Your message dated Thu, 09 Aug 2018 13:34:49 +0000 with message-id <[email protected]> and subject line Bug#904825: fixed in openmpi 3.1.1.real-5 has caused the Debian Bug report #904825, regarding aces3 ftbfs in unstable to be marked as done.
This means that you claim that the problem has been dealt with. If this is not the case it is now your responsibility to reopen the Bug report if necessary, and/or fix the problem forthwith. (NB: If you are a system administrator and have no idea what this message is talking about, this may indicate a serious mail system misconfiguration somewhere. Please contact [email protected] immediately.) -- 904825: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=904825 Debian Bug Tracking System Contact [email protected] with problems
--- Begin Message ---Package: src:aces3 Version: 3.0.8-5.1 Tags: sid buster Severity: serious aces3 ftbfs in unstable: [...] mpif77 -DMPIF2C -DMPI2 -DC_SUFFIX -DCB_SUFFIX -D__fortran -D__fortran77 -g -O2 -Wall -fno-aggressive-loop-optimizations -o xaces3 \ find_seg.o reorder_coefficients.o reorder_rohf.o joda_exit.o clear_static_data_requests.o init_data.o nuclear_nuclear_repulsion_energy.o worker_termination.o check_jodadone.o find_jobflow.o write_default_sial_programs.o int_send_common.o int_gen_sizer.o geometry.o reset_internal_system_data.o write_zmat_auto.o get_sial_config_params.o aces_com_parallel_aces.o nuclear_nuclear_gradient.o beta.o scf_init.o set_ecp_charges.o worker_work.o decode_fmo_params.o timer_data.o descramble_coefficients.o int_gen_init.o handle_gradient.o molread.o det_segsizes.o handle_hessian.o worker_init.o joda_prep.o verify_aces2_params.o c_exit.o sumz.o ../sia/manager/check_consistency.o ../sia/manager/check_for_server_array.o ../sia/manager/check_preparesum_work.o ../sia/manager/check_work_stack_for_delay.o ../sia/manager/claim_memory_block.o ../sia/manager/clear_server_stats.o ../sia/manager/diskcall.o ../sia/manager/distribute_server_info.o ../sia/manager/do_backup.o ../sia/manager/find_clean_block.o ../sia/manager/find_free_diskloc.o ../sia/manager/find_oldest_dirty_block.o ../sia/manager/find_server_table_ptr.o ../sia/manager/insert_work_node.o ../sia/manager/make_free_block.o ../sia/manager/mark_block_clean.o ../sia/manager/mark_block_dirty.o ../sia/manager/pop_clean_block.o ../sia/manager/pop_work_node.o ../sia/manager/prequest_copy_slice.o ../sia/manager/print_server_data.o ../sia/manager/process_prepare_message.o ../sia/manager/process_preparesum_message.o ../sia/manager/process_prequest_message.o ../sia/manager/process_request_message.o ../sia/manager/process_server_blocks_to_list_msg.o ../sia/manager/process_server_blocks_to_list_no_mpi_io.o ../sia/manager/process_server_checkpoint_msg.o ../sia/manager/process_server_commit_msg.o ../sia/manager/process_server_copy_message.o ../sia/manager/process_server_delete_message.o ../sia/manager/process_server_list_to_blocks_msg.o ../sia/manager/process_server_restart_msg.o ../sia/manager/process_work_queue_entry.o ../sia/manager/ptr_check.o ../sia/manager/push_clean_block.o ../sia/manager/push_work_node.o ../sia/manager/remove_from_dirty_list.o ../sia/manager/remove_work_head.o ../sia/manager/server_abort_job.o ../sia/manager/sip_server_init.o ../sia/manager/sip_server_work.o ../sia/manager/syscopy.o ../sia/manager/translate_key.o ../sia/worker/block_map_table_setup.o ../sia/worker/build_segment_table.o ../sia/worker/built_cmp2zmat.o ../sia/worker/determine_stack_blocksizes.o ../sia/worker/fragment_orbitals.o ../sia/worker/fshells_to_segments.o ../sia/worker/get_subrange_segments.o ../sia/worker/get_symbolic_constant.o ../sia/worker/init_c.o ../sia/worker/init_eps.o ../sia/worker/init_fock.o ../sia/worker/init_fockrohf.o ../sia/worker/init_oed_integrals.o ../sia/worker/print_symbolic_constants.o ../sia/worker/refill_block_map_table.o ../sia/worker/remap.o ../sia/worker/send_static_data.o ../sia/worker/shells_to_segments.o ../sia/worker/sial_compile_and_send_tables.o ../sia/worker/sial_compile_and_send_tables1.o ../sia/worker/sip_fmain.o ../sia/worker/stack_distribution.o ../sia/worker/vmlgen.o ../sia/worker/vtdemo_init.o ../sia/worker/write_eig_data.o ../aces/aces_library/special_directory/direct_integral/aces_to_erd.o ../aces/aces_library/special_directory/direct_integral/binpack.o ../aces/aces_library/special_directory/direct_integral/comp_dipole_moment.o ../aces/aces_library/special_directory/direct_integral/comp_first_moment.o ../aces/aces_library/special_directory/direct_integral/comp_fock_der.o ../aces/aces_library/special_directory/direct_integral/comp_overlap_der.o ../aces/aces_library/special_directory/direct_integral/comp_return_derv_xyz.o ../aces/aces_library/special_directory/direct_integral/comp_return_h1.o ../aces/aces_library/special_directory/direct_integral/comp_return_h1_nodiag.o ../aces/aces_library/special_directory/direct_integral/comp_return_ovl.o ../aces/aces_library/special_directory/direct_integral/comp_return_x.o ../aces/aces_library/special_directory/direct_integral/comp_return_xx.o ../aces/aces_library/special_directory/direct_integral/comp_return_xy.o ../aces/aces_library/special_directory/direct_integral/comp_return_xz.o ../aces/aces_library/special_directory/direct_integral/comp_return_y.o ../aces/aces_library/special_directory/direct_integral/comp_return_yy.o ../aces/aces_library/special_directory/direct_integral/comp_return_yz.o ../aces/aces_library/special_directory/direct_integral/comp_return_z.o ../aces/aces_library/special_directory/direct_integral/comp_return_zz.o ../aces/aces_library/special_directory/direct_integral/comp_second_moment.o ../aces/aces_library/special_directory/direct_integral/compute_der2_batch.o ../aces/aces_library/special_directory/direct_integral/compute_der_batch.o ../aces/aces_library/special_directory/direct_integral/compute_erd3.o ../aces/aces_library/special_directory/direct_integral/compute_erd_2e_Sderv_integrals.o ../aces/aces_library/special_directory/direct_integral/compute_erd_2e_derv_integrals.o ../aces/aces_library/special_directory/direct_integral/compute_integrals.o ../aces/aces_library/special_directory/direct_integral/compute_integrals_wrapper.o ../aces/aces_library/special_directory/direct_integral/compute_oed_integrals.o ../aces/aces_library/special_directory/direct_integral/compute_return_1soix.o ../aces/aces_library/special_directory/direct_integral/compute_return_1soiy.o ../aces/aces_library/special_directory/direct_integral/compute_return_1soiz.o ../aces/aces_library/special_directory/direct_integral/compute_return_2soix.o ../aces/aces_library/special_directory/direct_integral/compute_return_2soiy.o ../aces/aces_library/special_directory/direct_integral/compute_return_2soiz.o ../aces/aces_library/special_directory/direct_integral/contract_ecp_derv_integrals.o ../aces/aces_library/special_directory/direct_integral/contract_erd_2der.o ../aces/aces_library/special_directory/direct_integral/contract_oed_2derv_integrals.o ../aces/aces_library/special_directory/direct_integral/contract_oed_2derv_num.o ../aces/aces_library/special_directory/direct_integral/contract_oed_2derv_type1.o ../aces/aces_library/special_directory/direct_integral/contract_oed_2derv_type1_numint.o ../aces/aces_library/special_directory/direct_integral/contract_oed_2derv_type1a.o ../aces/aces_library/special_directory/direct_integral/contract_oed_2derv_type1b.o ../aces/aces_library/special_directory/direct_integral/contract_oed_derv_integrals.o ../aces/aces_library/special_directory/direct_integral/ecp_renorm.o ../aces/aces_library/special_directory/direct_integral/ecp_to_erd.o ../aces/aces_library/special_directory/direct_integral/erd_scratch_mem_calc.o ../aces/aces_library/special_directory/direct_integral/fast_erd_scratch_mem_calc.o ../aces/aces_library/special_directory/direct_integral/get1e.o ../aces/aces_library/special_directory/direct_integral/lookup_shell.o ../aces/aces_library/special_directory/direct_integral/move_integrals.o ../aces/aces_library/special_directory/direct_integral/nn_repulsion_energy.o ../aces/aces_library/special_directory/direct_integral/pack_coeffs.o ../aces/aces_library/special_directory/direct_integral/pack_coeffs_oed.o ../aces/aces_library/special_directory/direct_integral/pack_coeffs_ovl3c.o ../aces/aces_library/special_directory/direct_integral/segment_mol.o ../aces/aces_library/special_directory/direct_integral/setup_ccbeg.o ../aces/aces_library/special_directory/direct_integral/sip_integral_init.o ../aces/aces_library/special_directory/direct_integral/test2d_numint.o ../aces/aces_library/special_directory/direct_integral/tester_MRT1.o ../aces/aces_library/special_directory/direct_integral/tester_MRT2.o ../aces/aces_library/special_directory/direct_integral/tester_MRT3.o ../aces/aces_library/special_directory/direct_integral/tester_MRT4.o \ -L../../lib -L/usr/lib -lstdc++ -lsip1 -lsip2 -lsialinst -lsip_shared -lframelib -laces2 -lgeopt -lsymcor -laces2 -lprop_ints -lerd -loed -lecp -ldup -lsip1 -lsip2 -lsialinst -lerd_F12 -lF12grid -loed_F12 -lsip1 -lsip2 -lblas -llapack && test -x xaces3 || rm -f xaces3 /usr/bin/ld: ../../lib/libsip2.a(generate_scratch_filename.o): in function `generate_scratch_filename_': /<<PKGBUILDDIR>>/src/sia/sip/sip_instructions/generate_scratch_filename.c:31: warning: the use of `mktemp' is dangerous, better use `mkstemp' or `mkdtemp' cp xaces3 ../../bin/xaces3 rm -f make.out make.err make[3]: Leaving directory '/<<PKGBUILDDIR>>/src/main' make[2]: Leaving directory '/<<PKGBUILDDIR>>/src' make[2]: Entering directory '/<<PKGBUILDDIR>>/src/aces/aces_sial' rm -f make.out make.err make[2]: Leaving directory '/<<PKGBUILDDIR>>/src/aces/aces_sial' make[2]: Entering directory '/<<PKGBUILDDIR>>/test_compare' rm -f make.out make.err mpif77 -c -DMPIF2C -DMPI2 -DC_SUFFIX -DCB_SUFFIX -D__fortran -D__fortran77 -g -O2 -Wall -fno-aggressive-loop-optimizations -I$MPIHOME/include test_compare.f 1>>make.out 2>>make.err mpif77 -DMPIF2C -DMPI2 -DC_SUFFIX -DCB_SUFFIX -D__fortran -D__fortran77 -g -O2 -Wall -fno-aggressive-loop-optimizations -o xtest_compare \ test_compare.o \ -L../lib -L/usr/lib -lstdc++ -lsip1 -lsip2 -lsip_shared -lframelib -laces2 -lgeopt -lsymcor -laces2 -lerd -loed -ldup -lsip1 -lsip2 -lblas -llapack && test -x xtest_compare || rm -f xtest_compare cp xtest_compare ../bin/xtest_compare rm -f make.out make.err make[2]: Leaving directory '/<<PKGBUILDDIR>>/test_compare' make[2]: Entering directory '/<<PKGBUILDDIR>>/tests' make[2]: Leaving directory '/<<PKGBUILDDIR>>/tests' make[1]: Leaving directory '/<<PKGBUILDDIR>>' debian/rules override_dh_auto_test make[1]: Entering directory '/<<PKGBUILDDIR>>' (cd tests; OMPI_MCA_orte_rsh_agent=/bin/false csh ./runscript-quick) Running 1.1.1.1 -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 1 in communicator MPI_COMM_WORLD with errorcode 1. 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. -------------------------------------------------------------------------- E: Build killed with signal TERM after 150 minutes of inactivity --------------------------------------------------------------------------------
--- End Message ---
--- Begin Message ---Source: openmpi Source-Version: 3.1.1.real-5 We believe that the bug you reported is fixed in the latest version of openmpi, which is due to be installed in the Debian FTP archive. A summary of the changes between this version and the previous one is attached. Thank you for reporting the bug, which will now be closed. If you have further comments please address them to [email protected], and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Alastair McKinstry <[email protected]> (supplier of updated openmpi package) (This message was generated automatically at their request; if you believe that there is a problem with it please contact the archive administrators by mailing [email protected]) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA256 Format: 1.8 Date: Thu, 09 Aug 2018 12:55:50 +0100 Source: openmpi Binary: openmpi-bin libopenmpi-dev libopenmpi3 openmpi-common openmpi-doc Architecture: source amd64 all Version: 3.1.1.real-5 Distribution: unstable Urgency: medium Maintainer: Alastair McKinstry <[email protected]> Changed-By: Alastair McKinstry <[email protected]> Description: libopenmpi-dev - high performance message passing library -- header files libopenmpi3 - high performance message passing library -- shared library openmpi-bin - high performance message passing library -- binaries openmpi-common - high performance message passing library -- common files openmpi-doc - high performance message passing library -- man pages Closes: 904825 Changes: openmpi (3.1.1.real-5) unstable; urgency=medium . * Include zlib1g-dev to build against * Use internal libpmix, libevent to fix hang on MPI_Abort. Closes: #904825. 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