April 2014 - discuss - mailman3.cels.anl.gov

Re: [mpich-discuss] problem with mpiexec
by Gilles Gouaillardet 11 Apr '14

11 Apr '14

Hi, did you create a file called machinefile ? if yes, can you send its content ? an easier way to start with mpiexec is : mpiexec -n 5 -host localhost ./examples/cpi Cheers, Gilles

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problem with mpiexec
by Mojtaba S. Moghani 11 Apr '14

11 Apr '14

hi why im seeing this errors? im doing everything based on the manual! thanks, [mojtaba@Mojtaba mpich-3.1]# mpiexec -n 5 -f ./machinefile ./examples/cpi [mpiexec@Mojtaba] HYDU_parse_hostfile (utils/args/args.c:319): unable to open host file: ./machinefile [mpiexec@Mojtaba] mfile_fn (ui/mpich/utils.c:336): error parsing hostfile [mpiexec@Mojtaba] match_arg (utils/args/args.c:152): match handler returned error [mpiexec@Mojtaba] HYDU_parse_array (utils/args/args.c:174): argument matching returned error [mpiexec@Mojtaba] parse_args (ui/mpich/utils.c:1596): error parsing input array [mpiexec@Mojtaba] HYD_uii_mpx_get_parameters (ui/mpich/utils.c:1648): unable to parse user arguments [mpiexec@Mojtaba] main (ui/mpich/mpiexec.c:153): error parsing parameters -- Mojtaba S. Moghani Faculty of Environment University of Tehran

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Re: [mpich-discuss] Run MPICH without mpiexec
by Kenneth Raffenetti 10 Apr '14

10 Apr '14

Hi Jackey, To clarify in my first email, MPICH supports singleton init. However, MPICH does not support launching dynamic MPI processes (MPI_Comm_spawn or MPI_Comm_spawn_multiple) from a singleton init. For this you need to use mpiexec. The crash you see in from the code below is a known bug: http://trac.mpich.org/projects/mpich/ticket/1541. I will see if we can fix this for an upcoming release. Ken On 04/10/2014 01:21 PM, Jackey Yan wrote: > Hi Kenneth, > > === Here is my MPICH info=== > HYDRA build details: > Version: 3.1 > Release Date: Thu Feb 20 11:41:13 CST 2014 > CC: gcc > CXX: g++ > F77: gfortran > F90: gfortran > Configure options: '--disable-option-checking' '--prefix=/icd/placement/zyan/tools/mpitch-install' '-enable-fast' '--cache-file=/dev/null' '--srcdir=/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra' 'CC=gcc' 'CFLAGS= -DNDEBUG -DNVALGRIND -O2' 'LDFLAGS= ' 'LIBS=-lrt -lpthread ' 'CPPFLAGS= -I/icd/placement/zyan/tools/build/mpich-3.1/src/mpl/include -I/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/mpl/include -I/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/openpa/src -I/icd/placement/zyan/tools/build/mpich-3.1/src/openpa/src -I/icd/placement/zyan/tools/build/mpich-3.1/src/mpi/romio/include' > 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 > > === Here is partial sample of my code=== > int world_size, universe_size, *universe_sizep, flag, rank; > MPI_Comm everyone; /* intercommunicator */ > char worker_program[100]; > char hostname[1024]; > gethostname(hostname, 1024); > std::cout << "Hi, I'm the master. host: " << hostname << " pid: " << getpid() << std::endl; > MPI_Init(&argc, &argv); > MPI_Comm_size(MPI_COMM_WORLD, &world_size); > MPI_Comm_rank(MPI_COMM_WORLD, &rank); > > std::cout << "Hi, I'm the master again. host: " << hostname << " rank: " << rank > << ". pid: " << getpid() << " world_size: " << world_size << std::endl; > > if (world_size != 1) std::cout << "Top heavy with management" << std::endl; > MPI_Comm_get_attr(MPI_COMM_WORLD, MPI_UNIVERSE_SIZE, > &universe_sizep, &flag); > ........ > > === Here is the error message I got without using mpiexec=== > Hi, I'm the master. host: place37 pid: 31698 > Hi, I'm the master again. host: place37 rank: 0. pid: 31698 world_size: 1 > [mpiexec@place37] match_arg (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/utils/args/args.c:159): unrecognized argument pmi_args > [mpiexec@place37] HYDU_parse_array (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/utils/args/args.c:174): argument matching returned error > [mpiexec@place37] parse_args (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/ui/mpich/utils.c:1596): error parsing input array > [mpiexec@place37] HYD_uii_mpx_get_parameters (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/ui/mpich/utils.c:1648): unable to parse user arguments > [mpiexec@place37] main (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/ui/mpich/mpiexec.c:153): error parsing parameters > > > Looks like the error happens in the code line of calling MPI_Comm_get_attr(). > > Thanks, > > Jackey > > -----Original Message----- > From: discuss-bounces(a)mpich.org [mailto:[email protected]] On Behalf Of Kenneth Raffenetti > Sent: Thursday, April 10, 2014 11:08 AM > To: discuss(a)mpich.org > Subject: Re: [mpich-discuss] Run MPICH without mpiexec > > MPICH supports these dynamic process features. Can you tell us more > information about your version of MPICH and provide a small example code > that can reproduce the error you are getting? > > On 04/10/2014 01:00 PM, Jackey Yan wrote: >> Hi everyone, >> >> In MPICH, do I have to use mpiexec in the command line, in order to >> launch a MPI run? >> >> I know that in MPI-2 standard, it supports the “dynamic process” >> feature, i.e., dynamically generate/spawn processes from existing >> singleton process. >> >> So it is not required to use mpiexec/mpirun in the command line, in >> order to launch a singleton MPI. >> >> But, I tried to run without mpiexec in MPICH, but it error out when >> parsing the arguments in Hydra… >> >> Thanks, >> >> Jackey >> >> >> >> >> >> _______________________________________________ >> 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] MPIExec.hydra allocates too many CPU's on SLURM
by Ruben Faelens 10 Apr '14

10 Apr '14

Hi list, I specified the hosts because mpich2-1.2 did not seem to detect I was using slurm. Not specifying the -hosts parameter made mpiexec launch using slurm, but using host 'localhost' (which is not a slurm compute node). I have now compiled mpich-3.1 from source, installed it on all nodes in the cluster, and everything works beautifully. salloc -n 8 mpiexec.hydra -n 1 ./master : -n 7 ./slave Thank you for the support! / Ruben On Thu, Apr 10, 2014 at 2:24 PM, Kenneth Raffenetti <raffenet(a)mcs.anl.gov>wrote: > What version of mpich are you using? Why are you specifying -hosts in your > mpiexec command? Are you allocating resources in some other way prior to > launching your job? > > You are correct about the normal behavior of hydra. It launches a proxies > on all nodes which then launch the MPI processes. > > > On 04/10/2014 06:49 AM, Ruben Faelens wrote: > >> Hello list, >> >> I have been messing around with SLURM and MPICH2 for about a week now, >> in order to run NONMEM on my cluster. >> >> I start my job using the following command line: >> > mpiexec.hydra -hosts node2-a,node2-b -bootstrap slurm -rmk slurm -n 1 >> ./master : -n 7 ./slave >> >> Using pstree, I can see that this launches the following command: >> > srun -N 4 -n 4 /usr/local/bin/hydra_pmi_proxy --control-port >> node2-head:38860 --rmk slurm --launcher slurm --demux poll --pgid 0 >> --retries 10 --usize -2 --proxy-id -1 >> >> Apparently, Hydra launches one single 'hydra_pmi_proxy' per node, after >> which the hydra_pmi_proxy launches the other processes. This completely >> screws up allocation rules in SLURM. >> >> Is this normal behaviour? I would rather have mpiexec.hydra allocate the >> right number of resources on SLURM, instead of seemingly deciding on its >> own which hosts to use. >> >> Kind regards, >> Ruben FAELENS >> >> >> _______________________________________________ >> 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 > -- / Ruben FAELENS +32 494 06 72 59

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Re: [mpich-discuss] Run MPICH without mpiexec
by Jackey Yan 10 Apr '14

10 Apr '14

Hi Kenneth, === Here is my MPICH info=== HYDRA build details: Version: 3.1 Release Date: Thu Feb 20 11:41:13 CST 2014 CC: gcc CXX: g++ F77: gfortran F90: gfortran Configure options: '--disable-option-checking' '--prefix=/icd/placement/zyan/tools/mpitch-install' '-enable-fast' '--cache-file=/dev/null' '--srcdir=/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra' 'CC=gcc' 'CFLAGS= -DNDEBUG -DNVALGRIND -O2' 'LDFLAGS= ' 'LIBS=-lrt -lpthread ' 'CPPFLAGS= -I/icd/placement/zyan/tools/build/mpich-3.1/src/mpl/include -I/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/mpl/include -I/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/openpa/src -I/icd/placement/zyan/tools/build/mpich-3.1/src/openpa/src -I/icd/placement/zyan/tools/build/mpich-3.1/src/mpi/romio/include' 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 === Here is partial sample of my code=== int world_size, universe_size, *universe_sizep, flag, rank; MPI_Comm everyone; /* intercommunicator */ char worker_program[100]; char hostname[1024]; gethostname(hostname, 1024); std::cout << "Hi, I'm the master. host: " << hostname << " pid: " << getpid() << std::endl; MPI_Init(&argc, &argv); MPI_Comm_size(MPI_COMM_WORLD, &world_size); MPI_Comm_rank(MPI_COMM_WORLD, &rank); std::cout << "Hi, I'm the master again. host: " << hostname << " rank: " << rank << ". pid: " << getpid() << " world_size: " << world_size << std::endl; if (world_size != 1) std::cout << "Top heavy with management" << std::endl; MPI_Comm_get_attr(MPI_COMM_WORLD, MPI_UNIVERSE_SIZE, &universe_sizep, &flag); ........ === Here is the error message I got without using mpiexec=== Hi, I'm the master. host: place37 pid: 31698 Hi, I'm the master again. host: place37 rank: 0. pid: 31698 world_size: 1 [mpiexec@place37] match_arg (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/utils/args/args.c:159): unrecognized argument pmi_args [mpiexec@place37] HYDU_parse_array (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/utils/args/args.c:174): argument matching returned error [mpiexec@place37] parse_args (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/ui/mpich/utils.c:1596): error parsing input array [mpiexec@place37] HYD_uii_mpx_get_parameters (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/ui/mpich/utils.c:1648): unable to parse user arguments [mpiexec@place37] main (/icd/placement/zyan/tools/DOWNLOAD/mpich-3.1/src/pm/hydra/ui/mpich/mpiexec.c:153): error parsing parameters Looks like the error happens in the code line of calling MPI_Comm_get_attr(). Thanks, Jackey -----Original Message----- From: discuss-bounces(a)mpich.org [mailto:[email protected]] On Behalf Of Kenneth Raffenetti Sent: Thursday, April 10, 2014 11:08 AM To: discuss(a)mpich.org Subject: Re: [mpich-discuss] Run MPICH without mpiexec MPICH supports these dynamic process features. Can you tell us more information about your version of MPICH and provide a small example code that can reproduce the error you are getting? On 04/10/2014 01:00 PM, Jackey Yan wrote: > Hi everyone, > > In MPICH, do I have to use mpiexec in the command line, in order to > launch a MPI run? > > I know that in MPI-2 standard, it supports the “dynamic process” > feature, i.e., dynamically generate/spawn processes from existing > singleton process. > > So it is not required to use mpiexec/mpirun in the command line, in > order to launch a singleton MPI. > > But, I tried to run without mpiexec in MPICH, but it error out when > parsing the arguments in Hydra… > > Thanks, > > Jackey > > > > > > _______________________________________________ > 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] Run MPICH without mpiexec
by Kenneth Raffenetti 10 Apr '14

10 Apr '14

MPICH supports these dynamic process features. Can you tell us more information about your version of MPICH and provide a small example code that can reproduce the error you are getting? On 04/10/2014 01:00 PM, Jackey Yan wrote: > Hi everyone, > > In MPICH, do I have to use mpiexec in the command line, in order to > launch a MPI run? > > I know that in MPI-2 standard, it supports the “dynamic process” > feature, i.e., dynamically generate/spawn processes from existing > singleton process. > > So it is not required to use mpiexec/mpirun in the command line, in > order to launch a singleton MPI. > > But, I tried to run without mpiexec in MPICH, but it error out when > parsing the arguments in Hydra… > > Thanks, > > Jackey > > > > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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Run MPICH without mpiexec
by Jackey Yan 10 Apr '14

10 Apr '14

Hi everyone, In MPICH, do I have to use mpiexec in the command line, in order to launch a MPI run? I know that in MPI-2 standard, it supports the "dynamic process" feature, i.e., dynamically generate/spawn processes from existing singleton process. So it is not required to use mpiexec/mpirun in the command line, in order to launch a singleton MPI. But, I tried to run without mpiexec in MPICH, but it error out when parsing the arguments in Hydra... Thanks, Jackey

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Re: [mpich-discuss] mpiexec
by Gus Correa 10 Apr '14

10 Apr '14

On 04/09/2014 05:22 PM, Balaji, Pavan wrote: > > On Apr 9, 2014, at 12:53 PM, Gus Correa <gus(a)ldeo.columbia.edu> wrote: >> For the benefit of new users, >> this information could be more visible, though. >> Perhaps an entry in the User's Guide or the FAQ. > > Good idea. Iï¿½ll add it to the user guide. FAQ is probably not appropriate for this, > unless, of course, we get this question frequently enough. :-) > > ï¿½ Pavan Thank you! Gus Correa

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Re: [mpich-discuss] Reference paper for ROMIO
by Matthieu Dorier 10 Apr '14

10 Apr '14

Thank you! Matthieu Dorier PhD student at ENS Rennes http://people.irisa.fr/Matthieu.Dorier ----- Mail original ----- > De: "Rajeev Thakur" <thakur(a)mcs.anl.gov> > À: discuss(a)mpich.org > Envoyé: Jeudi 10 Avril 2014 18:33:08 > Objet: Re: [mpich-discuss] Reference paper for ROMIO > > Perhaps the second paper listed here: > http://www.mcs.anl.gov/~thakur/papers/papers.html#MPIO > (On Implementing…) It is a bit old. > > Rajeev > > On Apr 10, 2014, at 9:15 AM, Matthieu Dorier <matthieu.dorier(a)irisa.fr> > wrote: > > > Hi, > > > > For citation, what is the reference paper for ROMIO? > > Thanks, > > > > Matthieu Dorier > > PhD student at ENS Rennes > > 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 >

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Re: [mpich-discuss] Reference paper for ROMIO
by Rajeev Thakur 10 Apr '14

10 Apr '14

Perhaps the second paper listed here: http://www.mcs.anl.gov/~thakur/papers/papers.html#MPIO (On Implementing…) It is a bit old. Rajeev On Apr 10, 2014, at 9:15 AM, Matthieu Dorier <matthieu.dorier(a)irisa.fr> wrote: > Hi, > > For citation, what is the reference paper for ROMIO? > Thanks, > > Matthieu Dorier > PhD student at ENS Rennes > 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

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