81520 2005-02-10 10:55 0000 Numeric ebuild doesn't recognize atlas 2007-02-07 17:23:23 0000 1 1 1 Unclassified Gentoo Linux Applications unspecified All Linux RESOLVED FIXED P2 normal --- 1 dsdale24@gmail.com python@gentoo.org bicatali@gentoo.org cbm@m.fsf.org rak088+gentoobugzilla@casbah.it.northwestern.edu sci@gentoo.org dsdale24@gmail.com 2005-02-10 10:55:28 0000 I suggest that if atlas is listed in the USE flags, that Numeric should depend on lapack-atlas and blas-atlas. I suggest that sci-libs/atlas is not a good alternative, because it does not have a full lapack implementation. The setup.py file should be modified, I'll post a patch. Reproducible: Always Steps to Reproduce: 1. 2. 3. dsdale24@gmail.com 2005-02-10 11:04:56 0000 Created an attachment (id=50930) patch for setup.py to recognize atlas on gentoo Here is the setup.py patch for an ebuild to recognize lapack-atlas. I dont have experience writing ebuilds, but I will try to propose a new one that depends on lapack-atlas if USE="atlas". This patch would be applied instead of the existing patch, again if USE="atlas". dsdale24@gmail.com 2005-02-10 12:12:38 0000 Created an attachment (id=50945) patch for numeric to recognize atlas successfully built numeric with this patch, and the following ebuild... dsdale24@gmail.com 2005-02-10 12:17:53 0000 Created an attachment (id=50946) proposed ebuild for numeric-23.7-r1 I was able to link numeric-23.7 to atlas-tuned blas and lapack using this ebuild and patch 50945. If USE="atlas", then lapack-atlas is required. kugelfang@gentoo.org 2005-02-11 03:18:46 0000 Hi Darren! Ok, what I don't like on this idea is the following: We currently have a working system to switch between different BLAS and LAPACK implementations. So it makes no sense to apply this patch to circumvent the current system. A much better patch would make it look like this: library_dirs_list = ['/usr/lib/'] libraries_list = ['lapack', 'cblas', 'blas', 'atlas', 'g2c'] This way, any user of numeric could switch between the implementations using blas-config and lapack-config. dsdale24@gmail.com 2005-02-11 06:55:33 0000 Created an attachment (id=50997) updated patch to play nice with blas-config and lapack-config The use flag in the above ebuild is in question, but this patch is offerred as suggested in the last comment. kugelfang@gentoo.org 2005-02-16 04:05:09 0000 [As a side note: please submit always patches against ebuilds you want to be modified. This eases the devs job twice: 1st) he sees the actual differences, 2nd) he can commit w/o problems even if other parts of the ebuild have been altered in between submission and commit. ;-) ] Darren, as we already talked about on gentoo-science ML, we need to remove the "atlas" USE flag from your ebuild submission... @Python-herd: I'd like to see this in the tree. Mind if I commit it myself and add the Scientific Herd to the metadata ? --- numeric-23.7.ebuild 2005-02-16 13:01:25.403085728 +0100 +++ numeric-23.7-r1.ebuild 2005-02-16 13:01:08.422667144 +0100 @@ -11,19 +11,21 @@ SRC_URI="mirror://sourceforge/numpy/${MY_P}.tar.gz" HOMEPAGE="http://www.pfdubois.com/numpy/" -IUSE="" +IUSE="lapack" SLOT="0" KEYWORDS="~x86 ~ppc ~sparc ~alpha ~hppa ~amd64" LICENSE="as-is" # 2.1 gave sandbox violations see #21 -DEPEND=">=dev-lang/python-2.2" +DEPEND=">=dev-lang/python-2.2 + lapack? ( virtual/lapack )" src_unpack() { unpack ${A} cd ${S} epatch ${FILESDIR}/${P}.patch + epatch ${FILESDIR}/${P}-lapack.patch } src_install() { dsdale24@gmail.com 2005-02-16 07:01:20 0000 Thats excellent, thank you Danny. One final comment, the homepage for Numeric is now: http://numeric.scipy.org/ It should be reflected in the ebuild. bicatali@gentoo.org 2006-06-07 10:33:47 0000 The Gentoo Scientific overlay in http://gentooscience.org contains an updated ebuild of numeric allowing lapack and also makes some fixes. bicatali@gentoo.org 2006-09-13 09:16:26 0000 The ebuild in the gentooscience.org overlay fixes a decent number of numeric problems. From the ChangeLog: +files/numeric-arrayobject.patch, +files/numeric-lapack.patch, +numeric-24.2-r1.ebuild: fixed a memory leak, and added the possibility to compile linear algebra with installed blas/cblas/lapack. Tested against gcc41 and gcc34 on amd64, x86. Added longdescription in metadata.xml. Closes bugs #81520 and #114885. May be it would be worth a bump in the main tree? bicatali@gentoo.org 2007-02-07 17:23:23 0000 added lapack support in numeric-24.2-r2, now in cvs. 50930 2005-02-10 11:04 0000 patch for setup.py to recognize atlas on gentoo setup.py.diff text/plain NDMsNDRjNDMsNDQKPCBsaWJyYXJ5X2RpcnNfbGlzdCA9IFsnL3Vzci9saWIvYXRsYXMnXQo8IGxp YnJhcmllc19saXN0ID0gWydsYXBhY2snLCAnY2JsYXMnLCAnZjc3YmxhcycsICdhdGxhcycsICdn MmMnXSAKLS0tCj4gbGlicmFyeV9kaXJzX2xpc3QgPSBbXQo+IGxpYnJhcmllc19saXN0ID0gWyds YXBhY2snLCAnY2JsYXMnLCAnYmxhcycsICdhdGxhcycsICdnMmMnXSAK 50945 2005-02-10 12:12 0000 patch for numeric to recognize atlas numeric-23.7.atlas.patch text/plain LS0tIHNldHVwLnB5CTIwMDUtMDEtMDYgMTc6MTY6MTMuMDAwMDAwMDAwIC0wNTAwCisrKyBzZXR1 cC5weS5uZXcJMjAwNS0wMi0xMCAxNDozNzo1MC4wOTQ3NTA5MDQgLTA1MDAKQEAgLTQwLDggKzQw LDggQEAKICAgICAgICAgICAgICBdCiAjIHNldCB0aGVzZSB0byB1c2UgeW91ciBvd24gQkxBUzsK IAotbGlicmFyeV9kaXJzX2xpc3QgPSBbJy91c3IvbGliL2F0bGFzJ10KLWxpYnJhcmllc19saXN0 ID0gWydsYXBhY2snLCAnY2JsYXMnLCAnZjc3YmxhcycsICdhdGxhcycsICdnMmMnXSAKK2xpYnJh cnlfZGlyc19saXN0ID0gW10KK2xpYnJhcmllc19saXN0ID0gWydsYXBhY2snLCAnY2JsYXMnLCAn YmxhcycsICdhdGxhcycsICdnMmMnXSAKIAogIyBzZXQgdG8gdHJ1ZSAoMSksIGlmIHlvdSBhbHNv IHdhbnQgQkxBUyBvcHRpbWl6ZWQgbWF0cml4bXVsdGlwbHkvZG90L2lubmVycHJvZHVjdAogdXNl X2RvdGJsYXMgPSAxIAo= 50946 2005-02-10 12:17 0000 proposed ebuild for numeric-23.7-r1 numeric-23.7-r1.ebuild text/plain IyBDb3B5cmlnaHQgMTk5OS0yMDA1IEdlbnRvbyBGb3VuZGF0aW9uCiMgRGlzdHJpYnV0ZWQgdW5k ZXIgdGhlIHRlcm1zIG9mIHRoZSBHTlUgR2VuZXJhbCBQdWJsaWMgTGljZW5zZSB2MgojICRIZWFk ZXI6IC92YXIvY3Zzcm9vdC9nZW50b28teDg2L2Rldi1weXRob24vbnVtZXJpYy9udW1lcmljLTIz LjcuZWJ1aWxkLHYgMS4xIDIwMDUvMDEvMjEgMTY6NDk6NTcgY2FybG8gRXhwICQKCmluaGVyaXQg ZGlzdHV0aWxzIGV1dGlscwoKTVlfUD0ke1Avbi9OfQpTPSR7V09SS0RJUn0vJHtNWV9QfQoKREVT Q1JJUFRJT049Ik51bWVyaWNhbCBQeXRob24gYWRkcyBhIGZhc3QsIGNvbXBhY3QsIG11bHRpZGlt ZW5zaW9uYWwgYXJyYXkgbGFuZ3VhZ2UgZmFjaWxpdHkgdG8gUHl0aG9uLiIKU1JDX1VSST0ibWly cm9yOi8vc291cmNlZm9yZ2UvbnVtcHkvJHtNWV9QfS50YXIuZ3oiCkhPTUVQQUdFPSJodHRwOi8v d3d3LnBmZHVib2lzLmNvbS9udW1weS8iCgpJVVNFPSJhdGxhcyIKU0xPVD0iMCIKS0VZV09SRFM9 In54ODYgfnBwYyB+c3BhcmMgfmFscGhhIH5ocHBhIH5hbWQ2NCIKTElDRU5TRT0iYXMtaXMiCgoj IDIuMSBnYXZlIHNhbmRib3ggdmlvbGF0aW9ucyBzZWUgIzIxCkRFUEVORD0iPj1kZXYtbGFuZy9w eXRob24tMi4yCglhdGxhcz8gKD49c2NpLWxpYnMvbGFwYWNrLWF0bGFzLTMuNi4wKSIKCnNyY191 bnBhY2soKSB7Cgl1bnBhY2sgJHtBfQoKCWNkICR7U30KCWlmIHVzZSBhdGxhcyA7IHRoZW4KCQll cGF0Y2ggJHtGSUxFU0RJUn0vJHtQfS5hdGxhcy5wYXRjaAoJZWxzZQoJCWVwYXRjaCAke0ZJTEVT RElSfS8ke1B9LnBhdGNoCglmaQp9CgpzcmNfaW5zdGFsbCgpIHsKCglkaXN0dXRpbHNfc3JjX2lu c3RhbGwKCWRpc3R1dGlsc19weXRob25fdmVyc2lvbgoKCSNOdW1lcmljYWwgVHV0b3JpYWwgaXMg bmljZSBmb3IgdGVzdGluZyBhbmQgbGVhcm5pbmcKCWluc2ludG8gL3Vzci9saWIvcHl0aG9uJHtQ WVZFUn0vc2l0ZS1wYWNrYWdlcy9OdW1UdXQKCWRvaW5zIERlbW8vTnVtVHV0LyoKCn0K 50997 2005-02-11 06:55 0000 updated patch to play nice with blas-config and lapack-config setup.py.diff text/plain LS0tIHNldHVwLnB5CTIwMDUtMDEtMDYgMTc6MTY6MTMuMDAwMDAwMDAwIC0wNTAwCisrKyBzZXR1 cC5weS5uZXcJMjAwNS0wMi0xMCAxNDozNzo1MC4wOTQ3NTA5MDQgLTA1MDAKQEAgLTQwLDggKzQw LDggQEAKICAgICAgICAgICAgICBdCiAjIHNldCB0aGVzZSB0byB1c2UgeW91ciBvd24gQkxBUzsK IAotbGlicmFyeV9kaXJzX2xpc3QgPSBbJy91c3IvbGliL2F0bGFzJ10KLWxpYnJhcmllc19saXN0 ID0gWydsYXBhY2snLCAnY2JsYXMnLCAnZjc3YmxhcycsICdhdGxhcycsICdnMmMnXSAKK2xpYnJh cnlfZGlyc19saXN0ID0gWycvdXNyL2xpYiddCitsaWJyYXJpZXNfbGlzdCA9IFsnbGFwYWNrJywg J2NibGFzJywgJ2JsYXMnLCAnYXRsYXMnLCAnZzJjJ10gCiAKICMgc2V0IHRvIHRydWUgKDEpLCBp ZiB5b3UgYWxzbyB3YW50IEJMQVMgb3B0aW1pemVkIG1hdHJpeG11bHRpcGx5L2RvdC9pbm5lcnBy b2R1Y3QKIHVzZV9kb3RibGFzID0gMQo=