Your message dated Fri, 07 Sep 2012 00:02:41 +0000 with message-id <e1t9m1x-00074r...@franck.debian.org> and subject line Bug#686874: fixed in cp2k 2.2.426-6 has caused the Debian Bug report #686874, regarding cp2k: segfaults on i386 due to not aligning FFT arrays to 16 bytes for SSE2 and reusing them 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.) -- 686874: http://bugs.debian.org/cgi-bin/bugreport.cgi?bug=686874 Debian Bug Tracking System Contact ow...@bugs.debian.org with problems
--- Begin Message ---Package: cp2k Version: 2.2.426-1 Severity: serious Since some months ago, fftw3 is using SSE2 instructions for fast fourier transforms if the CPU supports it. One requirement for this is that the incoming arrays must be aligned to 16 bytes for the SIMD instructions. This is the case on amd64 by default, but not on i386. Usually, fftw3 will detect unaligned arrays and not use SSE2. However, if the same plan is originally executed with a properly aligned array and then re-executed with another, unaligned array, a segfault will occur, see e.g. https://buildd.debian.org/status/fetch.php?pkg=cp2k&arch=i386&ver=2.2.426-5&stamp=1346699763 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx /build/buildd-cp2k_2.2.426-5-i386-rUGkvz/cp2k-2.2.426/tools/..//TEST-Linux-i686-gfortran-popt-2012-09-03T19:08:13+0000/QS/regtest-nmr-1/H2O-NMR-12.inp.out max_diis: 4 -------------------------------------------------------- eps_scf: 1.00E-05 eps_scf_history: 0.00E+00 eps_diis: 1.00E-01 eps_eigval: 1.00E-05 -------------------------------------------------------- level_shift [a.u.]: 0.00 -------------------------------------------------------- Mixing method: DIRECT_P_MIXING -------------------------------------------------------- No outer SCF Program received signal SIGSEGV: Segmentation fault - invalid memory reference. Backtrace for this error: #0 0x56A8FF6B #1 0x56A905AC #2 0x555733FF #3 0x55FE3C0B #4 0x55F2008B #5 0x55F22E9B #6 0x55F23402 #7 0x55F22E9B #8 0x55FC558B #9 0x9666567 in fftw33d_ at fftw3_lib.F:196 #10 0x966195B in fft_3d_ at fft_lib.f90:135 #11 0x80C77D3 in __fft_tools_MOD_fft3d_s at fft_tools.F:441 #12 0x8340A58 in __pw_methods_MOD_fft_wrap_pw1pw2 at pw_methods.F:1462 #13 0x8EABD6D in __qs_collocate_density_MOD_density_rs2pw at qs_collocate_density.F:3433 #14 0x8EC0EF2 in __qs_collocate_density_MOD_calculate_rho_elec at qs_collocate_density.F:1392 #15 0x849ADDE in __qs_rho_methods_MOD_qs_rho_update_rho at qs_rho_methods.F:391 #16 0x84A1E30 in __qs_scf_MOD_scf_env_initial_rho_setup at qs_scf.F:2277 #17 0x84A9F28 in __qs_scf_MOD_init_scf_run at qs_scf.F:1810 #18 0x84B53A7 in __qs_scf_MOD_scf at qs_scf.F:368 #19 0x836FA1C in __qs_energy_MOD_qs_energies_scf at qs_energy.F:231 #20 0x80CD15C in __force_env_methods_MOD_force_env_calc_energy_force at force_env_methods.F:231 #21 0x8054D39 in __cp2k_runs_MOD_cp2k_run at cp2k_runs.F:403 #22 0x8058C1D in __cp2k_runs_MOD_run_input at cp2k_runs.F:1143 #23 0x804E2C5 in cp2k at cp2k.F:285 xxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxxx This problem is common enough (1/3 of the test cases segfaulted on the autobuilder) that it makes cp2k pretty much unusable on i386. Michael
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--- Begin Message ---Source: cp2k Source-Version: 2.2.426-6 We believe that the bug you reported is fixed in the latest version of cp2k, 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 686...@bugs.debian.org, and the maintainer will reopen the bug report if appropriate. Debian distribution maintenance software pp. Michael Banck <mba...@debian.org> (supplier of updated cp2k 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...@debian.org) -----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Format: 1.8 Date: Fri, 07 Sep 2012 00:27:39 +0200 Source: cp2k Binary: cp2k cp2k-data Architecture: source amd64 all Version: 2.2.426-6 Distribution: unstable Urgency: low Maintainer: Michael Banck <mba...@debian.org> Changed-By: Michael Banck <mba...@debian.org> Description: cp2k - Ab Initio Molecular Dynamics cp2k-data - Ab Initio Molecular Dynamics (data files) Closes: 686874 Changes: cp2k (2.2.426-6) unstable; urgency=low . * debian/rules (FFTW3_ALIGN): New variable, set to '-D__FFTW3_UNALIGNED' on i386. * debian/patches/makeflags.patch: Include $(FFTW3_ALIGN) environment variable in $(DFLAGS). * debian/patches/fftw3_unaligned.patch: New patch, unconditionally adds the FFTW_UNALIGNED flag to the FFTW3 plan if __FFTW3_UNALIGNED is defined, thanks to Julian Taylor (Closes: #686874). * debian/control (Description): Added Metadynamics to capabilities. Checksums-Sha1: dd4f40227eb4025013887341b91aa6742d1dde26 1734 cp2k_2.2.426-6.dsc 6265440f95fc44a752dab6e9f4a331f5b30aa3b5 12069 cp2k_2.2.426-6.debian.tar.gz 866d15c46a1b1d7b6c950d03693a402c03f35eae 12497096 cp2k_2.2.426-6_amd64.deb d1dd6fb57070c40c4d6778b9d557a331766e7490 9357214 cp2k-data_2.2.426-6_all.deb Checksums-Sha256: 528ff5fcff0b638053707a2e02418b3c55f324b23ca4301f795a70614a30a36b 1734 cp2k_2.2.426-6.dsc 5b953c31b1358c1532fa0b4af0801af467aeef37acb0d14c75eae703d78df375 12069 cp2k_2.2.426-6.debian.tar.gz 48878763786cd8b17789ae838c834854b34e8afeef3dea2d7986b1ab6a969baa 12497096 cp2k_2.2.426-6_amd64.deb 05ae31c502cf5ea1e2fcb9833aba9496572941c7e5b0115782cbc5637b9d6341 9357214 cp2k-data_2.2.426-6_all.deb Files: c2c65867a4e95fde5ed8df9981e338b3 1734 science optional cp2k_2.2.426-6.dsc fbcfb6af512bf6595d1305130f0380ce 12069 science optional cp2k_2.2.426-6.debian.tar.gz 9c78a74f9f1a954156a5b3694114c8f2 12497096 science optional cp2k_2.2.426-6_amd64.deb 8feb9006b10b18126fee3a42c8226cae 9357214 science optional cp2k-data_2.2.426-6_all.deb -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.4.10 (GNU/Linux) iEYEARECAAYFAlBJLt0ACgkQmHaJYZ7RAb8aAACfbzXv/nTukxfAuIBTDxnWFD4u EmYAoIGbds1hruJJ14493DfenDUmd8J3 =u0Am -----END PGP SIGNATURE-----
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