> On Oct 4, 2015, at 13:07, Viv Kendon <v...@trellick.org> wrote: > > On 4 Oct 2015, at 20:59, Alexander Hansen <alexanderk.han...@gmail.com > <mailto:alexanderk.han...@gmail.com>> wrote: > >>>> >>>> A rebuild normally includes a reinstall if you’re building the same >>>> version as the currently installed one, so that’s not surprising. >>>> However, if those files were indeed changed by the openmpi-shlibs install, >>>> that would be another matter, since the pre-removal and post-install >>>> scripts are run for the main package only. >>>> >>>> At least we’ve determined that vtCC wasn’t present in the root directory. >>>> What happens if you remove openmpi (leaving the shlibs) and install it? >>> >>> openmpi is not installed (according to fink), which is why only >>> openmpi-shlibs was reinstalled. So trying to install openmpi gives the >>> same error: >>> >>> fink list openmpi >>> Information about 9257 packages read in 1 seconds. >>> openmpi 1.10.0-1 MPI implementation for parallel computing >>> i openmpi-shlibs 1.10.0-1 Shared libraries for openmpi package >>> fink install openmpi >>> Password: >>> Information about 9257 packages read in 0 seconds. >>> The following package will be installed or updated: >>> openmpi >>> Reading buildlock packages... >>> All buildlocks accounted for. >>> /sw/bin/dpkg-lockwait -i >>> /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.0-1_darwin-x86_64.deb >>> (Reading database ... 380816 files and directories currently installed.) >>> Preparing to replace openmpi 1.10.0-1 (using >>> .../openmpi_1.10.0-1_darwin-x86_64.deb) ... >>> Unpacking replacement openmpi ... >>> Setting up openmpi (1.10.0-1) ... >>> Clearing dependency_libs of .la files being installed >>> ln: /sw/bin/vtCC: File exists >>> /sw/bin/dpkg: error processing openmpi (--install): >>> subprocess post-installation script returned error exit status 1 >>> Errors were encountered while processing: >>> openmpi >>> ### execution of /sw/bin/dpkg-lockwait failed, exit code 1 >>> Failed: can't install package openmpi-1.10.0-1 >>> >>> ls -l /sw/bin/vt* >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 20:36 /sw/bin/vtCC@ -> vtwrapper >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 20:36 /sw/bin/vtc++@ -> vtwrapper >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 20:36 /sw/bin/vtcxx@ -> vtwrapper >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 20:36 /sw/bin/vtf77@ -> vtwrapper >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 20:36 /sw/bin/vtf90@ -> vtwrapper >>> 624 -rwxr-xr-x 1 root admin 318760 Oct 4 19:48 /sw/bin/vtfilter* >>> 664 -rwxr-xr-x 1 root admin 336860 Oct 4 19:48 /sw/bin/vtfilter-mpi* >>> 8 lrwxr-xr-x 1 root admin 8 Oct 4 20:36 /sw/bin/vtfiltergen@ -> >>> vtfilter >>> 8 lrwxr-xr-x 1 root admin 12 Oct 4 20:36 /sw/bin/vtfiltergen-mpi@ >>> -> vtfilter-mpi >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 20:36 /sw/bin/vtfort@ -> >>> vtwrapper >>> 24 -rwxr-xr-x 1 root admin 9205 Oct 4 19:48 /sw/bin/vtrun* >>> 8 -rwxr-xr-x 1 root admin 1612 Oct 4 19:48 /sw/bin/vtsetup* >>> 1096 -rw-r--r-- 1 root admin 557402 Oct 4 19:48 /sw/bin/vtsetup.jar >>> 1104 -rwxr-xr-x 1 root admin 563296 Oct 4 19:48 /sw/bin/vtunify* >>> 1272 -rwxr-xr-x 1 root admin 649392 Oct 4 19:48 /sw/bin/vtunify-mpi* >>> 328 -rwxr-xr-x 1 root admin 166016 Oct 4 19:48 /sw/bin/vtwrapper* >>> >>> 19:48 is the rebuild time, i.e., when the openmpi deb was created, 20:36 is >>> the attempt to install openmpi time. So for the record, the 18:02 >>> timestamp above was from another failed attempt to install openmpi, when I >>> kicked off update-all again. >>> >>> fink remove openmpi >>> Information about 9257 packages read in 1 seconds. >>> WARNING: openmpi is not installed, skipping. >>> No packages to remove >>> >>> So it looks like it doesn’t clean up after the failed attempt to install. >>> Is there another way to get rid of the not quite installed files and try >>> again? >>> >>> many thanks, >>> — Viv >>> >>> >> >> Use “sudo dpkg -r openmpi” to remove the partially installed package (dpkg >> has a slightly different view of what is installed than fink does). Then >> verify whether /sw/bin/vtCC is still around. If it is, manually remove it. >> If not then try to “fink install openmpi” again. > > Great, that worked: > > sudo dpkg -r openmpi > Password: > dpkg: dependency problems prevent removal of openmpi: > fftw-mpi depends on openmpi. > /sw/bin/dpkg: error processing openmpi (--remove): > dependency problems - not removing > Errors were encountered while processing: > openmpi > fink remove fftw-mpi > Information about 9257 packages read in 1 seconds. > Reading buildlock packages... > All buildlocks accounted for. > /sw/bin/dpkg-lockwait --remove fftw-mpi > (Reading database ... 380816 files and directories currently installed.) > Removing fftw-mpi ... > install-info(fftw.info <http://fftw.info/>): deleting entry `* fftw: (fftw) > ...' > sudo dpkg -r openmpi > (Reading database ... 380755 files and directories currently installed.) > Removing openmpi ... > ls -l /sw/bin/vt* > ls: /sw/bin/vt*: No such file or directory > fink install openmpi > Information about 9257 packages read in 1 seconds. > The following package will be installed or updated: > openmpi > Reading buildlock packages... > All buildlocks accounted for. > /sw/bin/dpkg-lockwait -i > /sw/fink/dists/stable/main/binary-darwin-x86_64/devel/openmpi_1.10.0-1_darwin-x86_64.deb > Selecting previously deselected package openmpi. > (Reading database ... 379368 files and directories currently installed.) > Unpacking openmpi (from .../openmpi_1.10.0-1_darwin-x86_64.deb) ... > Setting up openmpi (1.10.0-1) ... > Clearing dependency_libs of .la files being installed > > fink list fftw-mpi > Information about 9257 packages read in 1 seconds. > fftw-mpi 2.1.5-1122 Discrete Fourier Transform Library > (i) fftw-mpi-shlibs 2.1.5-1122 Discrete Fourier Transform Library > > ls -l /sw/bin/vt* > 8 lrwxr-xr-x 1 root admin 17 Oct 4 21:04 /sw/bin/vtCC@ -> > /sw/bin/vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 21:04 /sw/bin/vtc++@ -> vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 21:04 /sw/bin/vtcc@ -> vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 21:04 /sw/bin/vtcxx@ -> vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 21:04 /sw/bin/vtf77@ -> vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 21:04 /sw/bin/vtf90@ -> vtwrapper > 624 -rwxr-xr-x 1 root admin 318760 Oct 4 19:48 /sw/bin/vtfilter* > 664 -rwxr-xr-x 1 root admin 336860 Oct 4 19:48 /sw/bin/vtfilter-mpi* > 8 lrwxr-xr-x 1 root admin 8 Oct 4 21:04 /sw/bin/vtfiltergen@ -> > vtfilter > 8 lrwxr-xr-x 1 root admin 12 Oct 4 21:04 /sw/bin/vtfiltergen-mpi@ > -> vtfilter-mpi > 8 lrwxr-xr-x 1 root admin 9 Oct 4 21:04 /sw/bin/vtfort@ -> > vtwrapper > 24 -rwxr-xr-x 1 root admin 9205 Oct 4 19:48 /sw/bin/vtrun* > 8 -rwxr-xr-x 1 root admin 1612 Oct 4 19:48 /sw/bin/vtsetup* > 1096 -rw-r--r-- 1 root admin 557402 Oct 4 19:48 /sw/bin/vtsetup.jar > 1104 -rwxr-xr-x 1 root admin 563296 Oct 4 19:48 /sw/bin/vtunify* > 1272 -rwxr-xr-x 1 root admin 649392 Oct 4 19:48 /sw/bin/vtunify-mpi* > 328 -rwxr-xr-x 1 root admin 166016 Oct 4 19:48 /sw/bin/vtwrapper* > > I’ll go back to “update-all”, and fftw-mpi will get reinstalled if needed. I > guess the original failure was due to the previous version still being > installed? > > many thanks, > — Viv
Yes, though I’m not completely sure what the problem was. It seems like the prior pre-removal script was possibly not handling vtCC correctly. -- Alexander Hansen, Ph.D. Fink User Liaison
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