[Wien] parallel segmentation fault
Hi Luis, You were right. The problem was in the parallel options. I had to change this library and also recompile fftw3_mpi library with the correct openmpi compiler. Regards!! Arturo El 06/02/13 14:04, Luis Ogando escribi?: Hi Arturo, You have to check the compilation options for the parallel version (not the serial one) and change-lmkl_blacs_lp64 by -lmkl_blacs_openmpi_lp64in the RP_LIB(SCALAPACK+PBLAS):line. Good luck, Luis 2013/2/6 Arturo artginer at bifi.es mailto:artginer at bifi.es Hi Luis, First of all, thanks for help!! In the first suggestion, how can I know if I'm using this library? In the compilations options, I don't use that library. I used: -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread So the solution you suggest is to add the library mkl_blacs_openmpi_lp64 to this line? Regards El 06/02/13 13:32, Luis Ogando escribi?: Hi Arturo, Try http://zeus.theochem.tuwien.ac.at/pipermail/wien/2012-July/017207.html The first suggestion given by Prof. Marks solved a similar problem to me. All the best, Luis 2013/2/6 Arturo artginer at bifi.es mailto:artginer at bifi.es Hi, We are trying to run wien2k v12, compiled with openmpi 1.5.4 and intel compilers 12.1 but it gives us a segmentations fault while executing the following: mpirun -np 4 /cm/shared/apps/WIEN2k_12/lapw1_mpi uplapw1_1.defcat The errors are these: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 91. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- Child id 0 SIGSEGV, contact developers Child id 1 SIGSEGV, contact developers Child id 2 SIGSEGV, contact developers Child id 3 SIGSEGV, contact developers -- mpirun has exited due to process rank 2 with PID 25559 on node node042 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [node042:25556] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [node042:25556] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages And the ulimit -s is unlimited. Could you help us executing wien2k in parallel mode? Sequential is working fine. Best Regards Arturo ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at mailto:Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at mailto:Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at mailto:Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130208/0f8f2d03/attachment.htm
[Wien] parallel segmentation fault
Hi Arturo, Actually, Prof. Marks were right !! :) All the best, Luis 2013/2/8 Arturo artginer at bifi.es Hi Luis, You were right. The problem was in the parallel options. I had to change this library and also recompile fftw3_mpi library with the correct openmpi compiler. Regards!! Arturo El 06/02/13 14:04, Luis Ogando escribi?: Hi Arturo, You have to check the compilation options for the parallel version (not the serial one) and change-lmkl_blacs_lp64by -lmkl_blacs_openmpi_lp64in theRP_LIB(SCALAPACK+PBLAS):line. Good luck, Luis 2013/2/6 Arturo artginer at bifi.es Hi Luis, First of all, thanks for help!! In the first suggestion, how can I know if I'm using this library? In the compilations options, I don't use that library. I used: -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread So the solution you suggest is to add the library mkl_blacs_openmpi_lp64 to this line? Regards El 06/02/13 13:32, Luis Ogando escribi?: Hi Arturo, Try http://zeus.theochem.tuwien.ac.at/pipermail/wien/2012-July/017207.html The first suggestion given by Prof. Marks solved a similar problem to me. All the best, Luis 2013/2/6 Arturo artginer at bifi.es Hi, We are trying to run wien2k v12, compiled with openmpi 1.5.4 and intel compilers 12.1 but it gives us a segmentations fault while executing the following: mpirun -np 4 /cm/shared/apps/WIEN2k_12/lapw1_mpi uplapw1_1.defcat The errors are these: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 91. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- Child id 0 SIGSEGV, contact developers Child id 1 SIGSEGV, contact developers Child id 2 SIGSEGV, contact developers Child id 3 SIGSEGV, contact developers -- mpirun has exited due to process rank 2 with PID 25559 on node node042 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [node042:25556] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [node042:25556] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages And the ulimit -s is unlimited. Could you help us executing wien2k in parallel mode? Sequential is working fine. Best Regards Arturo ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing listWien at zeus.theochem.tuwien.ac.athttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing listWien at zeus.theochem.tuwien.ac.athttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130208/8ecb6ed4/attachment.htm
[Wien] parallel segmentation fault
Hi, We are trying to run wien2k v12, compiled with openmpi 1.5.4 and intel compilers 12.1 but it gives us a segmentations fault while executing the following: mpirun -np 4 /cm/shared/apps/WIEN2k_12/lapw1_mpi uplapw1_1.defcat The errors are these: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 91. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- Child id 0 SIGSEGV, contact developers Child id 1 SIGSEGV, contact developers Child id 2 SIGSEGV, contact developers Child id 3 SIGSEGV, contact developers -- mpirun has exited due to process rank 2 with PID 25559 on node node042 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [node042:25556] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [node042:25556] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages And the ulimit -s is unlimited. Could you help us executing wien2k in parallel mode? Sequential is working fine. Best Regards Arturo -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130206/57176701/attachment.htm
[Wien] parallel segmentation fault
Hi Arturo, Try http://zeus.theochem.tuwien.ac.at/pipermail/wien/2012-July/017207.html The first suggestion given by Prof. Marks solved a similar problem to me. All the best, Luis 2013/2/6 Arturo artginer at bifi.es Hi, We are trying to run wien2k v12, compiled with openmpi 1.5.4 and intel compilers 12.1 but it gives us a segmentations fault while executing the following: mpirun -np 4 /cm/shared/apps/WIEN2k_12/lapw1_mpi uplapw1_1.defcat The errors are these: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 91. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- Child id 0 SIGSEGV, contact developers Child id 1 SIGSEGV, contact developers Child id 2 SIGSEGV, contact developers Child id 3 SIGSEGV, contact developers -- mpirun has exited due to process rank 2 with PID 25559 on node node042 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [node042:25556] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [node042:25556] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages And the ulimit -s is unlimited. Could you help us executing wien2k in parallel mode? Sequential is working fine. Best Regards Arturo ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130206/dfa2b7e7/attachment.htm
[Wien] parallel segmentation fault
Hi Luis, First of all, thanks for help!! In the first suggestion, how can I know if I'm using this library? In the compilations options, I don't use that library. I used: -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread So the solution you suggest is to add the library mkl_blacs_openmpi_lp64 to this line? Regards El 06/02/13 13:32, Luis Ogando escribi?: Hi Arturo, Try http://zeus.theochem.tuwien.ac.at/pipermail/wien/2012-July/017207.html The first suggestion given by Prof. Marks solved a similar problem to me. All the best, Luis 2013/2/6 Arturo artginer at bifi.es mailto:artginer at bifi.es Hi, We are trying to run wien2k v12, compiled with openmpi 1.5.4 and intel compilers 12.1 but it gives us a segmentations fault while executing the following: mpirun -np 4 /cm/shared/apps/WIEN2k_12/lapw1_mpi uplapw1_1.defcat The errors are these: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 91. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- Child id 0 SIGSEGV, contact developers Child id 1 SIGSEGV, contact developers Child id 2 SIGSEGV, contact developers Child id 3 SIGSEGV, contact developers -- mpirun has exited due to process rank 2 with PID 25559 on node node042 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [node042:25556] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [node042:25556] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages And the ulimit -s is unlimited. Could you help us executing wien2k in parallel mode? Sequential is working fine. Best Regards Arturo ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at mailto:Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130206/9f1c3af8/attachment.htm
[Wien] parallel segmentation fault
Hi Arturo, You have to check the compilation options for the parallel version (not the serial one) and change-lmkl_blacs_lp64by -lmkl_blacs_openmpi_lp64in theRP_LIB(SCALAPACK+PBLAS):line. Good luck, Luis 2013/2/6 Arturo artginer at bifi.es Hi Luis, First of all, thanks for help!! In the first suggestion, how can I know if I'm using this library? In the compilations options, I don't use that library. I used: -lmkl_lapack95_lp64 -lmkl_intel_lp64 -lmkl_intel_thread -lmkl_core -openmp -lpthread So the solution you suggest is to add the library mkl_blacs_openmpi_lp64 to this line? Regards El 06/02/13 13:32, Luis Ogando escribi?: Hi Arturo, Try http://zeus.theochem.tuwien.ac.at/pipermail/wien/2012-July/017207.html The first suggestion given by Prof. Marks solved a similar problem to me. All the best, Luis 2013/2/6 Arturo artginer at bifi.es Hi, We are trying to run wien2k v12, compiled with openmpi 1.5.4 and intel compilers 12.1 but it gives us a segmentations fault while executing the following: mpirun -np 4 /cm/shared/apps/WIEN2k_12/lapw1_mpi uplapw1_1.defcat The errors are these: w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault w2k_dispatch_signal(): received: Segmentation fault -- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 91. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -- Child id 0 SIGSEGV, contact developers Child id 1 SIGSEGV, contact developers Child id 2 SIGSEGV, contact developers Child id 3 SIGSEGV, contact developers -- mpirun has exited due to process rank 2 with PID 25559 on node node042 exiting without calling finalize. This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -- [node042:25556] 3 more processes have sent help message help-mpi-api.txt / mpi-abort [node042:25556] Set MCA parameter orte_base_help_aggregate to 0 to see all help / error messages And the ulimit -s is unlimited. Could you help us executing wien2k in parallel mode? Sequential is working fine. Best Regards Arturo ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing listWien at zeus.theochem.tuwien.ac.athttp://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien ___ Wien mailing list Wien at zeus.theochem.tuwien.ac.at http://zeus.theochem.tuwien.ac.at/mailman/listinfo/wien -- next part -- An HTML attachment was scrubbed... URL: http://zeus.theochem.tuwien.ac.at/pipermail/wien/attachments/20130206/5ad08383/attachment.htm
