December 2013 - discuss - mailman3.cels.anl.gov

MPI_Send/MPI_Recv - getting delayed indeffinitely
by Madhawa Bandara 22 Dec '13

22 Dec '13

Hello everyone, I use mpich2 on a small cluster of 3 nodes and each node has Ubuntu 12.04 installed. I use this cluster to do the following. 1. *Master *node send some matrices to the 2 *workers* 2. Workers perform some calculations and send the resulted matrices back to the master. 3. Master perform some final calculations. code snippet: //n*n is the matrix size //master(taskid=0) MPI_Send(ha11, n / 2 * n / 2, MPI_DOUBLE, 1, 1, MPI_COMM_WORLD); //to worker 1 MPI_Send(ha11, n / 2 * n / 2, MPI_DOUBLE, 2, 1, MPI_COMM_WORLD); //to worker 2 MPI_Recv(hM1, n / 2 * n / 2, MPI_DOUBLE, 1, 2, MPI_COMM_WORLD,&status); //from worker 1 MPI_Recv(hM2, n / 2 * n / 2, MPI_DOUBLE, 2, 2, MPI_COMM_WORLD,&status);//from worker 2 //final calculations using hM1,hM2 //worker 1 (taskid=1) MPI_Recv(ha11, n / 2 * n / 2, MPI_DOUBLE, 0, 1, MPI_COMM_WORLD,&status); //does some calculations MPI_Send(hM1, n / 2 * n / 2, MPI_DOUBLE, 0, 2, MPI_COMM_WORLD); //sends back //worker 2(taskid=2) MPI_Recv(ha11, n / 2 * n / 2, MPI_DOUBLE, 0, 1, MPI_COMM_WORLD,&status); //does some calculations MPI_Send(hM2, n / 2 * n / 2, MPI_DOUBLE, 0, 2, MPI_COMM_WORLD); //sends back This worked fine at first, for n=128 to n=2048. But after I pushed 'n' beyond 2048 I got a segmentation fault from the worker 1. Since then, code works fine for the small n values. But whenever I set the value n=128 or greater, worker 1 is getting delayed indefinitely while the rest of the nodes works fine. What could be the reason for this? And how can I resolve this? If I have done any mistakes please point out. Thanks in advance. -- Regards, *H.K. Madhawa Bandara*

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Re: [mpich-discuss] Erroneous MPI type tag warning
by Junchao Zhang 22 Dec '13

22 Dec '13

Hi, Markus, I think you should change MPI_Reduce(in, out, 1, MPI_2INT, MPI_MAXLOC, 0, MPI_COMM_WORLD) to MPI_Reduce(in, out, 2, INT, MPI_MAXLOC, 0, MPI_COMM_WORLD). I guess the warning has nothing to do with padding. For MPI_Reduce(in, out, 1, MPI_2INT, ...), the compiler tries to match int, i.e., typeof(*in), with MPI_2INT. Whatever the layout of MPI_2INT is defined (e.g., struct {int i1; int i2} or int[2]), the compiler fails at matching. If you want to use MPI_2INT, then in, out should be defined as of type struct {int v1; int v2}. I agree that MPI_Reduce(in, out, 1, MPI_2INT, ...) is absolutely right. I think the only reason for the warning is that the compiler is not smart enough. For example, when matching a pointer P with a type T, the compiler should try to match typeof(*P) ~ T, typeof(*P)[2] ~T, typeof(*P)[3] ~ T, etc. --Junchao Zhang On Sun, Dec 22, 2013 at 3:56 AM, Markus Geimer <m.geimer(a)fz-juelich.de>wrote: > Dear MPICH developers, > > When compiling the attached example with MPICH 3.1rc2 using Clang 3.3, > I get the following compiler warnings: > > -------------------- snip -------------------- > mpi2int.c:17:20: warning: argument type 'int *' doesn't match specified > 'MPI' type tag [-Wtype-safety] > MPI_Reduce(in, out, 1, MPI_2INT, MPI_MAXLOC, 0, MPI_COMM_WORLD); > ^~~ ~~~~~~~~ > mpi2int.c:17:16: warning: argument type 'int *' doesn't match specified > 'MPI' type tag [-Wtype-safety] > MPI_Reduce(in, out, 1, MPI_2INT, MPI_MAXLOC, 0, MPI_COMM_WORLD); > ^~ ~~~~~~~~ > 2 warnings generated. > -------------------- snip -------------------- > > According to the MPI standard, however, MPI_2INT is a datatype as if > defined by > > MPI_Type_contiguous(2, MPI_INT, MPI_2INT) > > i.e., 'int[2]' should be a perfect match. This is not necessarily true > for the type used for comparison, > > struct mpich_struct_mpi_2int { int i1; int i2; }; > > which will only be contiguous if the compiler does not add any padding. > > Is there any chance this gets fixed for the final 3.1 release? Or did > I miss something? > > Thanks, > Markus > > -- > Dr. Markus Geimer > Juelich Supercomputing Centre > Institute for Advanced Simulation > Forschungszentrum Juelich GmbH > 52425 Juelich, Germany > > Phone: +49-2461-61-1773 > Fax: +49-2461-61-6656 > E-mail: m.geimer(a)fz-juelich.de > WWW: http://www.fz-juelich.de/jsc/ > > > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > Forschungszentrum Juelich GmbH > 52425 Juelich > Sitz der Gesellschaft: Juelich > Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 > Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher > Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), > Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, > Prof. Dr. Sebastian M. Schmidt > > ------------------------------------------------------------------------------------------------ > > ------------------------------------------------------------------------------------------------ > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Re: [mpich-discuss] MPI_Dims_create() fails for nproc >1000000
by Jeff Hammond 22 Dec '13

22 Dec '13

Thanks! This has been filed as https://trac.mpich.org/projects/mpich/ticket/1992. Best, Jeff On Thu, Dec 19, 2013 at 2:51 PM, Andreas Schäfer <gentryx(a)gmx.de> wrote: > Hi, > > sure, please see attached. > > Best > -Andreas > > > On 10:55 Thu 19 Dec , Jeff Hammond wrote: >> Can you provide a short test that reproduces the issue you are seeing? >> I will add a Trac ticket for it. >> >> Thanks, >> >> Jeff >> >> On Thu, Dec 19, 2013 at 9:49 AM, Andreas Schäfer <gentryx(a)gmx.de> wrote: >> > Hi, >> > >> > I noticed that MPICH's MPI_Dims_create() fails with a floating point >> > exception, if the number of processes is larger than 10^6. Apparently >> > the reason is that the prime factors are hard coded into the code and >> > are limited to 1000 (or sqrt(10^6)). Open MPI's implementation has no >> > such limitation. >> > >> > Best >> > -Andreas >> > >> > >> > -- >> > ========================================================== >> > Andreas Schäfer >> > HPC and Grid Computing >> > Chair of Computer Science 3 >> > Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany >> > +49 9131 85-27910 >> > PGP/GPG key via keyserver >> > http://www.libgeodecomp.org >> > ========================================================== >> > >> > (\___/) >> > (+'.'+) >> > (")_(") >> > This is Bunny. Copy and paste Bunny into your >> > signature to help him gain world domination! >> > >> > _______________________________________________ >> > discuss mailing list discuss(a)mpich.org >> > To manage subscription options or unsubscribe: >> > https://lists.mpich.org/mailman/listinfo/discuss >> >> >> >> -- >> Jeff Hammond >> jeff.science(a)gmail.com >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > -- > ========================================================== > Andreas Schäfer > HPC and Grid Computing > Chair of Computer Science 3 > Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany > +49 9131 85-27910 > PGP/GPG key via keyserver > http://www.libgeodecomp.org > ========================================================== > > (\___/) > (+'.'+) > (")_(") > This is Bunny. Copy and paste Bunny into your > signature to help him gain world domination! > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond jeff.science(a)gmail.com

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Erroneous MPI type tag warning
by Markus Geimer 22 Dec '13

22 Dec '13

Dear MPICH developers, When compiling the attached example with MPICH 3.1rc2 using Clang 3.3, I get the following compiler warnings: -------------------- snip -------------------- mpi2int.c:17:20: warning: argument type 'int *' doesn't match specified 'MPI' type tag [-Wtype-safety] MPI_Reduce(in, out, 1, MPI_2INT, MPI_MAXLOC, 0, MPI_COMM_WORLD); ^~~ ~~~~~~~~ mpi2int.c:17:16: warning: argument type 'int *' doesn't match specified 'MPI' type tag [-Wtype-safety] MPI_Reduce(in, out, 1, MPI_2INT, MPI_MAXLOC, 0, MPI_COMM_WORLD); ^~ ~~~~~~~~ 2 warnings generated. -------------------- snip -------------------- According to the MPI standard, however, MPI_2INT is a datatype as if defined by MPI_Type_contiguous(2, MPI_INT, MPI_2INT) i.e., 'int[2]' should be a perfect match. This is not necessarily true for the type used for comparison, struct mpich_struct_mpi_2int { int i1; int i2; }; which will only be contiguous if the compiler does not add any padding. Is there any chance this gets fixed for the final 3.1 release? Or did I miss something? Thanks, Markus -- Dr. Markus Geimer Juelich Supercomputing Centre Institute for Advanced Simulation Forschungszentrum Juelich GmbH 52425 Juelich, Germany Phone: +49-2461-61-1773 Fax: +49-2461-61-6656 E-mail: m.geimer(a)fz-juelich.de WWW: http://www.fz-juelich.de/jsc/ ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ Forschungszentrum Juelich GmbH 52425 Juelich Sitz der Gesellschaft: Juelich Eingetragen im Handelsregister des Amtsgerichts Dueren Nr. HR B 3498 Vorsitzender des Aufsichtsrats: MinDir Dr. Karl Eugen Huthmacher Geschaeftsfuehrung: Prof. Dr. Achim Bachem (Vorsitzender), Karsten Beneke (stellv. Vorsitzender), Prof. Dr.-Ing. Harald Bolt, Prof. Dr. Sebastian M. Schmidt ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------

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Re: [mpich-discuss] Please explain
by Andreas Schäfer 22 Dec '13

22 Dec '13

Hi Soheil, first of all, it is considered good style to post complete, minimal, programs, not just excerpts, so that others can quickly reproduce the problem you're reporting. To solve your homework, consider the following hints: 1. which lines of code does the for-loop enclose? 2. Which rank will send data to which other rank? 3. Which rank will receive data from which remote rank? (I'm using rank synonymous to process.) Best -Andreas On 07:17 Sun 22 Dec , Soheil Hooshdaran wrote: > Hello. > This program deadlocks and I cannot see the reason. Would you please > explain it to me? > > Thanks in advance > > int send_buf[10]; > int recv_buf[10]; > int i; > for(i=0;i<world_size;++i) > if (world_rank == 0) { > // If we are rank 0, set the number to -1 and send it to process 1 > printf("sent to process %d\n", i); > MPI_Send(send_buf, 10, MPI_INT, 1, 0, MPI_COMM_WORLD); > } > printf("process %d\n", world_rank); > MPI_Recv(recv_buf, 10, MPI_INT, 0, 0, MPI_COMM_WORLD, > MPI_STATUS_IGNORE); > printf("Process %d received %d bytes from process 0\n", world_rank, 10); > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- ========================================================== Andreas Schäfer HPC and Grid Computing Chair of Computer Science 3 Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany +49 9131 85-27910 PGP/GPG key via keyserver http://www.libgeodecomp.org ========================================================== (\___/) (+'.'+) (")_(") This is Bunny. Copy and paste Bunny into your signature to help him gain world domination!

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Re: [mpich-discuss] MPI memory allocation.
by Anatoly G 21 Dec '13

21 Dec '13

Good morning Pavan. Do you see process memory raise & network throughput low behavior? Anatoly. On Thu, Dec 19, 2013 at 7:09 PM, Anatoly G <anatolyrishon(a)gmail.com> wrote: > No. You can see memory increase using monitor like "qps", or any other. > The stack trace that I send I get when I stop my real program (not > simulation) with TotalView debugger. > if you monitor network traffic, you will see network speed which becomes > low until it reaches almost 0. > > Anatoly. > > > On Thu, Dec 19, 2013 at 5:16 PM, Pavan Balaji <balaji(a)mcs.anl.gov> wrote: > >> >> Are you printing it out? >> >> — Pavan >> >> On Dec 19, 2013, at 10:51 PM, Anatoly G <anatolyrishon(a)gmail.com> wrote: >> >> > Can you please remove comment from section >> > /* >> > // swap tag & enter blocked recv >> > MPI_Status stat; >> > tags[slaveIdx] = (tags[slaveIdx] == TAG1) ? TAG2 : TAG1; >> > MPI_Recv(RcvBufs[slaveIdx], BUF_SZ, MPI::CHAR, slaveRank, >> tags[slaveIdx], MPI_COMM_WORLD, &stat); >> > >> > ++SlavesRcvIters[slaveIdx]; >> > */ >> > >> > And then run it. >> > Do you see memory allocation increase? >> > >> > Regards, >> > Anatoly. >> > >> > >> > On Thu, Dec 19, 2013 at 4:29 PM, Pavan Balaji <balaji(a)mcs.anl.gov> >> wrote: >> > >> > I’m not sure what I should look for. I ran the program and it >> completed fine. >> > >> > — Pavan >> > >> > On Dec 19, 2013, at 7:16 PM, Anatoly G <anatolyrishon(a)gmail.com> wrote: >> > >> > > Good afternoon. >> > > My program enters a lot to attached stack functions. >> > > Can you please explain if it's ok? >> > > Did you success to execute simulation from previous mail. >> > > Did you see the memory raise when MPI_Recv not in comments? >> > > >> > > Regards, >> > > Anatoly. >> > > >> > > >> > > On Thu, Dec 12, 2013 at 9:36 PM, Anatoly G <anatolyrishon(a)gmail.com> >> wrote: >> > > Hi. >> > > Finally, I got an additional info. >> > > I build short simulation of my real application. >> > > >> > > The short description of real scenario. >> > > I have Master + N slaves. Each slave sends to Master 2 types of >> messages: >> > > • constant length message with predefined fields (one of it's >> fields is length of second message). >> > > • second message - length of this message each time is >> different and passed in first message. >> > > Master should use MPI_Irecv commands, in order to be tolerant to >> slaves failure (blocked MPI_Recv is blocking Master in the failure case). >> > > Master executes MPI_Irecv to each slave with buffer size equal to the >> constant size of first message type. After receiving first type of message, >> Master allocates expected buffer for second message and performs receive >> too. This happens in endless loop for each slaves. I use MPI_Waitany to >> monitor all receives. >> > > In order to separate messages Master & slaves use different tags (as >> ids) for first & second messages. >> > > >> > > Simulation description: >> > > All passed buffers (first & second) have the same size. >> > > Slave (SndSyncSlave) sends messages and swaps 2 tags between them >> (like 2 types of messages, but second one has constant size too). >> > > Master routine (Rcv_WaitAny function) executes MPI_Irecv for first >> message, and after receive executes MPI_Irecv for the second one. >> > > >> > > In this scenario: 5 processes works fine, but if I execute 20 >> processes and remove comment from line "usleep(200000)" I see 800 Mbit/s >> on network at the test beginning, but after 1-2 second network speed become >> 200-300Kbit/s and not increased back any more. >> > > >> > > If I add MPI_Recv block in Master (remove comment from "MPI_Recv" and >> line around) I see that Master starts increase memory as my real >> application, but again on 5 processes this not happens. This is scenario >> used in my real application. >> > > >> > > Command line: mpiexec.hydra -genvall -f MpiConfigMachines.txt >> -launcher=ssh -n 20 mpi_rcv_any_multithread 100000 1000000 out >> > > >> > > where >> > > 100000 - number of sends from each slave >> > > 1000000 - scale to separate input from each scale (used for debug >> only) >> > > out - prefix of output file. Each process produce out_"rank".txt file. >> > > >> > > MpiConfigMachines.txt - configuration file for my computers, 2 >> computers back to back 1 Gbit/s network. >> > > >> > > >> > > Can you please test this case, and give me yours suggestions. >> > > >> > > Thank you, >> > > Anatoly. >> > > >> > > >> > > >> > > On Mon, Dec 9, 2013 at 9:55 PM, Anatoly G <anatolyrishon(a)gmail.com> >> wrote: >> > > Yes, I understand that. I"ll try to make my stand alone test closer >> to real application. Thank you. >> > > >> > > >> > > On Mon, Dec 9, 2013 at 9:31 PM, Pavan Balaji <balaji(a)mcs.anl.gov> >> wrote: >> > > >> > > It sounds like MPICH is working correctly. Without a test case, it’s >> unfortunately quite hard for us to even know what to look for. It’s also >> possible that there’s a bug in your code which might be causing some bad >> behavior. >> > > >> > > — Pavan >> > > >> > > On Dec 9, 2013, at 1:27 PM, Anatoly G <anatolyrishon(a)gmail.com> >> wrote: >> > > >> > > > Yes, I"m actually need Fault tolerance, and it was the main reason >> for choosing MPICH2. I use fault tolerance for unpredictable bugs in the >> future. My system should survive partially. But in the regular case I just >> need full performance. I"m suspect that I don't use MPI correctly, but on >> slow rate everything works fine. The fail caused by increasing rate of >> MPI_Isend or increasing data buffer size. I didn't find yet any strong >> dependence, only main stream. >> > > > >> > > > Unfortunately I have a complex system which has a number of threads >> in each process. Part of the threads use different communicators. >> > > > >> > > > I try to simulate the same MPI behavior in simple stand alone test, >> but stand alone test works fine. It shows a full network performance, when >> I slow down master (on stand alone test), all slaves are stopped too and >> are waiting for master to continue. Can I open any MPICH log to send you >> the results? >> > > > >> > > > >> > > > On Mon, Dec 9, 2013 at 8:10 PM, Pavan Balaji <balaji(a)mcs.anl.gov> >> wrote: >> > > > >> > > > Do you actually need Fault Tolerance (one of your previous emails >> seemed to indicate that)? >> > > > >> > > > It sounds like there a bug in either your application or in the >> MPICH stack and you are trying to trace that down, and don’t really care >> about fault tolerance. Is that a correct assessment? >> > > > >> > > > Do you have a simplified program that reproduces this error, that >> we can try? >> > > > >> > > > — Pavan >> > > > >> > > > On Dec 9, 2013, at 11:44 AM, Anatoly G <anatolyrishon(a)gmail.com> >> wrote: >> > > > >> > > > > No. Hardware is Ok. Master process allocates memory (check with >> MemoryScape doesn't show any sufficient memory allocation in my code). Then >> network traffic become low, and then Master process crashes w/o saving core >> file. I have unlimited size of core files. The same fail (w/o core) I see >> when I call MPI_Abort, but I don't call it. >> > > > > >> > > > > >> > > > > On Mon, Dec 9, 2013 at 7:28 PM, Wesley Bland <wbland(a)mcs.anl.gov> >> wrote: >> > > > > Are you actually seeing hardware failure or is your code just >> crashing? It's odd that one specific process would fail so often in the >> same way if it were a hardware problem. >> > > > > >> > > > > Thanks, >> > > > > Wesley >> > > > > >> > > > > On Dec 9, 2013, at 11:15 AM, Anatoly G <anatolyrishon(a)gmail.com> >> wrote: >> > > > > >> > > > >> One more interesting fact. Each time I have a failure, the fails >> only master process, but slaves are still exists together with >> mpiexec.hydra. I thought that slaves should fail too, but slaves are live. >> > > > >> >> > > > >> >> > > > >> On Mon, Dec 9, 2013 at 10:30 AM, Anatoly G < >> anatolyrishon(a)gmail.com> wrote: >> > > > >> I configure MPICH-3.1rc2 build w/o "so" files. But instead of >> MPICH2 & MPICH-3.0.4 I get so files. What should I change in configure line >> to link MPI with my application statically. >> > > > >> >> > > > >> >> > > > >> >> > > > >> On Mon, Dec 9, 2013 at 9:47 AM, Pavan Balaji <balaji(a)mcs.anl.gov> >> wrote: >> > > > >> >> > > > >> Can you try mpich-3.1rc2? There were several fixes for this in >> this version and it’ll be good to try that out before we go digging too far >> into this. >> > > > >> >> > > > >> — Pavan >> > > > >> >> > > > >> On Dec 9, 2013, at 1:46 AM, Anatoly G <anatolyrishon(a)gmail.com> >> wrote: >> > > > >> >> > > > >> > With MPICH - 3.0.4 the situation repeated. It looks like MPI >> allocates memory for messages. >> > > > >> > Can you please advice about scenario when MPI or may be TCP >> under MPI allocates memory due to high transfer rate? >> > > > >> > >> > > > >> > >> > > > >> > On Mon, Dec 9, 2013 at 9:32 AM, Anatoly G < >> anatolyrishon(a)gmail.com> wrote: >> > > > >> > Thank you very much. >> > > > >> > Issend - is not so good, It can't support me Fault tolerance. >> If slave process fails, the master stall. >> > > > >> > I tried mpich-3.0.4 with hydra-3.0.4 but my program which uses >> MPI Fault tolerance doesn't recognize failure of slave process, but >> recognizes failure with MPICH2. May be you can suggest solution? >> > > > >> > I tried to use hydra from MPICH2 but link my program with >> MPICH3. This combination recognizes failures, but I"m not sure that such >> combination is stable enough. >> > > > >> > Can you please advice? >> > > > >> > Anatoly. >> > > > >> > >> > > > >> > >> > > > >> > >> > > > >> > On Sat, Dec 7, 2013 at 5:20 PM, Pavan Balaji < >> balaji(a)mcs.anl.gov> wrote: >> > > > >> > >> > > > >> > As much as I hate saying this — some people find it easier to >> think of it as “MPICH3”. >> > > > >> > >> > > > >> > — Pavan >> > > > >> > >> > > > >> > On Dec 7, 2013, at 7:37 AM, Wesley Bland <wbland(a)mcs.anl.gov> >> wrote: >> > > > >> > >> > > > >> > > MPICH is just the new version of MPICH2. We renamed it when >> we went past version 3.0. >> > > > >> > > >> > > > >> > > On Dec 7, 2013, at 3:55 AM, Anatoly G < >> anatolyrishon(a)gmail.com> wrote: >> > > > >> > > >> > > > >> > >> Ok. I"ll try both Issend, and next step to upgrade MPICH to >> 3.0.4. >> > > > >> > >> I thought before that MPICH & MPICH2 are two different >> branches, when MPICH2 partially supports Fault tolerance, but MPICH not. >> Now I understand, that I was wrong and MPICH2 is just main version of MPICH. >> > > > >> > >> >> > > > >> > >> Thank you very much, >> > > > >> > >> Anatoly. >> > > > >> > >> >> > > > >> > >> >> > > > >> > >> >> > > > >> > >> On Thu, Dec 5, 2013 at 11:01 PM, Rajeev Thakur < >> thakur(a)mcs.anl.gov> wrote: >> > > > >> > >> The master is receiving too many incoming messages than it >> can match quickly enough with Irecvs. Try using MPI_Issend instead of >> MPI_Isend. >> > > > >> > >> >> > > > >> > >> Rajeev >> > > > >> > >> >> > > > >> > >> On Dec 5, 2013, at 2:58 AM, Anatoly G < >> anatolyrishon(a)gmail.com> wrote: >> > > > >> > >> >> > > > >> > >> > Hello. >> > > > >> > >> > I"m using MPICH2 1.5. >> > > > >> > >> > My system contains master and 16 slaves. >> > > > >> > >> > System uses number of communicators. >> > > > >> > >> > The single communicator used for below scenario: >> > > > >> > >> > Each slave sends non-stop 2Kbyte data buffer using >> MPI_Isend and waits using MPI_Wait. >> > > > >> > >> > Master starts with MPI_Irecv to each slave >> > > > >> > >> > Then in endless loop: >> > > > >> > >> > MPI_Waitany and MPI_Irecv on rank returned by MPI_Waitany. >> > > > >> > >> > >> > > > >> > >> > Another communicator used for broadcast communication >> (commands between master + slaves), >> > > > >> > >> > but it's not used in parallel with previous communicator, >> > > > >> > >> > only before or after data transfer. >> > > > >> > >> > >> > > > >> > >> > The system executed on two computers linked by 1Gbit/s >> Ethernet. >> > > > >> > >> > Master executed on first computer, all slaves on other >> one. >> > > > >> > >> > Network traffic is ~800Mbit/s. >> > > > >> > >> > >> > > > >> > >> > After 1-2 minutes of execution, master process starts to >> increase it's memory allocation and network traffic becomes low. >> > > > >> > >> > This memory allocation & network traffic slow down >> continues until fail of MPI, >> > > > >> > >> > without core file save. >> > > > >> > >> > My program doesn't allocate memory. Can you please >> explain this behaviour. >> > > > >> > >> > How can I cause MPI to stop sending slaves if Master >> can't serve such traffic, instead of memory allocation and fail? >> > > > >> > >> > >> > > > >> > >> > >> > > > >> > >> > Thank you, >> > > > >> > >> > Anatoly. >> > > > >> > >> > >> > > > >> > >> > P.S. >> > > > >> > >> > On my stand alone test, I simulate similar behaviour, but >> with single thread on each process (master & hosts). >> > > > >> > >> > When I start stand alone test, master stops slaves until >> it completes accumulated data processing and MPI doesn't increase memory >> allocation. >> > > > >> > >> > When Master is free slaves continue to send data. >> > > > >> > >> > _______________________________________________ >> > > > >> > >> > discuss mailing list discuss(a)mpich.org >> > > > >> > >> > To manage subscription options or unsubscribe: >> > > > >> > >> > https://lists.mpich.org/mailman/listinfo/discuss >> > > > >> > >> >> > > > >> > >> _______________________________________________ >> > > > >> > >> discuss mailing list discuss(a)mpich.org >> > > > >> > >> To manage subscription options or unsubscribe: >> > > > >> > >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > >> > >> >> > > > >> > >> _______________________________________________ >> > > > >> > >> discuss mailing list discuss(a)mpich.org >> > > > >> > >> To manage subscription options or unsubscribe: >> > > > >> > >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > >> > > _______________________________________________ >> > > > >> > > discuss mailing list discuss(a)mpich.org >> > > > >> > > To manage subscription options or unsubscribe: >> > > > >> > > https://lists.mpich.org/mailman/listinfo/discuss >> > > > >> > >> > > > >> > -- >> > > > >> > Pavan Balaji >> > > > >> > http://www.mcs.anl.gov/~balaji >> > > > >> > >> > > > >> > _______________________________________________ >> > > > >> > discuss mailing list discuss(a)mpich.org >> > > > >> > To manage subscription options or unsubscribe: >> > > > >> > https://lists.mpich.org/mailman/listinfo/discuss >> > > > >> > >> > > > >> > >> > > > >> > _______________________________________________ >> > > > >> > discuss mailing list discuss(a)mpich.org >> > > > >> > To manage subscription options or unsubscribe: >> > > > >> > https://lists.mpich.org/mailman/listinfo/discuss >> > > > >> >> > > > >> -- >> > > > >> Pavan Balaji >> > > > >> http://www.mcs.anl.gov/~balaji >> > > > >> >> > > > >> _______________________________________________ >> > > > >> discuss mailing list discuss(a)mpich.org >> > > > >> To manage subscription options or unsubscribe: >> > > > >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > >> >> > > > >> >> > > > >> _______________________________________________ >> > > > >> discuss mailing list discuss(a)mpich.org >> > > > >> To manage subscription options or unsubscribe: >> > > > >> https://lists.mpich.org/mailman/listinfo/discuss >> > > > > >> > > > > 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https://lists.mpich.org/mailman/listinfo/discuss >> >> -- >> Pavan Balaji >> http://www.mcs.anl.gov/~balaji >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > >

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Please explain
by Soheil Hooshdaran 21 Dec '13

21 Dec '13

Hello. This program deadlocks and I cannot see the reason. Would you please explain it to me? Thanks in advance int send_buf[10]; int recv_buf[10]; int i; for(i=0;i<world_size;++i) if (world_rank == 0) { // If we are rank 0, set the number to -1 and send it to process 1 printf("sent to process %d\n", i); MPI_Send(send_buf, 10, MPI_INT, 1, 0, MPI_COMM_WORLD); } printf("process %d\n", world_rank); MPI_Recv(recv_buf, 10, MPI_INT, 0, 0, MPI_COMM_WORLD, MPI_STATUS_IGNORE); printf("Process %d received %d bytes from process 0\n", world_rank, 10);

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Re: [mpich-discuss] fairness
by Raffenetti, Kenneth J. 19 Dec '13

19 Dec '13

What makes you think they aren't executing? We'll need more information and a way to reproduce the problem in order to provide any help. ________________________________________ From: discuss-bounces(a)mpich.org [discuss-bounces(a)mpich.org] on behalf of Soheil Hooshdaran [shooshdaran577(a)gmail.com] Sent: Thursday, December 19, 2013 9:51 PM To: Balaji, Pavan Cc: discuss(a)mpich.org Subject: [mpich-discuss] fairness Hello. In my MPI program, some processes seem not to execute at all. How to overcome this problem? Regards Soheil Hooshdaran

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fairness
by Soheil Hooshdaran 19 Dec '13

19 Dec '13

Hello. In my MPI program, some processes seem not to execute at all. How to overcome this problem? Regards Soheil Hooshdaran

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Re: [mpich-discuss] MPI_Dims_create() fails for nproc >1000000
by Andreas Schäfer 19 Dec '13

19 Dec '13

Hi, sure, please see attached. Best -Andreas On 10:55 Thu 19 Dec , Jeff Hammond wrote: > Can you provide a short test that reproduces the issue you are seeing? > I will add a Trac ticket for it. > > Thanks, > > Jeff > > On Thu, Dec 19, 2013 at 9:49 AM, Andreas Schäfer <gentryx(a)gmx.de> wrote: > > Hi, > > > > I noticed that MPICH's MPI_Dims_create() fails with a floating point > > exception, if the number of processes is larger than 10^6. Apparently > > the reason is that the prime factors are hard coded into the code and > > are limited to 1000 (or sqrt(10^6)). Open MPI's implementation has no > > such limitation. > > > > Best > > -Andreas > > > > > > -- > > ========================================================== > > Andreas Schäfer > > HPC and Grid Computing > > Chair of Computer Science 3 > > Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany > > +49 9131 85-27910 > > PGP/GPG key via keyserver > > http://www.libgeodecomp.org > > ========================================================== > > > > (\___/) > > (+'.'+) > > (")_(") > > This is Bunny. Copy and paste Bunny into your > > signature to help him gain world domination! > > > > _______________________________________________ > > discuss mailing list discuss(a)mpich.org > > To manage subscription options or unsubscribe: > > https://lists.mpich.org/mailman/listinfo/discuss > > > > -- > Jeff Hammond > jeff.science(a)gmail.com > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- ========================================================== Andreas Schäfer HPC and Grid Computing Chair of Computer Science 3 Friedrich-Alexander-Universität Erlangen-Nürnberg, Germany +49 9131 85-27910 PGP/GPG key via keyserver http://www.libgeodecomp.org ========================================================== (\___/) (+'.'+) (")_(") This is Bunny. Copy and paste Bunny into your signature to help him gain world domination!

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