I commited the updated version of the package into sci overlay for testing. There I added following new things 1. bump to 1.1.0 2. Fix for bug 252662 3. removed some automagic and buddled lib support and replaced it with USE 4. USE="mpi" now uses mpi for compilation * NEW FEATURES o Moved APBS user guide and tutorial to MediaWiki o Added in support for OpenMPI for parallel calculations o Added in command line support for Opal job submissions (Code by Samir Unni) o Allowed pathname containing spaces in input file, as long as the whole pathname is in quotes ("") o Documented 'make test' and related features * MODIFICATIONS o Modified the function bcCalc to march through the data array linearly when setting boundary conditions. This removes duplication of grid points on the edge of the array and corners. o Clarified documentation on the IDs assigned to input maps, PQRs, parameter files, etc. o Updated tutorial to warn against spaces in APBS working directory path in VMD; updated user guide to warn against spaces in APBS installation path on Windows o 'make test' has been reconfigured to run before issuing make install (can be run from top directory) o Removed tools/visualization/vmd from tools directory in lieu of built-in support in VMD o Path lengths can now be larger than 80 characters o Expanded authorship list o Added in 'make test-opal' as a post install test (run from the examples install directory) o Added additional concentrations to protein-rna test case to better encompass experimental conditions used by Garcia-Garcia and Draper; this improves agreement with the published data * BUG FIXES o Fixed typos in User Guide (ion keyword) and clarified SMPBE keyword usage o Fixed typo in User Guide (writemat: poission -> poisson) o Updated psize.py with to fix inconsistent assignment of fine grid numbers in some (very) rare cases o Fixed bug with boundary condition assignment. This could potentially affect all calculations; however, probably has limited impact: many test cases gave identical results after the bug fix; the largest change in value was < 0.07%.
http://git.overlays.gentoo.org/gitweb/?p=proj/sci.git;a=tree;f=sci-chemistry/apbs;h=7a55d7e464017d8dbe1ac3b1722cfb46b2638e81;hb=HEAD
apbs-1.1.0's filesize is incorrect in the manifest. Whenever I try to install it I get the following: ======= >>> Emerging (2 of 5) sci-chemistry/apbs-1.1.0 from science * Fetching files in the background. To view fetch progress, run * `tail -f /var/log/emerge-fetch.log` in another terminal. >>> Downloading 'http://distfiles.gentoo.org/distfiles/apbs-1.1.0-source.tar.gz' --2009-04-21 09:26:33-- http://distfiles.gentoo.org/distfiles/apbs-1.1.0-source.tar.gz Resolviendo distfiles.gentoo.org... 140.211.166.134, 156.56.247.195, 216.165.129.135, ... Connecting to distfiles.gentoo.org|140.211.166.134|:80... conectado. Petición HTTP enviada, esperando respuesta... 404 Not Found 2009-04-21 09:26:44 ERROR 404: Not Found. >>> Downloading 'http://distro.ibiblio.org/pub/linux/distributions/gentoo/distfiles/apbs-1.1.0-source.tar.gz' --2009-04-21 09:26:44-- http://distro.ibiblio.org/pub/linux/distributions/gentoo/distfiles/apbs-1.1.0-source.tar.gz Resolviendo distro.ibiblio.org... 152.46.7.109 Connecting to distro.ibiblio.org|152.46.7.109|:80... conectado. Petición HTTP enviada, esperando respuesta... 404 Not Found 2009-04-21 09:26:44 ERROR 404: Not Found. >>> Downloading 'http://osdn.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz' --2009-04-21 09:26:44-- http://osdn.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz Resolviendo osdn.dl.sourceforge.net... 216.34.181.56 Connecting to osdn.dl.sourceforge.net|216.34.181.56|:80... conectado. Petición HTTP enviada, esperando respuesta... 200 OK Longitud: 10582742 (10M) [application/octet-stream] Saving to: `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' 100%[=====================================================================>] 10.582.742 23,6K/s in 5m 54s 2009-04-21 09:32:50 (29,2 KB/s) - `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' saved [10582742/10582742] ('Filesize does not match recorded size', 10582742L, 10582216) !!! Fetched file: apbs-1.1.0-source.tar.gz VERIFY FAILED! !!! Reason: Filesize does not match recorded size !!! Got: 10582742 !!! Expected: 10582216 Refetching... File renamed to '/usr/portage/distfiles/apbs-1.1.0-source.tar.gz._checksum_failure_.C6kpqa' >>> Downloading 'http://kent.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz' --2009-04-21 09:32:50-- http://kent.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz Resolviendo kent.dl.sourceforge.net... 212.219.56.167 Connecting to kent.dl.sourceforge.net|212.219.56.167|:80... conectado. Petición HTTP enviada, esperando respuesta... 200 OK Longitud: 10582742 (10M) [application/x-gzip] Saving to: `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' 100%[=====================================================================>] 10.582.742 493K/s in 17s 2009-04-21 09:33:18 (592 KB/s) - `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' saved [10582742/10582742] ('Filesize does not match recorded size', 10582742L, 10582216) !!! Fetched file: apbs-1.1.0-source.tar.gz VERIFY FAILED! !!! Reason: Filesize does not match recorded size !!! Got: 10582742 !!! Expected: 10582216 Refetching... File renamed to '/usr/portage/distfiles/apbs-1.1.0-source.tar.gz._checksum_failure_.C6kpqa' >>> Downloading 'http://mesh.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz' --2009-04-21 09:33:18-- http://mesh.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz Resolviendo mesh.dl.sourceforge.net... 213.203.218.122 Connecting to mesh.dl.sourceforge.net|213.203.218.122|:80... conectado. Petición HTTP enviada, esperando respuesta... 302 Found Localización: http://213.203.218.125/a/ap/apbs/apbs-1.1.0-source.tar.gz [siguiendo] --2009-04-21 09:33:28-- http://213.203.218.125/a/ap/apbs/apbs-1.1.0-source.tar.gz Connecting to 213.203.218.125:80... conectado. Petición HTTP enviada, esperando respuesta... 200 OK Longitud: 10582742 (10M) [application/octet-stream] Saving to: `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' 100%[=====================================================================>] 10.582.742 1,03M/s in 14s 2009-04-21 09:33:42 (732 KB/s) - `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' saved [10582742/10582742] ('Filesize does not match recorded size', 10582742L, 10582216) !!! Fetched file: apbs-1.1.0-source.tar.gz VERIFY FAILED! !!! Reason: Filesize does not match recorded size !!! Got: 10582742 !!! Expected: 10582216 Refetching... File renamed to '/usr/portage/distfiles/apbs-1.1.0-source.tar.gz._checksum_failure_.C6kpqa' >>> Downloading 'http://switch.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz' --2009-04-21 09:33:43-- http://switch.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz Resolviendo switch.dl.sourceforge.net... 130.59.138.21, 2001:620:0:1b::21 Connecting to switch.dl.sourceforge.net|130.59.138.21|:80... conectado. Petición HTTP enviada, esperando respuesta... 200 OK Longitud: 10582742 (10M) [application/x-gzip] Saving to: `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' 100%[=====================================================================>] 10.582.742 1,33M/s in 7,2s 2009-04-21 09:33:50 (1,40 MB/s) - `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' saved [10582742/10582742] ('Filesize does not match recorded size', 10582742L, 10582216) !!! Fetched file: apbs-1.1.0-source.tar.gz VERIFY FAILED! !!! Reason: Filesize does not match recorded size !!! Got: 10582742 !!! Expected: 10582216 Refetching... File renamed to '/usr/portage/distfiles/apbs-1.1.0-source.tar.gz._checksum_failure_.C6kpqa' >>> Downloading 'http://jaist.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz' --2009-04-21 09:33:50-- http://jaist.dl.sourceforge.net/sourceforge/apbs/apbs-1.1.0-source.tar.gz Resolviendo jaist.dl.sourceforge.net... 150.65.7.130 Connecting to jaist.dl.sourceforge.net|150.65.7.130|:80... conectado. Petición HTTP enviada, esperando respuesta... 200 OK Longitud: 10582742 (10M) [application/x-gzip] Saving to: `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' 100%[=====================================================================>] 10.582.742 70,2K/s in 74s 2009-04-21 09:35:15 (140 KB/s) - `/usr/portage/distfiles/apbs-1.1.0-source.tar.gz' saved [10582742/10582742] ('Filesize does not match recorded size', 10582742L, 10582216) !!! Fetched file: apbs-1.1.0-source.tar.gz VERIFY FAILED! !!! Reason: Filesize does not match recorded size !!! Got: 10582742 !!! Expected: 10582216 Refetching... File renamed to '/usr/portage/distfiles/apbs-1.1.0-source.tar.gz._checksum_failure_.C6kpqa' !!! Couldn't download 'apbs-1.1.0-source.tar.gz'. Aborting. * Fetch failed for 'sci-chemistry/apbs-1.1.0', Log file: * '/var/tmp/portage/sci-chemistry/apbs-1.1.0/temp/build.log'
confirmed, upstream changed the tarball and the patches doesn't aply anymore. Will fix that asap.
(In reply to comment #3) > confirmed, upstream changed the tarball and the patches doesn't aply anymore. > Will fix that asap. > I fixed it, but discovered some bad things. So the current ebuild is working again, but will be replaced by a new one soon.
Iwill do the bump in the overlay the next days.
I am working on it. It should be in portage soon(ish). Thanks, Markus
apbs-1.2 is now in portage (without opal support until ppc is on board with the opal client). Thanks, Markus
There are a couple of other things missing like openmp support, fetk and tinker support. Is it respecting LDFLAGS? Didn't test it yet but the version in sci overlay has a LDFLAGS patch.
openmp and LDFLAGS work as far as I can tell. fetk is missing since we need to add punc which I have yet to look at. Similarly, tinker integration is awaiting keywording on amd64 and ppc. Hopefully we can work on getting these integrated soon. Thanks, Markus
(In reply to comment #9) > openmp and LDFLAGS work as far as I can tell. Okay you are right the LDFLAGS patch is unneeded and the I overlooked the openmp support while diffing the ebuilds. > > fetk is missing since we need to add punc which I have punc is in sci overlay and quite a simple ebuild > yet to look at. Similarly, tinker integration > is awaiting keywording on amd64 and ppc. > > Hopefully we can work on getting these integrated > soon. > > Thanks, > Markus >
