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

Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Pavan Balaji 13 Jun '13

13 Jun '13

I just saw your older email. Why are you using smpd instead of the default process manager (hydra)? -- Pavan On 06/13/2013 08:05 AM, Pavan Balaji wrote: > > What's "-phrase"? That's not a recognized option. I'm not sure where > the /dev/mem check is coming from. Try running ~/main without mpiexec > first. > > -- Pavan > > On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: >> Hello all, >> >> I am trying to use two raspberry-pi to sample and then process some >> data. The first process samples while the second processes and vice >> versa. To do this I use gpio and also mpich-3.0.4 with the process >> manager smpd. I have successfully run cpi on both machines (from the >> master machine). I have also managed to run a similar program but >> without the MPI, this involved compiling with gcc and when running >> putting sudo in front of the binary file. >> >> When I combine these two processes I get various error messages. >> For input: >> mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >> the error is: >> Can't open /dev/mem >> Did you forget to use 'sudo .. ?' >> >> For input: >> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >> the error is: >> sudo: mpiexec: Command not found >> >> I therefore put mpiexec into /usr/bin >> >> now for input: >> sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main >> the error is: >> Can't open /dev/mem >> Did you forget to use 'sudo .. ?' >> >> Does anyone know how I can work around this? >> Thanks, >> Eibhlin >> >> >> >> _______________________________________________ >> 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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How to keep the VS console window open on exceptions during debug of a parallel code
by Feng Xiao 13 Jun '13

13 Jun '13

Hello, I am writing about how to keep the console window open on exceptions during debug of a parallel code (either F5 or Ctrl+F5). I am running MPICH2 FORTRAN program in Visual Studio 2010, everything works fine, expect that I could not see the exception/error messages on the console window, it closes right after the program exits on exceptions. I do know how to keep the console window open when program meets the end, or put a read statement to pause the program during the execution. I did some google search, the only relevant solution I could find is http://www.boost.org/doc/libs/1_36_0/libs/test/doc/html/utf/usage-recommend…, which is about making debugger break at the point the failure by adding extra command line argument and seeing the runtime error in the output window. However, it looks like something for a serial code without mpiexec.exe in the command line, and I am not a advanced VS user, so I don't know how to do it for a parallel code, or if there is any other way out. Thanks in advance! -- Feng Xiao Doctoral Student Petroleum Engineering Colorado School of Mines Cell 918-814-2644

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Re: [mpich-discuss] Running an mpi program that needs to access /dev/mem
by Pavan Balaji 13 Jun '13

13 Jun '13

What's "-phrase"? That's not a recognized option. I'm not sure where the /dev/mem check is coming from. Try running ~/main without mpiexec first. -- Pavan On 06/13/2013 06:56 AM, Lee, Eibhlin wrote: > Hello all, > > I am trying to use two raspberry-pi to sample and then process some > data. The first process samples while the second processes and vice > versa. To do this I use gpio and also mpich-3.0.4 with the process > manager smpd. I have successfully run cpi on both machines (from the > master machine). I have also managed to run a similar program but > without the MPI, this involved compiling with gcc and when running > putting sudo in front of the binary file. > > When I combine these two processes I get various error messages. > For input: > mpiexec -phrase cat -machinefile machinefile -n 2 ~/main > the error is: > Can't open /dev/mem > Did you forget to use 'sudo .. ?' > > For input: > sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main > the error is: > sudo: mpiexec: Command not found > > I therefore put mpiexec into /usr/bin > > now for input: > sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main > the error is: > Can't open /dev/mem > Did you forget to use 'sudo .. ?' > > Does anyone know how I can work around this? > Thanks, > Eibhlin > > > > _______________________________________________ > 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] Running an mpi program that needs to access /dev/mem
by Jeff Hammond 13 Jun '13

13 Jun '13

Just su to root instead of using sudo. Jeff On Thu, Jun 13, 2013 at 6:56 AM, Lee, Eibhlin <eibhlin.lee10(a)imperial.ac.uk> wrote: > Hello all, > > I am trying to use two raspberry-pi to sample and then process some data. > The first process samples while the second processes and vice versa. To do > this I use gpio and also mpich-3.0.4 with the process manager smpd. I have > successfully run cpi on both machines (from the master machine). I have also > managed to run a similar program but without the MPI, this involved > compiling with gcc and when running putting sudo in front of the binary > file. > > When I combine these two processes I get various error messages. > For input: > mpiexec -phrase cat -machinefile machinefile -n 2 ~/main > the error is: > Can't open /dev/mem > Did you forget to use 'sudo .. ?' > > For input: > sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main > the error is: > sudo: mpiexec: Command not found > > I therefore put mpiexec into /usr/bin > > now for input: > sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main > the error is: > Can't open /dev/mem > Did you forget to use 'sudo .. ?' > > Does anyone know how I can work around this? > Thanks, > Eibhlin > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond ALCF docs: http://www.alcf.anl.gov/user-guides

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Running an mpi program that needs to access /dev/mem
by Lee, Eibhlin 13 Jun '13

13 Jun '13

Hello all, I am trying to use two raspberry-pi to sample and then process some data. The first process samples while the second processes and vice versa. To do this I use gpio and also mpich-3.0.4 with the process manager smpd. I have successfully run cpi on both machines (from the master machine). I have also managed to run a similar program but without the MPI, this involved compiling with gcc and when running putting sudo in front of the binary file. When I combine these two processes I get various error messages. For input: mpiexec -phrase cat -machinefile machinefile -n 2 ~/main the error is: Can't open /dev/mem Did you forget to use 'sudo .. ?' For input: sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main the error is: sudo: mpiexec: Command not found I therefore put mpiexec into /usr/bin now for input: sudo mpiexec -phrase cat -machinefile machinefile -n 2 ~/main the error is: Can't open /dev/mem Did you forget to use 'sudo .. ?' Does anyone know how I can work around this? Thanks, Eibhlin

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Re: [mpich-discuss] Issue on compiling MPICH 3.0.4 with intel compiler on scientific linux
by Zheng Li 12 Jun '13

12 Jun '13

Thank you for comment. Regards, Lee 2013/6/12 Jeff Hammond <jhammond(a)alcf.anl.gov> > A large fraction of compile warnings are for innocuous aspects of the > code. It's appropriate for developers to look at warnings carefully > to ensure that they aren't indicative of problems, but users are > better off just running the test suite to determine if the build is > successful or not. In your case, 797/797 is a very good indication of > a proper build of MPICH. > > Best, > > Jeff > > On Wed, Jun 12, 2013 at 9:20 AM, Zheng Li <seraphzl(a)gmail.com> wrote: > > I did the 'make testing' according to the README in the > mpich-3.0.4.tar.gz > > file. All 797 tests passed, and the log files were attached. Yes, it > seems > > that the build was ok in spite of many warnings in the 'make' step. I > will > > run the cpi example further to test it. Thank you for your help. > > > > 2013/6/12 Rajeev Thakur <thakur(a)mcs.anl.gov> > >> > >> The build seems to have completed. Can you run the example programs? Try > >> running the cpi example in the examples directory. > >> > >> > >> On Jun 12, 2013, at 1:15 AM, Zheng Li wrote: > >> > >> > Dear All, > >> > > >> > I tried to compile the MPICH 3.0.4 with Intel C/C++/Fortran compiler > >> > 13.1.1 on scientific linux 6.4 x64 platform. The building steps were > as > >> > follows: > >> > > >> > export CC=icc CXX=icpc CPP='icc -E' CXXCPP='icpc -E' F77=ifort > FC=ifort > >> > CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' CXXFLAGS='-O3 > -xHost -ip > >> > -no-prec-div -static-intel' FFLAGS='-O3 -xHost -ip -no-prec-div > >> > -static-intel' > >> > configure --prefix=/home/sl/mpich-3.0.4 --disable-fast 2>&1 | tee > c.log > >> > make 2>&1 | tee m.log > >> > make install 2>&1 | tee mi.log > >> > > >> > The terminal reported many warning of pragma during 'make', such like > >> > the following: > >> > > >> > ../src/binding/f77/fdebug.c(22): warning #20: identifier > >> > "MPIR_IS_BOTTOM" is undefined > >> > #pragma weak MPIR_IS_BOTTOM = mpir_is_bottom_ > >> > ^ > >> > > >> > The log files were attached. How can I resolve this issue? Thanks in > >> > advance. > >> > > >> > > >> > > <c.log><config.log><m.log><mi.log>_______________________________________________ > >> > 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 > > > > -- > Jeff Hammond > Argonne Leadership Computing Facility > University of Chicago Computation Institute > jhammond(a)alcf.anl.gov / (630) 252-5381 > http://www.linkedin.com/in/jeffhammond > https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond > ALCF docs: http://www.alcf.anl.gov/user-guides > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > <seraphzl(a)gmail.com>

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Re: [mpich-discuss] Issue on compiling MPICH 3.0.4 with intel compiler on scientific linux
by Jeff Hammond 12 Jun '13

12 Jun '13

A large fraction of compile warnings are for innocuous aspects of the code. It's appropriate for developers to look at warnings carefully to ensure that they aren't indicative of problems, but users are better off just running the test suite to determine if the build is successful or not. In your case, 797/797 is a very good indication of a proper build of MPICH. Best, Jeff On Wed, Jun 12, 2013 at 9:20 AM, Zheng Li <seraphzl(a)gmail.com> wrote: > I did the 'make testing' according to the README in the mpich-3.0.4.tar.gz > file. All 797 tests passed, and the log files were attached. Yes, it seems > that the build was ok in spite of many warnings in the 'make' step. I will > run the cpi example further to test it. Thank you for your help. > > 2013/6/12 Rajeev Thakur <thakur(a)mcs.anl.gov> >> >> The build seems to have completed. Can you run the example programs? Try >> running the cpi example in the examples directory. >> >> >> On Jun 12, 2013, at 1:15 AM, Zheng Li wrote: >> >> > Dear All, >> > >> > I tried to compile the MPICH 3.0.4 with Intel C/C++/Fortran compiler >> > 13.1.1 on scientific linux 6.4 x64 platform. The building steps were as >> > follows: >> > >> > export CC=icc CXX=icpc CPP='icc -E' CXXCPP='icpc -E' F77=ifort FC=ifort >> > CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' CXXFLAGS='-O3 -xHost -ip >> > -no-prec-div -static-intel' FFLAGS='-O3 -xHost -ip -no-prec-div >> > -static-intel' >> > configure --prefix=/home/sl/mpich-3.0.4 --disable-fast 2>&1 | tee c.log >> > make 2>&1 | tee m.log >> > make install 2>&1 | tee mi.log >> > >> > The terminal reported many warning of pragma during 'make', such like >> > the following: >> > >> > ../src/binding/f77/fdebug.c(22): warning #20: identifier >> > "MPIR_IS_BOTTOM" is undefined >> > #pragma weak MPIR_IS_BOTTOM = mpir_is_bottom_ >> > ^ >> > >> > The log files were attached. How can I resolve this issue? Thanks in >> > advance. >> > >> > >> > <c.log><config.log><m.log><mi.log>_______________________________________________ >> > 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 > > > > > -- > Dr. Zheng Li > Research Assistant > State Key Laboratory of Environmental Aquatic Chemistry > Research Center for Eco-Environmental Sciences > Chinese Academy of Sciences > P. O. Box 2871, Beijing, 100085 China > seraphzl(a)gmail.com > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss -- Jeff Hammond Argonne Leadership Computing Facility University of Chicago Computation Institute jhammond(a)alcf.anl.gov / (630) 252-5381 http://www.linkedin.com/in/jeffhammond https://wiki.alcf.anl.gov/parts/index.php/User:Jhammond ALCF docs: http://www.alcf.anl.gov/user-guides

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Re: [mpich-discuss] Issue on compiling MPICH 3.0.4 with intel compiler on scientific linux
by Zheng Li 12 Jun '13

12 Jun '13

I did the 'make testing' according to the README in the mpich-3.0.4.tar.gz file. All 797 tests passed, and the log files were attached. Yes, it seems that the build was ok in spite of many warnings in the 'make' step. I will run the cpi example further to test it. Thank you for your help. 2013/6/12 Rajeev Thakur <thakur(a)mcs.anl.gov> > The build seems to have completed. Can you run the example programs? Try > running the cpi example in the examples directory. > > > On Jun 12, 2013, at 1:15 AM, Zheng Li wrote: > > > Dear All, > > > > I tried to compile the MPICH 3.0.4 with Intel C/C++/Fortran compiler > 13.1.1 on scientific linux 6.4 x64 platform. The building steps were as > follows: > > > > export CC=icc CXX=icpc CPP='icc -E' CXXCPP='icpc -E' F77=ifort FC=ifort > CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' CXXFLAGS='-O3 -xHost -ip > -no-prec-div -static-intel' FFLAGS='-O3 -xHost -ip -no-prec-div > -static-intel' > > configure --prefix=/home/sl/mpich-3.0.4 --disable-fast 2>&1 | tee c.log > > make 2>&1 | tee m.log > > make install 2>&1 | tee mi.log > > > > The terminal reported many warning of pragma during 'make', such like > the following: > > > > ../src/binding/f77/fdebug.c(22): warning #20: identifier > "MPIR_IS_BOTTOM" is undefined > > #pragma weak MPIR_IS_BOTTOM = mpir_is_bottom_ > > ^ > > > > The log files were attached. How can I resolve this issue? Thanks in > advance. > > > > > <c.log><config.log><m.log><mi.log>_______________________________________________ > > 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 > -- Dr. Zheng Li Research Assistant State Key Laboratory of Environmental Aquatic Chemistry Research Center for Eco-Environmental Sciences Chinese Academy of Sciences P. O. Box 2871, Beijing, 100085 China seraphzl(a)gmail.com

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Re: [mpich-discuss] Issue on compiling MPICH 3.0.4 with intel compiler on scientific linux
by Rajeev Thakur 12 Jun '13

12 Jun '13

The build seems to have completed. Can you run the example programs? Try running the cpi example in the examples directory. On Jun 12, 2013, at 1:15 AM, Zheng Li wrote: > Dear All, > > I tried to compile the MPICH 3.0.4 with Intel C/C++/Fortran compiler 13.1.1 on scientific linux 6.4 x64 platform. The building steps were as follows: > > export CC=icc CXX=icpc CPP='icc -E' CXXCPP='icpc -E' F77=ifort FC=ifort CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' > configure --prefix=/home/sl/mpich-3.0.4 --disable-fast 2>&1 | tee c.log > make 2>&1 | tee m.log > make install 2>&1 | tee mi.log > > The terminal reported many warning of pragma during 'make', such like the following: > > ../src/binding/f77/fdebug.c(22): warning #20: identifier "MPIR_IS_BOTTOM" is undefined > #pragma weak MPIR_IS_BOTTOM = mpir_is_bottom_ > ^ > > The log files were attached. How can I resolve this issue? Thanks in advance. > > <c.log><config.log><m.log><mi.log>_______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss

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Issue on compiling MPICH 3.0.4 with intel compiler on scientific linux
by Zheng Li 12 Jun '13

12 Jun '13

Dear All, I tried to compile the MPICH 3.0.4 with Intel C/C++/Fortran compiler 13.1.1 on scientific linux 6.4 x64 platform. The building steps were as follows: export CC=icc CXX=icpc CPP='icc -E' CXXCPP='icpc -E' F77=ifort FC=ifort CFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' CXXFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' FFLAGS='-O3 -xHost -ip -no-prec-div -static-intel' configure --prefix=/home/sl/mpich-3.0.4 --disable-fast 2>&1 | tee c.log make 2>&1 | tee m.log make install 2>&1 | tee mi.log The terminal reported many warning of pragma during 'make', such like the following: ../src/binding/f77/fdebug.c(22): warning #20: identifier "MPIR_IS_BOTTOM" is undefined #pragma weak MPIR_IS_BOTTOM = mpir_is_bottom_ ^ The log files were attached. How can I resolve this issue? Thanks in advance. <seraphzl(a)gmail.com>

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