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

Re: [mpich-discuss] Run R script via MPICH
by Balaji, Pavan 30 Dec '14

30 Dec '14

Riccardo, Can you run mpirun with the --verbose option and send us the output? Thanks, -- Pavan > On Dec 30, 2014, at 4:00 PM, Riccardo Romoli <ric.romoli(a)gmail.com> wrote: > > The error I get became from the syntax I used to run my script. Fynally I've been able to run my R script uning mpirun. This is the string I used: > > $ mpirun -n 1 -hosts node02 R --slave -f /home/mpiuser/R_scripts/prova_clust.R > > I get a fatal errors using R with MPI in interactive mode: > > [mpiexec@master] match_arg (./utils/args/args.c:122): unrecognized argument pmi_args// > [mpiexec@master] HYDU_parse_array (./utils/args/args.c:140): argument matching returned error// > [mpiexec@master] parse_args (./ui/mpich/utils.c:1387): error parsing input array// > [mpiexec@master] HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1438): unable to parse user arguments// > > Usage: ./mpiexec [global opts] [exec1 local opts] : [exec2 local opts] : ...// > > Please see the intructions provided at// > http://wiki.mcs.anl.gov/mpich2/index.php/Using_the_Hydra_Process_Manager// > for further details// > > > After that R stops work. > > > All the best, Riccardo > > On 30/12/14 04:25, discuss-request(a)mpich.org wrote: > >> Message: 4 >> Date: Mon, 22 Dec 2014 11:23:22 -0600 >> From: Kenneth Raffenetti <raffenet(a)mcs.anl.gov> >> To: <discuss(a)mpich.org> >> Subject: Re: [mpich-discuss] Run R script via MPICH >> Message-ID: <5498538A.7000609(a)mcs.anl.gov> >> Content-Type: text/plain; charset="utf-8"; format=flowed >> >> It seems your MPICH installation is working fine. Are you sure the error >> is coming from MPICH? A quick google search suggests it may be a shell >> syntax error. >> >> Ken >> >> On 12/22/2014 11:03 AM, Riccardo Romoli wrote: >>> Hi my name is Riccardo, I have a linux cluster based on ubuntu with >>> mpich2 installed. I try to run the examples: >>> >>> mpiexec.hydra -f hosts -n 4 /home/mpiuser/bin/cpi >>> >>> and all works. So I try to run a simple R script but I get an error: >>> >>> Syntax error: word unexpected >>> >>> How can I overcome this error? >>> >>> Regards, Riccardo >>> _______________________________________________ >>> 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

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Re: [mpich-discuss] /lib/cpp fails sanity check
by Balaji, Pavan 30 Dec '14

30 Dec '14

Laura, You are using an ancient version of mpich. Can you try the latest version from our download page: http://www.mpich.org -- Pavan > On Dec 30, 2014, at 3:04 PM, Laura Fowler <ldfowler58(a)icloud.com> wrote: > > Hello: > > I am trying to compile mpich2-1.5 using OS X 10.10.1 on my laptop. I installed gfortran-5.0 and gcc-5.0. I used the following configurations: > > export FC=/usr/local/bin/gfortran > export F77=/usr/local/bin/gfortran > export CC=/usr/local/bin/gcc > export CXX=/usr/local/bin/g++ > export CPP=/usr/local/bin/cpp > export CXXCPP=/usr/local/bin/cpp > > I ran sudo ./configure --prefix=/usr/local/mpich2-1.5-gfortran-5.0/ 2>&1 | sudo tee c.txt to install mpich2 in my /usr/local directory. > > I got the following error message at the bottom of the c.txt file: > > checking whether to build shared libraries... no > checking whether to build static libraries... yes > checking whether make supports nested variables... (cached) yes > checking for c++... c++ > checking whether we are using the GNU C++ compiler... no > checking whether c++ accepts -g... no > checking dependency style of c++... none > checking how to run the C++ preprocessor... /lib/cpp > configure: error: in `/usr/local/src/mpich2/mpich2-1.5': > configure: error: C++ preprocessor "/lib/cpp" fails sanity check > See `config.log' for more details > > Also see attached config.log file. I do not understand where the error comes from and I need help figuring it out. Note that using the same configuration, I was able to completely install mpich-3.1.3, so I do not undertand where the configure crashes in this case. I hope that somebody can help me figure this out as I really need to use mpich2 and not mpich. > > Thanks, > Laura > > !===================================================== > ! Laura D. Fowler > ! e-mail: ldfowler58(a)icloud.com > ! Phone: 970-215-0516 > !===================================================== > > _______________________________________________ > 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

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Re: Re: Run R script via MPICH
by Riccardo Romoli 30 Dec '14

30 Dec '14

The error I get became from the syntax I used to run my script. Fynally I've been able to run my R script uning mpirun. This is the string I used: $ mpirun -n 1 -hosts node02 R --slave -f /home/mpiuser/R_scripts/prova_clust.R I get a fatal errors using R with MPI in interactive mode: [mpiexec@master] match_arg (./utils/args/args.c:122): unrecognized argument pmi_args// [mpiexec@master] HYDU_parse_array (./utils/args/args.c:140): argument matching returned error// [mpiexec@master] parse_args (./ui/mpich/utils.c:1387): error parsing input array// [mpiexec@master] HYD_uii_mpx_get_parameters (./ui/mpich/utils.c:1438): unable to parse user arguments// Usage: ./mpiexec [global opts] [exec1 local opts] : [exec2 local opts] : ...// Please see the intructions provided at// http://wiki.mcs.anl.gov/mpich2/index.php/Using_the_Hydra_Process_Manager// for further details// After that R stops work. All the best, Riccardo On 30/12/14 04:25, discuss-request(a)mpich.org wrote: > Message: 4 > Date: Mon, 22 Dec 2014 11:23:22 -0600 > From: Kenneth Raffenetti <raffenet(a)mcs.anl.gov> > To: <discuss(a)mpich.org> > Subject: Re: [mpich-discuss] Run R script via MPICH > Message-ID: <5498538A.7000609(a)mcs.anl.gov> > Content-Type: text/plain; charset="utf-8"; format=flowed > > It seems your MPICH installation is working fine. Are you sure the error > is coming from MPICH? A quick google search suggests it may be a shell > syntax error. > > Ken > > On 12/22/2014 11:03 AM, Riccardo Romoli wrote: >> Hi my name is Riccardo, I have a linux cluster based on ubuntu with >> mpich2 installed. I try to run the examples: >> >> mpiexec.hydra -f hosts -n 4 /home/mpiuser/bin/cpi >> >> and all works. So I try to run a simple R script but I get an error: >> >> Syntax error: word unexpected >> >> How can I overcome this error? >> >> Regards, Riccardo >> _______________________________________________ >> discuss mailing list discuss(a)mpich.org >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/mailman/listinfo/discuss > > > ------------------------------

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/lib/cpp fails sanity check
by Laura Fowler 30 Dec '14

30 Dec '14

Hello: I am trying to compile mpich2-1.5 using OS X 10.10.1 on my laptop. I installed gfortran-5.0 and gcc-5.0. I used the following configurations: export FC=/usr/local/bin/gfortran export F77=/usr/local/bin/gfortran export CC=/usr/local/bin/gcc export CXX=/usr/local/bin/g++ export CPP=/usr/local/bin/cpp export CXXCPP=/usr/local/bin/cpp I ran sudo ./configure --prefix=/usr/local/mpich2-1.5-gfortran-5.0/ 2>&1 | sudo tee c.txt to install mpich2 in my /usr/local directory. I got the following error message at the bottom of the c.txt file: checking whether to build shared libraries... no checking whether to build static libraries... yes checking whether make supports nested variables... (cached) yes checking for c++... c++ checking whether we are using the GNU C++ compiler... no checking whether c++ accepts -g... no checking dependency style of c++... none checking how to run the C++ preprocessor... /lib/cpp configure: error: in `/usr/local/src/mpich2/mpich2-1.5': configure: error: C++ preprocessor "/lib/cpp" fails sanity check See `config.log' for more details Also see attached config.log file. I do not understand where the error comes from and I need help figuring it out. Note that using the same configuration, I was able to completely install mpich-3.1.3, so I do not undertand where the configure crashes in this case. I hope that somebody can help me figure this out as I really need to use mpich2 and not mpich. Thanks, Laura !===================================================== ! Laura D. Fowler ! e-mail: ldfowler58(a)icloud.com ! Phone: 970-215-0516 !===================================================== _______________________________________________ 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] mpe for mpich 3.1.3
by Junchao Zhang 29 Dec '14

29 Dec '14

See also this discussion thread http://lists.mpich.org/pipermail/discuss/2014-December/003553.html --Junchao Zhang On Mon, Dec 29, 2014 at 6:33 PM, Seo, Sangmin <sseo(a)anl.gov> wrote: > Hi Huijun, > > We were integrating MPE into the MPICH tarball until 2012, but we now > distribute it separately (i.e., MPICH 3.1.3 does not contain MPE in its > tarball). You can obtain the latest MPE from http://git.mpich.org/mpe.git/. > Please note that MPE is a separate project. > > However, since MPE is not officially supported by MPICH now, you can try > http://wiki.mpich.org/mpich/index.php/Debug_Event_Logging for event > logging and debugging. > > Best regards, > -- > Sangmin Seo > Postdoctoral Appointee > Mathematics and Computer Science Division > Argonne National Laboratory > http://www.mcs.anl.gov/~sseo/ > > > On Dec 29, 2014, at 11:20 AM, Alexander <hjunqq(a)gmail.com> wrote: > > i want to know does the mpich 3.1.3 have mpe . i want to use mpe to make > a log about a program and i cann't find how to use it. the wiki gives the > mpich 1.4.1 with mpe. but after i complied mpich 3.1.3 i cann't find > /src/mpe so i cann't follow the instruciton in wiki. can someone help me ? > thanks very much! > > > > huijun qi > _______________________________________________ > 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] mpe for mpich 3.1.3
by Seo, Sangmin 29 Dec '14

29 Dec '14

Hi Huijun, We were integrating MPE into the MPICH tarball until 2012, but we now distribute it separately (i.e., MPICH 3.1.3 does not contain MPE in its tarball). You can obtain the latest MPE from http://git.mpich.org/mpe.git/. Please note that MPE is a separate project. However, since MPE is not officially supported by MPICH now, you can try http://wiki.mpich.org/mpich/index.php/Debug_Event_Logging for event logging and debugging. Best regards, -- Sangmin Seo Postdoctoral Appointee Mathematics and Computer Science Division Argonne National Laboratory http://www.mcs.anl.gov/~sseo/ On Dec 29, 2014, at 11:20 AM, Alexander <hjunqq(a)gmail.com<mailto:[email protected]>> wrote: i want to know does the mpich 3.1.3 have mpe . i want to use mpe to make a log about a program and i cann't find how to use it. the wiki gives the mpich 1.4.1 with mpe. but after i complied mpich 3.1.3 i cann't find /src/mpe so i cann't follow the instruciton in wiki. can someone help me ? thanks very much! huijun qi _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> 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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mpe for mpich 3.1.3
by Alexander 28 Dec '14

28 Dec '14

i want to know does the mpich 3.1.3 have mpe . i want to use mpe to make a log about a program and i cann't find how to use it. the wiki gives the mpich 1.4.1 with mpe. but after i complied mpich 3.1.3 i cann't find /src/mpe so i cann't follow the instruciton in wiki. can someone help me ? thanks very much! huijun qi _______________________________________________ discuss mailing list discuss(a)mpich.org To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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mpiexec.hydra creates unexpectable TCP socket.
by Anatoly G 24 Dec '14

24 Dec '14

Dear MPICH. I'm using mpich 3.1 (hydra+MPI). I execute main application (Main) which calls mpiexec.hydra in following way: mpiexec.hydra -genvall -disable-auto-cleanup -f MpiConfigMachines.txt -launcher=ssh -n 3 MPI_Prog MpiConfigMachines.txt content: 10.3.2.100:1 10.3.2.101:2 Where 10.3.2.100 is a local host. As result I get - Main + single MPI_Prog processes on local computer - 2 MPI_Prog processes on remote one. Main application establish TCP socket with local MPI_Prog. Main application establish TCP socket with controller on other computer 10.3.2.170, which is not included in MpiConfigMachines.txt file. After executing some time (hours, sometimes days) I see via netstat that created new connection from mpiexec.hydra and controller. Before executing mpiexec.hydra I set environment variable setenv MPIEXEC_PORT_RANGE 50010:65535 According to manual this variable limits hydra destination ports to [50010:65535]. I see that hydra uses these ports with MPI_Prog, but connection with controller done on port 701 (controller computer). Controller program is a server. It can accept connections only. Can you please advice how to stand with this problem? How hydra recognizes controller IP and establish connection with it? Sincerely, Anatoly. _______________________________________________ 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 R script via MPICH
by Kenneth Raffenetti 22 Dec '14

22 Dec '14

It seems your MPICH installation is working fine. Are you sure the error is coming from MPICH? A quick google search suggests it may be a shell syntax error. Ken On 12/22/2014 11:03 AM, Riccardo Romoli wrote: > Hi my name is Riccardo, I have a linux cluster based on ubuntu with > mpich2 installed. I try to run the examples: > > mpiexec.hydra -f hosts -n 4 /home/mpiuser/bin/cpi > > and all works. So I try to run a simple R script but I get an error: > > Syntax error: word unexpected > > How can I overcome this error? > > Regards, Riccardo > _______________________________________________ > 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 R script via MPICH
by Lu, Huiwei 22 Dec '14

22 Dec '14

It looks like the problem came from the script. Can you run the script directly without MPI? — Huiwei > On Dec 22, 2014, at 11:03 AM, Riccardo Romoli <ric.romoli(a)gmail.com> wrote: > > Hi my name is Riccardo, I have a linux cluster based on ubuntu with mpich2 installed. I try to run the examples: > > mpiexec.hydra -f hosts -n 4 /home/mpiuser/bin/cpi > > and all works. So I try to run a simple R script but I get an error: > > Syntax error: word unexpected > > How can I overcome this error? > > Regards, Riccardo > _______________________________________________ > 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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