| Summary: | emerge sci-libs/scipy-0.6.0-r3 failed | ||
|---|---|---|---|
| Product: | Gentoo Linux | Reporter: | Qiangning Hong <hongqn> |
| Component: | Current packages | Assignee: | Gentoo Science Related Packages <sci> |
| Status: | VERIFIED TEST-REQUEST | ||
| Severity: | normal | CC: | Nylan |
| Priority: | High | ||
| Version: | unspecified | ||
| Hardware: | AMD64 | ||
| OS: | Linux | ||
| Whiteboard: | |||
| Package list: | Runtime testing required: | --- | |
| Attachments: |
output of emerge scipy-0.6.0-r3
Quick fix. contains phenom, nocona patch and some other minor fixes |
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Description
Qiangning Hong
2007-06-26 10:54:20 UTC
Hi Qiangning, It seems that numpy distutils does not get the nocona as an x86_64 arch, which I think was fixed on some recent numpy version. Could you provide the installed numpy version? Sébastien When I submitted this bug, my installed version of numpy is 1.0.2. But after I upgraded numpy from 1.0.2 to 1.0.3, this problem still exists. # emerge numpy -vp These are the packages that would be merged, in order: Calculating dependencies... done! [ebuild R ] dev-python/numpy-1.0.3 USE="-debug -lapack" 0 kB I could not reproduce this bug, although I'm testing on an opteron but forcing my flags to match yours. It really looks like a numpy bug which was fixed in later versions: http://projects.scipy.org/scipy/numpy/ticket/438 Are you sure you don't have another numpy in your system? Could you provide the results of this bit: $ python -c "import numpy; print numpy.__version__" The way numpy is detecting whether your arch is a "nocona" type is by looking at the results of: $ grep "model name" /proc/cpuinfo $ uname -m Could you also provide the results of those too? Thanks Sébastien $ python -c "import numpy; print numpy.__version__" 1.0.3 $ grep "model name" /proc/cpuinfo model name : Genuine Intel(R) CPU @ 2.40GHz model name : Genuine Intel(R) CPU @ 2.40GHz $ uname -m x86_64 Hi, It looks like the nocona based chips are recognized by parsing the /proc/cpuinfo and look for Core2 or Pentium IV string in the numpy distutils module. Unfortunately I have no nocona-based chip around on which I could test. (sci team, any one with nocona?). Post your entire "cat /proc/cpuinfo" here and when I find some time, I'll look it up. You could also test the numpy svn from upstream, and if the problem subsists, file a ticket on their track website [1]? Sébastien [1] http://projects.scipy.org/scipy/numpy/ Thanks very much! Here is the cpuinfo: $ cat /proc/cpuinfo processor : 0 vendor_id : GenuineIntel cpu family : 6 model : 15 model name : Genuine Intel(R) CPU @ 2.40GHz stepping : 4 cpu MHz : 2400.130 cache size : 4096 KB physical id : 0 siblings : 2 core id : 0 cpu cores : 2 fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall nx lm constant_tsc pni monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr lahf_lm bogomips : 4802.95 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: processor : 1 vendor_id : GenuineIntel cpu family : 6 model : 15 model name : Genuine Intel(R) CPU @ 2.40GHz stepping : 4 cpu MHz : 2400.130 cache size : 4096 KB physical id : 0 siblings : 2 core id : 1 cpu cores : 2 fpu : yes fpu_exception : yes cpuid level : 10 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm syscall nx lm constant_tsc pni monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr lahf_lm bogomips : 4800.31 clflush size : 64 cache_alignment : 64 address sizes : 36 bits physical, 48 bits virtual power management: Hi Is this problem still on with numpy-1.0.3.1 and scipy-0.5.2.1? Sebastien Please, get back to us. Current is 0.6.0-r3. Created attachment 140598 [details] output of emerge scipy-0.6.0-r3 scipy-0.6.0-r3 is still not compilable in my intel 64bit box. I attached the output of emerge. fyi, my numpy has upgraded to 1.0.4. $ python -c "import numpy; print numpy.__version__" 1.0.4 my current `emerge --info` followed: Portage 2.1.3.19 (default-linux/amd64/2007.0/desktop, gcc-4.1.2, glibc-2.6.1-r0, 2.6.19-gentoo-r5 x86_64) ================================================================= System uname: 2.6.19-gentoo-r5 x86_64 Genuine Intel(R) CPU @ 2.40GHz Timestamp of tree: Thu, 10 Jan 2008 08:46:01 +0000 app-shells/bash: 3.2_p17 dev-lang/python: 2.4.4-r4, 2.5.1-r3 dev-python/pycrypto: 2.0.1-r6 sys-apps/baselayout: 1.12.6 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.61-r1 sys-devel/automake: 1.6.3, 1.9.6-r2, 1.10 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.3.16 sys-devel/libtool: 1.5.24 virtual/os-headers: 2.6.22-r2 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=nocona -O3 -pipe" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc" CONFIG_PROTECT_MASK="/etc/env.d /etc/gconf /etc/revdep-rebuild /etc/terminfo" CXXFLAGS="-march=nocona -O3 -pipe" DISTDIR="/usr/portage/distfiles" FEATURES="ccache distlocks metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="ftp://ftp3.tsinghua.edu.cn/mirror/gentoo http://mirror.datapipe.net/gentoo" MAKEOPTS="-j3" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --delete-after --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages --filter=H_**/files/digest-*" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.asia.gentoo.org/gentoo-portage" USE="acl acpi amd64 arts bitmap-fonts cairo cdr cli cracklib crypt dbus dri dvd dvdr dvdread eds emboss encode esd evo fam firefox gif gnome gstreamer hal iconv isdnlog jpeg kde kerberos mad midi mikmod mmx mp3 mpeg mudflap ncurses nls nptl nptlonly ogg opengl openmp oss pam pcre pdf png pppd python qt3 qt3support qt4 quicktime readline reflection session spell spl sse sse2 ssl svg tcpd tiff truetype truetype-fonts type1-fonts unicode vorbis xml xorg xv zlib" ALSA_CARDS="ali5451 als4000 atiixp atiixp-modem bt87x ca0106 cmipci emu10k1x ens1370 ens1371 es1938 es1968 fm801 hda-intel intel8x0 intel8x0m maestro3 trident usb-audio via82xx via82xx-modem ymfpci" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="keyboard mouse evdev" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" USERLAND="GNU" VIDEO_CARDS="apm ark chips cirrus cyrix dummy fbdev glint i128 i810 mach64 mga neomagic nv r128 radeon rendition s3 s3virge savage siliconmotion sis sisusb tdfx tga trident tseng v4l vesa vga via vmware voodoo" Unset: CPPFLAGS, CTARGET, EMERGE_DEFAULT_OPTS, INSTALL_MASK, LANG, LC_ALL, LDFLAGS, LINGUAS, PORTAGE_COMPRESS, PORTAGE_COMPRESS_FLAGS, PORTAGE_RSYNC_EXTRA_OPTS Hi Qiangning, Could you report your problem upstream? I don't have nocona-based hardware on which I could test, so I can't follow-up the bug. To file a new ticket at the numpy page (see comment #5) you will need to register. Thanks, I vote for numpy bug. My cpuinfo is different and scipy compiles fine. When I copy Qiangning's cpuinfo and force numpy to use it, scipy fails in the same manner. I was able to fix this with a small patch to numpy which I readily admit probably isn't good, but shows this does appear to be a numpy problem. Created attachment 140653 [details, diff]
Quick fix.
Comment on attachment 140653 [details, diff]
Quick fix.
I should mention I do have nocona-based hardware :)
Submitted upstream: http://scipy.org/scipy/numpy/ticket/644 dev-python/numpy-1.4.0-r1 is in cvs. I've added a real patch that fixes this issue for me locally. Qiangning, please test and let us know if this works for you. Yes, it works. Thank you all! (In reply to comment #16) > Yes, it works. Thank you all! > emerge sci-libs/scipy-0.6.0-r4 fails on AMD Phenom Quad Core I've tried to patch cpuinfo.py without success. (similar to the nocona patch) [EMERGE LOG] Fortran f77 compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -march=k6-2 -mmmx -m3dnow -msse2 -msse Fortran f90 compiler: /usr/bin/gfortran -Wall -fno-second-underscore -fPIC -O3 -funroll-loops -march=k6-2 -mmmx -m3dnow -msse2 -msse Fortran fix compiler: /usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -Wall -fno-second-underscore -fPIC -O3 -funroll-loops -march=k6-2 -mmmx -m3dnow -msse2 -msse creating build/temp.linux-x86_64-2.4 creating build/temp.linux-x86_64-2.4/scipy creating build/temp.linux-x86_64-2.4/scipy/fftpack creating build/temp.linux-x86_64-2.4/scipy/fftpack/dfftpack compile options: '-c' gfortran:f77: scipy/fftpack/dfftpack/dcosqi.f scipy/fftpack/dfftpack/dcosqi.f:0: error: CPU you selected does not support x86-64 instruction set scipy/fftpack/dfftpack/dcosqi.f:0: error: CPU you selected does not support x86-64 instruction set scipy/fftpack/dfftpack/dcosqi.f:0: error: CPU you selected does not support x86-64 instruction set scipy/fftpack/dfftpack/dcosqi.f:0: error: CPU you selected does not support x86-64 instruction set error: Command "/usr/bin/gfortran -Wall -ffixed-form -fno-second-underscore -fPIC -O3 -funroll-loops -march=k6-2 -mmmx -m3dnow -msse2 -msse -c -c scipy/fftpack/dfftpack/dcosqi.f -o build/temp.linux-x86_64-2.4/scipy/fftpack/dfftpack/dcosqi.o" failed with exit status 1 * * ERROR: sci-libs/scipy-0.6.0-r4 failed. * Call stack: * ebuild.sh, line 49: Called src_compile * environment, line 3329: Called distutils_src_compile 'src_compile' 'src_compile' * environment, line 959: Called die * The specific snippet of code: * ${python} setup.py build "$@" || die "compilation failed" * The die message: * compilation failed * * If you need support, post the topmost build error, and the call stack if relevant. * A complete build log is located at '/var/tmp/portage/sci-libs/scipy-0.6.0-r4/temp/build.log'. * The ebuild environment file is located at '/var/tmp/portage/sci-libs/scipy-0.6.0-r4/temp/environment'. [EMERGE INFO] Portage 2.1.4.4 (default-linux/amd64/2007.0, gcc-4.1.2, glibc-2.6.1-r0, 2.6.24-gentoo-r5 x86_64) ================================================================= System uname: 2.6.24-gentoo-r5 x86_64 AMD Phenom(tm) 9750 Quad-Core Processor Timestamp of tree: Sat, 17 May 2008 10:03:01 +0000 ccache version 2.4 [disabled] app-shells/bash: 3.2_p33 dev-java/java-config: 1.3.7, 2.1.6 dev-lang/python: 2.4.4-r9 dev-python/pycrypto: 2.0.1-r6 dev-util/ccache: 2.4-r7 sys-apps/baselayout: 1.12.11.1 sys-apps/sandbox: 1.2.18.1-r2 sys-devel/autoconf: 2.13, 2.61-r1 sys-devel/automake: 1.5, 1.7.9-r1, 1.8.5-r3, 1.9.6-r2, 1.10.1 sys-devel/binutils: 2.18-r1 sys-devel/gcc-config: 1.4.0-r4 sys-devel/libtool: 1.5.26 virtual/os-headers: 2.6.23-r3 ACCEPT_KEYWORDS="amd64" CBUILD="x86_64-pc-linux-gnu" CFLAGS="-march=k8 -O2 -pipe -msse3" CHOST="x86_64-pc-linux-gnu" CONFIG_PROTECT="/etc /usr/kde/3.5/env /usr/kde/3.5/share/config /usr/kde/3.5/shutdown /usr/share/config /var/lib/hsqldb" CONFIG_PROTECT_MASK="/etc/env.d /etc/env.d/java/ /etc/fonts/fonts.conf /etc/gconf /etc/php/apache2-php5/ext-active/ /etc/php/cgi-php5/ext-active/ /etc/php/cli-php5/ext-active/ /etc/revdep-rebuild /etc/terminfo /etc/texmf/web2c /etc/udev/rules.d" CXXFLAGS="-march=k8 -O2 -pipe -msse3" DISTDIR="/usr/portage/distfiles" FEATURES="distlocks keeptemp metadata-transfer parallel-fetch sandbox sfperms strict unmerge-orphans userfetch" GENTOO_MIRRORS="http://mirror.switch.ch/ftp/mirror/gentoo/ ftp://mirror.switch.ch/mirror/gentoo/ http://gentoo.inode.at/ ftp://gentoo.inode.at/source/" LINGUAS="de it en en_GB" MAKEOPTS="-j5" PKGDIR="/usr/portage/packages" PORTAGE_RSYNC_OPTS="--recursive --links --safe-links --perms --times --compress --force --whole-file --delete --stats --timeout=180 --exclude=/distfiles --exclude=/local --exclude=/packages" PORTAGE_TMPDIR="/var/tmp" PORTDIR="/usr/portage" PORTDIR_OVERLAY="/usr/local/portage" SYNC="rsync://rsync.gentoo.org/gentoo-portage" USE="X acl acpi alsa amd64 avahi berkdb cdr cli cracklib crypt cups daap dbus dri dvd firefox fortran gdbm gnome gpm gstreamer gtk gtk+ hal iconv isdnlog jpeg live matroska midi mmx mp3 mpeg mudflap ncurses nls nptl nptlonly nsplugin openmp pam pcre perl png pppd python qt3 qt4 readline reflection samba session speex spl sse sse2 ssl svg tcpd tiff truetype type1 unicode x264 xinerama xorg zlib" ALSA_CARDS="emu10k1 intel8x0" ALSA_PCM_PLUGINS="adpcm alaw asym copy dmix dshare dsnoop empty extplug file hooks iec958 ioplug ladspa lfloat linear meter mulaw multi null plug rate route share shm softvol" APACHE2_MODULES="actions alias auth_basic authn_alias authn_anon authn_dbm authn_default authn_file authz_dbm authz_default authz_groupfile authz_host authz_owner authz_user autoindex cache dav dav_fs dav_lock deflate dir disk_cache env expires ext_filter file_cache filter headers include info log_config logio mem_cache mime mime_magic negotiation rewrite setenvif speling status unique_id userdir usertrack vhost_alias" ELIBC="glibc" INPUT_DEVICES="evdev keyboard mouse" KERNEL="linux" LCD_DEVICES="bayrad cfontz cfontz633 glk hd44780 lb216 lcdm001 mtxorb ncurses text" LINGUAS="de it en en_GB" USERLAND="GNU" VIDEO_CARDS="apm ark chips cirrus cyrix dummy fbdev glint i128 i810 mach64 mga neomagic nv r128 radeon rendition s3 s3virge savage siliconmotion sis sisusb tdfx tga trident tseng v4l vesa vga via vmware voodoo" [CPUINFO] processor : 3 vendor_id : AuthenticAMD cpu family : 16 model : 2 model name : AMD Phenom(tm) 9750 Quad-Core Processor stepping : 3 cpu MHz : 2400.000 cache size : 512 KB physical id : 0 siblings : 4 core id : 3 cpu cores : 4 fpu : yes fpu_exception : yes cpuid level : 5 wp : yes flags : fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush mmx fxsr sse sse2 ht syscall nx mmxext fxsr_opt pdpe1gb rdtscp lm 3dnowext 3dnow constant_tsc rep_good pni cx16 popcnt lahf_lm cmp_legacy svm extapic cr8_legacy abm sse4a misalignsse 3dnowprefetch osvw ibs bogomips : 4814.73 TLB size : 1024 4K pages clflush size : 64 cache_alignment : 64 address sizes : 48 bits physical, 48 bits virtual power management: ts ttp tm stc 100mhzsteps hwpstate Created attachment 153691 [details, diff]
contains phenom, nocona patch and some other minor fixes
nocona and other minor fixes are based on the latest cpuinfo.py in numpy cvs repository.
Note_1:Makes nocona patch obsolete
Note_2:Windows part is untested
Note_3:First patch ever, don't crucify me!
Hi Nylan, Thanks a lot for the patch. I've applied it in cvs. Please next time open a new bug (this one was set as closed). Also upstream might be interested in your patch. Why don't you submit it at http://projects.scipy.org/scipy/numpy/wiki. |
