[OMPI users] open-mpi error
Hello, i have some problem with mpi, i looked in the FAQ and google already but i couldnt find a solution. To build mpi i used this: shell$ ./configure --prefix=/opt/mpirun <...lots of output...> shell$ make all install Worked fine so far. I am using dlpoly, and this makefile: $(MAKE) LD="mpif90 -o" LDFLAGS="-O3" \ FC="mpif90 -c" FCFLAGS="-O3" \ EX=$(EX) BINROOT=$(BINROOT) $(TYPE) This worked fine too, the problem occurs when i want to run a job with mpiexec -n 4 ./DLPOLY.Z or mpirun -n 4 ./DLPOLY.z I get this error: -- [linux-6wa6:02927] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543 markus@linux-6wa6:/media/808CCB178CCB069E/MD Simulations/Test Simu1> sudo mpiexec -n 4 ./DLPOLY.Z [linux-6wa6:03731] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_base_select failed --> Returned value Not found (-13) instead of ORTE_SUCCESS -- [linux-6wa6:03731] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543 Some Informations: I use Open MPI 1.4.4, Suse 64bit, AMD quadcore make check gives: make: *** No rule to make target `check'. Stop. I attached the ompi_info. Thx alot for your help, regards, Markus markus@linux-6wa6:/media/808CCB178CCB069E/MD Simulations/Test Simu1> ompi_info --all Package: Open MPI abuild@build08 Distribution Open MPI: 1.4.3 Open MPI SVN revision: r23834 Open MPI release date: Oct 05, 2010 Open RTE: 1.4.3 Open RTE SVN revision: r23834 Open RTE release date: Oct 05, 2010 OPAL: 1.4.3 OPAL SVN revision: r23834 OPAL release date: Oct 05, 2010 Ident string: 1.4.3 MCA backtrace: execinfo (MCA v2.0, API v2.0, Component v1.4.3) MCA memory: ptmalloc2 (MCA v2.0, API v2.0, Component v1.4.3) MCA timer: linux (MCA v2.0, API v2.0, Component v1.4.3) MCA installdirs: env (MCA v2.0, API v2.0, Component v1.4.3) MCA installdirs: config (MCA v2.0, API v2.0, Component v1.4.3) Prefix: /usr/lib64/mpi/gcc/openmpi Exec_prefix: /usr/lib64/mpi/gcc/openmpi Bindir: /usr/lib64/mpi/gcc/openmpi/bin Sbindir: /usr/lib64/mpi/gcc/openmpi/sbin Libdir: /usr/lib64/mpi/gcc/openmpi/lib64 Incdir: /usr/lib64/mpi/gcc/openmpi/include Mandir: /usr/lib64/mpi/gcc/openmpi/share/man Pkglibdir: /usr/lib64/mpi/gcc/openmpi/lib64/openmpi Libexecdir: /usr/lib64/mpi/gcc/openmpi/lib Datarootdir: /usr/lib64/mpi/gcc/openmpi/share Datadir: /usr/lib64/mpi/gcc/openmpi/share Sysconfdir: /etc Sharedstatedir: /usr/lib64/mpi/gcc/openmpi/com Localstatedir: /var Infodir: /usr/lib64/mpi/gcc/openmpi/share/info Pkgdatadir: /usr/lib64/mpi/gcc/openmpi/share/openmpi Pkglibdir: /usr/lib64/mpi/gcc/openmpi/lib64/openmpi Pkgincludedir: /usr/lib64/mpi/gcc/openmpi/include/openmpi Configured architecture: x86_64-suse-linux-gnu Configure host: build08 Configured by: abuild Configured on: Sat Oct 29 15:50:22 UTC 2011 Configure host: build08 Built by: abuild Built on: Sat Oct 29 16:04:18 UTC 2011 Built host: build08 C bindings: yes C++ bindings: yes Fortran77 bindings: yes (all) Fortran90 bindings: yes Fortran90 bindings size: small C compiler: gcc C compiler absolute: /usr/bin/gcc C char size: 1 C bool size: 1 C short size: 2 C int size: 4 C long size: 8 C float size: 4 C double size: 8 C pointer size: 8 C char align: 1 C bool align: 1 C int align: 4 C float align: 4 C double align: 8 C++ compiler: g++ C++ compiler absolute: /usr/bin/g++ Fortran77 compiler: gfortran Fortran77 compiler abs: /usr/bin/gfortran Fortran90 compiler: gfortran Fortran90 compiler abs: /usr/bin/gfortran Fort integer size: 4 Fort logical size: 4 Fort logical value true: 1 Fort have integer1: yes Fort have integ
Re: [OMPI users] open-mpi error
On 11/24/2011 10:08 PM, MM wrote: Hi I get the same error while linking against home built 1.5.4 openmpi libs on win32. I didn't get this error against the prebuilt libs. I see you use Suse. There probably is a openmpi.rpm or openmpi.dpkg already available for Suse which contains the libraries and you could link against those and that may work MM -Original Message- From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Markus Stiller Sent: 24 November 2011 20:41 To: us...@open-mpi.org Subject: [OMPI users] open-mpi error Hello, i have some problem with mpi, i looked in the FAQ and google already but i couldnt find a solution. To build mpi i used this: shell$ ./configure --prefix=/opt/mpirun <...lots of output...> shell$ make all install Worked fine so far. I am using dlpoly, and this makefile: $(MAKE) LD="mpif90 -o" LDFLAGS="-O3" \ FC="mpif90 -c" FCFLAGS="-O3" \ EX=$(EX) BINROOT=$(BINROOT) $(TYPE) This worked fine too, the problem occurs when i want to run a job with mpiexec -n 4 ./DLPOLY.Z or mpirun -n 4 ./DLPOLY.z I get this error: -- [linux-6wa6:02927] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543 markus@linux-6wa6:/media/808CCB178CCB069E/MD Simulations/Test Simu1> sudo mpiexec -n 4 ./DLPOLY.Z [linux-6wa6:03731] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_base_select failed --> Returned value Not found (-13) instead of ORTE_SUCCESS -- [linux-6wa6:03731] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543 Some Informations: I use Open MPI 1.4.4, Suse 64bit, AMD quadcore make check gives: make: *** No rule to make target `check'. Stop. I attached the ompi_info. Thx alot for your help, regards, Markus ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users Hi, thx for your answer. When i try this (with mpich) i get problems with dl_poly itself: /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: cannot find -lmpi_f90 /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: cannot find -lmpi_f77 /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: cannot find -lmpi /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: cannot find -lopen-rte /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../x86_64-suse-linux/bin/ld: cannot find -lopen-pal I do not really know how to get rid of this either ^^
Re: [OMPI users] open-mpi error
On 11/24/2011 10:08 PM, MM wrote: Hi I get the same error while linking against home built 1.5.4 openmpi libs on win32. I didn't get this error against the prebuilt libs. I see you use Suse. There probably is a openmpi.rpm or openmpi.dpkg already available for Suse which contains the libraries and you could link against those and that may work MM -Original Message- From: users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Markus Stiller Sent: 24 November 2011 20:41 To: us...@open-mpi.org Subject: [OMPI users] open-mpi error Hello, i have some problem with mpi, i looked in the FAQ and google already but i couldnt find a solution. To build mpi i used this: shell$ ./configure --prefix=/opt/mpirun <...lots of output...> shell$ make all install Worked fine so far. I am using dlpoly, and this makefile: $(MAKE) LD="mpif90 -o" LDFLAGS="-O3" \ FC="mpif90 -c" FCFLAGS="-O3" \ EX=$(EX) BINROOT=$(BINROOT) $(TYPE) This worked fine too, the problem occurs when i want to run a job with mpiexec -n 4 ./DLPOLY.Z or mpirun -n 4 ./DLPOLY.z I get this error: -- [linux-6wa6:02927] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543 markus@linux-6wa6:/media/808CCB178CCB069E/MD Simulations/Test Simu1> sudo mpiexec -n 4 ./DLPOLY.Z [linux-6wa6:03731] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_base_select failed --> Returned value Not found (-13) instead of ORTE_SUCCESS -- [linux-6wa6:03731] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543 Some Informations: I use Open MPI 1.4.4, Suse 64bit, AMD quadcore make check gives: make: *** No rule to make target `check'. Stop. I attached the ompi_info. Thx alot for your help, regards, Markus ___ users mailing list us...@open-mpi.org http://www.open-mpi.org/mailman/listinfo.cgi/users Now i made open mpi new, but now im ggetting stuff like this: .. /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `lam_ssi_base_param_find' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `asc_parse' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `lam_ssi_base_param_register_string' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `lam_ssi_base_param_register_int' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `lampanic' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `lam_thread_self' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `lam_debug_close' /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_CONVERSION_FN_NULL' /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_read_at_all' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `sfh_sock_set_buf_size' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `blktype' /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_preallocate' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `ao_init' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `lam_mutex_destroy' /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_iread_shared' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `al_init' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `stoi' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `lam_ssi_base_hostmap' /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_FORTRAN_ERRCODES_IGNORE' /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_File_close' /usr/lib64/gcc/x86_64-suse-linux/4.6/../../../../lib64/libmpi.so: undefined reference to `al_next' /usr/local/lib64/libmpi_f77.so: undefined reference to `MPI_Register_datarep' /usr/loca
Re: [OMPI users] open-mpi error
Hi Castain, You have some major problems with confused installations of MPIs. First, you cannot compile an application against>MPICH and expect to run it with OMPI - the two are not binary compatible. You need to compile against the MPI>installation you intend to run against. I did this, sry i didnt tell this. I tried mpich and openmpi, and of course for each case i compiled againt mpich and opem mpi Second, your errors appear to be because you are not pointing your library path at the OMPI installation, and so the>libraries are not being found. You need to set LD_LIBRARY_PATH to include the path to where you installed OMPI.>Based on the configure line you give, that would mean ensuring that /opt/mpirun/lib was in that envar. Likewise,>/opt/mpirun/bin needs to be in your PATH. hmmi installed openmpi in the std location, changed the variables to this and this works now But now i have the same problem again (the problem why i wrote u in the first place): markus@linux-6wa6:/media/808CCB178CCB069E/MD Simulations/Test Simu1> sudo mpirun -n 4 ./DLPOLY.Z root's password: [linux-6wa6:05565] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; here's some additional information (which may only be relevant to an Open MPI developer): orte_ess_base_select failed --> Returned value Not found (-13) instead of ORTE_SUCCESS -- [linux-6wa6:05565] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543 What can i do with this? Thx, Markus On 11/25/2011 03:42 AM, Ralph Castain wrote: Hi Markus You have some major problems with confused installations of MPIs. First, you cannot compile an application against MPICH and expect to run it with OMPI - the two are not binary compatible. You need to compile against the MPI installation you intend to run against. Second, your errors appear to be because you are not pointing your library path at the OMPI installation, and so the libraries are not being found. You need to set LD_LIBRARY_PATH to include the path to where you installed OMPI. Based on the configure line you give, that would mean ensuring that /opt/mpirun/lib was in that envar. Likewise, /opt/mpirun/bin needs to be in your PATH. Once you have those correctly set, and build your app against the appropriate mpicc, you should be able to run. BTW: your last message indicates that you built against an old LAM MPI, so you appear to have some pretty old software laying around. Perhaps cleaning out some of the old MPI installations would help. On Nov 24, 2011, at 4:32 PM, Markus Stiller wrote: On 11/24/2011 10:08 PM, MM wrote: Hi I get the same error while linking against home built 1.5.4 openmpi libs on win32. I didn't get this error against the prebuilt libs. I see you use Suse. There probably is a openmpi.rpm or openmpi.dpkg already available for Suse which contains the libraries and you could link against those and that may work MM -Original Message- From:users-boun...@open-mpi.org [mailto:users-boun...@open-mpi.org] On Behalf Of Markus Stiller Sent: 24 November 2011 20:41 To:us...@open-mpi.org Subject: [OMPI users] open-mpi error Hello, i have some problem with mpi, i looked in the FAQ and google already but i couldnt find a solution. To build mpi i used this: shell$ ./configure --prefix=/opt/mpirun <...lots of output...> shell$ make all install Worked fine so far. I am using dlpoly, and this makefile: $(MAKE) LD="mpif90 -o" LDFLAGS="-O3" \ FC="mpif90 -c" FCFLAGS="-O3" \ EX=$(EX) BINROOT=$(BINROOT) $(TYPE) This worked fine too, the problem occurs when i want to run a job with mpiexec -n 4 ./DLPOLY.Z or mpirun -n 4 ./DLPOLY.z I get this error: -- [linux-6wa6:02927] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file orterun.c at line 543 markus@linux-6wa6:/media/808CCB178CCB069E/MD Simulations/Test Simu1> sudo mpiexec -n 4 ./DLPOLY.Z [linux-6wa6:03731] [[INVALID],INVALID] ORTE_ERROR_LOG: Not found in file runtime/orte_init.c at line 125 -- It looks like orte_init failed for some reason; your parallel process is likely to abort. There are many reasons that a parallel process can fail during orte_init; some of which are due to configuration or environment problems. This failure appears to be an internal failure; he
