Re: [AMBER] amber 18 compilation issue

From: Vlad Cojocaru <>
Date: Wed, 7 Nov 2018 16:54:51 +0100

Dear Dave, Dear Stephan,

Thanks for answering. So, I just managed a few minutes ago to solve the
issue by adding the "-lpthread" explicitly to LIBS in the Makefiles of
packmol-memgen ... (both src and python). I modified all Makefiles and I
don't know if all modifications are needed but with them, the serial
compilation worked now ....

Anyhow, maybe this helps to add a patch that fixes this issue ...

Best wishes

On 11/7/18 4:21 PM, Stephan Schott wrote:
> 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 (<>)
> 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/ 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

Vlad Cojocaru, PD (Habil.), Ph.D.
Project Group Leader
Department of Cell and Developmental Biology
Max Planck Institute for Molecular Biomedicine
Röntgenstrasse 20, 48149 Münster, Germany
Tel: +49-251-70365-324; Fax: +49-251-70365-399
Email: vlad.cojocaru[at]
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Received on Wed Nov 07 2018 - 08:00:02 PST
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