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

Re: [mpich-discuss] libmpi.so.12 error
by Sophie Norman 09 Sep '14

09 Sep '14

Sure Sangmin, here you go $ mpiexec -n 4 -machinefile /home/pi/mpi_testing/machinefile which mpiexec /usr/bin/mpiexec /usr/bin/mpiexec /usr/bin/mpiexec /usr/bin/mpiexec Sophie On 9 September 2014 13:27, Seo, Sangmin <sseo(a)anl.gov> wrote: > To verify the path to mpiexec on nodes, can you try the following? > > mpiexec -n 4 -machinefile /home/pi/mpi_testing/__machinefile which > mpiexec > > > — Sangmin > > > On Sep 9, 2014, at 6:37 AM, Sophie Norman <sophie.norman(a)gmail.com> > wrote: > > I've looked and there's definitely no OpenMPI installation, there is > however a Python-mpi4py installation, could that be causing the problem? > > On 9 September 2014 12:08, Kenneth Raffenetti <raffenet(a)mcs.anl.gov> > wrote: > >> That looks like an error message from OpenMPI's mpiexec. That is surely >> part of the problem here. Do you have an OpenMPI installation somewhere >> that may be conflicting with your MPICH? One solution would be to make sure >> that the path to MPICH's mpiexec is first in your environment. >> >> Ken >> >> On 09/09/2014 05:31 PM, Sophie Norman wrote: >> >>> Hi Ken >>> >>> When I run that code I get the following error >>> >>> ------------------------------------------------------------ >>> -------------- >>> mpiexec was unable to launch the specified application as it could not >>> find an executable: >>> >>> Executable: -l >>> Node: raspberrypi >>> >>> while attempting to start process rank 0. >>> ------------------------------------------------------------ >>> -------------- >>> >>> Sophie >>> >>> On 9 September 2014 02:07, Kenneth Raffenetti <raffenet(a)mcs.anl.gov >>> <mailto:[email protected]>> wrote: >>> >>> Let's try to verify that the library is properly located on all the >>> nodes you are running. We can do a simple test with mpiexec. Try >>> running: >>> >>> mpiexec -n 4 -machinefile /home/pi/mpi_testing/____machinefile -l >>> ls /home/rpimpi/mpich3-install/__lib/libmpi.so.12 >>> >>> Ken >>> >>> On 09/08/2014 07:03 PM, Sophie Norman wrote: >>> >>> Hi Ken, >>> Yes I used mpicc to build the binary >>> >>> the oputput of mpicc -show is >>> >>> gcc -I/home/rpimpi/mpich3-install/__include >>> -L/home/rpimpi/mpich3-install/__lib -Wl,-rpath >>> -Wl,/home/rpimpi/mpich3-__install/lib -Wl,--enable-new-dtags >>> -lmpi -lrt >>> -lpthread >>> >>> >>> Sophie >>> >>> On 9 September 2014 00:48, Kenneth Raffenetti >>> <raffenet(a)mcs.anl.gov <mailto:[email protected]> >>> <mailto:[email protected] <mailto:[email protected]>>> >>> wrote: >>> >>> Did you use mpicc to build your binary? What is the output >>> of 'mpicc >>> -show'. The compile wrappers should encode an RPATH tag in >>> your >>> program so that setting an LD_LIBRARY_PATH to find >>> libmpi.so is >>> unncessary. >>> >>> Ken >>> >>> >>> On 09/08/2014 06:44 PM, Sophie Norman wrote: >>> >>> Hi, >>> >>> When running NAS parallel benchmarks using 4 Raspberry >>> Pi nodes each >>> running MPICH-3.1.2 I get the following error when I >>> try to run the >>> integer sort benchmark >>> >>> ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile >>> /home/pi/mpi_testing/____machinefile ./is.S.4 >>> >>> >>> NAS Parallel Benchmarks 3.3 -- IS Benchmark >>> >>> Size: 65536 (class S) >>> Iterations: 10 >>> Number of processes: 1 >>> >>> ERROR: compiled for 4 processes >>> Number of active processes: 1 >>> Exiting program! >>> >>> ./is.S.4: error while loading shared libraries: >>> libmpi.so.12: cannot >>> open shared object file: No such file or directory >>> ./is.S.4: error while loading shared libraries: >>> libmpi.so.12: cannot >>> open shared object file: No such file or directory >>> ./is.S.4: error while loading shared libraries: >>> libmpi.so.12: cannot >>> open shared object file: No such file or directory >>> >>> >>> >>> I have tried >>> export >>> >>> LD_LIBRARY_PATH=$LD_LIBRARY_____PATH:/home/rpimpi/mpich3-___ >>> _install/lib >>> on each of the nodes, and each node works individually >>> when run with >>> the file ./is.S.1 >>> >>> $ldd ./is.S.4 give the following output for the master >>> node >>> >>> /usr/lib/arm-linux-gnueabihf/____libcofi_rpi.so >>> (0xb6edf000) >>> libmpi.so.12 => >>> /home/rpimpi/mpich3-install/____lib/libmpi.so.12 >>> (0xb6ca3000) >>> libc.so.6 => /lib/arm-linux-gnueabihf/libc.____so.6 >>> (0xb6b68000) >>> librt.so.1 => /lib/arm-linux-gnueabihf/____librt.so.1 >>> (0xb6b59000) >>> libpthread.so.0 => >>> /lib/arm-linux-gnueabihf/____libpthread.so.0 >>> (0xb6b3a000) >>> libgfortran.so.3 => >>> /usr/lib/arm-linux-gnueabihf/____libgfortran.so.3 >>> (0xb6a93000) >>> libm.so.6 => /lib/arm-linux-gnueabihf/libm.____so.6 >>> (0xb6a22000) >>> libgcc_s.so.1 => /lib/arm-linux-gnueabihf/____ >>> libgcc_s.so.1 >>> (0xb69fa000) >>> /lib/ld-linux-armhf.so.3 (0xb6eed000) >>> >>> >>> please help >>> >>> Thanks >>> >>> Sophie >>> >>> >>> ___________________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> <mailto:[email protected]> <mailto:[email protected] >>> <mailto:[email protected]>> >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/____mailman/listinfo/discuss >>> <https://lists.mpich.org/__mailman/listinfo/discuss> >>> <https://lists.mpich.org/__mailman/listinfo/discuss >>> <https://lists.mpich.org/mailman/listinfo/discuss>> >>> >>> ___________________________________________________ >>> discuss mailing list discuss(a)mpich.org >>> <mailto:[email protected]> <mailto:[email protected] >>> <mailto:[email protected]>> >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/____mailman/listinfo/discuss >>> <https://lists.mpich.org/__mailman/listinfo/discuss> >>> <https://lists.mpich.org/__mailman/listinfo/discuss >>> <https://lists.mpich.org/mailman/listinfo/discuss>> >>> >>> >>> >>> >>> _________________________________________________ >>> discuss mailing list discuss(a)mpich.org <mailto:[email protected] >>> > >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/__mailman/listinfo/discuss >>> <https://lists.mpich.org/mailman/listinfo/discuss> >>> >>> _________________________________________________ >>> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >>> To manage subscription options or unsubscribe: >>> https://lists.mpich.org/__mailman/listinfo/discuss >>> <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 >> > > _______________________________________________ > 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] libmpi.so.12 error
by Seo, Sangmin 09 Sep '14

09 Sep '14

To verify the path to mpiexec on nodes, can you try the following? mpiexec -n 4 -machinefile /home/pi/mpi_testing/__machinefile which mpiexec — Sangmin On Sep 9, 2014, at 6:37 AM, Sophie Norman <sophie.norman(a)gmail.com<mailto:[email protected]>> wrote: I've looked and there's definitely no OpenMPI installation, there is however a Python-mpi4py installation, could that be causing the problem? On 9 September 2014 12:08, Kenneth Raffenetti <raffenet(a)mcs.anl.gov<mailto:[email protected]>> wrote: That looks like an error message from OpenMPI's mpiexec. That is surely part of the problem here. Do you have an OpenMPI installation somewhere that may be conflicting with your MPICH? One solution would be to make sure that the path to MPICH's mpiexec is first in your environment. Ken On 09/09/2014 05:31 PM, Sophie Norman wrote: Hi Ken When I run that code I get the following error -------------------------------------------------------------------------- mpiexec was unable to launch the specified application as it could not find an executable: Executable: -l Node: raspberrypi while attempting to start process rank 0. -------------------------------------------------------------------------- Sophie On 9 September 2014 02:07, Kenneth Raffenetti <raffenet(a)mcs.anl.gov<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>>> wrote: Let's try to verify that the library is properly located on all the nodes you are running. We can do a simple test with mpiexec. Try running: mpiexec -n 4 -machinefile /home/pi/mpi_testing/____machinefile -l ls /home/rpimpi/mpich3-install/__lib/libmpi.so.12 Ken On 09/08/2014 07:03 PM, Sophie Norman wrote: Hi Ken, Yes I used mpicc to build the binary the oputput of mpicc -show is gcc -I/home/rpimpi/mpich3-install/__include -L/home/rpimpi/mpich3-install/__lib -Wl,-rpath -Wl,/home/rpimpi/mpich3-__install/lib -Wl,--enable-new-dtags -lmpi -lrt -lpthread Sophie On 9 September 2014 00:48, Kenneth Raffenetti <raffenet(a)mcs.anl.gov<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> <mailto:[email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>>>> wrote: Did you use mpicc to build your binary? What is the output of 'mpicc -show'. The compile wrappers should encode an RPATH tag in your program so that setting an LD_LIBRARY_PATH to find libmpi.so is unncessary. Ken On 09/08/2014 06:44 PM, Sophie Norman wrote: Hi, When running NAS parallel benchmarks using 4 Raspberry Pi nodes each running MPICH-3.1.2 I get the following error when I try to run the integer sort benchmark ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile /home/pi/mpi_testing/____machinefile ./is.S.4 NAS Parallel Benchmarks 3.3 -- IS Benchmark Size: 65536 (class S) Iterations: 10 Number of processes: 1 ERROR: compiled for 4 processes Number of active processes: 1 Exiting program! ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory I have tried export LD_LIBRARY_PATH=$LD_LIBRARY_____PATH:/home/rpimpi/mpich3-____install/lib on each of the nodes, and each node works individually when run with the file ./is.S.1 $ldd ./is.S.4 give the following output for the master node /usr/lib/arm-linux-gnueabihf/____libcofi_rpi.so (0xb6edf000) libmpi.so.12 => /home/rpimpi/mpich3-install/____lib/libmpi.so.12 (0xb6ca3000) libc.so.6 => /lib/arm-linux-gnueabihf/libc.____so.6 (0xb6b68000) librt.so.1 => /lib/arm-linux-gnueabihf/____librt.so.1 (0xb6b59000) libpthread.so.0 => /lib/arm-linux-gnueabihf/____libpthread.so.0 (0xb6b3a000) libgfortran.so.3 => /usr/lib/arm-linux-gnueabihf/____libgfortran.so.3 (0xb6a93000) libm.so.6 => /lib/arm-linux-gnueabihf/libm.____so.6 (0xb6a22000) libgcc_s.so.1 => /lib/arm-linux-gnueabihf/____libgcc_s.so.1 (0xb69fa000) /lib/ld-linux-armhf.so.3 (0xb6eed000) please help Thanks Sophie ___________________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> <mailto:[email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>>> To manage subscription options or unsubscribe: https://lists.mpich.org/____mailman/listinfo/discuss <https://lists.mpich.org/__mailman/listinfo/discuss> <https://lists.mpich.org/__mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss>> ___________________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> <mailto:[email protected]<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>>> To manage subscription options or unsubscribe: https://lists.mpich.org/____mailman/listinfo/discuss <https://lists.mpich.org/__mailman/listinfo/discuss> <https://lists.mpich.org/__mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss>> _________________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> To manage subscription options or unsubscribe: https://lists.mpich.org/__mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss> _________________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> <mailto:[email protected]<mailto:[email protected]>> To manage subscription options or unsubscribe: https://lists.mpich.org/__mailman/listinfo/discuss <https://lists.mpich.org/mailman/listinfo/discuss> _______________________________________________ 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<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss _______________________________________________ discuss mailing list discuss(a)mpich.org<mailto:[email protected]> To manage subscription options or unsubscribe: https://lists.mpich.org/mailman/listinfo/discuss

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Re: [mpich-discuss] libmpi.so.12 error
by Sophie Norman 09 Sep '14

09 Sep '14

I've looked and there's definitely no OpenMPI installation, there is however a Python-mpi4py installation, could that be causing the problem? On 9 September 2014 12:08, Kenneth Raffenetti <raffenet(a)mcs.anl.gov> wrote: > That looks like an error message from OpenMPI's mpiexec. That is surely > part of the problem here. Do you have an OpenMPI installation somewhere > that may be conflicting with your MPICH? One solution would be to make sure > that the path to MPICH's mpiexec is first in your environment. > > Ken > > On 09/09/2014 05:31 PM, Sophie Norman wrote: > >> Hi Ken >> >> When I run that code I get the following error >> >> ------------------------------------------------------------ >> -------------- >> mpiexec was unable to launch the specified application as it could not >> find an executable: >> >> Executable: -l >> Node: raspberrypi >> >> while attempting to start process rank 0. >> ------------------------------------------------------------ >> -------------- >> >> Sophie >> >> On 9 September 2014 02:07, Kenneth Raffenetti <raffenet(a)mcs.anl.gov >> <mailto:[email protected]>> wrote: >> >> Let's try to verify that the library is properly located on all the >> nodes you are running. We can do a simple test with mpiexec. Try >> running: >> >> mpiexec -n 4 -machinefile /home/pi/mpi_testing/____machinefile -l >> ls /home/rpimpi/mpich3-install/__lib/libmpi.so.12 >> >> Ken >> >> On 09/08/2014 07:03 PM, Sophie Norman wrote: >> >> Hi Ken, >> Yes I used mpicc to build the binary >> >> the oputput of mpicc -show is >> >> gcc -I/home/rpimpi/mpich3-install/__include >> -L/home/rpimpi/mpich3-install/__lib -Wl,-rpath >> -Wl,/home/rpimpi/mpich3-__install/lib -Wl,--enable-new-dtags >> -lmpi -lrt >> -lpthread >> >> >> Sophie >> >> On 9 September 2014 00:48, Kenneth Raffenetti >> <raffenet(a)mcs.anl.gov <mailto:[email protected]> >> <mailto:[email protected] <mailto:[email protected]>>> >> wrote: >> >> Did you use mpicc to build your binary? What is the output >> of 'mpicc >> -show'. The compile wrappers should encode an RPATH tag in >> your >> program so that setting an LD_LIBRARY_PATH to find libmpi.so >> is >> unncessary. >> >> Ken >> >> >> On 09/08/2014 06:44 PM, Sophie Norman wrote: >> >> Hi, >> >> When running NAS parallel benchmarks using 4 Raspberry >> Pi nodes each >> running MPICH-3.1.2 I get the following error when I >> try to run the >> integer sort benchmark >> >> ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile >> /home/pi/mpi_testing/____machinefile ./is.S.4 >> >> >> NAS Parallel Benchmarks 3.3 -- IS Benchmark >> >> Size: 65536 (class S) >> Iterations: 10 >> Number of processes: 1 >> >> ERROR: compiled for 4 processes >> Number of active processes: 1 >> Exiting program! >> >> ./is.S.4: error while loading shared libraries: >> libmpi.so.12: cannot >> open shared object file: No such file or directory >> ./is.S.4: error while loading shared libraries: >> libmpi.so.12: cannot >> open shared object file: No such file or directory >> ./is.S.4: error while loading shared libraries: >> libmpi.so.12: cannot >> open shared object file: No such file or directory >> >> >> >> I have tried >> export >> >> LD_LIBRARY_PATH=$LD_LIBRARY_____PATH:/home/rpimpi/mpich3-___ >> _install/lib >> on each of the nodes, and each node works individually >> when run with >> the file ./is.S.1 >> >> $ldd ./is.S.4 give the following output for the master >> node >> >> /usr/lib/arm-linux-gnueabihf/____libcofi_rpi.so >> (0xb6edf000) >> libmpi.so.12 => >> /home/rpimpi/mpich3-install/____lib/libmpi.so.12 >> (0xb6ca3000) >> libc.so.6 => /lib/arm-linux-gnueabihf/libc.____so.6 >> (0xb6b68000) >> librt.so.1 => /lib/arm-linux-gnueabihf/____librt.so.1 >> (0xb6b59000) >> libpthread.so.0 => >> /lib/arm-linux-gnueabihf/____libpthread.so.0 >> (0xb6b3a000) >> libgfortran.so.3 => >> /usr/lib/arm-linux-gnueabihf/____libgfortran.so.3 >> (0xb6a93000) >> libm.so.6 => /lib/arm-linux-gnueabihf/libm.____so.6 >> (0xb6a22000) >> libgcc_s.so.1 => /lib/arm-linux-gnueabihf/____ >> libgcc_s.so.1 >> (0xb69fa000) >> /lib/ld-linux-armhf.so.3 (0xb6eed000) >> >> >> please help >> >> Thanks >> >> Sophie >> >> >> ___________________________________________________ >> discuss mailing list discuss(a)mpich.org >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/____mailman/listinfo/discuss >> <https://lists.mpich.org/__mailman/listinfo/discuss> >> <https://lists.mpich.org/__mailman/listinfo/discuss >> <https://lists.mpich.org/mailman/listinfo/discuss>> >> >> ___________________________________________________ >> discuss mailing list discuss(a)mpich.org >> <mailto:[email protected]> <mailto:[email protected] >> <mailto:[email protected]>> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/____mailman/listinfo/discuss >> <https://lists.mpich.org/__mailman/listinfo/discuss> >> <https://lists.mpich.org/__mailman/listinfo/discuss >> <https://lists.mpich.org/mailman/listinfo/discuss>> >> >> >> >> >> _________________________________________________ >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/__mailman/listinfo/discuss >> <https://lists.mpich.org/mailman/listinfo/discuss> >> >> _________________________________________________ >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/__mailman/listinfo/discuss >> <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] libmpi.so.12 error
by Kenneth Raffenetti 09 Sep '14

09 Sep '14

That looks like an error message from OpenMPI's mpiexec. That is surely part of the problem here. Do you have an OpenMPI installation somewhere that may be conflicting with your MPICH? One solution would be to make sure that the path to MPICH's mpiexec is first in your environment. Ken On 09/09/2014 05:31 PM, Sophie Norman wrote: > Hi Ken > > When I run that code I get the following error > > -------------------------------------------------------------------------- > mpiexec was unable to launch the specified application as it could not > find an executable: > > Executable: -l > Node: raspberrypi > > while attempting to start process rank 0. > -------------------------------------------------------------------------- > > Sophie > > On 9 September 2014 02:07, Kenneth Raffenetti <raffenet(a)mcs.anl.gov > <mailto:[email protected]>> wrote: > > Let's try to verify that the library is properly located on all the > nodes you are running. We can do a simple test with mpiexec. Try > running: > > mpiexec -n 4 -machinefile /home/pi/mpi_testing/____machinefile -l > ls /home/rpimpi/mpich3-install/__lib/libmpi.so.12 > > Ken > > On 09/08/2014 07:03 PM, Sophie Norman wrote: > > Hi Ken, > Yes I used mpicc to build the binary > > the oputput of mpicc -show is > > gcc -I/home/rpimpi/mpich3-install/__include > -L/home/rpimpi/mpich3-install/__lib -Wl,-rpath > -Wl,/home/rpimpi/mpich3-__install/lib -Wl,--enable-new-dtags > -lmpi -lrt > -lpthread > > > Sophie > > On 9 September 2014 00:48, Kenneth Raffenetti > <raffenet(a)mcs.anl.gov <mailto:[email protected]> > <mailto:[email protected] <mailto:[email protected]>>> wrote: > > Did you use mpicc to build your binary? What is the output > of 'mpicc > -show'. The compile wrappers should encode an RPATH tag in your > program so that setting an LD_LIBRARY_PATH to find libmpi.so is > unncessary. > > Ken > > > On 09/08/2014 06:44 PM, Sophie Norman wrote: > > Hi, > > When running NAS parallel benchmarks using 4 Raspberry > Pi nodes each > running MPICH-3.1.2 I get the following error when I > try to run the > integer sort benchmark > > ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile > /home/pi/mpi_testing/____machinefile ./is.S.4 > > > NAS Parallel Benchmarks 3.3 -- IS Benchmark > > Size: 65536 (class S) > Iterations: 10 > Number of processes: 1 > > ERROR: compiled for 4 processes > Number of active processes: 1 > Exiting program! > > ./is.S.4: error while loading shared libraries: > libmpi.so.12: cannot > open shared object file: No such file or directory > ./is.S.4: error while loading shared libraries: > libmpi.so.12: cannot > open shared object file: No such file or directory > ./is.S.4: error while loading shared libraries: > libmpi.so.12: cannot > open shared object file: No such file or directory > > > > I have tried > export > > LD_LIBRARY_PATH=$LD_LIBRARY_____PATH:/home/rpimpi/mpich3-____install/lib > on each of the nodes, and each node works individually > when run with > the file ./is.S.1 > > $ldd ./is.S.4 give the following output for the master node > > /usr/lib/arm-linux-gnueabihf/____libcofi_rpi.so > (0xb6edf000) > libmpi.so.12 => > /home/rpimpi/mpich3-install/____lib/libmpi.so.12 > (0xb6ca3000) > libc.so.6 => /lib/arm-linux-gnueabihf/libc.____so.6 > (0xb6b68000) > librt.so.1 => /lib/arm-linux-gnueabihf/____librt.so.1 > (0xb6b59000) > libpthread.so.0 => > /lib/arm-linux-gnueabihf/____libpthread.so.0 > (0xb6b3a000) > libgfortran.so.3 => > /usr/lib/arm-linux-gnueabihf/____libgfortran.so.3 > (0xb6a93000) > libm.so.6 => /lib/arm-linux-gnueabihf/libm.____so.6 > (0xb6a22000) > libgcc_s.so.1 => /lib/arm-linux-gnueabihf/____libgcc_s.so.1 > (0xb69fa000) > /lib/ld-linux-armhf.so.3 (0xb6eed000) > > > please help > > Thanks > > Sophie > > > ___________________________________________________ > discuss mailing list discuss(a)mpich.org > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>> > To manage subscription options or unsubscribe: > https://lists.mpich.org/____mailman/listinfo/discuss > <https://lists.mpich.org/__mailman/listinfo/discuss> > <https://lists.mpich.org/__mailman/listinfo/discuss > <https://lists.mpich.org/mailman/listinfo/discuss>> > > ___________________________________________________ > discuss mailing list discuss(a)mpich.org > <mailto:[email protected]> <mailto:[email protected] > <mailto:[email protected]>> > To manage subscription options or unsubscribe: > https://lists.mpich.org/____mailman/listinfo/discuss > <https://lists.mpich.org/__mailman/listinfo/discuss> > <https://lists.mpich.org/__mailman/listinfo/discuss > <https://lists.mpich.org/mailman/listinfo/discuss>> > > > > > _________________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/__mailman/listinfo/discuss > <https://lists.mpich.org/mailman/listinfo/discuss> > > _________________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/__mailman/listinfo/discuss > <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] libmpi.so.12 error
by Sophie Norman 09 Sep '14

09 Sep '14

Hi Ken When I run that code I get the following error -------------------------------------------------------------------------- mpiexec was unable to launch the specified application as it could not find an executable: Executable: -l Node: raspberrypi while attempting to start process rank 0. -------------------------------------------------------------------------- Sophie On 9 September 2014 02:07, Kenneth Raffenetti <raffenet(a)mcs.anl.gov> wrote: > Let's try to verify that the library is properly located on all the nodes > you are running. We can do a simple test with mpiexec. Try running: > > mpiexec -n 4 -machinefile /home/pi/mpi_testing/__machinefile -l ls > /home/rpimpi/mpich3-install/lib/libmpi.so.12 > > Ken > > On 09/08/2014 07:03 PM, Sophie Norman wrote: > >> Hi Ken, >> Yes I used mpicc to build the binary >> >> the oputput of mpicc -show is >> >> gcc -I/home/rpimpi/mpich3-install/include >> -L/home/rpimpi/mpich3-install/lib -Wl,-rpath >> -Wl,/home/rpimpi/mpich3-install/lib -Wl,--enable-new-dtags -lmpi -lrt >> -lpthread >> >> >> Sophie >> >> On 9 September 2014 00:48, Kenneth Raffenetti <raffenet(a)mcs.anl.gov >> <mailto:[email protected]>> wrote: >> >> Did you use mpicc to build your binary? What is the output of 'mpicc >> -show'. The compile wrappers should encode an RPATH tag in your >> program so that setting an LD_LIBRARY_PATH to find libmpi.so is >> unncessary. >> >> Ken >> >> >> On 09/08/2014 06:44 PM, Sophie Norman wrote: >> >> Hi, >> >> When running NAS parallel benchmarks using 4 Raspberry Pi nodes >> each >> running MPICH-3.1.2 I get the following error when I try to run >> the >> integer sort benchmark >> >> ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile >> /home/pi/mpi_testing/__machinefile ./is.S.4 >> >> >> NAS Parallel Benchmarks 3.3 -- IS Benchmark >> >> Size: 65536 (class S) >> Iterations: 10 >> Number of processes: 1 >> >> ERROR: compiled for 4 processes >> Number of active processes: 1 >> Exiting program! >> >> ./is.S.4: error while loading shared libraries: libmpi.so.12: >> cannot >> open shared object file: No such file or directory >> ./is.S.4: error while loading shared libraries: libmpi.so.12: >> cannot >> open shared object file: No such file or directory >> ./is.S.4: error while loading shared libraries: libmpi.so.12: >> cannot >> open shared object file: No such file or directory >> >> >> >> I have tried >> export >> LD_LIBRARY_PATH=$LD_LIBRARY___PATH:/home/rpimpi/mpich3-__ >> install/lib >> on each of the nodes, and each node works individually when run >> with >> the file ./is.S.1 >> >> $ldd ./is.S.4 give the following output for the master node >> >> /usr/lib/arm-linux-gnueabihf/__libcofi_rpi.so (0xb6edf000) >> libmpi.so.12 => /home/rpimpi/mpich3-install/__lib/libmpi.so.12 >> (0xb6ca3000) >> libc.so.6 => /lib/arm-linux-gnueabihf/libc.__so.6 (0xb6b68000) >> librt.so.1 => /lib/arm-linux-gnueabihf/__librt.so.1 (0xb6b59000) >> libpthread.so.0 => /lib/arm-linux-gnueabihf/__libpthread.so.0 >> (0xb6b3a000) >> libgfortran.so.3 => /usr/lib/arm-linux-gnueabihf/_ >> _libgfortran.so.3 >> (0xb6a93000) >> libm.so.6 => /lib/arm-linux-gnueabihf/libm.__so.6 (0xb6a22000) >> libgcc_s.so.1 => /lib/arm-linux-gnueabihf/__libgcc_s.so.1 >> (0xb69fa000) >> /lib/ld-linux-armhf.so.3 (0xb6eed000) >> >> >> please help >> >> Thanks >> >> Sophie >> >> >> _________________________________________________ >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/__mailman/listinfo/discuss >> <https://lists.mpich.org/mailman/listinfo/discuss> >> >> _________________________________________________ >> discuss mailing list discuss(a)mpich.org <mailto:[email protected]> >> To manage subscription options or unsubscribe: >> https://lists.mpich.org/__mailman/listinfo/discuss >> <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] libmpi.so.12 error
by Jan Bierbaum 09 Sep '14

09 Sep '14

On 09.09.2014 01:44, Sophie Norman wrote: > I have tried > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/rpimpi/mpich3-install/lib > on each of the nodes, and each node works individually when run with > the file ./is.S.1 Where did you put that 'export'? Hydra/mpiexec establishes connections to all the nodes itself so any changes you do to the environment of an interactive ssh session will not apply. Try putting that 'LD_LIBRARY_PATH' line into '.profile' on each of the compute nodes so it gets executed for every session. Or just make sure that the directory structure is the same on all nodes as Kenneth suggested. Regards, Jan

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Re: [mpich-discuss] libmpi.so.12 error
by Kenneth Raffenetti 08 Sep '14

08 Sep '14

Let's try to verify that the library is properly located on all the nodes you are running. We can do a simple test with mpiexec. Try running: mpiexec -n 4 -machinefile /home/pi/mpi_testing/__machinefile -l ls /home/rpimpi/mpich3-install/lib/libmpi.so.12 Ken On 09/08/2014 07:03 PM, Sophie Norman wrote: > Hi Ken, > Yes I used mpicc to build the binary > > the oputput of mpicc -show is > > gcc -I/home/rpimpi/mpich3-install/include > -L/home/rpimpi/mpich3-install/lib -Wl,-rpath > -Wl,/home/rpimpi/mpich3-install/lib -Wl,--enable-new-dtags -lmpi -lrt > -lpthread > > > Sophie > > On 9 September 2014 00:48, Kenneth Raffenetti <raffenet(a)mcs.anl.gov > <mailto:[email protected]>> wrote: > > Did you use mpicc to build your binary? What is the output of 'mpicc > -show'. The compile wrappers should encode an RPATH tag in your > program so that setting an LD_LIBRARY_PATH to find libmpi.so is > unncessary. > > Ken > > > On 09/08/2014 06:44 PM, Sophie Norman wrote: > > Hi, > > When running NAS parallel benchmarks using 4 Raspberry Pi nodes each > running MPICH-3.1.2 I get the following error when I try to run the > integer sort benchmark > > ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile > /home/pi/mpi_testing/__machinefile ./is.S.4 > > > NAS Parallel Benchmarks 3.3 -- IS Benchmark > > Size: 65536 (class S) > Iterations: 10 > Number of processes: 1 > > ERROR: compiled for 4 processes > Number of active processes: 1 > Exiting program! > > ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot > open shared object file: No such file or directory > ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot > open shared object file: No such file or directory > ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot > open shared object file: No such file or directory > > > > I have tried > export > LD_LIBRARY_PATH=$LD_LIBRARY___PATH:/home/rpimpi/mpich3-__install/lib > on each of the nodes, and each node works individually when run with > the file ./is.S.1 > > $ldd ./is.S.4 give the following output for the master node > > /usr/lib/arm-linux-gnueabihf/__libcofi_rpi.so (0xb6edf000) > libmpi.so.12 => /home/rpimpi/mpich3-install/__lib/libmpi.so.12 > (0xb6ca3000) > libc.so.6 => /lib/arm-linux-gnueabihf/libc.__so.6 (0xb6b68000) > librt.so.1 => /lib/arm-linux-gnueabihf/__librt.so.1 (0xb6b59000) > libpthread.so.0 => /lib/arm-linux-gnueabihf/__libpthread.so.0 > (0xb6b3a000) > libgfortran.so.3 => /usr/lib/arm-linux-gnueabihf/__libgfortran.so.3 > (0xb6a93000) > libm.so.6 => /lib/arm-linux-gnueabihf/libm.__so.6 (0xb6a22000) > libgcc_s.so.1 => /lib/arm-linux-gnueabihf/__libgcc_s.so.1 > (0xb69fa000) > /lib/ld-linux-armhf.so.3 (0xb6eed000) > > > please help > > Thanks > > Sophie > > > _________________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/__mailman/listinfo/discuss > <https://lists.mpich.org/mailman/listinfo/discuss> > > _________________________________________________ > discuss mailing list discuss(a)mpich.org <mailto:[email protected]> > To manage subscription options or unsubscribe: > https://lists.mpich.org/__mailman/listinfo/discuss > <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] libmpi.so.12 error
by Sophie Norman 08 Sep '14

08 Sep '14

Hi Ken, Yes I used mpicc to build the binary the oputput of mpicc -show is gcc -I/home/rpimpi/mpich3-install/include -L/home/rpimpi/mpich3-install/lib -Wl,-rpath -Wl,/home/rpimpi/mpich3-install/lib -Wl,--enable-new-dtags -lmpi -lrt -lpthread Sophie On 9 September 2014 00:48, Kenneth Raffenetti <raffenet(a)mcs.anl.gov> wrote: > Did you use mpicc to build your binary? What is the output of 'mpicc > -show'. The compile wrappers should encode an RPATH tag in your program so > that setting an LD_LIBRARY_PATH to find libmpi.so is unncessary. > > Ken > > > On 09/08/2014 06:44 PM, Sophie Norman wrote: > >> Hi, >> >> When running NAS parallel benchmarks using 4 Raspberry Pi nodes each >> running MPICH-3.1.2 I get the following error when I try to run the >> integer sort benchmark >> >> ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile >> /home/pi/mpi_testing/machinefile ./is.S.4 >> >> >> NAS Parallel Benchmarks 3.3 -- IS Benchmark >> >> Size: 65536 (class S) >> Iterations: 10 >> Number of processes: 1 >> >> ERROR: compiled for 4 processes >> Number of active processes: 1 >> Exiting program! >> >> ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot >> open shared object file: No such file or directory >> ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot >> open shared object file: No such file or directory >> ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot >> open shared object file: No such file or directory >> >> >> >> I have tried >> export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/rpimpi/mpich3-install/lib >> on each of the nodes, and each node works individually when run with >> the file ./is.S.1 >> >> $ldd ./is.S.4 give the following output for the master node >> >> /usr/lib/arm-linux-gnueabihf/libcofi_rpi.so (0xb6edf000) >> libmpi.so.12 => /home/rpimpi/mpich3-install/lib/libmpi.so.12 (0xb6ca3000) >> libc.so.6 => /lib/arm-linux-gnueabihf/libc.so.6 (0xb6b68000) >> librt.so.1 => /lib/arm-linux-gnueabihf/librt.so.1 (0xb6b59000) >> libpthread.so.0 => /lib/arm-linux-gnueabihf/libpthread.so.0 (0xb6b3a000) >> libgfortran.so.3 => /usr/lib/arm-linux-gnueabihf/libgfortran.so.3 >> (0xb6a93000) >> libm.so.6 => /lib/arm-linux-gnueabihf/libm.so.6 (0xb6a22000) >> libgcc_s.so.1 => /lib/arm-linux-gnueabihf/libgcc_s.so.1 (0xb69fa000) >> /lib/ld-linux-armhf.so.3 (0xb6eed000) >> >> >> please help >> >> Thanks >> >> Sophie >> >> >> _______________________________________________ >> 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] libmpi.so.12 error
by Kenneth Raffenetti 08 Sep '14

08 Sep '14

Did you use mpicc to build your binary? What is the output of 'mpicc -show'. The compile wrappers should encode an RPATH tag in your program so that setting an LD_LIBRARY_PATH to find libmpi.so is unncessary. Ken On 09/08/2014 06:44 PM, Sophie Norman wrote: > Hi, > > When running NAS parallel benchmarks using 4 Raspberry Pi nodes each > running MPICH-3.1.2 I get the following error when I try to run the > integer sort benchmark > > ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile > /home/pi/mpi_testing/machinefile ./is.S.4 > > > NAS Parallel Benchmarks 3.3 -- IS Benchmark > > Size: 65536 (class S) > Iterations: 10 > Number of processes: 1 > > ERROR: compiled for 4 processes > Number of active processes: 1 > Exiting program! > > ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot > open shared object file: No such file or directory > ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot > open shared object file: No such file or directory > ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot > open shared object file: No such file or directory > > > > I have tried > export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/rpimpi/mpich3-install/lib > on each of the nodes, and each node works individually when run with > the file ./is.S.1 > > $ldd ./is.S.4 give the following output for the master node > > /usr/lib/arm-linux-gnueabihf/libcofi_rpi.so (0xb6edf000) > libmpi.so.12 => /home/rpimpi/mpich3-install/lib/libmpi.so.12 (0xb6ca3000) > libc.so.6 => /lib/arm-linux-gnueabihf/libc.so.6 (0xb6b68000) > librt.so.1 => /lib/arm-linux-gnueabihf/librt.so.1 (0xb6b59000) > libpthread.so.0 => /lib/arm-linux-gnueabihf/libpthread.so.0 (0xb6b3a000) > libgfortran.so.3 => /usr/lib/arm-linux-gnueabihf/libgfortran.so.3 > (0xb6a93000) > libm.so.6 => /lib/arm-linux-gnueabihf/libm.so.6 (0xb6a22000) > libgcc_s.so.1 => /lib/arm-linux-gnueabihf/libgcc_s.so.1 (0xb69fa000) > /lib/ld-linux-armhf.so.3 (0xb6eed000) > > > please help > > Thanks > > Sophie > > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss >

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libmpi.so.12 error
by Sophie Norman 08 Sep '14

08 Sep '14

Hi, When running NAS parallel benchmarks using 4 Raspberry Pi nodes each running MPICH-3.1.2 I get the following error when I try to run the integer sort benchmark ~/NPB3.3/NPB3.3-MPI/bin $ mpiexec -n 4 -machinefile /home/pi/mpi_testing/machinefile ./is.S.4 NAS Parallel Benchmarks 3.3 -- IS Benchmark Size: 65536 (class S) Iterations: 10 Number of processes: 1 ERROR: compiled for 4 processes Number of active processes: 1 Exiting program! ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory ./is.S.4: error while loading shared libraries: libmpi.so.12: cannot open shared object file: No such file or directory I have tried export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/rpimpi/mpich3-install/lib on each of the nodes, and each node works individually when run with the file ./is.S.1 $ldd ./is.S.4 give the following output for the master node /usr/lib/arm-linux-gnueabihf/libcofi_rpi.so (0xb6edf000) libmpi.so.12 => /home/rpimpi/mpich3-install/lib/libmpi.so.12 (0xb6ca3000) libc.so.6 => /lib/arm-linux-gnueabihf/libc.so.6 (0xb6b68000) librt.so.1 => /lib/arm-linux-gnueabihf/librt.so.1 (0xb6b59000) libpthread.so.0 => /lib/arm-linux-gnueabihf/libpthread.so.0 (0xb6b3a000) libgfortran.so.3 => /usr/lib/arm-linux-gnueabihf/libgfortran.so.3 (0xb6a93000) libm.so.6 => /lib/arm-linux-gnueabihf/libm.so.6 (0xb6a22000) libgcc_s.so.1 => /lib/arm-linux-gnueabihf/libgcc_s.so.1 (0xb69fa000) /lib/ld-linux-armhf.so.3 (0xb6eed000) please help Thanks Sophie

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