Created attachment 1473810 [details] Input example, sorry I can't share my actual molecule here but this is a department policy Description of problem: It is not possible to run a vibrational analysis using the CP2K provided on Fedora 28, but the same calculation runs OK on the precompiled binary version provided by the CP2K team. Version-Release number of selected component (if applicable): cp2k-common-5.1-3.fc28.x86_64 cp2k-openmpi-5.1-3.fc28.x86_64 cp2k-5.1-3.fc28.x86_64 cp2k-mpich-5.1-3.fc28.x86_64 How reproducible: The error happens every time. Steps to Reproduce: 1. cp2k.ssmp -i CoL3H2O.inp & Actual results: ******************************************************************************* ******************************************************************************* ** ** ** # # # # # # ## ** ** # # ### # ## ### #### ## # # ### # ** ** # # # # # ## # # # # # # ## # # # # ** ** ## # # # # # ## # # # # # # # ## # ** ** ## # ### # # # ## # ## # # # # ### ** ** ** ** ## ## # ** ** # # # # ### # # # ### ### ** ** # # ## # # # # # # ## # ## ** ** #### # # # ## # ### ## # ## N. Replicas: 1 ** ** # # # # # # ### # ### # ### N. Procs/Rep: 1 ** ** ## ** ** T. Laino and F. Schiffmann ** ** 2008 - 2015 ** ******************************************************************************* ******************************************************************************* REPLICA| layout of the replica grid, number of groups 1 REPLICA| layout of the replica grid, size of each group 1 REPLICA| MPI process to grid (group,rank) correspondence: ( 0 : 0, 0) VIB| Vibrational Analysis Info Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x7f577e5a739a #1 0x7f577e5a6513 #2 0x7f577da1606f #3 0x417d707d Segmentation fault (imagem do núcleo gravada) Expected results: The calculation should start Additional info: The same input worhs on the binary blob provided by the CP2K team and on Ubuntu.
Created attachment 1473811 [details] Potential file to use with the input
Created attachment 1473812 [details] Basis set to use with the input
Can you install the debuginfo packages, run under gdb and provide the full backtrace? Does it work when you use a different build, e.g. .sopt, .popt or .psmp? Assuming MPI build works, do both OpenMPI and MPICH work, too?
I have tested (with the same results) cp2k.psmp_openmpi cp2k.ssmp cp2k.popt_openmpi cp2k.sopt. Here is the GDB output (hope I got it right). [henrique@localhost CoL3H2O-1000-vib] $ gdb cp2k.ssmp GNU gdb (GDB) Fedora 8.1-25.fc28 Copyright (C) 2018 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later <http://gnu.org/licenses/gpl.html> This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-redhat-linux-gnu". Type "show configuration" for configuration details. For bug reporting instructions, please see: <http://www.gnu.org/software/gdb/bugs/>. Find the GDB manual and other documentation resources online at: <http://www.gnu.org/software/gdb/documentation/>. For help, type "help". Type "apropos word" to search for commands related to "word"... Reading symbols from cp2k.ssmp...Reading symbols from /usr/lib/debug/usr/bin/cp2k.ssmp-5.1-3.fc28.x86_64.debug...done. done. ------------------------------------ ******************************************************************************* ******************************************************************************* ** ** ** # # # # # # ## ** ** # # ### # ## ### #### ## # # ### # ** ** # # # # # ## # # # # # # ## # # # # ** ** ## # # # # # ## # # # # # # # ## # ** ** ## # ### # # # ## # ## # # # # ### ** ** ** ** ## ## # ** ** # # # # ### # # # ### ### ** ** # # ## # # # # # # ## # ## ** ** #### # # # ## # ### ## # ## N. Replicas: 1 ** ** # # # # # # ### # ### # ### N. Procs/Rep: 1 ** ** ## ** ** T. Laino and F. Schiffmann ** ** 2008 - 2015 ** ******************************************************************************* ******************************************************************************* REPLICA| layout of the replica grid, number of groups 1 REPLICA| layout of the replica grid, size of each group 1 REPLICA| MPI process to grid (group,rank) correspondence: ( 0 : 0, 0) VIB| Vibrational Analysis Info Thread 2 "cp2k.ssmp" received signal SIGSEGV, Segmentation fault. [Switching to Thread 0x7fffd9b57700 (LWP 9619)] 0x000000004000507d in ?? () --------------------------------------- (gdb) bt #0 0x000000004000507d in ?? () #1 0x00005555609ffda0 in ?? () #2 0x000000000000a68b in ?? () #3 0x0000000000001625 in ?? () #4 0x00007ffff3255b82 in dbcsr_mm_hostdrv::xsmm_process_mm_stack_d (stack_descr=..., params=..., stack_size=936, a_data=..., b_data=..., c_data=..., used_smm=.FALSE.) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_hostdrv.f90:238 #5 0x00007ffff32567fd in dbcsr_mm_hostdrv::dbcsr_mm_hostdrv_process (this=..., left=..., right=..., params=..., stack_size=936, stack_descr=..., success=.TRUE., used_smm=.FALSE.) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_hostdrv.F:225 #6 0x00007ffff326a7ed in dbcsr_mm_sched::dbcsr_mm_sched_process (this=..., left=..., right=..., stack_data=..., stack_fillcount=0x7fffc409a930, stack_descr=...) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_sched.F:429 #7 0x00007ffff325060b in dbcsr_mm_csr::flush_stacks (this=..., left=..., right=..., purge=<error reading variable: Cannot access memory at address 0x0>) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_csr.F:888 #8 0x00007ffff3253abe in dbcsr_mm_csr::dbcsr_mm_csr_multiply_low (b_norms=..., a_norms=..., b_index=<optimized out>, a_index=<optimized out>, c_hashes=..., stacks_fillcount=..., stacks_data=..., stack_map=0x7fffc4057e30, nk_stacks=-1006299336, nn_stacks=-1006299340, nm_stacks=-1006299344, k_size_maps_size=-1006299116, col_size_maps_size=-1006299120, row_size_maps_size=-1006299124, k_size_maps=0x7fffc4057f10, col_size_maps=0x7fffc4057e80, row_size_maps=0x7fffc4057c40, flop=140736482055904, row_max_epss=..., use_eps=<optimized out>, keep_sparsity=3288667012, c_has_symmetry=3288667008, c_local_cols=..., c_local_rows=..., k_sizes=..., n_sizes=..., m_sizes=..., datasize=1455311380, lastblk=1455311376, c_blk_p=..., c_col_i=..., c_row_i=..., bf=<optimized out>, bi=<optimized out>, af=<optimized out>, ai=<optimized out>, kf=<optimized out>, ki=<optimized out>, mf=<optimized out>, mi=<optimized out>, right=..., left=..., this=...) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_csr.F:442 #9 dbcsr_mm_csr::dbcsr_mm_csr_multiply (this=..., left=..., right=..., mi=56, mf=82, ni=1, nf=7, ki=1, kf=27, ai=2366, af=2851, bi=1, bf=189, m_sizes=..., n_sizes=..., k_sizes=..., c_local_rows=..., c_local_cols=..., c_has_symmetry=.FALSE., keep_sparsity=.FALSE., use_eps=.FALSE., row_max_epss=..., flop=25016160, a_index=..., b_index=..., a_norms=..., b_norms=...) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_csr.F:217 #10 0x00007ffff3265499 in dbcsr_mm_multrec::sparse_multrec (this=..., left=..., right=..., mi=56, mf=82, ni=1, nf=7, ki=1, kf=27, ai=2366, af=2851, a_index=..., bi=1, bf=189, b_index=..., d=4) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_multrec.F:649 #11 0x00007ffff3265068 in dbcsr_mm_multrec::sparse_multrec (this=..., left=..., right=..., mi=56, mf=110, ni=1, nf=7, ki=1, kf=27, ai=2366, af=3121, a_index=..., bi=1, bf=189, b_index=..., d=3) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_multrec.F:667 #12 0x00007ffff32651f0 in dbcsr_mm_multrec::sparse_multrec (this=..., left=..., right=..., mi=56, mf=110, ni=1, nf=7, ki=1, kf=55, ai=2366, af=3905, a_index=..., bi=1, bf=385, b_index=..., d=2) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_multrec.F:683 #13 0x00007ffff3265267 in dbcsr_mm_multrec::sparse_multrec (this=..., left=..., right=..., mi=1, mf=110, ni=1, nf=7, ki=1, kf=55, ai=2311, af=3905, a_index=..., bi=1, bf=385, b_index=..., d=1) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_multrec.F:685 #14 0x00007ffff32651f0 in dbcsr_mm_multrec::sparse_multrec (this=..., left=..., right=..., mi=1, mf=110, ni=1, nf=7, ki=1, kf=110, ai=2311, af=5500, a_index=..., bi=1, bf=770, b_index=..., d=0) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_multrec.F:683 ---Type <return> to continue, or q <return> to quit--- #15 0x00007ffff32667b8 in dbcsr_mm_multrec::dbcsr_mm_multrec_multiply (this=..., left=..., right=..., flop=0, a_norms=..., b_norms=..., k_sizes=...) at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_multrec.F:380 #16 0x00007ffff3256bf4 in dbcsr_mm_cannon::__dbcsr_mm_cannon_MOD_multiply_cannon._omp_fn.3 () at /usr/src/debug/cp2k-5.1-3.fc28.x86_64/src/dbcsr/mm/dbcsr_mm_cannon.F:1707 #17 0x00007fffdb519d1e in gomp_thread_start (xdata=<optimized out>) at ../../../libgomp/team.c:120 #18 0x00007fffdb942594 in start_thread () from /lib64/libpthread.so.0 #19 0x00007fffdbc540df in clone () from /lib64/libc.so.6
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