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

Re: [mpich-discuss] Checking level of thread support
by Matthieu Dorier 19 Mar '13

19 Mar '13

Great, thank you Jim! Matthieu ----- Mail original ----- > De: "Jim Dinan" <dinan(a)mcs.anl.gov> > À: discuss(a)mpich.org > Envoyé: Mardi 19 Mars 2013 15:55:39 > Objet: Re: [mpich-discuss] Checking level of thread support > > Hi Mattieu, > > MPI_Query_thread() can tell you this. > > ~Jim. > > On 3/19/13 9:47 AM, Matthieu Dorier wrote: > > Hi, > > > > I'm coding a library that can use threads in conjunction with MPI. > > I'd > > like to know if there is a way to check that the application using > > the > > library has called MPI_Init_thread with the proper level of thread > > support, in order to select if the library can or cannot use > > threads? > > > > Thanks, > > > > Matthieu Dorier > > PhD student at ENS Cachan Brittany and IRISA > > http://people.irisa.fr/Matthieu.Dorier > > > > > > _______________________________________________ > > 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 >

1 0

Re: [mpich-discuss] Checking level of thread support
by Jim Dinan 19 Mar '13

19 Mar '13

Hi Mattieu, MPI_Query_thread() can tell you this. ~Jim. On 3/19/13 9:47 AM, Matthieu Dorier wrote: > Hi, > > I'm coding a library that can use threads in conjunction with MPI. I'd > like to know if there is a way to check that the application using the > library has called MPI_Init_thread with the proper level of thread > support, in order to select if the library can or cannot use threads? > > Thanks, > > Matthieu Dorier > PhD student at ENS Cachan Brittany and IRISA > http://people.irisa.fr/Matthieu.Dorier > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

1 0

Checking level of thread support
by Matthieu Dorier 19 Mar '13

19 Mar '13

Hi, I'm coding a library that can use threads in conjunction with MPI. I'd like to know if there is a way to check that the application using the library has called MPI_Init_thread with the proper level of thread support, in order to select if the library can or cannot use threads? Thanks, Matthieu Dorier PhD student at ENS Cachan Brittany and IRISA http://people.irisa.fr/Matthieu.Dorier

1 0

Query regarding structure of dynamic array derived datatype
by Mahesh Doijade 19 Mar '13

19 Mar '13

Hi, I have a struct as - struct A { int size; int *lptr; }; And then I have array of such structure, I want to only send dynamic array present in each of the structs to other process. One of the options is to do it with MPI_Pack but then I have read it is not so good from performance point of view. What can be the other opt -- Regards, -- Mahesh Doijade MTech - II (CSE) , Walchand College of Engineering, Sangli

1 0

Re: [mpich-discuss] MPI_Comm_Spawn causing zombies of hydra_pmi_proxy
by Silvan Brändli 19 Mar '13

19 Mar '13

Dear Pavan, in the attached example I use mpich3, but still I get the zombies. Is there something wrong with - my MPI function calls? (disconnect, finalize) - my linked libraries? (see below) Thanks in advance! Best regards Silvan ldd_hi linux-vdso.so.1 (0x00007fffa01ff000) libmpichcxx.so.10 => /opt/mpich3/lib/libmpichcxx.so.10 (0x00007fdfec0e4000) libmpich.so.10 => /opt/mpich3/lib/libmpich.so.10 (0x00007fdfebc6f000) libopa.so.1 => /opt/mpich3/lib/libopa.so.1 (0x00007fdfeba6d000) libmpl.so.1 => /opt/mpich3/lib/libmpl.so.1 (0x00007fdfeb868000) libaio.so.1 => /lib64/libaio.so.1 (0x00007fdfeb666000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007fdfeb449000) libm.so.6 => /lib64/libm.so.6 (0x00007fdfeb14e000) libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libstdc++.so.6 (0x00007fdfeae47000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007fdfeac30000) libc.so.6 => /lib64/libc.so.6 (0x00007fdfea882000) libdl.so.2 => /lib64/libdl.so.2 (0x00007fdfea67e000) libgfortran.so.3 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libgfortran.so.3 (0x00007fdfea361000) libquadmath.so.0 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libquadmath.so.0 (0x00007fdfea12b000) /lib64/ld-linux-x86-64.so.2 (0x00007fdfec308000) librt.so.1 => /lib64/librt.so.1 (0x00007fdfe9f23000) ldd_main linux-vdso.so.1 (0x00007fffeb1ff000) libmpichcxx.so.10 => /opt/mpich3/lib/libmpichcxx.so.10 (0x00007f6fc797e000) libmpich.so.10 => /opt/mpich3/lib/libmpich.so.10 (0x00007f6fc7509000) libopa.so.1 => /opt/mpich3/lib/libopa.so.1 (0x00007f6fc7307000) libmpl.so.1 => /opt/mpich3/lib/libmpl.so.1 (0x00007f6fc7102000) libaio.so.1 => /lib64/libaio.so.1 (0x00007f6fc6f00000) libpthread.so.0 => /lib64/libpthread.so.0 (0x00007f6fc6ce3000) libm.so.6 => /lib64/libm.so.6 (0x00007f6fc69e8000) libstdc++.so.6 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libstdc++.so.6 (0x00007f6fc66e1000) libgcc_s.so.1 => /lib64/libgcc_s.so.1 (0x00007f6fc64ca000) libc.so.6 => /lib64/libc.so.6 (0x00007f6fc611c000) libdl.so.2 => /lib64/libdl.so.2 (0x00007f6fc5f18000) libgfortran.so.3 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libgfortran.so.3 (0x00007f6fc5bfb000) libquadmath.so.0 => /usr/lib/gcc/x86_64-pc-linux-gnu/4.7.2/libquadmath.so.0 (0x00007f6fc59c5000) /lib64/ld-linux-x86-64.so.2 (0x00007f6fc7ba2000) librt.so.1 => /lib64/librt.so.1 (0x00007f6fc57bd000) On 07.03.2013 17:23, Pavan Balaji wrote: > > I just tried this with the mpich master and it seems to work correctly, > and there are no zombie processes (though I reduced the number of > iterations to 10000, instead of 200000). This was a problem in mpich > once upon a time, but that was a few years ago. Are you using the > latest version of mpich (3.0.2)? > > -- Pavan > > On 03/07/2013 09:44 AM US Central Time, Silvan Brï¿½ndli wrote: >> PS: The attached programs are a simplification of my code. They >> reproduce the zombie problem. Waiting for the 32k zombies takes a >> while... but I expect the same behaviour as with my original code. >> >> Am I missing something when finishing the called program? I just use >> MPI_Comm_disconnect and MPI_Finalize. >> >> Best regards >> Silvan >> >> main.cpp >> >> #include <mpi.h>; >> >> int main(int argc, char *argv[]) >> { >> int myrank; >> int spawnerror; >> int value = 123; >> void *buf = &value; >> MPI_Comm child_comm; >> >> if (MPI_Init(&argc,&argv)!=MPI_SUCCESS) >> { >> printf("MPI_Init failed"); >> } >> >> MPI_Comm_rank(MPI_COMM_WORLD, &myrank); >> >> char* hiargv[] = {"23",NULL}; >> for(int i = 1; i <= 200000; i++) >> { >> value = i; >> printf("Main before spawn %d\n",i); >> MPI_Comm_spawn("./hi",hiargv, 1, MPI_INFO_NULL, myrank, >> MPI_COMM_SELF, &child_comm, &spawnerror); >> MPI_Send(buf, 1, MPI_INTEGER, 0, 1, child_comm); >> MPI_Comm_disconnect(&child_comm); >> } >> >> MPI_Finalize(); >> return 0; >> } >> >> hi.cpp: >> >> #include <mpi.h>; >> >> int main(int argc, char** argv) { >> MPI_Comm parent; >> MPI_Status status; >> int err; >> int value = -1; >> void* buf= &value; >> >> if (MPI_Init(&argc,&argv)!=MPI_SUCCESS) >> { >> printf("MPI_Init failed"); >> } >> MPI_Comm_get_parent(&parent); >> if (parent == MPI_COMM_NULL) printf("No parent!"); >> >> MPI_Recv(buf, 1, MPI_INTEGER, 0, MPI_ANY_TAG, parent, &status); >> MPI_Comm_disconnect(&parent); >> err = MPI_Finalize(); >> printf("hi finalized %d %d \n",err, value); >> return 0; >> } >> >> >> >> On 07.03.2013 12:38, Silvan Brï¿½ndli wrote: >>> Dear all, >>> >>> again I have a question related to spawning processes. I understand the >>> situation as follows: >>> >>> My program A spawns program B. Program B spawns program C1, C2 ... >>> C10000 ... >>> Program Cx terminates correctly before Cx+1 is called, however returning >>> 1 to mpiexec. To handle this I use the workaround as described in >>> http://lists.mpich.org/pipermail/discuss/2013-February/000429.html >>> >>> Now it looks like with every Spawn a "hydra_pmi_proxy" is started, the >>> calling program is mpiexec. When the program Cx is finished this >>> "hydra_pmi_proxy" remains as a zombie until the programs A, B and >>> mpiexec are finished. When approx. 32k of those "hydra_pmi_proxy" exist >>> I get some problems (too many processes or something similar). >>> >>> What can I do to finish "hydra_pmi_proxy" while my programs A, B and >>> mpiexec are still running? >>> >>> I'm glad about every hint. >>> >>> Best regards >>> Silvan >>> >> >> >> >> >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss >> > -- Dipl.-Ing. Silvan Brï¿½ndli Numerische Strukturanalyse mit Anwendungen in der Schiffstechnik (M-10) Technische Universitï¿½t Hamburg-Harburg Schwarzenbergstraï¿½e 95c 21073 Hamburg Tel. : +49 (0)40 42878 - 6187 Fax. : +49 (0)40 42878 - 6090 e-mail: silvan.braendli(a)tuhh.de www : http://www.tuhh.de/skf 5th GACM Colloquium on Computational Mechanics http://www.tu-harburg.de/gacm2013

1 0

MPI on Intel MIC
by Martin Rose 19 Mar '13

19 Mar '13

Dear all, I want to run an MPI program on an Intel Xeon Phi accelerator (MIC). I want to use an open source MPI library but I have not found any information about how to compile the MPI library for MIC. The link below leads to a paper about MVAPICH2 on MIC but the paper does not talk about compilation of the library. http://nowlab.cse.ohio-state.edu/publications/conf-papers/2012/potluri-tihp… I have tried to compile mpich-3.0.2 with icc anf ifort using a -dmmic as dummy flag. After running config, the dummy flag is replaced by -mmic. This got me pretty far but I do not have libnuma for MIC so the compilation could not complete. The announcement of MPICH2-1.5 states that the MIC architecture is supported. http://www.mpich.org/2012/10/08/mpich2-1-5-released-oct-8-2012/ Can anyone describe the build process to run a program compiled with MPICH on Intel MIC? Greetings, Martin

1 0

MPI I/O vs Sequential I/O
by Muhammad Zulfikar Handana 18 Mar '13

18 Mar '13

hello, i have some questions about MPI-I/O. 1) when i trying execute my program using MPI-I/O. why when iam execute with 1 proses, execute time more good than when iam execute with 2 proses. am i wrong? this is my source code. MPI_File_open (MPI_COMM_WORLD, file_akhir, MPI_MODE_CREATE | MPI_MODE_WRONLY, MPI_INFO_NULL, &hasil); int jumlah1 = (((block-1)*16)+pad); int jumlah = jumlah1 / size; MPI_File_set_view(hasil, rank * jumlah * sizeof(char),MPI_CHAR, MPI_CHAR, "native", MPI_INFO_NULL); MPI_File_write (hasil, output, jumlah1, MPI_CHAR, MPI_STATUS_IGNORE); MPI_File_close(&hasil); 2) and after that i have compared that source using MPI - I/O and with sequential I/O, apparently, sequential i / o is better than the parallel i / o. how it could be happen? this is my sequential source. if (rank==0) { hasil = fopen (file_akhir, "wb"); int test = (((block-1)*16)+pad); fwrite (output, sizeof(char), test, hasil ); fclose (hasil); } thanks a lot for your attention

1 0

Re: [mpich-discuss] Hydra fills in the MPIR_proctable[] incorrectly with multiple processes per node
by John DelSignore 18 Mar '13

18 Mar '13

Pavan Balaji wrote: > On 03/18/2013 11:56 AM US Central Time, John DelSignore wrote: >> But the bigger win is that tool would have to read only 513 separate >> strings using ptrace() or /proc, which represents a big time >> savings. > > Doesn't the tool still have to read all the strings? No. > Or are you > planning to compare pointers to check if they are the same and not read > the string again if they are the same? It could be done by comparing pointers, but the way TotalView implements it is through a "target address space data cache". Before TV reads from the target address space for the process (in any target read situation, not just MPIR), it looks in a data cache associated with the target address space, and if the data is already in the cache, there is no reason to reread it from the target address space using ptrace() or /proc. Cheers, John D. > > -- Pavan >

1 0

Call For Papers: EuroMPI 2013 Paper. Last days for submissions. Deadline: March 29th, 2013
by Francisco Javier Garcia Blas 18 Mar '13

18 Mar '13

Dear Sir or Madam, (We apologize if you receive multiple copies of this message) ============================================================ Recent Advances in Message Passing Interface. 20th European MPI Users' Group Meeting (EuroMPI 2013) EuroMPI 2013 is being held in cooperation with SIGHPC Madrid, Spain, September 15-18, 2013 www.eurompi2013.org BACKGROUND AND TOPICS ------------------------------- EuroMPI is the preeminent meeting for users, developers and researchers to interact and discuss new developments and applications of message-passing parallel computing, in particular in and related to the Message Passing Interface (MPI). The annual meeting has a long, rich tradition, and the 20th European MPI Users' Group Meeting will again be a lively forum for discussion of everything related to usage and implementation of MPI and other parallel programming interfaces. Traditionally, the meeting has focused on the efficient implementation of aspects of MPI, typically on high-performance computing platforms, benchmarking and tools for MPI, short-comings and extensions of MPI, parallel I/O and fault tolerance, as well as parallel applications using MPI. The meeting is open towards other topics, in particular application experience and alternative interfaces for high-performance heterogeneous, hybrid, distributed memory systems. Topics of interest include, but are not limited to: - MPI implementation issues and improvements - Extensions to and shortcomings of MPI - Tools and environments for MPI - Hybrid and heterogeneous programming with MPI and other interfaces - Relation of MPI to alternative interfaces for hybrid/heterogeneous distributed memory systems - Interaction between message-passing software and hardware, in particular new high performance architectures - Fault tolerance in message-passing implementations and systems - Performance evaluation for MPI and MPI based applications- - Automatic performance tuning of MPI applications and implementations - Verification of message passing applications and protocols - Applications using message-passing, in particular in Computational Science and Scientific Computing - Non-standard message-passing applications - Parallel algorithms in the message-passing paradigm - Algorithms using the message-passing paradigm The meeting will feature contributed talks on the selected, peer-reviewed papers, invited expert talks covering upcoming and future issues, a vendor session where selected vendors will present their new developments in hybrid and heterogeneous cluster and high-performance architectures, a poster session, and a tutorial day. The scientific part of the conference is organized in cooperation with ACM SIGHPC. Conference proceedings will be published in the ACM Digital Library, which includes short and long papers, workshop papers, and posters. Selected high quality papers will be published in an international journals. There will also be a reward for the overall best paper from the academic conference. WORKSHOPS ------------------------------- IMUDI SPECIAL SESSION ON IMPROVING MPI USER AND DEVELOPER INTERACTION The IMUDI special session, to be held as a full-day meeting at the EuroMPI 2013 conference in Madrid, Spain, focuses on bringing together the MPI end-user and MPI implementor communities through discussions on MPI usage experiences, techniques, and optimizations. This meeting will focus on evaluating the MPI standard from the perspective of the MPI end-user (application and library developers) and address concerns and insights of MPI implementors and vendors. Unlike workshops associated with other conferences, the IMUDI session is still considered to be a part of the Euro MPI conference. Submissions will be reviewed separately to facilitate bringing together research publications falling into these "special focus" areas. More info at: http://press.mcs.anl.gov/imudi/ ENERGY-EFFICIENT HIGH PERFORMANCE COMPUTING & COMMUNICATION WORKSHOP (E2HPC2) 2013 The first Energy-Efficient High Performance Computing & Communication workshop will be co-located with EuroMPI 2013 in Madrid. Energy-awareness is now a main topic for HPC systems. The goal of this workshop is to discuss latest researches on the impact and possibles leverages of communications for such systems. E2HPC2 solicits original and non-published or under-review articles on the field of energy-aware communication in HPC environment. This workshop is co-located with EuroMPI as MPI is the main communication interface in those environments. More info at: http://www.irit.fr/~Georges.Da-Costa/e2hpc2.html PBIO 2013: INTERNATIONAL WORKSHOP ON PARALLELISM IN BIOINFORMATICS In Bioinformatics, we can find a variety of problems which are affected by huge processing times and memory consumption, due to the large size of biological data sets and the inherent complexity of biological problems. In fact, Bioinformatics is one of the most exciting research areas in which Parallelism finds application. Successful examples are mpiBLAST or ClustalW-MPI, among many others. In conclusion, Bioinformatics allows and encourages the application of many different parallelism-based technologies. The focus of this workshop is on MPI-based approaches, but we welcome any technique based on: multicore and cluster computing, supercomputing, grid computing, cloud computing, hardware accelerators as GPUs, FPGAs, or Cell processors, etc. More info at: http://arco.unex.es/mavega/pbio2013/ SUBMISSION INFORMATION ------------------------------- Contributors are invited to submit a full paper as a PDF document not exceeding 6 pages in English. The title page should contain an abstract of at most 100 words and five specific, topical keywords. The paper must be formatted according to double-column ACM ICPS proceedings style. The usage of LaTeX for preparation of the contribution as well as the submission in camera ready format is strongly recommended. Style files can be found athttp://www.acm.org/publications/icps-instructions/. New work that is not yet mature for a full paper, short observations, and similar brief announcements are invited for the poster session. Contributions to the poster session should be submitted in the form of a two page abstract. All contributions will be fully peer reviewed by the program committee. Papers shall be submitted electronically via Easychair, seehttp://www.easychair.org/conferences/?conf=eurompi2013. NVIDIA BEST PAPER AWARD ------------------------------- The Program Committee of EuroMPI 2013 will give a best paper awards. Best Paper Awards will be given to the author(s) of a full paper presented at the conference, selected by the Organizing Committee. The Best Paper Award is a Tesla K20 computing processor, sponsored by NVIDIA, valued in $3,200. SCHEDULE, IMPORTANT DATES ------------------------------- - Submission of full papers and poster: March 29th, 2013 - Author notification: May 11th, 2013 - Camera Ready papers due: June 15th, 2013 - Tutorial(s): September 15th, 2012 - Conference: September 16th-18th, 2013 CONFERENCE SPONSORS ------------------------------- Platinum: CISCO Gold: Bull NVidia COMMITTEE ------------------------------- GENERAL CHAIR Jack Dongarra, University of Tennessee, Knoxville, USA ORGANIZERS, PC CHAIRS Javier Garcia Blas, Carlos III University (fjblas(a)inf.uc3m.es) Jesus Carretero, Carlos III University (jesus.carretero(a)uc3m.es) PROGRAM COMMITTEE Pavan Balaji, Argonne National Laboratory Siegfried Benkner, University of Vienna George Bosilca, Innovative Computing Laboratory - University of Tennessee Gil Bloch, Mellanox Technologies Ron Brightwell, Sandia National Laboratories Darius Buntinas, Argonne National Laboratory Franck Cappello, INRIA and University of Illinois at Urbana-Champaign Yiannis Cotronis, National and Kapodistrian University of Athens Chi-Yin Chow, Department of Computer Science, City University of Hong Kong Anthony Danalis, University of Tennessee Luiz Derose, Cray Christian Engelmann, Oak Ridge National Laboratory Edgar Gabriel, University of Houston Brice Goglin, INRIA Ganesh Gopalakrishnan, University of Utah David Goodell, Argonne National Laboratory Richard Graham, Oak Ridge National Laboratory William Gropp, University of Illinois at Urbana-Champaign Rainer Keller, HFT Stuttgart, University of Applied Science Julian Kunkel, Universitat Hamburg Thomas Herault, University of Tennessee Bronis De Supinski, Lawrence Livermore National Laboratory Thomas Ludwig, German Climate Computing Center and University of Hamburg David E. Singh, University Carlos III of Madrid Torsten Hoefler, ETH Zurich Atsushi Hori, RIKEN AICS Florin Isaila, University Carlos III of Madrid Akihiro Inokuchi, Osaka University Yutaka Ishikawa, Graduate School of Information Science and Technology / Information Technology Center, The University of Tokyo Emmanuel Jeannot, INRIA Dries Kimpe, Argonne National Laboratory Jesper Larsson Traf, Vienna University of Technology Alexey Lastovetsky, UCD School of Computer Science & Informatics Laurent Lefevre, INRIA Dong Li, Oak Rdige National Lab Ewing Lusk, Argonne National Laboratory Teng Ma, NetApp Inc Guillaume Mercier, ENSEIRB/INRIA Bernd Mohr, Juelich Supercomputing Center Raffaele Montella, Department of Applied Science - University of Naples Parthenope Julian David Morillo Pozo, Barcelona Supercomputing Center Matthias Mueller, ZIH, TU Dresden Jose Nelson Amaral, University of Alberta Jaechun No, Sejong University Maria S. Perez, Technical University of Madrid Rolf Rabenseifner, HLRS, University of Stuttgart Rolf Riesen, IBM Gudula Runge, Chemnitz University of Technology Mitsuhisa Sato, University of Tsukuba Christian Siebert, RWTH Aachen University Anna Sikora, DACSO - UAB Shinji Sumimoto, Fujitsu Laboratories Frederic Suter, IN2P3 Computing Center Jeff Squyres, Cisco Alexander Supalov, Intel GmbH Domenico Talia, Universita della Calabria Vinod Tipparaju, AMD Rajeev Thakur, Argonne National Laboratory Carsten Trinitis, University of Bedfordshire Yuichi Tsujita, Kinki University Denis Trystram, Grenoble university Keith Underwood, Intel Mateo Valero, Barcelona Supercomputing Center Alan Wagner, University of British Columbia Roland Wismulle, University of Siegen Roman Wyrzykowski, Czestochowa University of Technology Xin Yuan, Florida State University CONFERENCE FEES ------------------------------- The conference will hopefully be well supported by sponsors, which will help directly towards keeping the fees low. As far as possible, special student fees will be offered. ________________________________________________________ Francisco Javier García Blas Computer Architecture, Communications and Systems Area. Computer Science Department. UNIVERSIDAD CARLOS III DE MADRID Avda. de la Universidad, 30 28911 Leganés (Madrid), SPAIN e-mail: fjblas(a)arcos.inf.uc3m.es fjblas(a)inf.uc3m.es Phone:(+34) 916249118 FAX: (+34) 916249129 ________________________________________________________

1 0

Re: [mpich-discuss] Hydra fills in the MPIR_proctable[] incorrectly with multiple processes per node
by Pavan Balaji 18 Mar '13

18 Mar '13

On 03/18/2013 11:56 AM US Central Time, John DelSignore wrote: > But the bigger win is that tool would have to read only 513 separate > strings using ptrace() or /proc, which represents a big time > savings. Doesn't the tool still have to read all the strings? Or are you planning to compare pointers to check if they are the same and not read the string again if they are the same? -- Pavan -- Pavan Balaji http://www.mcs.anl.gov/~balaji

1 0