On 4 Oct 2015, at 20:59, Alexander Hansen <[email protected]> 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): 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
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