I: pbuilder: network access will be disabled during build I: Current time: Tue Sep 29 13:26:09 -12 2020 I: pbuilder-time-stamp: 1601429169 I: Building the build Environment I: extracting base tarball [/var/cache/pbuilder/buster-reproducible-base.tgz] I: copying local configuration I: mounting /proc filesystem I: mounting /sys filesystem I: creating /{dev,run}/shm I: mounting /dev/pts filesystem I: redirecting /dev/ptmx to /dev/pts/ptmx I: policy-rc.d already exists I: Copying source file I: copying [amp_0.6.1-1.dsc] I: copying [./amp_0.6.1.orig.tar.gz] I: copying [./amp_0.6.1-1.debian.tar.xz] I: Extracting source gpgv: unknown type of key resource 'trustedkeys.kbx' gpgv: keyblock resource '/root/.gnupg/trustedkeys.kbx': General error gpgv: Signature made Sun Oct 28 03:09:16 2018 -12 gpgv: using RSA key 8B7868786C33E5C64C4D0A480816B9E18C762BAD gpgv: Can't check signature: No public key dpkg-source: warning: failed to verify signature on ./amp_0.6.1-1.dsc dpkg-source: info: extracting amp in amp-0.6.1 dpkg-source: info: unpacking amp_0.6.1.orig.tar.gz dpkg-source: info: unpacking amp_0.6.1-1.debian.tar.xz dpkg-source: info: using patch list from debian/patches/series dpkg-source: info: applying 01_Makefile.patch dpkg-source: info: applying 03_tools.patch I: using fakeroot in build. I: Installing the build-deps I: user script /srv/workspace/pbuilder/1582/tmp/hooks/D02_print_environment starting I: set BUILDDIR='/build' BUILDUSERGECOS='first user,first room,first work-phone,first home-phone,first other' BUILDUSERNAME='pbuilder1' BUILD_ARCH='armhf' DEBIAN_FRONTEND='noninteractive' DEB_BUILD_OPTIONS='buildinfo=+all reproducible=+all parallel=3' DISTRIBUTION='' HOME='/root' HOST_ARCH='armhf' IFS=' ' INVOCATION_ID='8a8a522aa54948059f5da4f31e73b8cd' LANG='C' LANGUAGE='en_US:en' LC_ALL='C' MAIL='/var/mail/root' OPTIND='1' PATH='/usr/sbin:/usr/bin:/sbin:/bin:/usr/games' PBCURRENTCOMMANDLINEOPERATION='build' PBUILDER_OPERATION='build' PBUILDER_PKGDATADIR='/usr/share/pbuilder' PBUILDER_PKGLIBDIR='/usr/lib/pbuilder' PBUILDER_SYSCONFDIR='/etc' PPID='1582' PS1='# ' PS2='> ' PS4='+ ' PWD='/' SHELL='/bin/bash' SHLVL='2' SUDO_COMMAND='/usr/bin/timeout -k 18.1h 18h /usr/bin/ionice -c 3 /usr/bin/nice /usr/sbin/pbuilder --build --configfile /srv/reproducible-results/rbuild-debian/tmp.voxbBpb8ga/pbuilderrc_el8x --hookdir /etc/pbuilder/first-build-hooks --debbuildopts -b --basetgz /var/cache/pbuilder/buster-reproducible-base.tgz --buildresult /srv/reproducible-results/rbuild-debian/tmp.voxbBpb8ga/b1 --logfile b1/build.log amp_0.6.1-1.dsc' SUDO_GID='114' SUDO_UID='109' SUDO_USER='jenkins' TERM='unknown' TZ='/usr/share/zoneinfo/Etc/GMT+12' USER='root' _='/usr/bin/systemd-run' http_proxy='http://10.0.0.15:8000/' I: uname -a Linux ff2b 4.19.0-11-armmp-lpae #1 SMP Debian 4.19.146-1 (2020-09-17) armv7l GNU/Linux I: ls -l /bin total 3328 -rwxr-xr-x 1 root root 767656 Apr 17 2019 bash -rwxr-xr-x 3 root root 26052 Jul 10 2019 bunzip2 -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzcat lrwxrwxrwx 1 root root 6 Jul 10 2019 bzcmp -> bzdiff -rwxr-xr-x 1 root root 2227 Jul 10 2019 bzdiff lrwxrwxrwx 1 root root 6 Jul 10 2019 bzegrep -> bzgrep -rwxr-xr-x 1 root root 4877 Jun 24 2019 bzexe lrwxrwxrwx 1 root root 6 Jul 10 2019 bzfgrep -> bzgrep -rwxr-xr-x 1 root root 3641 Jul 10 2019 bzgrep -rwxr-xr-x 3 root root 26052 Jul 10 2019 bzip2 -rwxr-xr-x 1 root root 9636 Jul 10 2019 bzip2recover lrwxrwxrwx 1 root root 6 Jul 10 2019 bzless -> bzmore -rwxr-xr-x 1 root root 1297 Jul 10 2019 bzmore -rwxr-xr-x 1 root root 22432 Feb 28 2019 cat -rwxr-xr-x 1 root root 38868 Feb 28 2019 chgrp -rwxr-xr-x 1 root root 38836 Feb 28 2019 chmod -rwxr-xr-x 1 root root 42972 Feb 28 2019 chown -rwxr-xr-x 1 root root 88376 Feb 28 2019 cp -rwxr-xr-x 1 root root 75516 Jan 17 2019 dash -rwxr-xr-x 1 root root 71648 Feb 28 2019 date -rwxr-xr-x 1 root root 51212 Feb 28 2019 dd -rwxr-xr-x 1 root root 55672 Feb 28 2019 df -rwxr-xr-x 1 root root 88444 Feb 28 2019 dir -rwxr-xr-x 1 root root 54872 Jan 9 2019 dmesg lrwxrwxrwx 1 root root 8 Sep 26 2018 dnsdomainname -> hostname lrwxrwxrwx 1 root root 8 Sep 26 2018 domainname -> hostname -rwxr-xr-x 1 root root 22364 Feb 28 2019 echo -rwxr-xr-x 1 root root 28 Jan 7 2019 egrep -rwxr-xr-x 1 root root 18260 Feb 28 2019 false -rwxr-xr-x 1 root root 28 Jan 7 2019 fgrep -rwxr-xr-x 1 root root 47356 Jan 9 2019 findmnt -rwsr-xr-x 1 root root 21980 Apr 22 07:38 fusermount -rwxr-xr-x 1 root root 124508 Jan 7 2019 grep -rwxr-xr-x 2 root root 2345 Jan 5 2019 gunzip -rwxr-xr-x 1 root root 6375 Jan 5 2019 gzexe -rwxr-xr-x 1 root root 64232 Jan 5 2019 gzip -rwxr-xr-x 1 root root 13784 Sep 26 2018 hostname -rwxr-xr-x 1 root root 43044 Feb 28 2019 ln -rwxr-xr-x 1 root root 34932 Jul 26 2018 login -rwxr-xr-x 1 root root 88444 Feb 28 2019 ls -rwxr-xr-x 1 root root 67036 Jan 9 2019 lsblk -rwxr-xr-x 1 root root 47168 Feb 28 2019 mkdir -rwxr-xr-x 1 root root 43040 Feb 28 2019 mknod -rwxr-xr-x 1 root root 26552 Feb 28 2019 mktemp -rwxr-xr-x 1 root root 26024 Jan 9 2019 more -rwsr-xr-x 1 root root 34268 Jan 9 2019 mount -rwxr-xr-x 1 root root 9688 Jan 9 2019 mountpoint -rwxr-xr-x 1 root root 84284 Feb 28 2019 mv lrwxrwxrwx 1 root root 8 Sep 26 2018 nisdomainname -> hostname lrwxrwxrwx 1 root root 14 Feb 14 2019 pidof -> /sbin/killall5 -rwxr-xr-x 1 root root 22416 Feb 28 2019 pwd lrwxrwxrwx 1 root root 4 Apr 17 2019 rbash -> bash -rwxr-xr-x 1 root root 26504 Feb 28 2019 readlink -rwxr-xr-x 1 root root 42968 Feb 28 2019 rm -rwxr-xr-x 1 root root 26496 Feb 28 2019 rmdir -rwxr-xr-x 1 root root 14136 Jan 21 2019 run-parts -rwxr-xr-x 1 root root 76012 Dec 22 2018 sed lrwxrwxrwx 1 root root 4 Sep 20 20:24 sh -> dash -rwxr-xr-x 1 root root 22384 Feb 28 2019 sleep -rwxr-xr-x 1 root root 51124 Feb 28 2019 stty -rwsr-xr-x 1 root root 42472 Jan 9 2019 su -rwxr-xr-x 1 root root 22392 Feb 28 2019 sync -rwxr-xr-x 1 root root 283324 Apr 23 2019 tar -rwxr-xr-x 1 root root 9808 Jan 21 2019 tempfile -rwxr-xr-x 1 root root 63464 Feb 28 2019 touch -rwxr-xr-x 1 root root 18260 Feb 28 2019 true -rwxr-xr-x 1 root root 9636 Apr 22 07:38 ulockmgr_server -rwsr-xr-x 1 root root 21976 Jan 9 2019 umount -rwxr-xr-x 1 root root 22380 Feb 28 2019 uname -rwxr-xr-x 2 root root 2345 Jan 5 2019 uncompress -rwxr-xr-x 1 root root 88444 Feb 28 2019 vdir -rwxr-xr-x 1 root root 21980 Jan 9 2019 wdctl -rwxr-xr-x 1 root root 946 Jan 21 2019 which lrwxrwxrwx 1 root root 8 Sep 26 2018 ypdomainname -> hostname -rwxr-xr-x 1 root root 1983 Jan 5 2019 zcat -rwxr-xr-x 1 root root 1677 Jan 5 2019 zcmp -rwxr-xr-x 1 root root 5879 Jan 5 2019 zdiff -rwxr-xr-x 1 root root 29 Jan 5 2019 zegrep -rwxr-xr-x 1 root root 29 Jan 5 2019 zfgrep -rwxr-xr-x 1 root root 2080 Jan 5 2019 zforce -rwxr-xr-x 1 root root 7584 Jan 5 2019 zgrep -rwxr-xr-x 1 root root 2205 Jan 5 2019 zless -rwxr-xr-x 1 root root 1841 Jan 5 2019 zmore -rwxr-xr-x 1 root root 4552 Jan 5 2019 znew I: user script /srv/workspace/pbuilder/1582/tmp/hooks/D02_print_environment finished -> Attempting to satisfy build-dependencies -> Creating pbuilder-satisfydepends-dummy package Package: pbuilder-satisfydepends-dummy Version: 0.invalid.0 Architecture: armhf Maintainer: Debian Pbuilder Team Description: Dummy package to satisfy dependencies with aptitude - created by pbuilder This package was created automatically by pbuilder to satisfy the build-dependencies of the package being currently built. Depends: debhelper-compat (= 11), dh-python, gfortran, python3-all-dev, python3-ase (>= 3.9.0~), python3-matplotlib, python3-nose, python3-numpy, python3-scipy, python3-setuptools, python3-pexpect, python3-zmq, openssh-server dpkg-deb: building package 'pbuilder-satisfydepends-dummy' in '/tmp/satisfydepends-aptitude/pbuilder-satisfydepends-dummy.deb'. Selecting previously unselected package pbuilder-satisfydepends-dummy. (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../pbuilder-satisfydepends-dummy.deb ... Unpacking pbuilder-satisfydepends-dummy (0.invalid.0) ... dpkg: pbuilder-satisfydepends-dummy: dependency problems, but configuring anyway as you requested: pbuilder-satisfydepends-dummy depends on debhelper-compat (= 11); however: Package debhelper-compat is not installed. pbuilder-satisfydepends-dummy depends on dh-python; however: Package dh-python is not installed. pbuilder-satisfydepends-dummy depends on gfortran; however: Package gfortran is not installed. pbuilder-satisfydepends-dummy depends on python3-all-dev; however: Package python3-all-dev is not installed. pbuilder-satisfydepends-dummy depends on python3-ase (>= 3.9.0~); however: Package python3-ase is not installed. pbuilder-satisfydepends-dummy depends on python3-matplotlib; however: Package python3-matplotlib is not installed. pbuilder-satisfydepends-dummy depends on python3-nose; however: Package python3-nose is not installed. pbuilder-satisfydepends-dummy depends on python3-numpy; however: Package python3-numpy is not installed. pbuilder-satisfydepends-dummy depends on python3-scipy; however: Package python3-scipy is not installed. pbuilder-satisfydepends-dummy depends on python3-setuptools; however: Package python3-setuptools is not installed. pbuilder-satisfydepends-dummy depends on python3-pexpect; however: Package python3-pexpect is not installed. pbuilder-satisfydepends-dummy depends on python3-zmq; however: Package python3-zmq is not installed. pbuilder-satisfydepends-dummy depends on openssh-server; however: Package openssh-server is not installed. Setting up pbuilder-satisfydepends-dummy (0.invalid.0) ... Reading package lists... Building dependency tree... Reading state information... Initializing package states... Writing extended state information... Building tag database... pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) pbuilder-satisfydepends-dummy is already installed at the requested version (0.invalid.0) The following NEW packages will be installed: autoconf{a} automake{a} autopoint{a} autotools-dev{a} bsdmainutils{a} debhelper{a} dh-autoreconf{a} dh-python{a} dh-strip-nondeterminism{a} dwz{a} file{a} fonts-font-awesome{a} fonts-glyphicons-halflings{a} fonts-lyx{a} gettext{a} gettext-base{a} gfortran{a} gfortran-8{a} groff-base{a} intltool-debian{a} libarchive-zip-perl{a} libblas3{a} libbsd0{a} libcroco3{a} libedit2{a} libelf1{a} libexpat1{a} libexpat1-dev{a} libfile-stripnondeterminism-perl{a} libfreetype6{a} libgfortran-8-dev{a} libgfortran5{a} libglib2.0-0{a} libgssapi-krb5-2{a} libicu63{a} libjs-bootstrap{a} libjs-jquery{a} libjs-jquery-ui{a} libk5crypto3{a} libkeyutils1{a} libkrb5-3{a} libkrb5support0{a} liblapack3{a} libmagic-mgc{a} libmagic1{a} libmpdec2{a} libncurses6{a} libnorm1{a} libpgm-5.2-0{a} libpipeline1{a} libpng16-16{a} libprocps7{a} libpython3-all-dev{a} libpython3-dev{a} libpython3-stdlib{a} libpython3.7{a} libpython3.7-dev{a} libpython3.7-minimal{a} libpython3.7-stdlib{a} libreadline7{a} libsigsegv2{a} libsodium23{a} libssl1.1{a} libtool{a} libuchardet0{a} libwrap0{a} libxml2{a} libzmq5{a} lsb-base{a} m4{a} man-db{a} mime-support{a} openssh-client{a} openssh-server{a} openssh-sftp-server{a} po-debconf{a} procps{a} python-matplotlib-data{a} python3{a} python3-all{a} python3-all-dev{a} python3-ase{a} python3-click{a} python3-colorama{a} python3-cycler{a} python3-dateutil{a} python3-decorator{a} python3-dev{a} python3-distutils{a} python3-flask{a} python3-itsdangerous{a} python3-jinja2{a} python3-kiwisolver{a} python3-lib2to3{a} python3-markupsafe{a} python3-matplotlib{a} python3-minimal{a} python3-nose{a} python3-numpy{a} python3-pexpect{a} python3-pkg-resources{a} python3-ptyprocess{a} python3-pyparsing{a} python3-scipy{a} python3-setuptools{a} python3-six{a} python3-spglib{a} python3-werkzeug{a} python3-zmq{a} python3.7{a} python3.7-dev{a} python3.7-minimal{a} readline-common{a} sensible-utils{a} ttf-bitstream-vera{a} ucf{a} The following packages are RECOMMENDED but will NOT be installed: curl javascript-common krb5-locales libarchive-cpio-perl libglib2.0-data libgpm2 libltdl-dev libmail-sendmail-perl libpam-elogind libpam-systemd lynx ncurses-term psmisc python3-blinker python3-openssl python3-pil python3-pyinotify python3-simplejson python3-tk shared-mime-info wget xauth xdg-user-dirs 0 packages upgraded, 116 newly installed, 0 to remove and 0 not upgraded. Need to get 112 MB of archives. After unpacking 282 MB will be used. Writing extended state information... Get: 1 http://deb.debian.org/debian buster/main armhf libbsd0 armhf 0.9.1-2 [103 kB] Get: 2 http://deb.debian.org/debian buster/main armhf bsdmainutils armhf 11.1.2+b1 [186 kB] Get: 3 http://deb.debian.org/debian buster/main armhf libuchardet0 armhf 0.0.6-3 [62.2 kB] Get: 4 http://deb.debian.org/debian buster/main armhf groff-base armhf 1.22.4-3 [828 kB] Get: 5 http://deb.debian.org/debian buster/main armhf libpipeline1 armhf 1.5.1-2 [26.8 kB] Get: 6 http://deb.debian.org/debian buster/main armhf man-db armhf 2.8.5-2 [1240 kB] Get: 7 http://deb.debian.org/debian buster/main armhf libssl1.1 armhf 1.1.1d-0+deb10u3 [1299 kB] Get: 8 http://deb.debian.org/debian buster/main armhf libpython3.7-minimal armhf 3.7.3-2+deb10u2 [582 kB] Get: 9 http://deb.debian.org/debian buster/main armhf libexpat1 armhf 2.2.6-2+deb10u1 [78.0 kB] Get: 10 http://deb.debian.org/debian buster/main armhf python3.7-minimal armhf 3.7.3-2+deb10u2 [1466 kB] Get: 11 http://deb.debian.org/debian buster/main armhf python3-minimal armhf 3.7.3-1 [36.6 kB] Get: 12 http://deb.debian.org/debian buster/main armhf mime-support all 3.62 [37.2 kB] Get: 13 http://deb.debian.org/debian buster/main armhf libmpdec2 armhf 2.4.2-2 [69.3 kB] Get: 14 http://deb.debian.org/debian buster/main armhf readline-common all 7.0-5 [70.6 kB] Get: 15 http://deb.debian.org/debian buster/main armhf libreadline7 armhf 7.0-5 [131 kB] Get: 16 http://deb.debian.org/debian buster/main armhf libpython3.7-stdlib armhf 3.7.3-2+deb10u2 [1660 kB] Get: 17 http://deb.debian.org/debian buster/main armhf python3.7 armhf 3.7.3-2+deb10u2 [330 kB] Get: 18 http://deb.debian.org/debian buster/main armhf libpython3-stdlib armhf 3.7.3-1 [20.0 kB] Get: 19 http://deb.debian.org/debian buster/main armhf python3 armhf 3.7.3-1 [61.5 kB] Get: 20 http://deb.debian.org/debian buster/main armhf libncurses6 armhf 6.1+20181013-2+deb10u2 [79.8 kB] Get: 21 http://deb.debian.org/debian buster/main armhf libprocps7 armhf 2:3.3.15-2 [58.7 kB] Get: 22 http://deb.debian.org/debian buster/main armhf lsb-base all 10.2019051400 [28.4 kB] Get: 23 http://deb.debian.org/debian buster/main armhf procps armhf 2:3.3.15-2 [248 kB] Get: 24 http://deb.debian.org/debian buster/main armhf sensible-utils all 0.0.12 [15.8 kB] Get: 25 http://deb.debian.org/debian buster/main armhf libmagic-mgc armhf 1:5.35-4+deb10u1 [242 kB] Get: 26 http://deb.debian.org/debian buster/main armhf libmagic1 armhf 1:5.35-4+deb10u1 [110 kB] Get: 27 http://deb.debian.org/debian buster/main armhf file armhf 1:5.35-4+deb10u1 [65.5 kB] Get: 28 http://deb.debian.org/debian buster/main armhf gettext-base armhf 0.19.8.1-9 [118 kB] Get: 29 http://deb.debian.org/debian buster/main armhf libedit2 armhf 3.1-20181209-1 [79.5 kB] Get: 30 http://deb.debian.org/debian buster/main armhf libkeyutils1 armhf 1.6-6 [13.9 kB] Get: 31 http://deb.debian.org/debian buster/main armhf libkrb5support0 armhf 1.17-3 [62.3 kB] Get: 32 http://deb.debian.org/debian buster/main armhf libk5crypto3 armhf 1.17-3 [119 kB] Get: 33 http://deb.debian.org/debian buster/main armhf libkrb5-3 armhf 1.17-3 [323 kB] Get: 34 http://deb.debian.org/debian buster/main armhf libgssapi-krb5-2 armhf 1.17-3 [137 kB] Get: 35 http://deb.debian.org/debian buster/main armhf openssh-client armhf 1:7.9p1-10+deb10u2 [704 kB] Get: 36 http://deb.debian.org/debian buster/main armhf ucf all 3.0038+nmu1 [69.0 kB] Get: 37 http://deb.debian.org/debian buster/main armhf libsigsegv2 armhf 2.12-2 [32.1 kB] Get: 38 http://deb.debian.org/debian buster/main armhf m4 armhf 1.4.18-2 [190 kB] Get: 39 http://deb.debian.org/debian buster/main armhf autoconf all 2.69-11 [341 kB] Get: 40 http://deb.debian.org/debian buster/main armhf autotools-dev all 20180224.1 [77.0 kB] Get: 41 http://deb.debian.org/debian buster/main armhf automake all 1:1.16.1-4 [771 kB] Get: 42 http://deb.debian.org/debian buster/main armhf autopoint all 0.19.8.1-9 [434 kB] Get: 43 http://deb.debian.org/debian buster/main armhf libtool all 2.4.6-9 [547 kB] Get: 44 http://deb.debian.org/debian buster/main armhf dh-autoreconf all 19 [16.9 kB] Get: 45 http://deb.debian.org/debian buster/main armhf libarchive-zip-perl all 1.64-1 [96.8 kB] Get: 46 http://deb.debian.org/debian buster/main armhf libfile-stripnondeterminism-perl all 1.1.2-1 [19.8 kB] Get: 47 http://deb.debian.org/debian buster/main armhf dh-strip-nondeterminism all 1.1.2-1 [13.0 kB] Get: 48 http://deb.debian.org/debian buster/main armhf libelf1 armhf 0.176-1.1 [158 kB] Get: 49 http://deb.debian.org/debian buster/main armhf dwz armhf 0.12-3 [72.0 kB] Get: 50 http://deb.debian.org/debian buster/main armhf libglib2.0-0 armhf 2.58.3-2+deb10u2 [1101 kB] Get: 51 http://deb.debian.org/debian buster/main armhf libicu63 armhf 63.1-6+deb10u1 [8005 kB] Get: 52 http://deb.debian.org/debian buster/main armhf libxml2 armhf 2.9.4+dfsg1-7+b3 [595 kB] Get: 53 http://deb.debian.org/debian buster/main armhf libcroco3 armhf 0.6.12-3 [133 kB] Get: 54 http://deb.debian.org/debian buster/main armhf gettext armhf 0.19.8.1-9 [1242 kB] Get: 55 http://deb.debian.org/debian buster/main armhf intltool-debian all 0.35.0+20060710.5 [26.8 kB] Get: 56 http://deb.debian.org/debian buster/main armhf po-debconf all 1.0.21 [248 kB] Get: 57 http://deb.debian.org/debian buster/main armhf debhelper all 12.1.1 [1016 kB] Get: 58 http://deb.debian.org/debian buster/main armhf python3-lib2to3 all 3.7.3-1 [76.7 kB] Get: 59 http://deb.debian.org/debian buster/main armhf python3-distutils all 3.7.3-1 [142 kB] Get: 60 http://deb.debian.org/debian buster/main armhf dh-python all 3.20190308 [99.3 kB] Get: 61 http://deb.debian.org/debian buster/main armhf fonts-font-awesome all 5.0.10+really4.7.0~dfsg-1 [515 kB] Get: 62 http://deb.debian.org/debian buster/main armhf fonts-glyphicons-halflings all 1.009~3.4.1+dfsg-1 [164 kB] Get: 63 http://deb.debian.org/debian buster/main armhf fonts-lyx all 2.3.2-1 [199 kB] Get: 64 http://deb.debian.org/debian buster/main armhf libgfortran5 armhf 8.3.0-6 [213 kB] Get: 65 http://deb.debian.org/debian buster/main armhf libgfortran-8-dev armhf 8.3.0-6 [260 kB] Get: 66 http://deb.debian.org/debian buster/main armhf gfortran-8 armhf 8.3.0-6 [7219 kB] Get: 67 http://deb.debian.org/debian buster/main armhf gfortran armhf 4:8.3.0-1 [1424 B] Get: 68 http://deb.debian.org/debian buster/main armhf libblas3 armhf 3.8.0-2 [109 kB] Get: 69 http://deb.debian.org/debian buster/main armhf libexpat1-dev armhf 2.2.6-2+deb10u1 [126 kB] Get: 70 http://deb.debian.org/debian buster/main armhf libpng16-16 armhf 1.6.36-6 [275 kB] Get: 71 http://deb.debian.org/debian buster/main armhf libfreetype6 armhf 2.9.1-3+deb10u1 [322 kB] Get: 72 http://deb.debian.org/debian buster/main armhf libjs-bootstrap all 3.4.1+dfsg-1 [173 kB] Get: 73 http://deb.debian.org/debian buster/main armhf libjs-jquery all 3.3.1~dfsg-3 [332 kB] Get: 74 http://deb.debian.org/debian buster/main armhf libjs-jquery-ui all 1.12.1+dfsg-5 [232 kB] Get: 75 http://deb.debian.org/debian buster/main armhf liblapack3 armhf 3.8.0-2 [1631 kB] Get: 76 http://deb.debian.org/debian buster/main armhf libnorm1 armhf 1.5.8+dfsg2-1 [243 kB] Get: 77 http://deb.debian.org/debian buster/main armhf libpgm-5.2-0 armhf 5.2.122~dfsg-3 [155 kB] Get: 78 http://deb.debian.org/debian buster/main armhf libpython3.7 armhf 3.7.3-2+deb10u2 [1281 kB] Get: 79 http://deb.debian.org/debian buster/main armhf libpython3.7-dev armhf 3.7.3-2+deb10u2 [47.2 MB] Get: 80 http://deb.debian.org/debian buster/main armhf libpython3-dev armhf 3.7.3-1 [20.1 kB] Get: 81 http://deb.debian.org/debian buster/main armhf libpython3-all-dev armhf 3.7.3-1 [1068 B] Get: 82 http://deb.debian.org/debian buster/main armhf libsodium23 armhf 1.0.17-1 [144 kB] Get: 83 http://deb.debian.org/debian buster/main armhf libwrap0 armhf 7.6.q-28 [55.9 kB] Get: 84 http://deb.debian.org/debian buster/main armhf libzmq5 armhf 4.3.1-4+deb10u2 [209 kB] Get: 85 http://deb.debian.org/debian buster/main armhf openssh-sftp-server armhf 1:7.9p1-10+deb10u2 [38.7 kB] Get: 86 http://deb.debian.org/debian buster/main armhf openssh-server armhf 1:7.9p1-10+deb10u2 [319 kB] Get: 87 http://deb.debian.org/debian buster/main armhf ttf-bitstream-vera all 1.10-8 [352 kB] Get: 88 http://deb.debian.org/debian buster/main armhf python-matplotlib-data all 3.0.2-2 [4138 kB] Get: 89 http://deb.debian.org/debian buster/main armhf python3-all armhf 3.7.3-1 [1068 B] Get: 90 http://deb.debian.org/debian buster/main armhf python3.7-dev armhf 3.7.3-2+deb10u2 [509 kB] Get: 91 http://deb.debian.org/debian buster/main armhf python3-dev armhf 3.7.3-1 [1264 B] Get: 92 http://deb.debian.org/debian buster/main armhf python3-all-dev armhf 3.7.3-1 [1064 B] Get: 93 http://deb.debian.org/debian buster/main armhf python3-pkg-resources all 40.8.0-1 [153 kB] Get: 94 http://deb.debian.org/debian buster/main armhf python3-numpy armhf 1:1.16.2-1 [1903 kB] Get: 95 http://deb.debian.org/debian buster/main armhf python3-decorator all 4.3.0-1.1 [14.5 kB] Get: 96 http://deb.debian.org/debian buster/main armhf python3-scipy armhf 1.1.0-7 [9090 kB] Get: 97 http://deb.debian.org/debian buster/main armhf python3-spglib armhf 1.12.2-1 [90.7 kB] Get: 98 http://deb.debian.org/debian buster/main armhf python3-colorama all 0.3.7-1 [18.1 kB] Get: 99 http://deb.debian.org/debian buster/main armhf python3-click all 7.0-1 [73.6 kB] Get: 100 http://deb.debian.org/debian buster/main armhf python3-itsdangerous all 0.24+dfsg1-2 [13.0 kB] Get: 101 http://deb.debian.org/debian buster/main armhf python3-markupsafe armhf 1.1.0-1 [14.2 kB] Get: 102 http://deb.debian.org/debian buster/main armhf python3-jinja2 all 2.10-2 [106 kB] Get: 103 http://deb.debian.org/debian buster/main armhf python3-werkzeug all 0.14.1+dfsg1-4+deb10u1 [196 kB] Get: 104 http://deb.debian.org/debian buster/main armhf python3-flask all 1.0.2-3 [93.0 kB] Get: 105 http://deb.debian.org/debian buster/main armhf python3-six all 1.12.0-1 [15.7 kB] Get: 106 http://deb.debian.org/debian buster/main armhf python3-dateutil all 2.7.3-3 [64.5 kB] Get: 107 http://deb.debian.org/debian buster/main armhf python3-pyparsing all 2.2.0+dfsg1-2 [89.6 kB] Get: 108 http://deb.debian.org/debian buster/main armhf python3-cycler all 0.10.0-1 [7556 B] Get: 109 http://deb.debian.org/debian buster/main armhf python3-kiwisolver armhf 1.0.1-2+b1 [58.9 kB] Get: 110 http://deb.debian.org/debian buster/main armhf python3-matplotlib armhf 3.0.2-2 [5288 kB] Get: 111 http://deb.debian.org/debian buster/main armhf python3-ase all 3.17.0-2 [1159 kB] Get: 112 http://deb.debian.org/debian buster/main armhf python3-nose all 1.3.7-4 [132 kB] Get: 113 http://deb.debian.org/debian buster/main armhf python3-ptyprocess all 0.6.0-1 [13.2 kB] Get: 114 http://deb.debian.org/debian buster/main armhf python3-pexpect all 4.6.0-1 [52.4 kB] Get: 115 http://deb.debian.org/debian buster/main armhf python3-setuptools all 40.8.0-1 [306 kB] Get: 116 http://deb.debian.org/debian buster/main armhf python3-zmq armhf 17.1.2-2+deb10u1 [248 kB] Fetched 112 MB in 13s (8316 kB/s) debconf: delaying package configuration, since apt-utils is not installed Selecting previously unselected package libbsd0:armhf. (Reading database ... (Reading database ... 5% (Reading database ... 10% (Reading database ... 15% (Reading database ... 20% (Reading database ... 25% (Reading database ... 30% (Reading database ... 35% (Reading database ... 40% (Reading database ... 45% (Reading database ... 50% (Reading database ... 55% (Reading database ... 60% (Reading database ... 65% (Reading database ... 70% (Reading database ... 75% (Reading database ... 80% (Reading database ... 85% (Reading database ... 90% (Reading database ... 95% (Reading database ... 100% (Reading database ... 18932 files and directories currently installed.) Preparing to unpack .../0-libbsd0_0.9.1-2_armhf.deb ... Unpacking libbsd0:armhf (0.9.1-2) ... Selecting previously unselected package bsdmainutils. Preparing to unpack .../1-bsdmainutils_11.1.2+b1_armhf.deb ... Unpacking bsdmainutils (11.1.2+b1) ... Selecting previously unselected package libuchardet0:armhf. Preparing to unpack .../2-libuchardet0_0.0.6-3_armhf.deb ... 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Unpacking liblapack3:armhf (3.8.0-2) ... Selecting previously unselected package libnorm1:armhf. Preparing to unpack .../57-libnorm1_1.5.8+dfsg2-1_armhf.deb ... Unpacking libnorm1:armhf (1.5.8+dfsg2-1) ... Selecting previously unselected package libpgm-5.2-0:armhf. Preparing to unpack .../58-libpgm-5.2-0_5.2.122~dfsg-3_armhf.deb ... Unpacking libpgm-5.2-0:armhf (5.2.122~dfsg-3) ... Selecting previously unselected package libpython3.7:armhf. Preparing to unpack .../59-libpython3.7_3.7.3-2+deb10u2_armhf.deb ... Unpacking libpython3.7:armhf (3.7.3-2+deb10u2) ... Selecting previously unselected package libpython3.7-dev:armhf. Preparing to unpack .../60-libpython3.7-dev_3.7.3-2+deb10u2_armhf.deb ... Unpacking libpython3.7-dev:armhf (3.7.3-2+deb10u2) ... Selecting previously unselected package libpython3-dev:armhf. Preparing to unpack .../61-libpython3-dev_3.7.3-1_armhf.deb ... Unpacking libpython3-dev:armhf (3.7.3-1) ... Selecting previously unselected package libpython3-all-dev:armhf. 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Unpacking python3-zmq (17.1.2-2+deb10u1) ... Setting up libpipeline1:armhf (1.5.1-2) ... Setting up lsb-base (10.2019051400) ... Setting up libkeyutils1:armhf (1.6-6) ... Setting up ttf-bitstream-vera (1.10-8) ... Setting up libsodium23:armhf (1.0.17-1) ... Setting up mime-support (3.62) ... Setting up libmagic-mgc (1:5.35-4+deb10u1) ... Setting up libarchive-zip-perl (1.64-1) ... Setting up libglib2.0-0:armhf (2.58.3-2+deb10u2) ... No schema files found: doing nothing. Setting up fonts-glyphicons-halflings (1.009~3.4.1+dfsg-1) ... Setting up fonts-lyx (2.3.2-1) ... Setting up libprocps7:armhf (2:3.3.15-2) ... Setting up libnorm1:armhf (1.5.8+dfsg2-1) ... Setting up libmagic1:armhf (1:5.35-4+deb10u1) ... Setting up gettext-base (0.19.8.1-9) ... Setting up file (1:5.35-4+deb10u1) ... Setting up libicu63:armhf (63.1-6+deb10u1) ... Setting up libkrb5support0:armhf (1.17-3) ... Setting up autotools-dev (20180224.1) ... Setting up libexpat1-dev:armhf (2.2.6-2+deb10u1) ... Setting up libwrap0:armhf (7.6.q-28) ... Setting up libncurses6:armhf (6.1+20181013-2+deb10u2) ... Setting up libsigsegv2:armhf (2.12-2) ... Setting up libpng16-16:armhf (1.6.36-6) ... Setting up autopoint (0.19.8.1-9) ... Setting up libk5crypto3:armhf (1.17-3) ... Setting up libgfortran5:armhf (8.3.0-6) ... Setting up sensible-utils (0.0.12) ... Setting up libuchardet0:armhf (0.0.6-3) ... Setting up procps (2:3.3.15-2) ... update-alternatives: using /usr/bin/w.procps to provide /usr/bin/w (w) in auto mode Setting up libkrb5-3:armhf (1.17-3) ... Setting up libmpdec2:armhf (2.4.2-2) ... Setting up libjs-jquery (3.3.1~dfsg-3) ... Setting up python-matplotlib-data (3.0.2-2) ... Setting up libbsd0:armhf (0.9.1-2) ... Setting up libelf1:armhf (0.176-1.1) ... Setting up readline-common (7.0-5) ... Setting up libxml2:armhf (2.9.4+dfsg1-7+b3) ... Setting up fonts-font-awesome (5.0.10+really4.7.0~dfsg-1) ... Setting up libjs-bootstrap (3.4.1+dfsg-1) ... Setting up libreadline7:armhf (7.0-5) ... Setting up libpgm-5.2-0:armhf (5.2.122~dfsg-3) ... Setting up libfile-stripnondeterminism-perl (1.1.2-1) ... Setting up libgfortran-8-dev:armhf (8.3.0-6) ... Setting up libpython3.7-stdlib:armhf (3.7.3-2+deb10u2) ... Setting up libpython3.7:armhf (3.7.3-2+deb10u2) ... Setting up libtool (2.4.6-9) ... Setting up gfortran-8 (8.3.0-6) ... Setting up libpython3.7-dev:armhf (3.7.3-2+deb10u2) ... Setting up libedit2:armhf (3.1-20181209-1) ... Setting up m4 (1.4.18-2) ... Setting up gfortran (4:8.3.0-1) ... update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f95 (f95) in auto mode update-alternatives: using /usr/bin/gfortran to provide /usr/bin/f77 (f77) in auto mode Setting up libblas3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/blas/libblas.so.3 to provide /usr/lib/arm-linux-gnueabihf/libblas.so.3 (libblas.so.3-arm-linux-gnueabihf) in auto mode Setting up libjs-jquery-ui (1.12.1+dfsg-5) ... Setting up libfreetype6:armhf (2.9.1-3+deb10u1) ... Setting up bsdmainutils (11.1.2+b1) ... update-alternatives: using /usr/bin/bsd-write to provide /usr/bin/write (write) in auto mode update-alternatives: using /usr/bin/bsd-from to provide /usr/bin/from (from) in auto mode Setting up libgssapi-krb5-2:armhf (1.17-3) ... Setting up libcroco3:armhf (0.6.12-3) ... Setting up ucf (3.0038+nmu1) ... Setting up autoconf (2.69-11) ... Setting up dwz (0.12-3) ... Setting up groff-base (1.22.4-3) ... Setting up libpython3-stdlib:armhf (3.7.3-1) ... Setting up automake (1:1.16.1-4) ... update-alternatives: using /usr/bin/automake-1.16 to provide /usr/bin/automake (automake) in auto mode Setting up python3.7 (3.7.3-2+deb10u2) ... Setting up liblapack3:armhf (3.8.0-2) ... update-alternatives: using /usr/lib/arm-linux-gnueabihf/lapack/liblapack.so.3 to provide /usr/lib/arm-linux-gnueabihf/liblapack.so.3 (liblapack.so.3-arm-linux-gnueabihf) in auto mode Setting up gettext (0.19.8.1-9) ... Setting up libpython3-dev:armhf (3.7.3-1) ... Setting up libzmq5:armhf (4.3.1-4+deb10u2) ... Setting up openssh-client (1:7.9p1-10+deb10u2) ... Setting up python3 (3.7.3-1) ... Setting up man-db (2.8.5-2) ... Not building database; man-db/auto-update is not 'true'. Setting up python3-markupsafe (1.1.0-1) ... Setting up python3.7-dev (3.7.3-2+deb10u2) ... Setting up intltool-debian (0.35.0+20060710.5) ... Setting up python3-six (1.12.0-1) ... Setting up python3-decorator (4.3.0-1.1) ... Setting up python3-jinja2 (2.10-2) ... Setting up python3-pyparsing (2.2.0+dfsg1-2) ... Setting up python3-werkzeug (0.14.1+dfsg1-4+deb10u1) ... Setting up libpython3-all-dev:armhf (3.7.3-1) ... Setting up python3-zmq (17.1.2-2+deb10u1) ... Setting up python3-cycler (0.10.0-1) ... Setting up python3-dateutil (2.7.3-3) ... Setting up python3-lib2to3 (3.7.3-1) ... Setting up python3-ptyprocess (0.6.0-1) ... Setting up python3-pkg-resources (40.8.0-1) ... Setting up python3-distutils (3.7.3-1) ... Setting up dh-python (3.20190308) ... Setting up openssh-sftp-server (1:7.9p1-10+deb10u2) ... Setting up python3-setuptools (40.8.0-1) ... Setting up openssh-server (1:7.9p1-10+deb10u2) ... Creating config file /etc/ssh/sshd_config with new version Creating SSH2 RSA key; this may take some time ... 2048 SHA256:4gPm5VWjOcgO3dr+rU6qG9TXGsGswtQ+XDkMosoluIQ root@ff2b (RSA) Creating SSH2 ECDSA key; this may take some time ... 256 SHA256:bi/7lCnULFHoN/lGg0ZLcfUUCLNypLvt1gWcc6NKQig root@ff2b (ECDSA) Creating SSH2 ED25519 key; this may take some time ... 256 SHA256:EH5skk4NVsWlLTfDmMYaG0PLWE8vgBdaKvRIL50HQjY root@ff2b (ED25519) invoke-rc.d: could not determine current runlevel invoke-rc.d: policy-rc.d denied execution of start. Setting up python3-colorama (0.3.7-1) ... Setting up po-debconf (1.0.21) ... Setting up python3-itsdangerous (0.24+dfsg1-2) ... Setting up python3-all (3.7.3-1) ... Setting up python3-click (7.0-1) ... Setting up python3-nose (1.3.7-4) ... Setting up python3-pexpect (4.6.0-1) ... Setting up python3-dev (3.7.3-1) ... Setting up python3-kiwisolver (1.0.1-2+b1) ... Setting up python3-numpy (1:1.16.2-1) ... Setting up python3-spglib (1.12.2-1) ... Setting up python3-all-dev (3.7.3-1) ... Setting up python3-matplotlib (3.0.2-2) ... Setting up python3-scipy (1.1.0-7) ... Setting up python3-flask (1.0.2-3) ... Setting up python3-ase (3.17.0-2) ... Setting up debhelper (12.1.1) ... Setting up dh-autoreconf (19) ... Setting up dh-strip-nondeterminism (1.1.2-1) ... Processing triggers for libc-bin (2.28-10) ... Reading package lists... Building dependency tree... Reading state information... Reading extended state information... Initializing package states... Writing extended state information... Building tag database... -> Finished parsing the build-deps Reading package lists... Building dependency tree... Reading state information... fakeroot is already the newest version (1.23-1). 0 upgraded, 0 newly installed, 0 to remove and 0 not upgraded. I: Building the package I: Running cd /build/amp-0.6.1/ && env PATH="/usr/sbin:/usr/bin:/sbin:/bin:/usr/games" HOME="/nonexistent/first-build" dpkg-buildpackage -us -uc -b dpkg-buildpackage: info: source package amp dpkg-buildpackage: info: source version 0.6.1-1 dpkg-buildpackage: info: source distribution unstable dpkg-buildpackage: info: source changed by Mattia Rizzolo dpkg-source --before-build . dpkg-buildpackage: info: host architecture armhf fakeroot debian/rules clean dh clean --with python3 --buildsystem=pybuild debian/rules override_dh_auto_clean make[1]: Entering directory '/build/amp-0.6.1' dh_auto_clean I: pybuild base:217: python3.7 setup.py clean running clean removing '/build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build' (and everything under it) 'build/bdist.linux-armhf' does not exist -- can't clean it 'build/scripts.linux-armhf-3.7' does not exist -- can't clean it /usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) rm -rf amp.egg-info/ find . -name "*.json" -delete find . -name "*-train-log.txt" -delete find . -name "*.pyc" -delete find . -name "*.o" -delete find . -name "*.mod" -delete find . -name "*.so" -delete make[1]: Leaving directory '/build/amp-0.6.1' dh_autoreconf_clean -O--buildsystem=pybuild dh_clean -O--buildsystem=pybuild debian/rules build dh build --with python3 --buildsystem=pybuild dh_update_autotools_config -O--buildsystem=pybuild dh_autoreconf -O--buildsystem=pybuild dh_auto_configure -O--buildsystem=pybuild I: pybuild base:217: python3.7 setup.py config running config /usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) dh_auto_build -O--buildsystem=pybuild I: pybuild pybuild:272: make -C amp python3.7 make[1]: Entering directory '/build/amp-0.6.1/amp' Building for python3.7 (3.7) make -C model make[2]: Entering directory '/build/amp-0.6.1/amp/model' gfortran -c neuralnetwork.f90 cp neuralnetwork.mod .. make[2]: Leaving directory '/build/amp-0.6.1/amp/model' make -C descriptor make[2]: Entering directory '/build/amp-0.6.1/amp/descriptor' gfortran -c cutoffs.f90 cp cutoffs.mod .. make[2]: Leaving directory '/build/amp-0.6.1/amp/descriptor' f2py3.7 -c -m fmodules model.f90 descriptor/cutoffs.f90 descriptor/gaussian.f90 descriptor/zernike.f90 model/neuralnetwork.f90 running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "fmodules" sources f2py options: [] f2py:> /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodulesmodule.c creating /tmp/tmpzebktwtd/src.linux-armhf-3.7 Reading fortran codes... Reading file 'model.f90' (format:fix) Line #99 in model.f90:" type:: image_forces " analyzeline: No name/args pattern found for line. Line #104 in model.f90:" type:: integer_one_d_array " analyzeline: No name/args pattern found for line. Line #109 in model.f90:" type:: embedded_real_one_one_d_array " analyzeline: No name/args pattern found for line. Line #114 in model.f90:" type:: embedded_real_one_two_d_array " analyzeline: No name/args pattern found for line. Line #119 in model.f90:" type:: embedded_integer_one_one_d_array " analyzeline: No name/args pattern found for line. Line #124 in model.f90:" type:: embedded_one_one_two_d_array " analyzeline: No name/args pattern found for line. Reading file 'descriptor/cutoffs.f90' (format:fix) Reading file 'descriptor/gaussian.f90' (format:free) Reading file 'descriptor/zernike.f90' (format:free) Reading file 'model/neuralnetwork.f90' (format:fix) Line #17 in model/neuralnetwork.f90:" type:: real_two_d_array " analyzeline: No name/args pattern found for line. Line #22 in model/neuralnetwork.f90:" type:: element_parameters " analyzeline: No name/args pattern found for line. Line #29 in model/neuralnetwork.f90:" type:: real_one_d_array " analyzeline: No name/args pattern found for line. Post-processing... Block: fmodules Block: check_version Block: fingerprint_props Block: model_props Block: images_props {} In: :fmodules:model.f90:calculate_loss:calculate_energy vars2fortran: No typespec for argument "image_no". {} In: :fmodules:model.f90:calculate_loss:calculate_forces vars2fortran: No typespec for argument "image_no". {} In: :fmodules:model.f90:calculate_loss:calculate_denergy_dparameters vars2fortran: No typespec for argument "image_no". {} In: :fmodules:model.f90:calculate_loss:calculate_numerical_denergy_dparameters vars2fortran: No typespec for argument "image_no". {} In: :fmodules:model.f90:calculate_loss:calculate_dforces_dparameters vars2fortran: No typespec for argument "image_no". {} In: :fmodules:model.f90:calculate_loss:calculate_numerical_dforces_dparameters vars2fortran: No typespec for argument "image_no". Block: calculate_loss In: :fmodules:model.f90:calculate_loss get_useparameters: no module neuralnetwork info used by calculate_loss Block: unknown_type In: :fmodules:model.f90:calculate_loss:unknown_type get_useparameters: no module neuralnetwork info used by unknown_type Block: unknown_type In: :fmodules:model.f90:calculate_loss:unknown_type get_useparameters: no module neuralnetwork info used by unknown_type Block: unknown_type In: :fmodules:model.f90:calculate_loss:unknown_type get_useparameters: no module neuralnetwork info used by unknown_type Block: unknown_type In: :fmodules:model.f90:calculate_loss:unknown_type get_useparameters: no module neuralnetwork info used by unknown_type Block: unknown_type In: :fmodules:model.f90:calculate_loss:unknown_type get_useparameters: no module neuralnetwork info used by unknown_type Block: unknown_type In: :fmodules:model.f90:calculate_loss:unknown_type get_useparameters: no module neuralnetwork info used by unknown_type Block: deallocate_variables In: :fmodules:model.f90:deallocate_variables get_useparameters: no module neuralnetwork info used by deallocate_variables Block: cutoffs Block: cutoff_fxn Block: cutoff_fxn_prime Block: calculate_g2 Block: calculate_g4 Block: calculate_g2_prime Block: calculate_g4_prime Block: calculate_zernike_prime Block: calculate_z Block: calculate_z_prime Block: calculate_q Block: binomial Block: neuralnetwork Block: unknown_type Block: unknown_type Block: unknown_type Block: calculate_image_energy Block: calculate_atomic_energy Block: calculate_force_ Block: calculate_force Block: calculate_denergy_dparameters_ Block: calculate_datomicenergy_dparameters Block: calculate_dforce_dparameters_ Block: calculate_dforce_dparameters Post-processing (stage 2)... Block: fmodules Block: unknown_interface Block: check_version Block: fingerprint_props Block: model_props Block: images_props Block: calculate_loss Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: deallocate_variables Block: cutoffs Block: cutoff_fxn Block: cutoff_fxn_prime Block: calculate_g2 Block: calculate_g4 Block: calculate_g2_prime Block: calculate_g4_prime Block: calculate_zernike_prime Block: calculate_z Block: calculate_z_prime Block: calculate_q Block: binomial Block: neuralnetwork Block: unknown_type Block: unknown_type Block: unknown_type Block: calculate_image_energy Block: calculate_atomic_energy Block: calculate_force_ Block: calculate_force Block: calculate_denergy_dparameters_ Block: calculate_datomicenergy_dparameters Block: calculate_dforce_dparameters_ Block: calculate_dforce_dparameters Building modules... Building module "fmodules"... Constructing wrapper function "check_version"... warning = check_version(version) Constructing wrapper function "calculate_loss"... loss,dloss_dparameters,energyloss,forceloss,energy_maxresid,force_maxresid = calculate_loss(parameters,lossprime,[num_parameters]) Constructing wrapper function "deallocate_variables"... deallocate_variables() Constructing wrapper function "calculate_g2"... ridge = calculate_g2(neighbornumbers,neighborpositions,g_number,g_eta,rc,cutofffn,ri,[p_gamma]) Constructing wrapper function "calculate_g4"... ridge = calculate_g4(neighbornumbers,neighborpositions,g_numbers,g_gamma,g_zeta,g_eta,rc,cutofffn,ri,[p_gamma]) Constructing wrapper function "calculate_g2_prime"... ridge = calculate_g2_prime(neighborindices,neighbornumbers,neighborpositions,g_number,g_eta,rc,cutofffn,i,ri,m,l,[p_gamma]) Constructing wrapper function "calculate_g4_prime"... ridge = calculate_g4_prime(neighborindices,neighbornumbers,neighborpositions,g_numbers,g_gamma,g_zeta,g_eta,rc,cutofffn,i,ri,m,l,[p_gamma]) Constructing wrapper function "calculate_zernike_prime"... norm_prime = calculate_zernike_prime(n,l,n_indices,numbers,rs,g_numbers,cutoff,indexx,home,p,q,factorial,cutofffn,[n_length,fac_length,p_gamma]) Constructing wrapper function "calculate_z"... output = calculate_z(n,l,m,x,y,z,factorial,[length]) Constructing wrapper function "calculate_z_prime"... output = calculate_z_prime(n,l,m,x,y,z,p,factorial,[length]) Constructing wrapper function "calculate_q"... output = calculate_q(nu,k,l,factorial,[length]) Constructing wrapper function "binomial"... output = binomial(n,k,factorial,[length]) Constructing F90 module support for "fingerprint_props"... Variables: num_fingerprints_of_elements raveled_fingerprints raveled_fingerprintprimes getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' Constructing F90 module support for "model_props"... Variables: mode_signal train_forces energy_coefficient force_coefficient overfit numericprime d Constructing F90 module support for "images_props"... Variables: num_images num_elements elements_numbers num_images_atoms atomic_numbers num_neighbors raveled_neighborlists actual_energies actual_forces num_atoms atomic_positions getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' Constructing F90 module support for "cutoffs"... Creating wrapper for Fortran function "cutoff_fxn"("cutoff_fxn")... Constructing wrapper function "cutoffs.cutoff_fxn"... cutoff_fxn = cutoff_fxn(r,rc,cutofffn,[p_gamma]) Creating wrapper for Fortran function "cutoff_fxn_prime"("cutoff_fxn_prime")... Constructing wrapper function "cutoffs.cutoff_fxn_prime"... cutoff_fxn_prime = cutoff_fxn_prime(r,rc,cutofffn,[p_gamma]) Constructing F90 module support for "neuralnetwork"... Variables: min_fingerprints max_fingerprints no_layers_of_elements no_nodes_of_elements activation_signal getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' Skipping type unknown_type Skipping type unknown_type Skipping type unknown_type Creating wrapper for Fortran function "calculate_image_energy"("calculate_image_energy")... Constructing wrapper function "neuralnetwork.calculate_image_energy"... calculate_image_energy = calculate_image_energy(inputs,parameters,[num_inputs,num_parameters]) Creating wrapper for Fortran function "calculate_atomic_energy"("calculate_atomic_energy")... Constructing wrapper function "neuralnetwork.calculate_atomic_energy"... calculate_atomic_energy = calculate_atomic_energy(symbol,fingerprint,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters]) Creating wrapper for Fortran function "calculate_force_"("calculate_force_")... Constructing wrapper function "neuralnetwork.calculate_force_"... calculate_force_ = calculate_force_(inputs,inputs_,parameters,[num_inputs,num_parameters]) Creating wrapper for Fortran function "calculate_force"("calculate_force")... Constructing wrapper function "neuralnetwork.calculate_force"... calculate_force = calculate_force(symbol,fingerprint,fingerprintprime,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters]) Creating wrapper for Fortran function "calculate_denergy_dparameters_"("calculate_denergy_dparameters_")... Constructing wrapper function "neuralnetwork.calculate_denergy_dparameters_"... calculate_denergy_dparameters_ = calculate_denergy_dparameters_(inputs,parameters,[num_inputs,num_parameters]) Creating wrapper for Fortran function "calculate_datomicenergy_dparameters"("calculate_datomicenergy_dparameters")... Constructing wrapper function "neuralnetwork.calculate_datomicenergy_dparameters"... calculate_datomicenergy_dparameters = calculate_datomicenergy_dparameters(symbol,fingerprint,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters]) Creating wrapper for Fortran function "calculate_dforce_dparameters_"("calculate_dforce_dparameters_")... Constructing wrapper function "neuralnetwork.calculate_dforce_dparameters_"... calculate_dforce_dparameters_ = calculate_dforce_dparameters_(inputs,inputs_,parameters,[num_inputs,num_parameters]) Creating wrapper for Fortran function "calculate_dforce_dparameters"("calculate_dforce_dparameters")... Constructing wrapper function "neuralnetwork.calculate_dforce_dparameters"... calculate_dforce_dparameters = calculate_dforce_dparameters(symbol,fingerprint,fingerprintprime,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters]) Wrote C/API module "fmodules" to file "/tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodulesmodule.c" Fortran 90 wrappers are saved to "/tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90" adding '/tmp/tmpzebktwtd/src.linux-armhf-3.7/fortranobject.c' to sources. adding '/tmp/tmpzebktwtd/src.linux-armhf-3.7' to include_dirs. copying /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.c -> /tmp/tmpzebktwtd/src.linux-armhf-3.7 copying /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.h -> /tmp/tmpzebktwtd/src.linux-armhf-3.7 adding '/tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'fmodules' extension compiling C sources C compiler: arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating /tmp/tmpzebktwtd/tmp creating /tmp/tmpzebktwtd/tmp/tmpzebktwtd creating /tmp/tmpzebktwtd/tmp/tmpzebktwtd/src.linux-armhf-3.7 compile options: '-I/tmp/tmpzebktwtd/src.linux-armhf-3.7 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c' arm-linux-gnueabihf-gcc: /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodulesmodule.c arm-linux-gnueabihf-gcc: /tmp/tmpzebktwtd/src.linux-armhf-3.7/fortranobject.c In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmpzebktwtd/src.linux-armhf-3.7/fortranobject.h:13, from /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodulesmodule.c:16: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from /tmp/tmpzebktwtd/src.linux-armhf-3.7/fortranobject.h:13, from /tmp/tmpzebktwtd/src.linux-armhf-3.7/fortranobject.c:2: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodulesmodule.c:144:12: warning: 'f2py_size' defined but not used [-Wunused-function] static int f2py_size(PyArrayObject* var, ...) ^~~~~~~~~ compiling Fortran 90 module sources Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops creating /tmp/tmpzebktwtd/descriptor creating /tmp/tmpzebktwtd/model compile options: '-I/tmp/tmpzebktwtd/src.linux-armhf-3.7 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c' extra options: '-J/tmp/tmpzebktwtd/ -I/tmp/tmpzebktwtd/' gfortran:f90: model.f90 model.f90:219:1: do j = 1, num_parameters 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:220:1: denergy_dparameters(j) = 0.0d0 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:221:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:269:1: do selfindex = 1, num_atoms 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:270:1: allocate(dforces_dparameters(& 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:271:1: selfindex)%twodarray(3, num_parameters)) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:272:1: do i = 1, 3 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:273:1: do j = 1, num_parameters 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:274:1: dforces_dparameters(& 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:275:1: selfindex)%twodarray(i, j) = 0.0d0 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:276:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:277:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:278:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:300:1: do p = 1, size(dforces_dparameters) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:301:1: deallocate(dforces_dparameters(p)%twodarray) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:302:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:303:1: deallocate(dforces_dparameters) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:323:1: doverfitloss_dparameters(j) = & 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:646:1: allocate(fplus(num_atoms, 3)) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:647:1: do selfindex = 1, num_atoms 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:648:1: do i = 1, 3 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:649:1: fplus(selfindex, i) = amp_forces(selfindex, i) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:650:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:651:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:655:1: allocate(fminus(num_atoms, 3)) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:656:1: do selfindex = 1, num_atoms 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:657:1: do i = 1, 3 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:658:1: fminus(selfindex, i) = amp_forces(selfindex, i) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:659:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] model.f90:660:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] gfortran:f90: descriptor/cutoffs.f90 gfortran:f90: model/neuralnetwork.f90 model/neuralnetwork.f90:1379:1: unraveled_dforce_dweights(layer)%twodarray(p, q) = & 1 Warning: Nonconforming tab character at (1) [-Wtabs] model/neuralnetwork.f90:1380:1: -1.0d0 * unraveled_dforce_dweights(layer)%twodarray(p, q) 1 Warning: Nonconforming tab character at (1) [-Wtabs] model/neuralnetwork.f90:1767:1: unraveled_dforce_dparameters(element)%slope = & 1 Warning: Nonconforming tab character at (1) [-Wtabs] model/neuralnetwork.f90:1768:1: -1.0d0 * unraveled_dforce_dparameters(element)%slope 1 Warning: Nonconforming tab character at (1) [-Wtabs] model/neuralnetwork.f90:1802:1: unraveled_dforce_dparameters(element)%weights(& 1 Warning: Nonconforming tab character at (1) [-Wtabs] compiling Fortran sources Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops compile options: '-I/tmp/tmpzebktwtd/src.linux-armhf-3.7 -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c' extra options: '-J/tmp/tmpzebktwtd/ -I/tmp/tmpzebktwtd/' gfortran:f90: descriptor/gaussian.f90 gfortran:f90: descriptor/zernike.f90 gfortran:f90: /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90 /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:102:10: use fingerprint_props, only : num_fingerprints_of_elements 1 Warning: Unused module variable 'num_fingerprints_of_elements' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:102:10: use fingerprint_props, only : num_fingerprints_of_elements 1 Warning: Unused module variable 'raveled_fingerprintprimes' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:102:10: use fingerprint_props, only : num_fingerprints_of_elements 1 Warning: Unused module variable 'raveled_fingerprints' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:379:10: use images_props, only : num_images 1 Warning: Unused module variable 'actual_energies' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:379:10: use images_props, only : num_images 1 Warning: Unused module variable 'actual_forces' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:379:10: use images_props, only : num_images 1 Warning: Unused module variable 'atomic_numbers' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:379:10: use images_props, only : num_images 1 Warning: Unused module variable 'atomic_positions' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:379:10: use images_props, only : num_images 1 Warning: Unused module variable 'elements_numbers' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:379:10: use images_props, only : num_images 1 Warning: Unused module variable 'num_images_atoms' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:379:10: use images_props, only : num_images 1 Warning: Unused module variable 'num_neighbors' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:379:10: use images_props, only : num_images 1 Warning: Unused module variable 'raveled_neighborlists' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:706:10: use neuralnetwork, only : min_fingerprints 1 Warning: Unused module variable 'max_fingerprints' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:706:10: use neuralnetwork, only : min_fingerprints 1 Warning: Unused module variable 'min_fingerprints' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:706:10: use neuralnetwork, only : min_fingerprints 1 Warning: Unused module variable 'no_layers_of_elements' which has been explicitly imported at (1) [-Wunused-variable] /tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.f90:706:10: use neuralnetwork, only : min_fingerprints 1 Warning: Unused module variable 'no_nodes_of_elements' which has been explicitly imported at (1) [-Wunused-variable] /usr/bin/gfortran -Wall -g -Wl,-z,relro -Wl,-z,now -shared /tmp/tmpzebktwtd/tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodulesmodule.o /tmp/tmpzebktwtd/tmp/tmpzebktwtd/src.linux-armhf-3.7/fortranobject.o /tmp/tmpzebktwtd/model.o /tmp/tmpzebktwtd/descriptor/cutoffs.o /tmp/tmpzebktwtd/model/neuralnetwork.o /tmp/tmpzebktwtd/descriptor/gaussian.o /tmp/tmpzebktwtd/descriptor/zernike.o /tmp/tmpzebktwtd/tmp/tmpzebktwtd/src.linux-armhf-3.7/fmodules-f2pywrappers2.o -L/usr/lib/gcc/arm-linux-gnueabihf/8 -L/usr/lib/gcc/arm-linux-gnueabihf/8 -lgfortran -o ./fmodules.cpython-37m-arm-linux-gnueabihf.so rmbadname1: Replacing "index" with "index_bn". /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:517: UserWarning: FFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). fflags = self.flag_vars.flags + dflags + oflags + aflags /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_so_flags = self.flag_vars.linker_so /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_exe_flags = self.flag_vars.linker_exe Removing build directory /tmp/tmpzebktwtd make[1]: Leaving directory '/build/amp-0.6.1/amp' I: pybuild base:217: /usr/bin/python3 setup.py build running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "amp.fmodules" sources f2py options: [] f2py:> build/src.linux-armhf-3.7/amp/fmodulesmodule.c creating build creating build/src.linux-armhf-3.7 creating build/src.linux-armhf-3.7/amp Reading fortran codes... Reading file 'amp/model/neuralnetwork.f90' (format:fix) Line #17 in amp/model/neuralnetwork.f90:" type:: real_two_d_array " analyzeline: No name/args pattern found for line. Line #22 in amp/model/neuralnetwork.f90:" type:: element_parameters " analyzeline: No name/args pattern found for line. Line #29 in amp/model/neuralnetwork.f90:" type:: real_one_d_array " analyzeline: No name/args pattern found for line. Reading file 'amp/descriptor/gaussian.f90' (format:free) Reading file 'amp/descriptor/cutoffs.f90' (format:fix) Reading file 'amp/descriptor/zernike.f90' (format:free) Reading file 'amp/model.f90' (format:fix) Line #99 in amp/model.f90:" type:: image_forces " analyzeline: No name/args pattern found for line. Line #104 in amp/model.f90:" type:: integer_one_d_array " analyzeline: No name/args pattern found for line. Line #109 in amp/model.f90:" type:: embedded_real_one_one_d_array " analyzeline: No name/args pattern found for line. Line #114 in amp/model.f90:" type:: embedded_real_one_two_d_array " analyzeline: No name/args pattern found for line. Line #119 in amp/model.f90:" type:: embedded_integer_one_one_d_array " analyzeline: No name/args pattern found for line. Line #124 in amp/model.f90:" type:: embedded_one_one_two_d_array " analyzeline: No name/args pattern found for line. Post-processing... Block: fmodules Block: neuralnetwork Block: unknown_type Block: unknown_type Block: unknown_type Block: calculate_image_energy Block: calculate_atomic_energy Block: calculate_force_ Block: calculate_force Block: calculate_denergy_dparameters_ Block: calculate_datomicenergy_dparameters Block: calculate_dforce_dparameters_ Block: calculate_dforce_dparameters Block: calculate_g2 In: :fmodules:amp/descriptor/gaussian.f90:calculate_g2 get_useparameters: no module cutoffs info used by calculate_g2 Block: calculate_g4 In: :fmodules:amp/descriptor/gaussian.f90:calculate_g4 get_useparameters: no module cutoffs info used by calculate_g4 Block: calculate_g2_prime In: :fmodules:amp/descriptor/gaussian.f90:calculate_g2_prime get_useparameters: no module cutoffs info used by calculate_g2_prime Block: calculate_g4_prime In: :fmodules:amp/descriptor/gaussian.f90:calculate_g4_prime get_useparameters: no module cutoffs info used by calculate_g4_prime Block: cutoffs Block: cutoff_fxn Block: cutoff_fxn_prime Block: calculate_zernike_prime Block: calculate_z Block: calculate_z_prime Block: calculate_q Block: binomial Block: check_version Block: fingerprint_props Block: model_props Block: images_props {} In: :fmodules:amp/model.f90:calculate_loss:calculate_energy vars2fortran: No typespec for argument "image_no". {} In: :fmodules:amp/model.f90:calculate_loss:calculate_forces vars2fortran: No typespec for argument "image_no". {} In: :fmodules:amp/model.f90:calculate_loss:calculate_denergy_dparameters vars2fortran: No typespec for argument "image_no". {} In: :fmodules:amp/model.f90:calculate_loss:calculate_numerical_denergy_dparameters vars2fortran: No typespec for argument "image_no". {} In: :fmodules:amp/model.f90:calculate_loss:calculate_dforces_dparameters vars2fortran: No typespec for argument "image_no". {} In: :fmodules:amp/model.f90:calculate_loss:calculate_numerical_dforces_dparameters vars2fortran: No typespec for argument "image_no". Block: calculate_loss Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: deallocate_variables Post-processing (stage 2)... Block: fmodules Block: unknown_interface Block: neuralnetwork Block: unknown_type Block: unknown_type Block: unknown_type Block: calculate_image_energy Block: calculate_atomic_energy Block: calculate_force_ Block: calculate_force Block: calculate_denergy_dparameters_ Block: calculate_datomicenergy_dparameters Block: calculate_dforce_dparameters_ Block: calculate_dforce_dparameters Block: calculate_g2 Block: calculate_g4 Block: calculate_g2_prime Block: calculate_g4_prime Block: cutoffs Block: cutoff_fxn Block: cutoff_fxn_prime Block: calculate_zernike_prime Block: calculate_z Block: calculate_z_prime Block: calculate_q Block: binomial Block: check_version Block: fingerprint_props Block: model_props Block: images_props Block: calculate_loss Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: unknown_type Block: deallocate_variables Building modules... Building module "fmodules"... Constructing wrapper function "calculate_g2"... ridge = calculate_g2(neighbornumbers,neighborpositions,g_number,g_eta,rc,cutofffn,ri,[p_gamma]) Constructing wrapper function "calculate_g4"... ridge = calculate_g4(neighbornumbers,neighborpositions,g_numbers,g_gamma,g_zeta,g_eta,rc,cutofffn,ri,[p_gamma]) Constructing wrapper function "calculate_g2_prime"... ridge = calculate_g2_prime(neighborindices,neighbornumbers,neighborpositions,g_number,g_eta,rc,cutofffn,i,ri,m,l,[p_gamma]) Constructing wrapper function "calculate_g4_prime"... ridge = calculate_g4_prime(neighborindices,neighbornumbers,neighborpositions,g_numbers,g_gamma,g_zeta,g_eta,rc,cutofffn,i,ri,m,l,[p_gamma]) Constructing wrapper function "calculate_zernike_prime"... norm_prime = calculate_zernike_prime(n,l,n_indices,numbers,rs,g_numbers,cutoff,indexx,home,p,q,factorial,cutofffn,[n_length,fac_length,p_gamma]) Constructing wrapper function "calculate_z"... output = calculate_z(n,l,m,x,y,z,factorial,[length]) Constructing wrapper function "calculate_z_prime"... output = calculate_z_prime(n,l,m,x,y,z,p,factorial,[length]) Constructing wrapper function "calculate_q"... output = calculate_q(nu,k,l,factorial,[length]) Constructing wrapper function "binomial"... output = binomial(n,k,factorial,[length]) Constructing wrapper function "check_version"... warning = check_version(version) Constructing wrapper function "calculate_loss"... loss,dloss_dparameters,energyloss,forceloss,energy_maxresid,force_maxresid = calculate_loss(parameters,lossprime,[num_parameters]) Constructing wrapper function "deallocate_variables"... deallocate_variables() Constructing F90 module support for "neuralnetwork"... Variables: min_fingerprints max_fingerprints no_layers_of_elements no_nodes_of_elements activation_signal getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' Skipping type unknown_type Skipping type unknown_type Skipping type unknown_type Creating wrapper for Fortran function "calculate_image_energy"("calculate_image_energy")... Constructing wrapper function "neuralnetwork.calculate_image_energy"... calculate_image_energy = calculate_image_energy(inputs,parameters,[num_inputs,num_parameters]) Creating wrapper for Fortran function "calculate_atomic_energy"("calculate_atomic_energy")... Constructing wrapper function "neuralnetwork.calculate_atomic_energy"... calculate_atomic_energy = calculate_atomic_energy(symbol,fingerprint,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters]) Creating wrapper for Fortran function "calculate_force_"("calculate_force_")... Constructing wrapper function "neuralnetwork.calculate_force_"... calculate_force_ = calculate_force_(inputs,inputs_,parameters,[num_inputs,num_parameters]) Creating wrapper for Fortran function "calculate_force"("calculate_force")... Constructing wrapper function "neuralnetwork.calculate_force"... calculate_force = calculate_force(symbol,fingerprint,fingerprintprime,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters]) Creating wrapper for Fortran function "calculate_denergy_dparameters_"("calculate_denergy_dparameters_")... Constructing wrapper function "neuralnetwork.calculate_denergy_dparameters_"... calculate_denergy_dparameters_ = calculate_denergy_dparameters_(inputs,parameters,[num_inputs,num_parameters]) Creating wrapper for Fortran function "calculate_datomicenergy_dparameters"("calculate_datomicenergy_dparameters")... Constructing wrapper function "neuralnetwork.calculate_datomicenergy_dparameters"... calculate_datomicenergy_dparameters = calculate_datomicenergy_dparameters(symbol,fingerprint,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters]) Creating wrapper for Fortran function "calculate_dforce_dparameters_"("calculate_dforce_dparameters_")... Constructing wrapper function "neuralnetwork.calculate_dforce_dparameters_"... calculate_dforce_dparameters_ = calculate_dforce_dparameters_(inputs,inputs_,parameters,[num_inputs,num_parameters]) Creating wrapper for Fortran function "calculate_dforce_dparameters"("calculate_dforce_dparameters")... Constructing wrapper function "neuralnetwork.calculate_dforce_dparameters"... calculate_dforce_dparameters = calculate_dforce_dparameters(symbol,fingerprint,fingerprintprime,elements_numbers,parameters,[len_of_fingerprint,num_elements,num_parameters]) Constructing F90 module support for "cutoffs"... Creating wrapper for Fortran function "cutoff_fxn"("cutoff_fxn")... Constructing wrapper function "cutoffs.cutoff_fxn"... cutoff_fxn = cutoff_fxn(r,rc,cutofffn,[p_gamma]) Creating wrapper for Fortran function "cutoff_fxn_prime"("cutoff_fxn_prime")... Constructing wrapper function "cutoffs.cutoff_fxn_prime"... cutoff_fxn_prime = cutoff_fxn_prime(r,rc,cutofffn,[p_gamma]) Constructing F90 module support for "fingerprint_props"... Variables: num_fingerprints_of_elements raveled_fingerprints raveled_fingerprintprimes getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' Constructing F90 module support for "model_props"... Variables: mode_signal train_forces energy_coefficient force_coefficient overfit numericprime d Constructing F90 module support for "images_props"... Variables: num_images num_elements elements_numbers num_images_atoms atomic_numbers num_neighbors raveled_neighborlists actual_energies actual_forces num_atoms atomic_positions getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' getarrdims:warning: assumed shape array, using 0 instead of ':' Wrote C/API module "fmodules" to file "build/src.linux-armhf-3.7/amp/fmodulesmodule.c" Fortran 90 wrappers are saved to "build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90" adding 'build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fortranobject.c' to sources. adding 'build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp' to include_dirs. creating build/src.linux-armhf-3.7/build creating build/src.linux-armhf-3.7/build/src.linux-armhf-3.7 creating build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp copying /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.c -> build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp copying /usr/lib/python3/dist-packages/numpy/f2py/src/fortranobject.h -> build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp adding 'build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_py creating /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp copying amp/utilities.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp copying amp/analysis.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp copying amp/__init__.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp creating /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor copying amp/descriptor/analysis.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor copying amp/descriptor/gaussian.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor copying amp/descriptor/__init__.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor copying amp/descriptor/zernike.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor copying amp/descriptor/cutoffs.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor copying amp/descriptor/example.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor copying amp/descriptor/bispectrum.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor creating /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/regression copying amp/regression/__init__.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/regression creating /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model copying amp/model/neuralnetwork.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model copying amp/model/__init__.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model copying amp/model/tflow.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model copying amp/model/__main__.py -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model copying amp/VERSION -> /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext building 'amp.fmodules' extension compiling C sources C compiler: arm-linux-gnueabihf-gcc -pthread -DNDEBUG -g -fwrapv -O2 -Wall -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -fPIC creating build/temp.linux-armhf-3.7/build creating build/temp.linux-armhf-3.7/build/src.linux-armhf-3.7 creating build/temp.linux-armhf-3.7/build/src.linux-armhf-3.7/amp creating build/temp.linux-armhf-3.7/build/src.linux-armhf-3.7/build creating build/temp.linux-armhf-3.7/build/src.linux-armhf-3.7/build/src.linux-armhf-3.7 creating build/temp.linux-armhf-3.7/build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp compile options: '-Ibuild/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c' arm-linux-gnueabihf-gcc: build/src.linux-armhf-3.7/amp/fmodulesmodule.c arm-linux-gnueabihf-gcc: build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fortranobject.c In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fortranobject.h:13, from build/src.linux-armhf-3.7/amp/fmodulesmodule.c:16: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ In file included from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarraytypes.h:1822, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/ndarrayobject.h:12, from /usr/lib/python3/dist-packages/numpy/core/include/numpy/arrayobject.h:4, from build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fortranobject.h:13, from build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fortranobject.c:2: /usr/lib/python3/dist-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION" [-Wcpp] #warning "Using deprecated NumPy API, disable it with " \ ^~~~~~~ build/src.linux-armhf-3.7/amp/fmodulesmodule.c:144:12: warning: 'f2py_size' defined but not used [-Wunused-function] static int f2py_size(PyArrayObject* var, ...) ^~~~~~~~~ compiling Fortran 90 module sources creating build/temp.linux-armhf-3.7/amp Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops creating build/temp.linux-armhf-3.7/amp/model creating build/temp.linux-armhf-3.7/amp/descriptor compile options: '-Ibuild/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c' extra options: '-Jbuild/temp.linux-armhf-3.7/amp -Ibuild/temp.linux-armhf-3.7/amp' gfortran:f90: amp/model/neuralnetwork.f90 amp/model/neuralnetwork.f90:1379:1: unraveled_dforce_dweights(layer)%twodarray(p, q) = & 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model/neuralnetwork.f90:1380:1: -1.0d0 * unraveled_dforce_dweights(layer)%twodarray(p, q) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model/neuralnetwork.f90:1767:1: unraveled_dforce_dparameters(element)%slope = & 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model/neuralnetwork.f90:1768:1: -1.0d0 * unraveled_dforce_dparameters(element)%slope 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model/neuralnetwork.f90:1802:1: unraveled_dforce_dparameters(element)%weights(& 1 Warning: Nonconforming tab character at (1) [-Wtabs] gfortran:f90: amp/descriptor/cutoffs.f90 gfortran:f90: amp/model.f90 amp/model.f90:219:1: do j = 1, num_parameters 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:220:1: denergy_dparameters(j) = 0.0d0 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:221:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:269:1: do selfindex = 1, num_atoms 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:270:1: allocate(dforces_dparameters(& 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:271:1: selfindex)%twodarray(3, num_parameters)) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:272:1: do i = 1, 3 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:273:1: do j = 1, num_parameters 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:274:1: dforces_dparameters(& 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:275:1: selfindex)%twodarray(i, j) = 0.0d0 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:276:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:277:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:278:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:300:1: do p = 1, size(dforces_dparameters) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:301:1: deallocate(dforces_dparameters(p)%twodarray) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:302:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:303:1: deallocate(dforces_dparameters) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:323:1: doverfitloss_dparameters(j) = & 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:646:1: allocate(fplus(num_atoms, 3)) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:647:1: do selfindex = 1, num_atoms 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:648:1: do i = 1, 3 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:649:1: fplus(selfindex, i) = amp_forces(selfindex, i) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:650:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:651:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:655:1: allocate(fminus(num_atoms, 3)) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:656:1: do selfindex = 1, num_atoms 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:657:1: do i = 1, 3 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:658:1: fminus(selfindex, i) = amp_forces(selfindex, i) 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:659:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] amp/model.f90:660:1: end do 1 Warning: Nonconforming tab character at (1) [-Wtabs] compiling Fortran sources Fortran f77 compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops Fortran f90 compiler: /usr/bin/gfortran -Wall -g -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops Fortran fix compiler: /usr/bin/gfortran -Wall -g -ffixed-form -fno-second-underscore -Wall -g -fno-second-underscore -g -O2 -ffile-prefix-map=/build/amp-0.6.1=. -fstack-protector-strong -fPIC -O3 -funroll-loops compile options: '-Ibuild/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp -I/usr/lib/python3/dist-packages/numpy/core/include -I/usr/include/python3.7m -c' extra options: '-Jbuild/temp.linux-armhf-3.7/amp -Ibuild/temp.linux-armhf-3.7/amp' gfortran:f90: amp/descriptor/gaussian.f90 gfortran:f90: amp/descriptor/zernike.f90 gfortran:f90: build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90 build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:256:10: use neuralnetwork, only : min_fingerprints 1 Warning: Unused module variable 'max_fingerprints' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:256:10: use neuralnetwork, only : min_fingerprints 1 Warning: Unused module variable 'min_fingerprints' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:256:10: use neuralnetwork, only : min_fingerprints 1 Warning: Unused module variable 'no_layers_of_elements' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:256:10: use neuralnetwork, only : min_fingerprints 1 Warning: Unused module variable 'no_nodes_of_elements' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:533:10: use fingerprint_props, only : num_fingerprints_of_elements 1 Warning: Unused module variable 'num_fingerprints_of_elements' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:533:10: use fingerprint_props, only : num_fingerprints_of_elements 1 Warning: Unused module variable 'raveled_fingerprintprimes' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:533:10: use fingerprint_props, only : num_fingerprints_of_elements 1 Warning: Unused module variable 'raveled_fingerprints' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:810:10: use images_props, only : num_images 1 Warning: Unused module variable 'actual_energies' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:810:10: use images_props, only : num_images 1 Warning: Unused module variable 'actual_forces' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:810:10: use images_props, only : num_images 1 Warning: Unused module variable 'atomic_numbers' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:810:10: use images_props, only : num_images 1 Warning: Unused module variable 'atomic_positions' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:810:10: use images_props, only : num_images 1 Warning: Unused module variable 'elements_numbers' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:810:10: use images_props, only : num_images 1 Warning: Unused module variable 'num_images_atoms' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:810:10: use images_props, only : num_images 1 Warning: Unused module variable 'num_neighbors' which has been explicitly imported at (1) [-Wunused-variable] build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90:810:10: use images_props, only : num_images 1 Warning: Unused module variable 'raveled_neighborlists' which has been explicitly imported at (1) [-Wunused-variable] /usr/bin/gfortran -Wall -g -Wl,-z,relro -Wl,-z,now -shared build/temp.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fmodulesmodule.o build/temp.linux-armhf-3.7/build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fortranobject.o build/temp.linux-armhf-3.7/amp/model/neuralnetwork.o build/temp.linux-armhf-3.7/amp/descriptor/cutoffs.o build/temp.linux-armhf-3.7/amp/model.o build/temp.linux-armhf-3.7/amp/descriptor/gaussian.o build/temp.linux-armhf-3.7/amp/descriptor/zernike.o build/temp.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.o -L/usr/lib/gcc/arm-linux-gnueabihf/8 -L/usr/lib/gcc/arm-linux-gnueabihf/8 -lgfortran -o /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/fmodules.cpython-37m-arm-linux-gnueabihf.so /usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) rmbadname1: Replacing "index" with "index_bn". /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:517: UserWarning: FFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). fflags = self.flag_vars.flags + dflags + oflags + aflags /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_so_flags = self.flag_vars.linker_so /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_exe_flags = self.flag_vars.linker_exe debian/rules override_dh_auto_test make[1]: Entering directory '/build/amp-0.6.1' PYBUILD_SYSTEM=custom \ PYBUILD_TEST_ARGS="cd {build_dir}; {interpreter} /usr/bin/nosetests3 tests" \ dh_auto_test make[1]: Leaving directory '/build/amp-0.6.1' create-stamp debian/debhelper-build-stamp fakeroot debian/rules binary dh binary --with python3 --buildsystem=pybuild dh_testroot -O--buildsystem=pybuild dh_prep -O--buildsystem=pybuild dh_auto_install -O--buildsystem=pybuild I: pybuild base:217: /usr/bin/python3 setup.py install --root /build/amp-0.6.1/debian/python3-amp running install running build running config_cc unifing config_cc, config, build_clib, build_ext, build commands --compiler options running config_fc unifing config_fc, config, build_clib, build_ext, build commands --fcompiler options running build_src build_src building extension "amp.fmodules" sources f2py options: [] adding 'build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp/fortranobject.c' to sources. adding 'build/src.linux-armhf-3.7/build/src.linux-armhf-3.7/amp' to include_dirs. adding 'build/src.linux-armhf-3.7/amp/fmodules-f2pywrappers2.f90' to sources. build_src: building npy-pkg config files running build_py running build_ext customize UnixCCompiler customize UnixCCompiler using build_ext get_default_fcompiler: matching types: '['gnu95', 'intel', 'lahey', 'pg', 'absoft', 'nag', 'vast', 'compaq', 'intele', 'intelem', 'gnu', 'g95', 'pathf95', 'nagfor']' customize Gnu95FCompiler Found executable /usr/bin/gfortran customize Gnu95FCompiler customize Gnu95FCompiler using build_ext running install_lib creating /build/amp-0.6.1/debian/python3-amp/usr creating /build/amp-0.6.1/debian/python3-amp/usr/lib creating /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7 creating /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages creating /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/utilities.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/analysis.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/fmodules.cpython-37m-arm-linux-gnueabihf.so -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/__init__.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/VERSION -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp creating /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/regression copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/regression/__init__.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/regression creating /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor/analysis.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor/gaussian.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor/__init__.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor/zernike.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor/cutoffs.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor/example.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/descriptor/bispectrum.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor creating /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model/neuralnetwork.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model/__init__.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model/tflow.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model copying /build/amp-0.6.1/.pybuild/cpython3_3.7_amp/build/amp/model/__main__.py -> /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/utilities.py to utilities.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/analysis.py to analysis.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/__init__.py to __init__.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/regression/__init__.py to __init__.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor/analysis.py to analysis.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor/gaussian.py to gaussian.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor/__init__.py to __init__.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor/zernike.py to zernike.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor/cutoffs.py to cutoffs.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor/example.py to example.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/descriptor/bispectrum.py to bispectrum.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model/neuralnetwork.py to neuralnetwork.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model/__init__.py to __init__.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model/tflow.py to tflow.cpython-37.pyc byte-compiling /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp/model/__main__.py to __main__.cpython-37.pyc running install_egg_info Writing /build/amp-0.6.1/debian/python3-amp/usr/lib/python3.7/dist-packages/amp_atomistics-0.6.1.egg-info running install_clib customize UnixCCompiler /usr/lib/python3.7/distutils/dist.py:274: UserWarning: Unknown distribution option: 'install_requires' warnings.warn(msg) /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:517: UserWarning: FFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). fflags = self.flag_vars.flags + dflags + oflags + aflags /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:530: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_so_flags = self.flag_vars.linker_so /usr/lib/python3/dist-packages/numpy/distutils/fcompiler/__init__.py:540: UserWarning: LDFLAGS is used as is, not appended to flags already defined by numpy.distutils! Use NPY_DISTUTILS_APPEND_FLAGS=1 to obtain appending behavior instead (this behavior will become default in a future release). linker_exe_flags = self.flag_vars.linker_exe I: pybuild pybuild:298: cp -r '/build/amp-0.6.1/tests' '/build/amp-0.6.1/debian/python3-amp//usr/lib/python3.7/dist-packages/amp' dh_install -O--buildsystem=pybuild dh_installdocs -O--buildsystem=pybuild dh_installchangelogs -O--buildsystem=pybuild debian/rules override_dh_python3 make[1]: Entering directory '/build/amp-0.6.1' dh_python3 W: dh_python3 fs:112: Paths differ: debian/python3-amp/usr/lib/python3.7/dist-packages/amp/fmodules.cpython-37m-arm-linux-gnueabihf.so and debian/python3-amp/usr/lib/python3/dist-packages/amp/fmodules.cpython-37m-arm-linux-gnueabihf.so I: dh_python3 tools:114: replacing shebang in debian/python3-amp/usr/bin/amp-compress I: dh_python3 tools:114: replacing shebang in debian/python3-amp/usr/bin/amp-plotconvergence dh_numpy3 dh_fixperms make[1]: Leaving directory '/build/amp-0.6.1' dh_installinit -O--buildsystem=pybuild dh_perl -O--buildsystem=pybuild dh_link -O--buildsystem=pybuild dh_strip_nondeterminism -O--buildsystem=pybuild dh_compress -O--buildsystem=pybuild dh_fixperms -O--buildsystem=pybuild dh_missing -O--buildsystem=pybuild dh_strip -O--buildsystem=pybuild dh_makeshlibs -O--buildsystem=pybuild dh_shlibdeps -O--buildsystem=pybuild dh_installdeb -O--buildsystem=pybuild dh_gencontrol -O--buildsystem=pybuild dpkg-gencontrol: warning: Breaks field of package python3-amp: substitution variable ${python3:Breaks} used, but is not defined dpkg-gencontrol: warning: package python3-amp: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-amp: substitution variable ${python3:Versions} unused, but is defined dpkg-gencontrol: warning: Breaks field of package python3-amp: substitution variable ${python3:Breaks} used, but is not defined dpkg-gencontrol: warning: package python3-amp: substitution variable ${python3:Provides} unused, but is defined dpkg-gencontrol: warning: package python3-amp: substitution variable ${python3:Versions} unused, but is defined dh_md5sums -O--buildsystem=pybuild dh_builddeb -O--buildsystem=pybuild dpkg-deb: building package 'python3-amp-dbgsym' in '../python3-amp-dbgsym_0.6.1-1_armhf.deb'. dpkg-deb: building package 'python3-amp' in '../python3-amp_0.6.1-1_armhf.deb'. dpkg-genbuildinfo --build=binary dpkg-genchanges --build=binary >../amp_0.6.1-1_armhf.changes dpkg-genchanges: info: binary-only upload (no source code included) dpkg-source --after-build . dpkg-buildpackage: info: binary-only upload (no source included) I: copying local configuration I: unmounting dev/ptmx filesystem I: unmounting dev/pts filesystem I: unmounting dev/shm filesystem I: unmounting proc filesystem I: unmounting sys filesystem I: cleaning the build env I: removing directory /srv/workspace/pbuilder/1582 and its subdirectories I: Current time: Tue Sep 29 13:30:12 -12 2020 I: pbuilder-time-stamp: 1601429412