Re: [AMBER] amber 18 compilation issue

From: David A Case <>
Date: Wed, 7 Nov 2018 08:05:23 -0500

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/ 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.)


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Received on Wed Nov 07 2018 - 05:30:03 PST
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