Your message dated Thu, 09 Aug 2018 13:34:49 +0000
with message-id <e1fnl5v-0000dc...@fasolo.debian.org>
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 ow...@bugs.debian.org
immediately.)
--
904825: https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=904825
Debian Bug Tracking System
Contact ow...@bugs.debian.org 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 904...@bugs.debian.org,
and the maintainer will reopen the bug report if appropriate.
Debian distribution maintenance software
pp.
Alastair McKinstry <mckins...@debian.org> (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 ftpmas...@ftp-master.debian.org)
-----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 <mckins...@debian.org>
Changed-By: Alastair McKinstry <mckins...@debian.org>
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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openmpi_3.1.1.real-5.debian.tar.xz
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