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

Re: [mpich-discuss] Configure/make fails when given flag --with-shared-memory=sysv
by Seo, Sangmin 09 Sep '14

09 Sep '14

Hi Åsmund, Thank you for emailing us, but this email needs to go to MVAPICH team. The correct mailing list will be mvapich-discuss(a)cse.ohio-state.edu<mailto:[email protected]> in http://mvapich.cse.ohio-state.edu/mailinglists/. Thanks, Sangmin On Sep 9, 2014, at 2:32 PM, Åsmund Ervik <asmund.ervik(a)ntnu.no<mailto:[email protected]>> wrote: Hello all, I'm compiling mvapich2 on an old quirky cluster where I'm not root. After having problems with shared memory using mvapich2 with plain configure/make (I had to disable shared memory for any jobs doing allreduce), I decided to try to configure/make using --with-shared-memory=sysv . This failed at the "make" step, with the following error: CC src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.lo src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c: In function 'mv2_allocate_shm_local': src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: 'O_CREAT' undeclared (first use in this function) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: (Each undeclared identifier is reported only once src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: for each function it appears in.) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: 'O_RDWR' undeclared (first use in this function) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: 'O_EXCL' undeclared (first use in this function) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c: In function 'mv2_rma_allocate_shm': src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:375: error: 'O_CREAT' undeclared (first use in this function) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:375: error: 'O_RDWR' undeclared (first use in this function) make[2]: *** [src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.lo] Error 1 The full configure command was ./configure --prefix=/home/asmunder/mvapich2-2.0 --with-ib-libpath=/cvos/shared/apps/ofed/1.3.1/lib64/ --with-ib-include=/cvos/shared/apps/ofed/1.3.1/include --with-shared-memory=sysv --enable-libpci In the end I traced this down to lines 22 and 26 in rdma_iba_1sc.c , which is an #ifdef that only includes fcntl.h (containing O_CREAT et al) when the flag _SMP_LIMIC_ is defined. Obviously this flag was not defined in my case. I removed these two lines, and now configure/make works fine. Also, in the end, I found that this flag was not necessary, and that the correct and much simpler solution was to set the environment variable MV2_SHMEM_DIR to the correct path. Regards, Åsmund _______________________________________________ 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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Configure/make fails when given flag --with-shared-memory=sysv
by Åsmund Ervik 09 Sep '14

09 Sep '14

Hello all, I'm compiling mvapich2 on an old quirky cluster where I'm not root. After having problems with shared memory using mvapich2 with plain configure/make (I had to disable shared memory for any jobs doing allreduce), I decided to try to configure/make using --with-shared-memory=sysv . This failed at the "make" step, with the following error: CC src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.lo src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c: In function 'mv2_allocate_shm_local': src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: 'O_CREAT' undeclared (first use in this function) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: (Each undeclared identifier is reported only once src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: for each function it appears in.) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: 'O_RDWR' undeclared (first use in this function) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:182: error: 'O_EXCL' undeclared (first use in this function) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c: In function 'mv2_rma_allocate_shm': src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:375: error: 'O_CREAT' undeclared (first use in this function) src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.c:375: error: 'O_RDWR' undeclared (first use in this function) make[2]: *** [src/mpid/ch3/channels/mrail/src/gen2/rdma_iba_1sc.lo] Error 1 The full configure command was ./configure --prefix=/home/asmunder/mvapich2-2.0 --with-ib-libpath=/cvos/shared/apps/ofed/1.3.1/lib64/ --with-ib-include=/cvos/shared/apps/ofed/1.3.1/include --with-shared-memory=sysv --enable-libpci In the end I traced this down to lines 22 and 26 in rdma_iba_1sc.c , which is an #ifdef that only includes fcntl.h (containing O_CREAT et al) when the flag _SMP_LIMIC_ is defined. Obviously this flag was not defined in my case. I removed these two lines, and now configure/make works fine. Also, in the end, I found that this flag was not necessary, and that the correct and much simpler solution was to set the environment variable MV2_SHMEM_DIR to the correct path. Regards, Åsmund

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Re: [mpich-discuss] Max Communicators Limit
by wesley＠wesbland.com 09 Sep '14

09 Sep '14

There is a maximum number of communicators, but it’s not exactly standardized or consistent between implementations. In MPICH, the context ID can be up to 32 bits but we reserve some of those so in the end you get something like 16 bits. In reality, you still don’t get all 65,536. Depending on how they are allocated, you’ll get some subset of that. So in the end, there’s not a good answer. Rob’s answer is probably the best. Try it until it breaks. Most people that we’ve heard running against the barrier have a problem after a few thousand. On Tue, Sep 9, 2014 at 1:19 PM, Vishwanath, Venkatram <venkat(a)anl.gov> wrote: > Hi, > There is a maximum # of communicators one can create. How can I query this limit for MPICH? Is there a standard way to query this limit across MPI implementations? > Regards, > Venkat > _______________________________________________ > 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] Max Communicators Limit
by Rob Latham 09 Sep '14

09 Sep '14

On 09/09/2014 01:19 PM, Venkat Vishwanath wrote: > There is a maximum # of communicators one can create. How can I query this limit for MPICH? Is there a standard way to query this limit across MPI implementations? > Huh. It would appear not: Cray uses an environment variable: http://docs.cray.com/books/S-2310-50/html-S-2310-50/z1026396842smg.html Intel asserts it's ~16k: - https://software.intel.com/en-us/forums/topic/279324 MPICH limit used to be 8189: - http://www.mcs.anl.gov/papers/P1621A.pdf I guess the way to query is "create until it fails" ? ==rob -- Rob Latham Mathematics and Computer Science Division Argonne National Lab, IL USA

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Max Communicators Limit
by Venkat Vishwanath 09 Sep '14

09 Sep '14

Hi, There is a maximum # of communicators one can create. How can I query this limit for MPICH? Is there a standard way to query this limit across MPI implementations? Regards, Venkat

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

09 Sep '14

On 9 September 2014 15:31, Seo, Sangmin <sseo(a)anl.gov> wrote: > export PATH=/home/rpimpi/mpich3-install/bin:$PATH > Thank you everyone, it's working great now Sophie

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Re: [mpich-discuss] libmpi.so.12 error
by Seo, Sangmin 09 Sep '14

09 Sep '14

To find /home/rpimpi/mpich3-install/bin/mpiexec first, you can set the PATH variable in your .bashrc (or .profile) file like: export PATH=/home/rpimpi/mpich3-install/bin:$PATH — Sangmin On Sep 9, 2014, at 9:21 AM, Sophie Norman <sophie.norman(a)gmail.com<mailto:[email protected]>> wrote: Oops there is a version of OpenMPI on the system that is didn't find before. Sangmin thank you, here are the two different versions $ /usr/bin/mpiexec --versionmpiexec (OpenRTE) 1.4.5 Report bugs to http://www.open-mpi.org/community/help/ $ /home/rpimpi/mpich3-install/bin/mpiexec --version HYDRA build details: Version: 3.1.2 Release Date: Mon Jul 21 16:00:21 CDT 2014 CC: gcc CXX: g++ F77: gfortran F90: gfortran Configure options: '--disable-option-checking' '--prefix=/home/rpimpi/mpich3-install' '--enable-shared' '--cache-file=/dev/null' '--srcdir=/home/pi/mpich3/mpich-3.1.2/src/pm/hydra' 'CC=gcc' 'CFLAGS= -O2' 'LDFLAGS= ' 'LIBS=-lrt -lpthread ' 'CPPFLAGS= -I/home/pi/mpich3/src/mpl/include -I/home/pi/mpich3/mpich-3.1.2/src/mpl/include -I/home/pi/mpich3/mpich-3.1.2/src/openpa/src -I/home/pi/mpich3/src/openpa/src -D_REENTRANT -I/home/pi/mpich3/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 Running the system so that it is MPICH that runs allowed the system to work as it should! so thank you all for your help. Just one last question, how can I set it so that it is the MPICH configuration that runs not the OpenMPI without having to type /home/rpimpi/mpich3-install/bin/mpiexec each time? Yours happily Sophie On 9 September 2014 15:01, Seo, Sangmin <sseo(a)anl.gov<mailto:[email protected]>> wrote: Did you install MPICH-3.1.2 to /home/rpimpi/mpich3-install/? If so and you did not specify --bindir, /usr/bin/mpiexec might be installed by a different MPI implementation. Can you try these? /usr/bin/mpiexec --version /home/rpimpi/mpich3-install/bin/mpiexec --version If they are different, can you also try to use /home/rpimpi/mpich3-install/bin/mpiexec to execute your application? — Sangmin On Sep 9, 2014, at 8:44 AM, Sophie Norman <sophie.norman(a)gmail.com<mailto:[email protected]>> wrote: 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<mailto:[email protected]>> 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<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 _______________________________________________ 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 _______________________________________________ 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 wesley＠wesbland.com 09 Sep '14

09 Sep '14

You can just set up your path in your shell config file to be /home/rpimpi/mpich3-install/bin/mpiexec. In Bash you can add: export PATH=/home/rpimpi/mpich3-install/bin/mpiexec:$PATH to your .bashrc file. Thanks, Wesley On Tue, Sep 9, 2014 at 9:21 AM, Sophie Norman <sophie.norman(a)gmail.com> wrote: > Oops there is a version of OpenMPI on the system that is didn't find before. > Sangmin thank you, here are the two different versions > $ /usr/bin/mpiexec --versionmpiexec (OpenRTE) 1.4.5 > Report bugs to http://www.open-mpi.org/community/help/ > $ /home/rpimpi/mpich3-install/bin/mpiexec --version > HYDRA build details: > Version: 3.1.2 > Release Date: Mon Jul 21 16:00:21 CDT 2014 > CC: gcc > CXX: g++ > F77: gfortran > F90: gfortran > Configure options: '--disable-option-checking' '--prefix=/home/rpimpi/mpich3-install' '--enable-shared' '--cache-file=/dev/null' '--srcdir=/home/pi/mpich3/mpich-3.1.2/src/pm/hydra' 'CC=gcc' 'CFLAGS= -O2' 'LDFLAGS= ' 'LIBS=-lrt -lpthread ' 'CPPFLAGS= -I/home/pi/mpich3/src/mpl/include -I/home/pi/mpich3/mpich-3.1.2/src/mpl/include -I/home/pi/mpich3/mpich-3.1.2/src/openpa/src -I/home/pi/mpich3/src/openpa/src -D_REENTRANT -I/home/pi/mpich3/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 > Running the system so that it is MPICH that runs allowed the system to work as it should! so thank you all for your help. > Just one last question, how can I set it so that it is the MPICH configuration that runs not the OpenMPI without having to type /home/rpimpi/mpich3-install/bin/mpiexec each time? > Yours happily > Sophie > On 9 September 2014 15:01, Seo, Sangmin <sseo(a)anl.gov<mailto:[email protected]>> wrote: > Did you install MPICH-3.1.2 to /home/rpimpi/mpich3-install/? If so and you did not specify --bindir, /usr/bin/mpiexec might be installed by a different MPI implementation. Can you try these? > /usr/bin/mpiexec --version > /home/rpimpi/mpich3-install/bin/mpiexec --version > If they are different, can you also try to use /home/rpimpi/mpich3-install/bin/mpiexec to execute your application? > — Sangmin > On Sep 9, 2014, at 8:44 AM, Sophie Norman <sophie.norman(a)gmail.com<mailto:[email protected]>> wrote: > 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<mailto:[email protected]>> 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<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 > 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Re: [mpich-discuss] libmpi.so.12 error
by Sophie Norman 09 Sep '14

09 Sep '14

Oops there is a version of OpenMPI on the system that is didn't find before. Sangmin thank you, here are the two different versions $ /usr/bin/mpiexec --versionmpiexec (OpenRTE) 1.4.5 Report bugs to http://www.open-mpi.org/community/help/ $ /home/rpimpi/mpich3-install/bin/mpiexec --version HYDRA build details: Version: 3.1.2 Release Date: Mon Jul 21 16:00:21 CDT 2014 CC: gcc CXX: g++ F77: gfortran F90: gfortran Configure options: '--disable-option-checking' '--prefix=/home/rpimpi/mpich3-install' '--enable-shared' '--cache-file=/dev/null' '--srcdir=/home/pi/mpich3/mpich-3.1.2/src/pm/hydra' 'CC=gcc' 'CFLAGS= -O2' 'LDFLAGS= ' 'LIBS=-lrt -lpthread ' 'CPPFLAGS= -I/home/pi/mpich3/src/mpl/include -I/home/pi/mpich3/mpich-3.1.2/src/mpl/include -I/home/pi/mpich3/mpich-3.1.2/src/openpa/src -I/home/pi/mpich3/src/openpa/src -D_REENTRANT -I/home/pi/mpich3/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 Running the system so that it is MPICH that runs allowed the system to work as it should! so thank you all for your help. Just one last question, how can I set it so that it is the MPICH configuration that runs not the OpenMPI without having to type /home/rpimpi/mpich3-install/bin/mpiexec each time? Yours happily Sophie On 9 September 2014 15:01, Seo, Sangmin <sseo(a)anl.gov> wrote: > Did you install MPICH-3.1.2 to /home/rpimpi/mpich3-install/? If so and > you did not specify --bindir, /usr/bin/mpiexec might be installed by a > different MPI implementation. Can you try these? > > /usr/bin/mpiexec --version > /home/rpimpi/mpich3-install/bin/mpiexec --version > > If they are different, can you also try to use > /home/rpimpi/mpich3-install/bin/mpiexec to execute your application? > > — Sangmin > > On Sep 9, 2014, at 8:44 AM, Sophie Norman <sophie.norman(a)gmail.com> > wrote: > > 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: >>>> discuss(a)mpich.org> >>>> 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 >> > > _______________________________________________ > discuss mailing list discuss(a)mpich.org > To manage subscription options or unsubscribe: > https://lists.mpich.org/mailman/listinfo/discuss > > > > _______________________________________________ > discuss mailing list 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Re: [mpich-discuss] libmpi.so.12 error
by Seo, Sangmin 09 Sep '14

09 Sep '14

Did you install MPICH-3.1.2 to /home/rpimpi/mpich3-install/? If so and you did not specify --bindir, /usr/bin/mpiexec might be installed by a different MPI implementation. Can you try these? /usr/bin/mpiexec --version /home/rpimpi/mpich3-install/bin/mpiexec --version If they are different, can you also try to use /home/rpimpi/mpich3-install/bin/mpiexec to execute your application? — Sangmin On Sep 9, 2014, at 8:44 AM, Sophie Norman <sophie.norman(a)gmail.com<mailto:[email protected]>> wrote: 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<mailto:[email protected]>> 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<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 _______________________________________________ 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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