> On Oct 4, 2015, at 11:56, Viv Kendon <v...@trellick.org> wrote: > > On 4 Oct 2015, at 19:32, Alexander Hansen <alexanderk.han...@gmail.com > <mailto:alexanderk.han...@gmail.com>> wrote: >> >>> On Oct 4, 2015, at 09:37, Viv Kendon <v...@trellick.org> wrote: >>> >>> Having trouble unpacking openmpi: >>> >>> /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 >>> >>> It didn’t give me a “please include this” set of info, let me know if I >>> left out anything you need about my configuration: 10.9.5, case-sensitive, >>> fink -V >>> Package manager version: 0.39.1 >>> >>> fink list -t openmpi >>> Information about 9257 packages read in 0 seconds. >>> openmpi 1.10.0-1 MPI implementation for parallel computing >>> i openmpi-shlibs 1.10.0-1 Shared libraries for openmpi package >>> >>> gcc -v >>> Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr >>> --with-gxx-include-dir=/usr/include/c++/4.2.1 >>> Apple LLVM version 6.0 (clang-600.0.57) (based on LLVM 3.5svn) >>> Target: x86_64-apple-darwin13.4.0 >>> >>> ls -l /sw/bin/vt* >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 15:56 /sw/bin/vtCC@ -> vtwrapper >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 15:56 /sw/bin/vtc++@ -> vtwrapper >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 15:56 /sw/bin/vtcxx@ -> vtwrapper >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 15:56 /sw/bin/vtf77@ -> vtwrapper >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 15:56 /sw/bin/vtf90@ -> vtwrapper >>> 624 -rwxr-xr-x 1 root admin 318760 Oct 4 14:53 /sw/bin/vtfilter* >>> 664 -rwxr-xr-x 1 root admin 336860 Oct 4 14:53 /sw/bin/vtfilter-mpi* >>> 8 lrwxr-xr-x 1 root admin 8 Oct 4 15:56 /sw/bin/vtfiltergen@ -> >>> vtfilter >>> 8 lrwxr-xr-x 1 root admin 12 Oct 4 15:56 /sw/bin/vtfiltergen-mpi@ >>> -> vtfilter-mpi >>> 8 lrwxr-xr-x 1 root admin 9 Oct 4 15:56 /sw/bin/vtfort@ -> >>> vtwrapper >>> 24 -rwxr-xr-x 1 root admin 9205 Oct 4 14:53 /sw/bin/vtrun* >>> 8 -rwxr-xr-x 1 root admin 1612 Oct 4 14:53 /sw/bin/vtsetup* >>> 1096 -rw-r--r-- 1 root admin 557402 Oct 4 14:53 /sw/bin/vtsetup.jar >>> 1104 -rwxr-xr-x 1 root admin 563296 Oct 4 14:53 /sw/bin/vtunify* >>> 1272 -rwxr-xr-x 1 root admin 649392 Oct 4 14:53 /sw/bin/vtunify-mpi* >>> 328 -rwxr-xr-x 1 root admin 166016 Oct 4 14:53 /sw/bin/vtwrapper* >>> >>> (the 14:53 timestamps are from when I tried it first, and openmpi-shlibs >>> was installed successfully; 15:56 is when it failed the second time, after >>> restarting “update-all") >>> >>> many thanks, >>> — Viv >>> ——————————————————————————————————————— >> >> There’s a note in the packaging about “case sensitive hackery”, but it >> appears not to have taken effect. It looks like vtCC still gets installed, >> and then the PostInstScript tries to run >> >> ln -s /sw/bin/vtwrapper /sw/bin/vtCC >> >> which fails due to vtCC already existing. >> >> Since I don’t have a case-sensisitve system handy, could I please get you to >> do a “fink -kK rebuild openmpi” ? That way I can do some forensics on the >> build and root directories to see whether the scripts are doing the right >> thing? >> >> The first thing to look for is the output of "ls >> /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vt* >> > done: > > ls /sw/src/fink.build/root-openmpi-1.10.0-1/sw > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtc++@ > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtcc@ > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtcxx@ > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtf77@ > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtf90@ > 624 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfilter* > 664 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfilter-mpi* > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfiltergen@ > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfiltergen-mpi@ > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtfort@ > 24 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtrun* > 8 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtsetup* > 1096 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtsetup.jar > 1104 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtunify* > 1272 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtunify-mpi* > 328 /sw/src/fink.build/root-openmpi-1.10.0-1/sw/bin/vtwrapper* > > note that despite the “rebuild” it reinstalled openmpi-shlibs, so I now have > > ls -l /sw/bin/vt* > 8 lrwxr-xr-x 1 root admin 9 Oct 4 18:02 /sw/bin/vtCC@ -> vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 18:02 /sw/bin/vtc++@ -> vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 18:02 /sw/bin/vtcxx@ -> vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 18:02 /sw/bin/vtf77@ -> vtwrapper > 8 lrwxr-xr-x 1 root admin 9 Oct 4 18:02 /sw/bin/vtf90@ -> vtwrapper > 624 -rwxr-xr-x 1 root admin 318760 Oct 4 14:53 /sw/bin/vtfilter* > 664 -rwxr-xr-x 1 root admin 336860 Oct 4 14:53 /sw/bin/vtfilter-mpi* > 8 lrwxr-xr-x 1 root admin 8 Oct 4 18:02 /sw/bin/vtfiltergen@ -> > vtfilter > 8 lrwxr-xr-x 1 root admin 12 Oct 4 18:02 /sw/bin/vtfiltergen-mpi@ > -> vtfilter-mpi > 8 lrwxr-xr-x 1 root admin 9 Oct 4 18:02 /sw/bin/vtfort@ -> > vtwrapper > 24 -rwxr-xr-x 1 root admin 9205 Oct 4 14:53 /sw/bin/vtrun* > 8 -rwxr-xr-x 1 root admin 1612 Oct 4 14:53 /sw/bin/vtsetup* > 1096 -rw-r--r-- 1 root admin 557402 Oct 4 14:53 /sw/bin/vtsetup.jar > 1104 -rwxr-xr-x 1 root admin 563296 Oct 4 14:53 /sw/bin/vtunify* > 1272 -rwxr-xr-x 1 root admin 649392 Oct 4 14:53 /sw/bin/vtunify-mpi* > 328 -rwxr-xr-x 1 root admin 166016 Oct 4 14:53 /sw/bin/vtwrapper* > > note later timestamps. > > many thanks, > — Viv > ———————————————————————————————————————
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? -- Alexander Hansen, Ph.D. Fink User Liaison
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