Hello again
Regarding Boost:
The boost version is stable 1.67.0, installed through Homebrew package manager.
The log-file contains no further information
ld: library not found for -lboost_thread
clang: error: linker command failed with exit code 1 (use -v to see invocation)
On 26 Apr 2018, at 10:59, Stephan Schott <schottve.hhu.de<mailto:schottve.hhu.de>> wrote:
Hi Gustaf,
You can find the boost.compile.err file under AmberTools/src/ . Could you
tell me what version of boost you have in your machine? The -mt libraries
are a way of distinguishing the multi-threaded variants of the libs, but
afaik this should be included in the main library after boost 1.5 or so. As
Hai mentioned, all the functionalities of Amber will work with the
exception of the automated protein orientation in membranes done by
memembed in packmol-memgen. This means that you can still use the workflow
but by providing a preoriented structure (with OPM for example). Thanks for
testing though, is very valuable info.
2018-04-26 9:32 GMT+02:00 Gustaf Olsson <gustaf.olsson.lnu.se<mailto:gustaf.olsson.lnu.se>>:
Hi Stephan (David and Hai as well).
Could you send me or attach the content of boost.compile.err?
I probably could if I knew where to find it though I sort of solved the
issue instead.
do you need to use packmol_memgen? If not, you can skip that warning and
go ahead "make install"
To be honest, I have not even read the info on packmol_memgen so I can’t
answer that question. This is more of an OCD related problem at this point.
Below you’ll find the output from ./configure. It now finds and tests
boost successfully.
Testing the clang++ compiler with boost:
clang++ -fPIC -lboost_thread -lboost_system -o testp testp.cpp
OK
Anyway, the initial issue seems to have been filenames. The mac-boost
libraries seems to ship with "libboost_thread-mt.a" and
"libboost_thread-mt.dylib” instead of the sought after "libboost_thread.a"
and “libboost_thread.dylib”, this means that a simple symbolic link
addition to usr/local/lib/ solved the issue with configuration.
I am not a programmer of any sort so apologies for my possibly crude
assumptions and horrible example though it seems that this could be solved
by including some sort of IF check along the lines of:
if os=OSX && homebrew=TRUE
$boost_threads_prefix=libboost_thread-mt
else
$boost_threads_prefix=libboost_thread
I realise that this would have to be more complex of course. It also seems
that OS X does not set BOOST_ROOT and BOOST_LIBDIR even with brew boost
installed and as I don’t know if these are called during config/install I
don’t know if this would be a part of the fix. Basically, make sure BOOST
can be found and cover both libboost_thread and libboost_thread-mt.
Unfortunately, even if the tests passed "make install" failed
clang: warning: libstdc++ is deprecated; move to libc++ with a minimum
deployment target of OS X 10.9 [-Wdeprecated]
src/ga.hpp:45:15: error: private field 'w' is not used
[-Werror,-Wunused-private-field]
unsigned int w, x, y, z, c;
^
1 error generated.
make[4]: *** [src/ga.o] Error 1
make[3]: *** [install.memembed] Error 2
cp: packmol_memgen/lib/memembed/bin/memembed: No such file or directory
make[2]: *** [packmol-memgen] Error 1
make[1]: *** [serial] Error 2
make: *** [install] Error 2
The warning is obviously an indication that there is a library conflict
between Mac and Brew, I am sure that either sorting out the priorities or
adding more symlinks can solve this as well though I have spend the time I
had allocated for today on this issue. It is still kind of strange, I am
assuming that the binary was not built and hence cannot be copied though I
have no other error indication that something failed.
I’ll keep looking for a working solution to these issues and if I manage
to sort it out I’ll post something here! Meanwhile, if someone else figures
out how to get this working, please do share!
// Gustaf
On 25 Apr 2018, at 16:53, Stephan Schott <schottve.hhu.de<mailto:schottve.hhu.de><mailto:schott
ve.hhu.de<mailto:ve.hhu.de>>> wrote:
Hi,
Could you send me or attach the content of boost.compile.err? Maybe we can
get a hint of what is going on from there.
2018-04-25 14:53 GMT+02:00 David A Case <david.case.rutgers.edu<mailto:david.case.rutgers.edu><mailto:
david.case.rutgers.edu<mailto:
david.case.rutgers.edu>>>:
On Wed, Apr 25, 2018, Gustaf Olsson wrote:
So I switched from MacPorts to Homebrew when switching computers. This
meant going from GNU compilers to using CLANG which worked without a
hitch on AmberTools17, though this time I’m getting an error.
./configure -macAccelerate gnu
Testing the clang++ compiler with boost:
clang++ -fPIC -lboost_thread -lboost_system -o testp testp.cpp
Warning: Could not link to boost. Ensure boost-thread, boost-system and
boost headers are installed.
Wow: homebrew seems weird to me. It looks like it is following Apple's
strange (to me) policy of having gcc (in spite of its name)
point to the clang compiler and not to the GNU compiler. If things work
without a hitch for you, that is great. But most users, and
certainly those using macports, should follow this rule:
if the "gcc" in your PATH is really clang, you should use the
clang option for configure, not the gnu option.
Concerning packmol_memgen: as far as I can tell, for now, this option
only works for Linux. I'm sure some smart Mac user can figure out how
to get the boost libraries either by compiling from source, or from
macports. If someone provides detailed instructions, we'll create an
update patch. We apologize for the inconvenience.
...dac
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Bioquímico / Licenciado en Bioquímica
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Received on Thu Apr 26 2018 - 03:00:02 PDT
