On 4 Oct 2015, at 20:20, Alexander Hansen <alexanderk.han...@gmail.com> wrote:
>
>> 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>
>> 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?
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
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