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Work/ag_parallel/src/mpi/tasks.cpp\"", + "file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/mpi/tasks.cpp" +}, +{ + "directory": "/home/noah/Documents/School/Thesis Work/ag_parallel/build", + "command": "/usr/bin/cc -I/usr/include/postgresql -I\"/home/noah/Documents/School/Thesis Work/ag_parallel/src\" -g -o CMakeFiles/dynstr_test.dir/src/util/mem.c.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/util/mem.c\"", + "file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/util/mem.c" +}, +{ + "directory": "/home/noah/Documents/School/Thesis Work/ag_parallel/build", + "command": "/usr/bin/cc -I/usr/include/postgresql -I\"/home/noah/Documents/School/Thesis Work/ag_parallel/src\" -g -o CMakeFiles/dynstr_test.dir/src/tests/mem_test.c.o -c \"/home/noah/Documents/School/Thesis Work/ag_parallel/src/tests/mem_test.c\"", + "file": "/home/noah/Documents/School/Thesis Work/ag_parallel/src/tests/mem_test.c" } ] \ No newline at end of file diff --git a/build/config.ini b/build/config.ini deleted file mode 100755 index f77efc8..0000000 --- a/build/config.ini +++ /dev/null @@ -1,6 +0,0 @@ -[database] -name = ag_gen -host = compute03 -port = 5240 -username = ag_gen -password = 8PZQc79NUZ3FjqSB diff --git a/build/slurm_reports/job.29742.err b/build/slurm_reports/job.29742.err deleted file mode 100644 index c8beb5c..0000000 --- a/build/slurm_reports/job.29742.err +++ /dev/null @@ -1,191 +0,0 @@ -terminate called after throwing an instance of 'DBException' -terminate called after throwing an instance of 'DBException' - what(): Database connection failed: dbname=tmp user=ag_gen host=login port=5420 password=8PZQc79NUZ3FjqSB -could not connect to server: Connection refused - Is the server running on host "login" (10.1.100.100) and accepting - TCP/IP connections on port 5420? - - what(): Database connection failed: dbname=tmp user=ag_gen host=login port=5420 password=8PZQc79NUZ3FjqSB -could not connect to server: Connection refused - Is the server running on host "login" (10.1.100.100) and accepting - TCP/IP connections on port 5420? - -[compute03:25307] *** Process received signal *** -[compute03:25307] Signal: Aborted (6) -[compute03:25307] Signal code: (-6) -[compute03:25306] *** Process received signal *** -[compute03:25306] Signal: Aborted (6) -[compute03:25306] Signal code: (-6) -[compute03:25307] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x7f9d3a1677e0] -[compute03:25307] [ 1] terminate called after throwing an instance of 'DBException' -[compute03:25306] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x7f6f98b587e0] -[compute03:25306] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x7f9d39df6495] -[compute03:25307] [ 2] /lib64/libc.so.6(gsignal+0x35)[0x7f6f987e7495] -[compute03:25306] [ 2] terminate called after throwing an instance of 'DBException' - what(): Database connection failed: dbname=tmp user=ag_gen host=login port=5420 password=8PZQc79NUZ3FjqSB -could not connect to server: Connection refused - Is the server running on host "login" (10.1.100.100) and accepting - TCP/IP connections on port 5420? - -[compute04:24809] *** Process received signal *** -/lib64/libc.so.6(abort+0x175)[0x7f9d39df7c75] -[compute03:25307] [ 3] /lib64/libc.so.6(abort+0x175)[0x7f6f987e8c75] -[compute03:25306] [ 3] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x915c2)[0x7f9d3aace5c2] -[compute03:25307] [ 4] what(): Database connection failed: dbname=tmp user=ag_gen host=login port=5420 password=8PZQc79NUZ3FjqSB -could not connect to server: Connection refused - Is the server running on host "login" (10.1.100.100) and accepting - TCP/IP connections on port 5420? - -[compute04:24810] *** Process received signal *** -[compute04:24810] Signal: Aborted (6) -[compute04:24810] Signal code: (-6) -/opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4a6)[0x7f9d3aacc4a6] -[compute03:25307] [ 5] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x915c2)[0x7f6f994bf5c2] -[compute03:25306] [ 4] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4e1)[0x7f9d3aacc4e1] -[compute03:25307] [ 6] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4a6)[0x7f6f994bd4a6] -[compute03:25306] [ 5] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f723)[0x7f9d3aacc723] -[compute03:25307] [ 7] [compute04:24809] Signal: Aborted (6) -[compute04:24809] Signal code: (-6) -[compute04:24809] [ 0] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4e1)[0x7f6f994bd4e1] -[compute03:25306] [ 6] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f723)[0x7f6f994bd723] -[compute03:25306] [ 7] [compute04:24810] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x7f88c631b7e0] -[compute04:24810] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x7f88c5faa495] -[compute04:24810] [ 2] ./ag_gen(_ZN10Connection7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x63cb74] -[compute03:25307] [ 8] /lib64/libpthread.so.0(+0xf7e0)[0x7f93996627e0] -[compute04:24809] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x7f93992f1495] -[compute04:24809] [ 2] /lib64/libc.so.6(abort+0x175)[0x7f93992f2c75] -./ag_gen(_ZN10Connection7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x63cb74] -[compute03:25306] [ 8] ./ag_gen(_ZN2DB7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x23)[0x63d10b] -[compute03:25307] [ 9] /lib64/libc.so.6(abort+0x175)[0x7f88c5fabc75] -[compute04:24810] [ 3] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x915c2)[0x7f88c6c825c2] -[compute04:24810] [ 4] [compute04:24809] [ 3] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x915c2)[0x7f9399fc95c2] -[compute04:24809] [ 4] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4a6)[0x7f88c6c804a6] -[compute04:24810] [ 5] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4e1)[0x7f88c6c804e1] -[compute04:24810] [ 6] ./ag_gen(_ZN2DB7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x23)[0x63d10b] -[compute03:25306] [ 9] ./ag_gen(_Z7init_dbNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1d)[0x634ab5] -[compute03:25307] [10] ./ag_gen(main+0x7e8)[0x5c2d8e] -[compute03:25307] [11] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4a6)[0x7f9399fc74a6] -[compute04:24809] [ 5] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4e1)[0x7f9399fc74e1] -[compute04:24809] [ 6] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f723)[0x7f9399fc7723] -[compute04:24809] [ 7] /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f9d39de2d1d] -[compute03:25307] [12] ./ag_gen[0x5c0c49] -[compute03:25307] *** End of error message *** -/opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f723)[0x7f88c6c80723] -[compute04:24810] [ 7] ./ag_gen(_Z7init_dbNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1d)[0x634ab5] -[compute03:25306] [10] ./ag_gen(main+0x7e8)[0x5c2d8e] -[compute03:25306] [11] ./ag_gen(_ZN10Connection7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x63cb74] -[compute04:24809] [ 8] /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f6f987d3d1d] -[compute03:25306] [12] ./ag_gen(_ZN10Connection7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x63cb74] -[compute04:24810] [ 8] terminate called after throwing an instance of 'DBException' -./ag_gen[0x5c0c49] -[compute03:25306] *** End of error message *** -terminate called after throwing an instance of 'DBException' -./ag_gen(_ZN2DB7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x23)[0x63d10b] -[compute04:24809] [ 9] terminate called after throwing an instance of 'DBException' - what(): Database connection failed: dbname=tmp user=ag_gen host=login port=5420 password=8PZQc79NUZ3FjqSB -could not connect to server: Connection refused - Is the server running on host "login" (10.1.100.100) and accepting - TCP/IP connections on port 5420? - -terminate called after throwing an instance of 'DBException' - what(): Database connection failed: dbname=tmp user=ag_gen host=login port=5420 password=8PZQc79NUZ3FjqSB -could not connect to server: Connection refused - Is the server running on host "login" (10.1.100.100) and accepting - TCP/IP connections on port 5420? - -./ag_gen(_ZN2DB7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x23)[0x63d10b] -[compute04:24810] [ 9] what(): Database connection failed: dbname=tmp user=ag_gen host=login port=5420 password=8PZQc79NUZ3FjqSB -could not connect to server: Connection refused - Is the server running on host "login" (10.1.100.100) and accepting - TCP/IP connections on port 5420? - -[compute06:24528] *** Process received signal *** -[compute06:24528] Signal: Aborted (6) -[compute06:24528] Signal code: (-6) - what(): Database connection failed: dbname=tmp user=ag_gen host=login port=5420 password=8PZQc79NUZ3FjqSB -could not connect to server: Connection refused - Is the server running on host "login" (10.1.100.100) and accepting - TCP/IP connections on port 5420? - -[compute05:24497] *** Process received signal *** -[compute05:24497] Signal: Aborted (6) -[compute05:24497] Signal code: (-6) -./ag_gen(_Z7init_dbNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1d)[0x634ab5] -[compute04:24809] [10] [compute06:24527] *** Process received signal *** -[compute06:24527] Signal: Aborted (6) -[compute06:24527] Signal code: (-6) -[compute05:24496] *** Process received signal *** -[compute05:24496] Signal: Aborted (6) -[compute05:24496] Signal code: (-6) -./ag_gen(_Z7init_dbNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1d)[0x634ab5] -[compute04:24810] [10] [compute06:24528] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x7f86803b07e0] -[compute06:24528] [ 1] [compute05:24497] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x7f1aef7697e0] -./ag_gen(main+0x7e8)[0x5c2d8e] -[compute04:24809] [11] /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f93992ddd1d] -[compute04:24809] [12] [compute06:24527] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x7fe3588c97e0] -[compute06:24527] [ 1] [compute05:24496] [ 0] /lib64/libpthread.so.0(+0xf7e0)[0x7fba08a7e7e0] -[compute05:24496] [ 1] ./ag_gen(main+0x7e8)[0x5c2d8e] -[compute04:24810] [11] /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f88c5f96d1d] -[compute04:24810] [12] /lib64/libc.so.6(gsignal+0x35)[0x7f868003f495] -[compute06:24528] [ 2] [compute05:24497] [ 1] /lib64/libc.so.6(gsignal+0x35)[0x7f1aef3f8495] -[compute05:24497] [ 2] ./ag_gen[0x5c0c49] -[compute04:24809] *** End of error message *** -/lib64/libc.so.6(gsignal+0x35)[0x7fe358558495] -[compute06:24527] [ 2] /lib64/libc.so.6(abort+0x175)[0x7fe358559c75] -[compute06:24527] [ 3] /lib64/libc.so.6(gsignal+0x35)[0x7fba0870d495] -[compute05:24496] [ 2] /lib64/libc.so.6(abort+0x175)[0x7fba0870ec75] -[compute05:24496] [ 3] ./ag_gen[0x5c0c49] -[compute04:24810] *** End of error message *** -/lib64/libc.so.6(abort+0x175)[0x7f8680040c75] -[compute06:24528] [ 3] /lib64/libc.so.6(abort+0x175)[0x7f1aef3f9c75] -[compute05:24497] [ 3] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x915c2)[0x7fe3592305c2] -[compute06:24527] [ 4] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x915c2)[0x7fba093e55c2] -[compute05:24496] [ 4] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x915c2)[0x7f8680d175c2] -[compute06:24528] [ 4] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4a6)[0x7f8680d154a6] -[compute06:24528] [ 5] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x915c2)[0x7f1af00d05c2] -[compute05:24497] [ 4] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4a6)[0x7f1af00ce4a6] -[compute05:24497] [ 5] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4a6)[0x7fe35922e4a6] -[compute06:24527] [ 5] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4a6)[0x7fba093e34a6] -[compute05:24496] [ 5] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4e1)[0x7fba093e34e1] -[compute05:24496] [ 6] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4e1)[0x7f8680d154e1] -[compute06:24528] [ 6] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f723)[0x7f8680d15723] -[compute06:24528] [ 7] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4e1)[0x7f1af00ce4e1] -[compute05:24497] [ 6] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f723)[0x7f1af00ce723] -[compute05:24497] [ 7] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f4e1)[0x7fe35922e4e1] -[compute06:24527] [ 6] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f723)[0x7fe35922e723] -[compute06:24527] [ 7] /opt/apps/gcc/8.2.0/lib64/libstdc++.so.6(+0x8f723)[0x7fba093e3723] -[compute05:24496] [ 7] ./ag_gen(_ZN10Connection7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x63cb74] -[compute06:24528] [ 8] ./ag_gen(_ZN10Connection7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x63cb74] -[compute05:24497] [ 8] ./ag_gen(_ZN10Connection7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x63cb74] -[compute06:24527] [ 8] ./ag_gen(_ZN10Connection7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x15e)[0x63cb74] -[compute05:24496] [ 8] ./ag_gen(_ZN2DB7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x23)[0x63d10b] -[compute06:24528] [ 9] ./ag_gen(_ZN2DB7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x23)[0x63d10b] -[compute05:24497] [ 9] ./ag_gen(_ZN2DB7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x23)[0x63d10b] -[compute06:24527] [ 9] ./ag_gen(_ZN2DB7connectERKNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x23)[0x63d10b] -[compute05:24496] [ 9] ./ag_gen(_Z7init_dbNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1d)[0x634ab5] -[compute06:24528] [10] ./ag_gen(_Z7init_dbNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1d)[0x634ab5] -[compute05:24497] [10] ./ag_gen(main+0x7e8)[0x5c2d8e] -[compute06:24528] [11] ./ag_gen(main+0x7e8)[0x5c2d8e] -[compute05:24497] [11] ./ag_gen(_Z7init_dbNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1d)[0x634ab5] -[compute06:24527] [10] ./ag_gen(_Z7init_dbNSt7__cxx1112basic_stringIcSt11char_traitsIcESaIcEEE+0x1d)[0x634ab5] -[compute05:24496] [10] /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f868002bd1d] -[compute06:24528] [12] /lib64/libc.so.6(__libc_start_main+0xfd)[0x7f1aef3e4d1d] -[compute05:24497] [12] ./ag_gen[0x5c0c49] -[compute06:24528] *** End of error message *** -./ag_gen[0x5c0c49] -[compute05:24497] *** End of error message *** -./ag_gen(main+0x7e8)[0x5c2d8e] -[compute06:24527] [11] /lib64/libc.so.6(__libc_start_main+0xfd)[0x7fe358544d1d] -[compute06:24527] [12] ./ag_gen(main+0x7e8)[0x5c2d8e] -[compute05:24496] [11] ./ag_gen[0x5c0c49] -[compute06:24527] *** End of error message *** -/lib64/libc.so.6(__libc_start_main+0xfd)[0x7fba086f9d1d] -[compute05:24496] [12] ./ag_gen[0x5c0c49] -[compute05:24496] *** End of error message *** --------------------------------------------------------------------------- -Primary job terminated normally, but 1 process returned -a non-zero exit code. Per user-direction, the job has been aborted. --------------------------------------------------------------------------- --------------------------------------------------------------------------- -mpirun noticed that process rank 0 with PID 0 on node compute03 exited on signal 6 (Aborted). --------------------------------------------------------------------------- diff --git a/config.ini b/config.ini deleted file mode 100755 index f77efc8..0000000 --- a/config.ini +++ /dev/null @@ -1,6 +0,0 @@ -[database] -name = ag_gen -host = compute03 -port = 5240 -username = ag_gen -password = 8PZQc79NUZ3FjqSB diff --git a/src/ag_gen/ag_gen.cpp b/src/ag_gen/ag_gen.cpp index 02eef77..09fe230 100755 --- a/src/ag_gen/ag_gen.cpp +++ b/src/ag_gen/ag_gen.cpp @@ -174,17 +174,21 @@ AGGenInstance &AGGen::generate(bool batch_process, int batch_size, int numThrd, } //Print out the groups if desired - std::cout <<"\nThere are "< factbases_dump; std::vector edges_dump; world.irecv(0, 7, factbases_dump); @@ -528,6 +539,7 @@ AGGenInstance &AGGen::generate(bool batch_process, int batch_size, int numThrd, instance.factbases = factbases_dump; instance.edges = edges_dump; //task_four(instance); + std::cout << "Task 4 finished." << std::endl; struct timeval t41,t42; gettimeofday(&t41,NULL); save_ag_to_db(instance, true); diff --git a/src/main.cpp b/src/main.cpp index 3fc6d3f..9c8296f 100755 --- a/src/main.cpp +++ b/src/main.cpp @@ -521,17 +521,18 @@ int main(int argc, char *argv[]) { boost::mpi::environment env(argc, argv, mt_level); mt ::level provided = env.thread_level(); - std::cout << "Asked the MPI environment to be created with threading level: "\ - << mt_level << std::endl; - std::cout << "MPI Environment was created with threading level: " << provided \ - << std::endl; - // std::cout << "Ensure that the MPI package has the MPI_THREAD_MULTIPLE build-time option enabled,"\ << "or change the environment creation to be use MPI threading level of single." << std::endl; // exit(EXIT_FAILURE); mpi::communicator world; + if (world.rank() == 0){ + std::cout << "Asked the MPI environment to be created with threading level: "\ + << mt_level << std::endl; + std::cout << "MPI Environment was created with threading level: " << provided \ + << std::endl; + } char hammer_host[256]; gethostname(hammer_host, 256); @@ -560,7 +561,9 @@ int main(int argc, char *argv[]) { //std::cout<> appl_exploits; unsigned long esize = exploit_list.size(); @@ -156,6 +156,8 @@ void task_two(AGGenInstance &instance, int alloc, int two_alloc, boost::mpi::com std::deque &localFrontier, double mem_threshold, boost::mpi::communicator &ttwo_comm,\ std::vector ex_groups, std::unordered_map &hash_map){ + std::cout << "Process rank " << world.rank() << " with " << two_alloc << " node(s) allocated has started Task 2." << std::endl; + NetworkState current_state; std::vector> appl_exploits; @@ -337,6 +339,7 @@ void task_three(AGGenInstance &instance, NetworkState &new_state, std::deque &hash_map){ + std::cout << "Started Task 3." << std::endl; auto hash_num = new_state.get_hash(instance.facts); //although local frontier is updated, the global hash is also updated to avoid testing on explored states.