Hi Vlad,
I have not tried with that particular version of OS/GCC. It seems like some
library links might have changed; I will do some tests and get back to you.
In the meanwhile, after you configure AMBER, you can go to the config.h
file that is created, and change the very last line from MEMEMBED=yes to
MEMEMBED=no, and the compiling process should continue. Let me know if it
works.
Cheers,
El mié., 7 nov. 2018 a las 14:05, David A Case (<david.case.rutgers.edu>)
escribió:
> On Tue, Nov 06, 2018, Vlad Cojocaru wrote:
> >
> > g++ -Wall -Wextra -Werror -O3 -fPIC -std=c++11 -Isrc -I../boost/1.66/
> > src/main.o src/pdb.o src/ga.o src/grid.o src/direct.o
> >
> -Wl,-rpath=/apps/amber/18_tools-18_openmpi-3.1.3_gnu-8.2.1/AmberTools/src/packmol_memgen/packmol_memgen/lib/memembed/../boost/1.66/stage/lib/
>
> >
> -L/apps/amber/18_tools-18_openmpi-3.1.3_gnu-8.2.1/AmberTools/src/packmol_memgen/packmol_memgen/lib/memembed/../boost/1.66/stage/lib/
>
> > -lboost_thread -lboost_system -o bin/memembed
> > /usr/lib64/gcc/x86_64-suse-linux/8/../../../../x86_64-suse-linux/bin/ld:
> > src/main.o: undefined reference to symbol
> > 'pthread_condattr_setclock@@GLIBC_2.3.3'
> > /usr/lib64/gcc/x86_64-suse-linux/8/../../../../x86_64-suse-linux/bin/ld:
> > /lib64/libpthread.so.0: error adding symbols: DSO missing from command
> line
> > collect2: error: ld returned 1 exit status
> > make[4]: *** [Makefile:25: memembed] Error 1
> > make[4]: Leaving directory
> >
> '/apps/amber/18_tools-18_openmpi-3.1.3_gnu-8.2.1/AmberTools/src/packmol_memgen/packmol_memgen/lib/memembed'
> > make[3]: *** [Makefile:17: install.memembed] Error 2
> > make[3]: Leaving directory
> >
> '/apps/amber/18_tools-18_openmpi-3.1.3_gnu-8.2.1/AmberTools/src/packmol_memgen/packmol_memgen'
>
> Sigh...the dependence on boost (and perhaps a particular version of boost,
> not to mention the dependence on python) makes packmol_memgen fragile.
> The only suggestion I have is to just comment out the "packmol-memgen"
> item in the python_serial target in $AMBERHOME/AmberTools/src/Makefile;
> and perhaps try AMBAT, which is an alternative way to build
> protein-membrane systems.
>
> (cc-ing to Stephan Schott in case he recognizes the problem.)
>
> ...dac
>
>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Wed Nov 07 2018 - 07:30:03 PST
