June 2016 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] Problem with Mpich3.0.4 build for WRF run across multiple nodes in a cluster.
by Rob Latham 21 Jun '16

21 Jun '16

On 06/21/2016 05:58 AM, Teck-Bin Arthur Lim wrote: > Hi , > > I met with a basic problem trying to get old mpich(3.0.4) version to do > parallel run across different machines in a mini-cluster. The error > messages > > while invoking the mpiruns are : > > *****************error messages******************** > > [limtba@fdns00_ws testenv-testlib]$ ./mpi-script > > [limtba@fdns00_ws testenv-testlib]$ more log.aout > > [mpiexec@fdns00_ws] HYDU_process_mfile_token (./utils/args/args.c:299): > token cpu not supported at this time > > [mpiexec@fdns00_ws] HYDU_parse_hostfile (./utils/args/args.c:347): > unable to process token what does your machine file look like? it sounds like you've got something in there that Hydra does not expect. ==rob > > [mpiexec@fdns00_ws] mfile_fn (./ui/mpich/utils.c:341): error parsing > hostfile > > [mpiexec@fdns00_ws] match_arg (./utils/args/args.c:153): match handler > returned error > > [mpiexec@fdns00_ws] HYDU_parse_array (./utils/args/args.c:175): argument > matching returned error > > [mpiexec@fdns00_ws] parse_args (./ui/mpich/utils.c:1609): error parsing > input array > > [mpiexec@fdns00_ws] HYD_uii_mpx_get_parameters > (./ui/mpich/utils.c:1660): unable to parse user arguments > > [mpiexec@fdns00_ws] main (./ui/mpich/mpiexec.c:153): error parsing > parameters > > Command exited with non-zero status 255 > > *****************error messages******************** > > This old version was downloaded from WRF site > (http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php#STEP2) > , and was built > > with essentially, all the default configuration settings without any > options arguments given in the configure/make/make-install process, as : > > Ø./configure –prefix=$DIR/mpich > > Ømake > > Ømake install > > There are no error messages during the built process, and the mpirun > works fine for parallel runs, using multiple processors, on a single > NODE only > > but met with the above error messages when attempting parallel run > across multiple machines. > > I need some advice as to how get this old mpich 3.0.4 working across > machines. The OS for these machines are Centos5.5, with gcc4.1.2 and > > gcc4.4.7 installations. As WRF needs gcc4.4 and higher version, I have > built the mpich3.04 using gcc4.4.7. > > Would appreciate any help and advices… > > Many Thanks. > > > > _______________________________________________ > 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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Problem with Mpich3.0.4 build for WRF run across multiple nodes in a cluster.
by Teck-Bin Arthur Lim 21 Jun '16

21 Jun '16

Hi , I met with a basic problem trying to get old mpich(3.0.4) version to do parallel run across different machines in a mini-cluster. The error messages while invoking the mpiruns are : *****************error messages******************** [limtba@fdns00_ws testenv-testlib]$ ./mpi-script [limtba@fdns00_ws testenv-testlib]$ more log.aout [mpiexec@fdns00_ws] HYDU_process_mfile_token (./utils/args/args.c:299): token cpu not supported at this time [mpiexec@fdns00_ws] HYDU_parse_hostfile (./utils/args/args.c:347): unable to process token [mpiexec@fdns00_ws] mfile_fn (./ui/mpich/utils.c:341): error parsing hostfile [mpiexec@fdns00_ws] match_arg (./utils/args/args.c:153): match handler returned error [mpiexec@fdns00_ws] HYDU_parse_array (./utils/args/args.c:175): argument matching returned error [mpiexec@fdns00_ws] parse_args (./ui/mpich/utils.c:1609): error parsing input array [mpiexec@fdns00_ws] HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1660): unable to parse user arguments [mpiexec@fdns00_ws] main (./ui/mpich/mpiexec.c:153): error parsing parameters Command exited with non-zero status 255 *****************error messages******************** This old version was downloaded from WRF site (http://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php#STEP2) , and was built with essentially, all the default configuration settings without any options arguments given in the configure/make/make-install process, as : Ø ./configure –prefix=$DIR/mpich Ø make Ø make install There are no error messages during the built process, and the mpirun works fine for parallel runs, using multiple processors, on a single NODE only but met with the above error messages when attempting parallel run across multiple machines. I need some advice as to how get this old mpich 3.0.4 working across machines. The OS for these machines are Centos5.5, with gcc4.1.2 and gcc4.4.7 installations. As WRF needs gcc4.4 and higher version, I have built the mpich3.04 using gcc4.4.7. Would appreciate any help and advices… Many Thanks. _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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mpi_f_sync_reg
by C.Friedrich 21 Jun '16

21 Jun '16

Dear all, in MPICH 3.2 (using "# include 'mpif.h' and "use mpi") I am missing the routine mpi_f_sync_reg which avoids problems with the optimization of Fortran compilers (e.g., assignment movements across MPI_WIN_FENCE). It seems to be available in the new module "mpi_f08", though. Well, I guess sooner or later I will have to switch to this Fortran 2008 compliant module... Regards Christoph ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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.-Ing. Wolfgang Marquardt (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] Race condition in MPI3 (Fortran, shared memory)
by C.Friedrich 21 Jun '16

21 Jun '16

Thank you. After some research I have been able to solve the problem: MPI_WIN_FENCE is correct, but an assignment like a=a+1 will always lead to race conditions. This assignment has to be replaced by calls to MPI_ACCUMULATE, which is "atomic" by design. So, calls to MPI_ACCUMULATEs do not have to be separated by "fences". However, we need fences to separate them from the local store (a=0) before and from the read (e.g., write(*,*) a) afterwards. In the present case, one could write ... b=1 tdisp=0 call mpe_win_fence(a,0,Nwin,err) do i = 1,10000 call mpi_accumulate(b,100,mpi_integer,0,tdisp,100,mpi_integer,mpi_sum,Nwin,err) enddo call mpe_win_fence(a,0,Nwin,err) ... Christoph ------------------------------------------------------------------------------------------------ ------------------------------------------------------------------------------------------------ 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.-Ing. Wolfgang Marquardt (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] mpich-master-v3.2-331-g44fd9c5f39e5: runtime error spawning processes
by Min Si 09 Jun '16

09 Jun '16

Hi Siegmar, It seems it is still caused by the unaligned memory access issue in MPICH. Unfortunately, the fix patch is still in our reviewing queue. I hope it can be pushed to master as soon as we can. Please check this ticket for tracking the status (it will be closed once we have pushed fix to master). Thanks. https://trac.mpich.org/projects/mpich/ticket/2309 Min On 6/8/16 1:14 AM, Siegmar Gross wrote: > Hi, > > I have built mpich-master-v3.2-331-g44fd9c5f39e5 on my machines (Solaris > 10 Sparc, Solaris 10 x86_64, and openSUSE Linux 12.1 x86_64) with > gcc-5.1.0 and Sun C 5.13. Most of the time I get an error with different > error messages spawning processes on a Sparc machine. > > > tyr spawn 107 mpiexec -np 1 --host tyr,tyr,tyr,tyr,tyr spawn_master > > Parent process 0 running on tyr.informatik.hs-fulda.de > I create 4 slave processes > > Parent process 0: tasks in MPI_COMM_WORLD: 1 > tasks in COMM_CHILD_PROCESSES local group: 1 > tasks in COMM_CHILD_PROCESSES remote group: 4 > > Slave process 0 of 4 running on tyr.informatik.hs-fulda.de > Slave process 1 of 4 running on tyr.informatik.hs-fulda.de > Slave process 2 of 4 running on tyr.informatik.hs-fulda.de > Slave process 3 of 4 running on tyr.informatik.hs-fulda.de > spawn_slave 0: argv[0]: spawn_slave > spawn_slave 1: argv[0]: spawn_slave > spawn_slave 2: argv[0]: spawn_slave > spawn_slave 3: argv[0]: spawn_slave > > > > tyr spawn 108 mpiexec -np 1 --host tyr,tyr,tyr,tyr,tyr spawn_master > > Parent process 0 running on tyr.informatik.hs-fulda.de > I create 4 slave processes > > Fatal error in MPI_Comm_spawn: Unknown error class, error stack: > MPI_Comm_spawn(141)...................: > MPI_Comm_spawn(cmd="spawn_slave", argv=0, maxprocs=4, MPI_INFO_NULL, > root=0, MPI_COMM_WORLD, intercomm=ffffffff7fffdf58, errors=0) failed > MPIDI_Comm_spawn_multiple(274)........: > MPID_Comm_accept(153).................: > MPIDI_Comm_accept(1039)...............: > MPIDU_Complete_posted_with_error(1137): Process failed > tyr spawn 109 > > > > tyr spawn 111 mpiexec -np 1 --host tyr,tyr,tyr,tyr,tyr spawn_master > > Parent process 0 running on tyr.informatik.hs-fulda.de > I create 4 slave processes > > > =================================================================================== > > = BAD TERMINATION OF ONE OF YOUR APPLICATION PROCESSES > = PID 3322 RUNNING AT tyr > = EXIT CODE: 10 > = CLEANING UP REMAINING PROCESSES > = YOU CAN IGNORE THE BELOW CLEANUP MESSAGES > =================================================================================== > > [proxy:0:[email protected]] HYD_pmcd_pmip_control_cmd_cb > (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/pm/pmiserv/pmip_cb.c:883): > assert (!closed) failed > [proxy:0:[email protected]] HYDT_dmxu_poll_wait_for_event > (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/tools/demux/demux_poll.c:77): > callback returned error status > [proxy:0:[email protected]] main > (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/pm/pmiserv/pmip.c:202): > demux engine error waiting for event > [mpiexec(a)tyr.informatik.hs-fulda.de] HYDT_bscu_wait_for_completion > (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/tools/bootstrap/utils/bscu_wait.c:76): > one of the processes terminated badly; aborting > [mpiexec(a)tyr.informatik.hs-fulda.de] HYDT_bsci_wait_for_completion > (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/tools/bootstrap/src/bsci_wait.c:23): > launcher returned error waiting for completion > [mpiexec(a)tyr.informatik.hs-fulda.de] HYD_pmci_wait_for_completion > (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/pm/pmiserv/pmiserv_pmci.c:218): > launcher returned error waiting for completion > [mpiexec(a)tyr.informatik.hs-fulda.de] main > (../../../../mpich-master-v3.2-331-g44fd9c5f39e5/src/pm/hydra/ui/mpich/mpiexec.c:340): > process manager error waiting for completion > tyr spawn 112 > > > > > I would be grateful if somebody can fix the problem. Please let me > know, if you need more information. Thank you very much for any help > in advance. > > > Kind regards > > Siegmar > _______________________________________________ > 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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Re: [mpich-discuss] logging
by Kanaev A.A. 09 Jun '16

09 Jun '16

Thanks for the response! I'll be glad to have an option of logging mpich 3.1 ________________________________________ From: Oden, Lena [loden(a)anl.gov] Sent: Thursday, June 09, 2016 3:38 PM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] logging Hello Anton, Unfortunately, you are right, the rlog support is broken for a while (I think i broke with our change to autogen) I was working on a fix for this, but had to work on other things. Give me a few days and I may will be able to fix it. I would be glad, If you are willing to test my patch. Thanks, Lena > On Jun 9, 2016, at 5:15 AM, Kanaev A.A. <kanaev(a)ibrae.ac.ru> wrote: > > Hello mpich-dev, > > Since version 2-1.5 there's no Makefile.in in src/util/logging/rlog folder > So when i run configure for mpich with --with-logging=rlog option i receive an error about Makefile.in absence in rlog folder > I tried to run autogen.sh prior to configure but it did nothing as well > > Thanks > Anton > _______________________________________________ > 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

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Re: [mpich-discuss] installation
by phani sri 09 Jun '16

09 Jun '16

thank you for the response, I cleared the problem by editing the makefile. On Thu, Jun 9, 2016 at 8:28 PM, Halim Amer <aamer(a)anl.gov> wrote: > As the error says, it cannot find the Fortran 90 MPI wrapper. You might > have installed MPICH without Fortran support. > > You can get the latest MPICH at https://www.mpich.org/downloads/ (Ubuntu > tarballs might be what you will need) and follow the instructions at > https://www.mpich.org/static/downloads/3.2/mpich-3.2-installguide.pdf for > a proper installation. > > --Halim > www.mcs.anl.gov/~aamer > > > On 6/9/16 4:52 AM, phani sri wrote: > >> I am a new user of FLASH4.3, which initiating the sample programme Sedov >> in 2d, I am not able to build it because when execute make it is showing >> the following error, I have installed the mpich2 in /usr/local but the >> following error it is showing. Can any one give a suggestion. >> Thank You >> >> -- >> D. P. S. L. Kameswari, >> Ph. D(Physics) >> ACRHEM >> University Of Hyderabad, >> Hyderabad, >> e-mail:[email protected] <mailto:id%[email protected]> >> >> >> _______________________________________________ >> 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 > -- D. P. S. L. Kameswari, Ph. D(Physics) ACRHEM University Of Hyderabad, Hyderabad, e-mail:[email protected] <id%3Aphanisri123(a)gmail.com> _______________________________________________ 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] installation
by Halim Amer 09 Jun '16

09 Jun '16

As the error says, it cannot find the Fortran 90 MPI wrapper. You might have installed MPICH without Fortran support. You can get the latest MPICH at https://www.mpich.org/downloads/ (Ubuntu tarballs might be what you will need) and follow the instructions at https://www.mpich.org/static/downloads/3.2/mpich-3.2-installguide.pdf for a proper installation. --Halim www.mcs.anl.gov/~aamer On 6/9/16 4:52 AM, phani sri wrote: > I am a new user of FLASH4.3, which initiating the sample programme Sedov > in 2d, I am not able to build it because when execute make it is showing > the following error, I have installed the mpich2 in /usr/local but the > following error it is showing. Can any one give a suggestion. > Thank You > > -- > D. P. S. L. Kameswari, > Ph. D(Physics) > ACRHEM > University Of Hyderabad, > Hyderabad, > e-mail:[email protected] <mailto:id%[email protected]> > > > _______________________________________________ > 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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Re: [mpich-discuss] logging
by Oden, Lena 09 Jun '16

09 Jun '16

Hello Anton, Unfortunately, you are right, the rlog support is broken for a while (I think i broke with our change to autogen) I was working on a fix for this, but had to work on other things. Give me a few days and I may will be able to fix it. I would be glad, If you are willing to test my patch. Thanks, Lena > On Jun 9, 2016, at 5:15 AM, Kanaev A.A. <kanaev(a)ibrae.ac.ru> wrote: > > Hello mpich-dev, > > Since version 2-1.5 there's no Makefile.in in src/util/logging/rlog folder > So when i run configure for mpich with --with-logging=rlog option i receive an error about Makefile.in absence in rlog folder > I tried to run autogen.sh prior to configure but it did nothing as well > > Thanks > Anton > _______________________________________________ > 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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logging
by Kanaev A.A. 09 Jun '16

09 Jun '16

Hello mpich-dev, Since version 2-1.5 there's no Makefile.in in src/util/logging/rlog folder So when i run configure for mpich with --with-logging=rlog option i receive an error about Makefile.in absence in rlog folder I tried to run autogen.sh prior to configure but it did nothing as well Thanks Anton _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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