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Re: [mpich-discuss] 1. Single file reading by all processors in MPI. 2.Difference between blocking and non-blocking call of MPI_neighbor_alltoallw
by Jeff Hammond 09 May '20

09 May '20

On Sat, May 9, 2020 at 10:10 AM hritikesh semwal via discuss < discuss(a)mpich.org> wrote: > Hello, > > I have following two questions with MPI, > > 1. Do I need to give a separate input file to each processor in a group or > all of them can read the input from a single file? All data inside the file > should be read by every processor. > You can read the input file from every process but it isn't a good idea. Read the input file from rank 0 and broadcast the contents. This assumes that your input file is small. If your input file is huge, then you should consider designing it for parallel reading with MPI_File_* functions. > 2. Can you please tell me what is the difference between > MPI_Neighbor_alltoallw and MPI_Ineighbor_alltoallw? As I read in MPI 3.0 > document that MPI_Neighbor_alltoallw also used non-blocking send and > receive inside its execution. > > MPI_Neighbor_alltoallw is a blocking function while MPI_Ineighbor_alltoallw is not. Using non-blocking send and receive inside its execution does not mean that MPI_Neighbor_alltoallw doesn't block - if that is how it's implemented, then there will be the equivalent of a MPI_Waitall before the function returns. But in any case, just because the MPI document suggests a possible implementation does not mean that is how all implementations work. Jeff > Thank you. > _______________________________________________ > 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 http://jeffhammond.github.io/

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1. Single file reading by all processors in MPI. 2.Difference between blocking and non-blocking call of MPI_neighbor_alltoallw
by hritikesh semwal 09 May '20

09 May '20

Hello, I have following two questions with MPI, 1. Do I need to give a separate input file to each processor in a group or all of them can read the input from a single file? All data inside the file should be read by every processor. 2. Can you please tell me what is the difference between MPI_Neighbor_alltoallw and MPI_Ineighbor_alltoallw? As I read in MPI 3.0 document that MPI_Neighbor_alltoallw also used non-blocking send and receive inside its execution. Thank you.

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Re: [mpich-discuss] Run mpich on localhost
by Tony Curtis 09 May '20

09 May '20

> On May 9, 2020, at 2:24 AM, Martin Ivanov <marto1980(a)gmail.com> wrote: > > Hello Tony, > Thank you very much for your reply. I followed your advice and gave the hostname 'dragonfly' to my machine. Then, in /etc/hosts I provided gave the alias 'dragonfly' to localhost as you suggested: > > " > marto@dragonfly% cat /etc/hosts > ::1 localhost dragonfly > 127.0.0.1 localhost dragonfly > " > > I compiled both the icpi and hellow examples. Now mpiexec seems to work, although not as reliably as I might wish. Running any of the examples with one core like this: > > mpiexec -n 1 mpich-3.0.4/examples/hellow > > is always successful. I could never get the command to finish with 2, 3, or 4 cores: it simply hangs. E.g. with 2 cores after running the above command I get: > > " > marto@dragonfly% ps x | grep hellow > 166493 ?? I6s 0:00.00 mpich-3.0.4/examples/hellow > 166494 ?? I6s 0:00.00 mpich-3.0.4/examples/hellow > " > Ok, good, that seemed like it was the obvious problem. Can you show all the processes involved in the launch, not just the application (i.e. also the mpirun and anything that is spawned)? This might provide a further clue about what is happening underneath. Tony

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Re: [mpich-discuss] Run mpich on localhost
by Martin Ivanov 09 May '20

09 May '20

Hello Tony, Thank you very much for your reply. I followed your advice and gave the hostname 'dragonfly' to my machine. Then, in /etc/hosts I provided gave the alias 'dragonfly' to localhost as you suggested: " marto@dragonfly% cat /etc/hosts ::1 localhost dragonfly 127.0.0.1 localhost dragonfly " I compiled both the icpi and hellow examples. Now mpiexec seems to work, although not as reliably as I might wish. Running any of the examples with one core like this: mpiexec -n 1 mpich-3.0.4/examples/hellow is always successful. I could never get the command to finish with 2, 3, or 4 cores: it simply hangs. E.g. with 2 cores after running the above command I get: " marto@dragonfly% ps x | grep hellow 166493 ?? I6s 0:00.00 mpich-3.0.4/examples/hellow 166494 ?? I6s 0:00.00 mpich-3.0.4/examples/hellow " With 5, 6, 7, or 8 cores most of the time the command is successful, that is all cores print as expected, but sometimes the command also hangs just as with 2 cores. Testing with icpi and 10^10 intervals gives the following output with 1 core: " marto@dragonfly% mpiexec -n 1 mpich-3.0.4/examples/icpi Enter the number of intervals: (0 quits) 10000000000 pi is approximately 3.1415926535895782, Error is 0.0000000000002149 wall clock time = 19.997830 " and the following with 5 cores, when it does not hang: " marto@dragonfly% mpiexec -n 5 mpich-3.0.4/examples/icpi Enter the number of intervals: (0 quits) 10000000000 pi is approximately 3.1415926535899605, Error is 0.0000000000001674 wall clock time = 4.475224 " As you can see, the calculation scales nicely. However, I am lost trying to figure out this unreliable behaviour. Maybe it has something to do with the hwloc warnings I get at configure? I am attaching the output of running the configure script. Thank you very much for your helpful advices. I am looking forward to your reply. Best regards, Martin On Fri, May 8, 2020 at 2:48 PM Tony Curtis <anthony.curtis(a)stonybrook.edu> wrote: > > > On May 8, 2020, at 1:41 AM, Martin Ivanov <marto1980(a)gmail.com> wrote: > > Hello, > Thank you for your replies. I think another version of MPICH may not work > as I am following a tutorial ( > https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php) > that requires specific library versions. > My /etc/hosts file contains only these two lines: > > " > ::1 localhost localhost.my.domain > 127.0.0.1 localhost localhost.my.domain > " > > uname -n returns an empty string as I have not set a hostname. I guess I > do not need this because I need to run MPICH only on this machine, that is > on localhost? uname -a gives the following output: > > > Thing is, though, your initial post showed ssh being used as launcher. So > in that case you would definitely need a hostname so you can resolve back > to yourself (your shell prompt was a big clue, by the way). Setting a > hostname and making it an alias of localhost in /etc/hosts would probably > do wonders no matter the underlying launch. > > The -info output is pretty much the same as I see on FreeBSD. > > If you run a hello world with a sleep in it to allow you to react, what > does “ps x” show? > > (Not familiar much with DragonFly beyond “poking at it” so I don’t have > any particular insight there.) > > Tony > > >

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Re: [mpich-discuss] Speed up issue with CFD solver.
by hritikesh semwal 08 May '20

08 May '20

What do you mean by logical partition? For 2 partitions it a single slice and for 4 partitions it is a plus shape slice partitioning. The computation is decreasing continuously but communication time is increasing from 0.69% to 8.9% of the total time from 2 to 4 processes. I am using MPI_Neighbor_alltoallw for exchanging data after forming distributed graph topology. On Fri, May 8, 2020 at 8:34 PM Zhou, Hui <zhouh(a)anl.gov> wrote: > I would first analyze the logical partition and the effects on computation > and communications. Do they continuously change from 2 process and up or is > there a bump? > > > > -- > Hui Zhou > > > > > > *From: *hritikesh semwal via discuss <discuss(a)mpich.org> > *Reply-To: *"discuss(a)mpich.org" <discuss(a)mpich.org> > *Date: *Thursday, May 7, 2020 at 11:19 PM > *To: *"discuss(a)mpich.org" <discuss(a)mpich.org> > *Cc: *hritikesh semwal <hritikesh.semwal(a)gmail.com> > *Subject: *[mpich-discuss] Speed up issue with CFD solver. > > > > Hello, > > > > I am developing a parallel CFD solver for unstructured grids with finite > volume explicit time integration method and the global mesh count is 97336 > cells. I am trying to get the speed up results of my code but something > strange is happening. Following are my timing results after the second time > step with the different number of processors; > > > > 2 processors- 182.284 seconds > > 4 processors- 251.7035 seconds > > 8 processors- 190.8578 seconds > > 16 processors- 129.7989 seconds > > 24 processors- 121.0303 seconds > > 32 processors- 111.3772 seconds > > > > I am not getting why there is a sharp rise in time from 2 processors to 4 > processors and after that, it is decreasing. I had run the same code 2 > weeks ago and at that time the results were different from the present > results and time was continuously decreasing at that time. Could someone > please help me with this matter by suggesting the probable cause/s of this > behaviour? > > > > Thank you. >

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Re: [mpich-discuss] Speed up issue with CFD solver.
by Zhou, Hui 08 May '20

08 May '20

I would first analyze the logical partition and the effects on computation and communications. Do they continuously change from 2 process and up or is there a bump? -- Hui Zhou From: hritikesh semwal via discuss <discuss(a)mpich.org> Reply-To: "discuss(a)mpich.org" <discuss(a)mpich.org> Date: Thursday, May 7, 2020 at 11:19 PM To: "discuss(a)mpich.org" <discuss(a)mpich.org> Cc: hritikesh semwal <hritikesh.semwal(a)gmail.com> Subject: [mpich-discuss] Speed up issue with CFD solver. Hello, I am developing a parallel CFD solver for unstructured grids with finite volume explicit time integration method and the global mesh count is 97336 cells. I am trying to get the speed up results of my code but something strange is happening. Following are my timing results after the second time step with the different number of processors; 2 processors- 182.284 seconds 4 processors- 251.7035 seconds 8 processors- 190.8578 seconds 16 processors- 129.7989 seconds 24 processors- 121.0303 seconds 32 processors- 111.3772 seconds I am not getting why there is a sharp rise in time from 2 processors to 4 processors and after that, it is decreasing. I had run the same code 2 weeks ago and at that time the results were different from the present results and time was continuously decreasing at that time. Could someone please help me with this matter by suggesting the probable cause/s of this behaviour? Thank you.

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Re: [mpich-discuss] Run mpich on localhost
by Tony Curtis 08 May '20

08 May '20

> On May 8, 2020, at 1:41 AM, Martin Ivanov <marto1980(a)gmail.com> wrote: > > Hello, > Thank you for your replies. I think another version of MPICH may not work as I am following a tutorial (https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php <https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php>) that requires specific library versions. > My /etc/hosts file contains only these two lines: > > " > ::1 localhost localhost.my.domain > 127.0.0.1 localhost localhost.my.domain > " > > uname -n returns an empty string as I have not set a hostname. I guess I do not need this because I need to run MPICH only on this machine, that is on localhost? uname -a gives the following output: > Thing is, though, your initial post showed ssh being used as launcher. So in that case you would definitely need a hostname so you can resolve back to yourself (your shell prompt was a big clue, by the way). Setting a hostname and making it an alias of localhost in /etc/hosts would probably do wonders no matter the underlying launch. The -info output is pretty much the same as I see on FreeBSD. If you run a hello world with a sleep in it to allow you to react, what does “ps x” show? (Not familiar much with DragonFly beyond “poking at it” so I don’t have any particular insight there.) Tony

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Re: [mpich-discuss] Run mpich on localhost
by Martin Ivanov 08 May '20

08 May '20

Hello, sorry for cross-posting, here is some more info: " marto@% mpiexec -info HYDRA build details: Version: 3.0.4 Release Date: Wed Apr 24 10:08:10 CDT 2013 CC: gcc -I/home/marto/WRF/Build_WRF/LIBRARIES/grib2/include -L/home/marto/WRF/Build_WRF/LIBRARIES/grib2/lib CXX: g++ -I/home/marto/WRF/Build_WRF/LIBRARIES/grib2/include -L/home/marto/WRF/Build_WRF/LIBRARIES/grib2/lib F77: gfortran -m64 -L/home/marto/WRF/Build_WRF/LIBRARIES/grib2/lib F90: gfortran -m64 -L/home/marto/WRF/Build_WRF/LIBRARIES/grib2/lib Configure options: '--disable-option-checking' '--prefix=/home/marto/WRF/Build_WRF/LIBRARIES/mpich' 'CC=gcc' 'LDFLAGS=-L/home/marto/WRF/Build_WRF/LIBRARIES/grib2/lib ' 'CPPFLAGS=-I/home/marto/WRF/Build_WRF/LIBRARIES/grib2/include -I/home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/mpl/include -I/home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/mpl/include -I/home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/openpa/src -I/home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/openpa/src -I/home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/mpi/romio/include' 'CXX=g++' 'F77=gfortran' 'FFLAGS=-m64 -O2' 'FC=gfortran' 'FCFLAGS=-m64 -O2' '--cache-file=/dev/null' '--srcdir=.' 'CFLAGS= -O2' 'LIBS=-lpthread ' Process Manager: pmi Launchers available: ssh rsh fork slurm ll lsf sge manual persist Topology libraries available: hwloc Resource management kernels available: user slurm ll lsf sge pbs cobalt Checkpointing libraries available: Demux engines available: poll select " Best regards, Martin On Fri, May 8, 2020 at 7:41 AM Martin Ivanov <marto1980(a)gmail.com> wrote: > Hello, > Thank you for your replies. I think another version of MPICH may not work > as I am following a tutorial ( > https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php) > that requires specific library versions. > My /etc/hosts file contains only these two lines: > > " > ::1 localhost localhost.my.domain > 127.0.0.1 localhost localhost.my.domain > " > > uname -n returns an empty string as I have not set a hostname. I guess I > do not need this because I need to run MPICH only on this machine, that is > on localhost? uname -a gives the following output: > > " > marto@% uname -a > DragonFly 5.8-RELEASE DragonFly v5.8.1-RELEASE #1: Thu May 7 08:26:21 > CEST 2020 root@:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 > " > > Apart from providing a --prefix, I configured MPICH with the default > options. During the configure step I got some interesting messages though: > > " > checking for architecture... x86_64 > configure: WARNING: Unknown architecture x86_64... proceeding anyway > ... > ### > ### Configuring hwloc core > ### > checking hwloc building mode... embedded > configure: hwloc builddir: > /home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc > configure: hwloc srcdir: > /home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc > checking if want hwloc maintainer support... disabled (embedded mode) > checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ > checking for hwloc symbol prefix... hwloc_ > checking size of void *... 8 > checking which OS support to include... Unsupported! > (x86_64-unknown-dragonfly5.8) > configure: WARNING: > *********************************************************** > configure: WARNING: *** hwloc does not support this system. > configure: WARNING: *** hwloc will *attempt* to build (but it may not > work). > configure: WARNING: *** hwloc run-time results may be reduced to showing > just one processor. > configure: WARNING: *** You have been warned. > configure: WARNING: *** Pausing to give you time to read this message... > configure: WARNING: > *********************************************************** > checking which CPU support to include... x86_64 > ... > configure: creating ./config.status > config.status: creating tools/topo/hwloc/hwloc/Makefile > config.status: creating tools/topo/hwloc/hwloc/include/Makefile > config.status: creating tools/topo/hwloc/hwloc/src/Makefile > config.status: creating Makefile > config.status: creating tools/bootstrap/src/bsci_init.c > config.status: creating hydra-doxygen.cfg > config.status: creating include/hydra_config.h > config.status: include/hydra_config.h is unchanged > config.status: creating > tools/topo/hwloc/hwloc/include/private/autogen/config.h > config.status: tools/topo/hwloc/hwloc/include/private/autogen/config.h is > unchanged > config.status: creating > tools/topo/hwloc/hwloc/include/hwloc/autogen/config.h > config.status: tools/topo/hwloc/hwloc/include/hwloc/autogen/config.h is > unchanged > " > I am looking forward to your replies. > > Best regards, > Martin > > On Thu, May 7, 2020 at 8:59 PM Tony Curtis via discuss <discuss(a)mpich.org> > wrote: > >> >> >> On May 7, 2020, at 2:30 PM, Zhou, Hui via discuss <discuss(a)mpich.org> >> wrote: >> >> Hi Martin, >> >> Could you try the latest version https://www.mpich.org/downloads/ ? >> >> -- >> Hui Zhou >> >> >> *From: *Martin Ivanov via discuss <discuss(a)mpich.org> >> *Reply-To: *"discuss(a)mpich.org" <discuss(a)mpich.org> >> *Date: *Thursday, May 7, 2020 at 11:35 AM >> *To: *"discuss(a)mpich.org" <discuss(a)mpich.org> >> *Cc: *Martin Ivanov <marto1980(a)gmail.com> >> *Subject: *[mpich-discuss] Run mpich on localhost >> >> Hello, >> I installed mpich-3.0.4 on a x86_64 BSD machine. I need to run MPI on >> this single machine, which has 8 cores. When I run the cpi example, I get: >> >> marto@% mpiexec -n 3 mpich-3.0.4/examples/cpi >> ssh: Could not resolve hostname : hostname nor servname provided, or not >> known >> >> >> >> Also, how did you configure MPICH? What is your hostname (uname -n), and >> what is in /etc/hosts? >> >> Tony >> >> _______________________________________________ >> 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] Run mpich on localhost
by Martin Ivanov 08 May '20

08 May '20

Hello, Thank you for your replies. I think another version of MPICH may not work as I am following a tutorial ( https://www2.mmm.ucar.edu/wrf/OnLineTutorial/compilation_tutorial.php) that requires specific library versions. My /etc/hosts file contains only these two lines: " ::1 localhost localhost.my.domain 127.0.0.1 localhost localhost.my.domain " uname -n returns an empty string as I have not set a hostname. I guess I do not need this because I need to run MPICH only on this machine, that is on localhost? uname -a gives the following output: " marto@% uname -a DragonFly 5.8-RELEASE DragonFly v5.8.1-RELEASE #1: Thu May 7 08:26:21 CEST 2020 root@:/usr/obj/usr/src/sys/X86_64_GENERIC x86_64 " Apart from providing a --prefix, I configured MPICH with the default options. During the configure step I got some interesting messages though: " checking for architecture... x86_64 configure: WARNING: Unknown architecture x86_64... proceeding anyway ... ### ### Configuring hwloc core ### checking hwloc building mode... embedded configure: hwloc builddir: /home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc configure: hwloc srcdir: /home/marto/WRF/Build_WRF/LIBRARIES/mpich-3.0.4/src/pm/hydra/tools/topo/hwloc/hwloc checking if want hwloc maintainer support... disabled (embedded mode) checking for hwloc directory prefix... tools/topo/hwloc/hwloc/ checking for hwloc symbol prefix... hwloc_ checking size of void *... 8 checking which OS support to include... Unsupported! (x86_64-unknown-dragonfly5.8) configure: WARNING: *********************************************************** configure: WARNING: *** hwloc does not support this system. configure: WARNING: *** hwloc will *attempt* to build (but it may not work). configure: WARNING: *** hwloc run-time results may be reduced to showing just one processor. configure: WARNING: *** You have been warned. configure: WARNING: *** Pausing to give you time to read this message... configure: WARNING: *********************************************************** checking which CPU support to include... x86_64 ... configure: creating ./config.status config.status: creating tools/topo/hwloc/hwloc/Makefile config.status: creating tools/topo/hwloc/hwloc/include/Makefile config.status: creating tools/topo/hwloc/hwloc/src/Makefile config.status: creating Makefile config.status: creating tools/bootstrap/src/bsci_init.c config.status: creating hydra-doxygen.cfg config.status: creating include/hydra_config.h config.status: include/hydra_config.h is unchanged config.status: creating tools/topo/hwloc/hwloc/include/private/autogen/config.h config.status: tools/topo/hwloc/hwloc/include/private/autogen/config.h is unchanged config.status: creating tools/topo/hwloc/hwloc/include/hwloc/autogen/config.h config.status: tools/topo/hwloc/hwloc/include/hwloc/autogen/config.h is unchanged " I am looking forward to your replies. Best regards, Martin On Thu, May 7, 2020 at 8:59 PM Tony Curtis via discuss <discuss(a)mpich.org> wrote: > > > On May 7, 2020, at 2:30 PM, Zhou, Hui via discuss <discuss(a)mpich.org> > wrote: > > Hi Martin, > > Could you try the latest version https://www.mpich.org/downloads/ ? > > -- > Hui Zhou > > > *From: *Martin Ivanov via discuss <discuss(a)mpich.org> > *Reply-To: *"discuss(a)mpich.org" <discuss(a)mpich.org> > *Date: *Thursday, May 7, 2020 at 11:35 AM > *To: *"discuss(a)mpich.org" <discuss(a)mpich.org> > *Cc: *Martin Ivanov <marto1980(a)gmail.com> > *Subject: *[mpich-discuss] Run mpich on localhost > > Hello, > I installed mpich-3.0.4 on a x86_64 BSD machine. I need to run MPI on this > single machine, which has 8 cores. When I run the cpi example, I get: > > marto@% mpiexec -n 3 mpich-3.0.4/examples/cpi > ssh: Could not resolve hostname : hostname nor servname provided, or not > known > > > > Also, how did you configure MPICH? What is your hostname (uname -n), and > what is in /etc/hosts? > > Tony > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Speed up issue with CFD solver.
by hritikesh semwal 07 May '20

07 May '20

Hello, I am developing a parallel CFD solver for unstructured grids with finite volume explicit time integration method and the global mesh count is 97336 cells. I am trying to get the speed up results of my code but something strange is happening. Following are my timing results after the second time step with the different number of processors; 2 processors- 182.284 seconds 4 processors- 251.7035 seconds 8 processors- 190.8578 seconds 16 processors- 129.7989 seconds 24 processors- 121.0303 seconds 32 processors- 111.3772 seconds I am not getting why there is a sharp rise in time from 2 processors to 4 processors and after that, it is decreasing. I had run the same code 2 weeks ago and at that time the results were different from the present results and time was continuously decreasing at that time. Could someone please help me with this matter by suggesting the probable cause/s of this behaviour? Thank you.

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