wrote: > > > Hi, > > > > Is it possible to get info

[OMPI users] Max Registerable Memory Warning

rtual memory (kbytes, -v) unlimited file locks (-x) unlimited Thank you, Saliya -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center Indiana University, Bloomington Cell 812-391-4914 http://saliy

Re: [OMPI users] Max Registerable Memory Warning

ing? If not latest, is it possible to > upgrade to latest OFED?. Otherwise, Can you try latest OMPI release (>= > v1.8.4), where this warning is ignored on older OFEDs > > -Devendar > > On Sun, Feb 8, 2015 at 12:37 PM, Saliya Ekanayake > wrote: > >> Hi, >>

[OMPI users] Process Binding Warning

[hwt 0]], socket 0[core 2[hwt 0]], socket 0[core 3[hwt 0]], socket 0[core 4[hwt 0]], socket 0[core 5[hwt 0]]: [B/B/B/B/B/B][./././././.][./././././.][./././././.] Thank you, Saliya -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center

Re: [OMPI users] Process Binding Warning

. > As the warning indicates, it can impact performance but won't stop you from > running > > > On Mar 12, 2015, at 12:51 PM, Saliya Ekanayake wrote: > > Hi, > > I am getting the following binding warning and wonde

Re: [OMPI users] Process Binding Warning

Thank you. It worked! On Fri, Mar 13, 2015 at 10:37 AM, Ralph Castain wrote: > You shouldn’t have to do so > > On Mar 13, 2015, at 7:14 AM, Saliya Ekanayake wrote: > > Thanks Ralph. Do I need to specify where to find numactl-devel when > compiling OpenMPI? > > On Thu,

[OMPI users] The effect of --bind-to in the presence of PE=N in --map-by

nd-to socket My understanding is that this will give each process 4 cores. Now, with bind to socket, does that mean it's possible that within a socket the assgined 4 cores for a process may change? Or will they stay in the same 4 cores always? Thank you, Saliya -- Saliya Ekanayake Ph.D.

Re: [OMPI users] The effect of --bind-to in the presence of PE=N in --map-by

3:46 PM, Ralph Castain wrote: > Perhaps we should error out, but at the moment, PE=4 forces bind-to-core > and so the bind-to socket is being ignored > > On May 19, 2016, at 12:06 PM, Saliya Ekanayake wrote: > > Hi, > > I understand --map-by will determine the process

Re: [OMPI users] The effect of --bind-to in the presence of PE=N in --map-by

t is what we will do - as I said, the > —bind-to socket directive will be ignored. > > On May 19, 2016, at 1:03 PM, Saliya Ekanayake wrote: > > So if bind-to-core is in effect, does that mean it'll run only on 1 core > even though I'd like it to be able to utilize 4 core

Re: [OMPI users] The effect of --bind-to in the presence of PE=N in --map-by

like to pin them to each core the process has been bound to. > > > > On Thu, May 19, 2016 at 3:46 PM, Ralph Castain wrote: > > Perhaps we should error out, but at the moment, PE=4 forces bind-to-core > and so the bind-to socket is being ignored > > > > On May 19, 2016, a

Re: [OMPI users] The effect of --bind-to in the presence of PE=N in --map-by

> It is true that we generally configure our schedulers to set the max > #slots on each node to equal the #cores on the node - but that is purely a > configuration choice. > > > On May 19, 2016, at 4:29 PM, Saliya Ekanayake wrote: > > Thank you, Tetsuya. So is a slot = core?

Re: [OMPI users] mpirun java

/www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2016/05/29285.php >> > > > ___ > users mailing list > us...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/05/29288.php > -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center Indiana University, Bloomington LibPath.java Description: Binary data

[OMPI users] Broadcast faster than barrier

Hi, I ran Ohio micro benchmarks for openmpi and noticed broadcast with smaller number of bytes is faster than a barrier - 2us vs 120us. I'm trying to understand how this could happen? Thank you Saliya

Re: [OMPI users] Broadcast faster than barrier

e times? > > Thanks, > > Matthieu > > -- > *From:* users [users-boun...@open-mpi.org] on behalf of Saliya Ekanayake [ > esal...@gmail.com] > *Sent:* Monday, May 30, 2016 7:53 AM > *To:* Open MPI Users > *Subject:* [OMPI users] Broadcast faster

Re: [OMPI users] Broadcast faster than barrier

l. > > Cheers, > > Gilles > > > On Monday, May 30, 2016, Saliya Ekanayake wrote: > >> Hi, >> >> I ran Ohio micro benchmarks for openmpi and noticed broadcast with >> smaller number of bytes is faster than a barrie

Re: [OMPI users] Broadcast faster than barrier

f Hammond > jeff.scie...@gmail.com > http://jeffhammond.github.io/ > > ___ > users mailing list > us...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi

[OMPI users] Why communication performance change with binding PEs?

Hi, I am trying to understand this peculiar behavior where the communication time in OpenMPI changes depending on the number of process elements (cores) the process is bound to. Is this expected? Thank you, saliya -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics

Re: [OMPI users] Why communication performance change with binding PEs?

o time sharing. > but if the task is bound on more than one core, then the task and the > helper run in parallel. > > > Cheers, > > Gilles > > On 6/23/2016 1:21 PM, Saliya Ekanayake wrote: > > Hi, > > I am trying to understand this peculiar behavior where

Re: [OMPI users] Why communication performance change with binding PEs?

process, i guess case 1 and case 2 > will become pretty close. > > i also suggest that for cases 2 and 3, you bind processes to a socket > instead of no binding at all > > Cheers, > > Gilles > > On 6/23/2016 2:41 PM, Saliya Ekanayake wrote: > > Thank you, Gilles for

[OMPI users] OpenMP explicit thread affinity with MPI

Core 4? P.S. I can manually achieve this within the program using *sched_setaffinity()*, but that's not portable. Thank you, Saliya -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center Indiana University, Bloomington

Re: [OMPI users] OpenMP explicit thread affinity with MPI

OCAL_RANK > envar, and then use that to calculate the offset location for your threads > (i.e., local rank 0 is on socket 0, local rank 1 is on socket 1, etc.). You > can then putenv the correct value of the GOMP envar > > > On Jun 28, 2016, at 8:40 PM, Saliya Ekanayake wrote: >

Re: [OMPI users] OpenMP explicit thread affinity with MPI

's version seem to support that, though. On Wed, Jun 29, 2016 at 1:20 AM, Saliya Ekanayake wrote: > Thank you, Ralph and Gilles. > > I didn't know about the OMPI_COMM_WORLD_LOCAL_RANK variable. Essentially, > this means I should be able to wrap my application call in a

[OMPI users] How to know if SM collective is being used?

Hi, I see in *mca_coll_sm_comm_query()* of *ompi/mca/coll/sm/coll_sm_module.c* that al allreduce and bcast have shared memory implementations. Is there a way to know if this implementation is being used when running my program that calls these collectives? Thank you, Saliya -- Saliya

[OMPI users] The ompi/mca/cool/sm will not be used on multi-nodes?

aliya -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center Indiana University, Bloomington

Re: [OMPI users] The ompi/mca/cool/sm will not be used on multi-nodes?

r is an inter > communicator or the communicator spans on several nodes. > > you can have a look at the source code, and you will not that bcast does > not use send/recv. instead, it uses a shared memory, so hopefully, it is > faster than other modules > > > Cheers, > > > Gilles

Re: [OMPI users] The ompi/mca/cool/sm will not be used on multi-nodes?

. Cheers, Gilles On Thursday, June 30, 2016, Saliya Ekanayake wrote: > Thank you, Gilles. > > What is the bcast I should look for? In general, how do I know which > module was used to for which communication - can I print this info? > On Jun 30, 2016 3:19 AM, "Gilles Gouaillardet

Re: [OMPI users] The ompi/mca/cool/sm will not be used on multi-nodes?

> (and libfabric, but I do not know the details...) > > Cheers, > > Gilles > > On Thursday, June 30, 2016, Saliya Ekanayake wrote: > >> OK, I am beginning to see how it works now. One question I still have is, >> in the case of a mult-node communicator it seems coll/tuned (o

Re: [OMPI users] The ompi/mca/cool/sm will not be used on multi-nodes?

try > mpirun --mca coll_ml_priority 100 ... > > Cheers, > > Gilles > > On Thursday, June 30, 2016, Saliya Ekanayake wrote: > >> Thank you, Gilles. The reason for digging into intra-node optimizations >> is that we've implemented several machine learning app

Re: [OMPI users] Java-OpenMPI returns with SIGSEGV

>>>> [titan01:01173] *** Process received signal *** >>>> [titan01:01173] Signal: Aborted (6) >>>> [titan01:01173] Signal code: (-6) >>>> [titan01:01172] [ 0] /usr/lib64/libpthread.so.0(+0xf100)[0x2b7e9596a100] >>>> [titan01:01172] [ 1] /usr/lib64/libc.so.6(gsignal+0x37)[0x2b7e95fc75f7] >>>> [titan01:01172] [ 2] /usr/lib64/libc.so.6(abort+0x148)[0x2b7e95fc8ce8] >>>> [titan01:01172] [ 3] >>>> /home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x742ac5)[0x2b7e96a95ac5] >>>> [titan01:01172] [ 4] >>>> /home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x8a2137)[0x2b7e96bf5137] >>>> [titan01:01172] [ 5] >>>> /home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(JVM_handle_linux_signal+0x140)[0x2b7e96a995e0] >>>> [titan01:01172] [ 6] [titan01:01173] [ 0] >>>> /usr/lib64/libpthread.so.0(+0xf100)[0x2af694ded100] >>>> [titan01:01173] [ 1] /usr/lib64/libc.so.6(+0x35670)[0x2b7e95fc7670] >>>> [titan01:01172] [ 7] [0x2b7e9c86e3a1] >>>> [titan01:01172] *** End of error message *** >>>> /usr/lib64/libc.so.6(gsignal+0x37)[0x2af69544a5f7] >>>> [titan01:01173] [ 2] /usr/lib64/libc.so.6(abort+0x148)[0x2af69544bce8] >>>> [titan01:01173] [ 3] >>>> /home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x742ac5)[0x2af695f18ac5] >>>> [titan01:01173] [ 4] >>>> /home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(+0x8a2137)[0x2af696078137] >>>> [titan01:01173] [ 5] >>>> /home/gl069/bin/jdk1.7.0_25/jre/lib/amd64/server/libjvm.so(JVM_handle_linux_signal+0x140)[0x2af695f1c5e0] >>>> [titan01:01173] [ 6] /usr/lib64/libc.so.6(+0x35670)[0x2af69544a670] >>>> [titan01:01173] [ 7] [0x2af69c0693a1] >>>> [titan01:01173] *** End of error message *** >>>> --- >>>> Primary job terminated normally, but 1 process returned >>>> a non-zero exit code. Per user-direction, the job has been aborted. >>>> --- >>>> >>>> -- >>>> mpirun noticed that process rank 1 with PID 0 on node titan01 exited on >>>> signal 6 (Aborted). >>>> >>>> >>>> CONFIGURATION: >>>> I used the ompi master sources from github: >>>> commit 267821f0dd405b5f4370017a287d9a49f92e734a >>>> Author: Gilles Gouaillardet >>>> Date: Tue Jul 5 13:47:50 2016 +0900 >>>> >>>> ./configure --enable-mpi-java >>>> --with-jdk-dir=/home/gl069/bin/jdk1.7.0_25 --disable-dlopen >>>> --disable-mca-dso >>>> >>>> Thanks a lot for your help! >>>> Gundram >>>> >>>> ___ >>>> users mailing list >>>> us...@open-mpi.org >>>> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users >>>> Link to this post: >>>> <http://www.open-mpi.org/community/lists/users/2016/07/29584.php> >>>> http://www.open-mpi.org/community/lists/users/2016/07/29584.php >>>> >>> >>> >>> >>> ___ >>> users mailing listus...@open-mpi.org >>> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users >>> Link to this post: >>> http://www.open-mpi.org/community/lists/users/2016/07/29585.php >>> >>> >>> >> >> ___ >> users mailing listus...@open-mpi.org >> Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users >> Link to this post: >> http://www.open-mpi.org/community/lists/users/2016/07/29587.php >> >> >> > > ___ > users mailing listus...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/07/29589.php > > > > ___ > users mailing list > us...@open-mpi.org > Subscription: https://www.open-mpi.org/mailman/listinfo.cgi/users > Link to this post: > http://www.open-mpi.org/community/lists/users/2016/07/29590.php > -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center Indiana University, Bloomington

[OMPI users] Forcing TCP btl

ssible for OpenMPI to use Infiniband and not TCP? Is there a way to guarantee that a test is using TCP, but not IB? Thank you, saliya -- Saliya Ekanayake Ph.D. Candidate | Research Assistant School of Informatics and Computing | Digital Science Center Indiana University, Bloomington

Re: [OMPI users] Forcing TCP btl

Thank you, but what's mxm? On Tue, Jul 19, 2016 at 12:52 AM, Nathan Hjelm wrote: > You probably will also want to run with -mca pml ob1 to make sure mxm is > not in use. The combination should be sufficient to force tcp usage. > > -Nathan > > > On Jul 18, 2016, at

Re: [OMPI users] Forcing TCP btl

for mxm, you need to > > - force pml/ob1 (so mtl/mxm cannot be used by pml/cm) > > and > > - blacklist btl/openib > > your mpirun command line looks like this > > mpirun --mca pml ob1 --mca btl ^openib ... > > > Cheers, > > > Gilles > On 7/

[OMPI users] OpenMPI Segfault when psm is enabled?

this module is and is there a disadvantage in terms of performance by disabling it? Thank you, Saliya -- Saliya Ekanayake, Ph.D Applied Computer Scientist Network Dynamics and Simulation Science Laboratory (NDSSL) Virginia Tech, Blacksburg ___ users ma

Re: [OMPI users] OpenMPI Segfault when psm is enabled?

l) >> that suggested to disable psm as a solution. >> >> It worked, but I would like to know what this module is and is there a >> disadvantage in terms of performance by disabling it? >> >> Thank you, >> Saliya >> >> -- >> Saliya Ekana

[OMPI users] UnsatisfiedLinkError - libmpi_java.so.0.0.0

;main" java.lang.UnsatisfiedLinkError: /N/u/sekanaya/build/lib/libmpi_java.so.0.0.0: /N/u/sekanaya/build/lib/libmpi.so.0: undefined symbol: opal_maffinity_setup Any suggestion on fixing this? Thank you in advance, Saliya -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

Re: [OMPI users] UnsatisfiedLinkError - libmpi_java.so.0.0.0

13, at 10:01 PM, Saliya Ekanayake wrote: > > Hi, > > I obtained the nightly build openmpi-1.9a1r28881 (on 7/19/13) and built it > with java enabled using, > > ./configure --enable-mpi-java --prefix=/N/u/sekanaya/build > > Then I wrote a simple MPI program to print the rank o

Re: [OMPI users] [EXTERNAL] MPI_THREAD_SINGLE vs. MPI_THREAD_FUNNELED

appears to hold up for all the MPI implementations of interest. The > > additional threads referred to are "inside the MPI rank," although I > suppose > > additional application threads not involved with MPI are possible. > > > > > > ___ > > users mailing list > > us...@open-mpi.org > > http://www.open-mpi.org/mailman/listinfo.cgi/users > > > > -- > Jeff Hammond > jeff.scie...@gmail.com > ___ > users mailing list > us...@open-mpi.org > http://www.open-mpi.org/mailman/listinfo.cgi/users > -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

[OMPI users] Reducing Varying Length Arrays

Hi, I want to contact bunch of strings from MPI processes. For example, say with 2 processes, P1 has text "hi" P2 has text "world" I have these stored as char arrays in processes. Is there a simple way to do a reduce operation to concat these? Thank you, Saliya -- S

Re: [OMPI users] Reducing Varying Length Arrays

Thanks Jeff, it solved the problem. Saliya On Sat, Nov 9, 2013 at 8:15 PM, Jeff Hammond wrote: > MPI_{Gather,Allgather}v are appropriate for this. See docs for details. > > Jeff > > Sent from my iPhone > > On Nov 9, 2013, at 6:15 PM, Saliya Ekanayake wrote: > >

[OMPI users] Equivalent to MPI.OBJECT in trunk

Hi, I was using MPI.OBJECT as datatype for custom Java classes, but this is no longer available. Could you please let me, which datatype should be used for such cases? Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

[OMPI users] Does sendrecv guarantee order?

Hi, Just want to verify if sendrecv provides any guarantees as to which operation (send or receive) happens first. I think it is not, is it? Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

[OMPI users] How to use non-primitive types with Java binding

Hi, Is it possible to use non-primitive types with MPI operations in OpenMPI's Java binding? At the moment in the trunk I only see Datatypes for primitive kinds. Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com

Re: [OMPI users] How to use non-primitive types with Java binding

you must create them with the Datatype > methods (createVector, createStruct,...). And the buffers that hold the > data must be arrays of a primitive type or direct buffers. > > Regards, > Oscar > > > Quoting Saliya Ekanayake : > > Hi, >> >> Is it possi

Re: [OMPI users] How to use non-primitive types with Java binding

struct data using direct buffers and avoiding > serialization. MPI.OBJECT could be implemented in a higher level layer, but > serialization is very bad for performance... > > Regards, > Oscar > > Quoting Saliya Ekanayake : > > Thank you Oscar. I was using an earlier n

Re: [OMPI users] How to use non-primitive types with Java binding

Thank you, this is exactly what I was hoping for!! Saliya On Jan 18, 2014 2:40 AM, "Siegmar Gross" < siegmar.gr...@informatik.hs-fulda.de> wrote: > Hi, > > > Anyway I wonder if there are some samples illustrating the use > > of complex structures in OpenMPI > > I'm not sure if my small programs a

Re: [OMPI users] Does sendrecv guarantee order?

e correct me here if I am wrong. Thank you, Saliya On Wed, Nov 27, 2013 at 6:00 AM, George Bosilca wrote: > Why do you need an order? If you plan to send and receive on the same > buffer, you should use the MPI constructs for that, namely MPI_IN_PLACE. > > George. > > On Nov 2

Re: [OMPI users] Does sendrecv guarantee order?

Thank you Jeff for the clarification. Saliya On Fri, Feb 14, 2014 at 7:06 AM, Jeff Squyres (jsquyres) wrote: > On Feb 13, 2014, at 10:59 PM, Saliya Ekanayake wrote: > > > Anyway, to answer your question I was trying to do sendrecv in a chain > where "toSend" and &q

[OMPI users] OpenMPI + Hadoop

e.org/jira/browse/MAPREDUCE-2911 Also, is there a place I can get more info on this effort? Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

Re: [OMPI users] OpenMPI + Hadoop

gt; > On Feb 23, 2014, at 10:42 AM, Saliya Ekanayake wrote: > > Hi, > > This is to get some info on the subject and not directly a question on > OpenMPI. > > I've Jeff's blog post on integrating OpenMPI with Hadoop ( > http://blogs.cisco.com/performance/resurre

Re: [OMPI users] OpenMPI + Hadoop

Thank you Ralph. I'll get back to you if I run into issues. On Mon, Feb 24, 2014 at 12:23 PM, Ralph Castain wrote: > > On Feb 24, 2014, at 7:55 AM, Saliya Ekanayake wrote: > > This is very interesting. I've been working on getting one of our > clu

[OMPI users] Binding to Core Warning

. Node: 192.168.0.19 This is a warning only; your job will continue, though performance may be degraded. Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

Re: [OMPI users] Binding to Core Warning

re installed, or you can turn off the warning > using "-mca hwloc_base_mem_bind_failure_action silent" > > > On Feb 25, 2014, at 10:32 PM, Saliya Ekanayake wrote: > > Hi, > > I tried to run an MPI Java program with --bind-to core. I receive the > following war

Re: [OMPI users] Binding to Core Warning

#x27;s the disadvantage of not using --bind-to core? Thank you, Saliya On Wed, Feb 26, 2014 at 11:01 AM, Saliya Ekanayake wrote: > Thank you Ralph, I'll check this. > > > On Wed, Feb 26, 2014 at 10:04 AM, Ralph Castain wrote: > >> It means that OMPI didn't get built a

Re: [OMPI users] Binding to Core Warning

, 2014, at 12:17 PM, Saliya Ekanayake wrote: > > I have a followup question on this. In our application we have parallel > for loops similar to OMP parallel for. I noticed that in order to gain > speedup with threads I've to set --bind-to none, otherwise multiple threads > wil

Re: [OMPI users] Binding to Core Warning

on in OMPI Thank you, Saliya On Wed, Feb 26, 2014 at 4:50 PM, Ralph Castain wrote: > Sorry, had to run some errands. > > On Feb 26, 2014, at 1:03 PM, Saliya Ekanayake wrote: > > Is it possible to bind to cores of multiple sockets? Say I have a machine > with 2 sockets each with

Re: [OMPI users] Binding to Core Warning

PM, Ralph Castain wrote: > > On Feb 26, 2014, at 4:29 PM, Saliya Ekanayake wrote: > > I see, so if I understand correctly, the best scenario for threads would > be to bind 2 procs to sockets as --map-by socket:pe=4 and use 4 threads in > each proc. > > > Yes, that would be t

Re: [OMPI users] Binding to Core Warning

ly, outside of that and the mpirun man page, there isn't much available > yet. I'm woefully far behind on it. > > > On Feb 26, 2014, at 4:47 PM, Saliya Ekanayake wrote: > > Thank you Ralph, this is very insightful and I think I can better > understand performance

[OMPI users] bind-to core warning even with numactl

l continue, though performance may* *be degraded.* Thank you, Saliya -- Saliya Ekanayake esal...@gmail.com Cell 812-391-4914 Home 812-961-6383 http://saliya.org

Re: [OMPI users] bind-to core warning even with numactl

built. > > If that still didn't solve your issue, please send all the information > listed here: > > http://www.open-mpi.org/community/help/ > > > > On Mar 4, 2014, at 6:57 AM, Saliya Ekanayake wrote: > > > Hi, > > > > In an earlier thread I m

Re: [OMPI users] bind-to core warning even with numactl

168.0.19 > where the problem happened in your most recent job. > Sometimes a node is down during a massive package install, > is forgotten, and never gets updated. > > I hope this helps, > Gus Correa > > > On 03/04/2014 12:15 PM, Saliya Ekanayake wrote: > >> I actually

[OMPI users] SIGSEV when running OMPI Java binding

linux-amd64 compressed oops) # Problematic frame: # C [libc.so.6+0x7b75b] memcpy+0x15b -- Saliya Ekanayake esal...@gmail.com http://saliya.org

Re: [OMPI users] SIGSEV when running OMPI Java binding

a particular > MPI function that you're using that results in this segv (e.g., perhaps we > have a specific bug somewhere)? > > Can you reduce the segv to a small example that we can reproduce (and > therefore fix)? > > > On Mar 10, 2014, at 12:05 AM, Saliya Ekanayake

Re: [OMPI users] SIGSEV when running OMPI Java binding

See if that enables > you to run (this particular component has nothing to do with Java). > > > On Mar 11, 2014, at 1:33 AM, Saliya Ekanayake wrote: > > > Just tested that this happens even with the simple Hello.java program > given in OMPI distribution. > > > > I&#

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