Dear All,
I tried to install Amber14/AmberTools15 on Ubuntu 14.04 LTS and got an error at compliation stage:
/usr/bin/ld: /home/kris/bin/amber14/lib/libnetcdff.a(fort-attio.o): relocation R_X86_64_PC32 against undefined symbol `strlen@@GLIBC_2.2.5' can not be used when making a shared object; recompile with -fPIC
/usr/bin/ld: final link failed: Bad value
collect2: error: ld returned 1 exit status
make[2]: *** [/home/kris/bin/amber14/lib/libsander.so] Error 1
make[2]: Leaving directory `/home/kris/bin/amber14/AmberTools/src/sander'
make[1]: *** [serial] Error 2
make[1]: Leaving directory `/home/kris/bin/amber14/AmberTools/src'
make: *** [install] Error 2
After untarring the amber files freshly, I executed the followings: ./configuregnu
/update_amber--upgrade
./configuregnu
make install
Can you help me to identify the problem?
This error was reported before in Re: [AMBER] Error when compile ambertools15 from Jason Swails on 2015-05-07 (Amber Archive May 2015) , where it iwas suggested the following:
> We tried that option, but didn't work. We have found that the problem is on
> shared x64 libraries
>
> We have modified the config.h in the C and C++ flag lines, adding the
> option -mcmodel=large
It is not clear to me which lines I need to modify in the config.h. What I tried produced the same error. line 59 :
CFLAGS=-fPIC -DSYSV -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -DBINTRAJ -DHASGZ -DHASBZ2 -D__PLUMED_HAS_DLOPEN $(CUSTOMBUILDFLAGS) $(AMBERBUILDFLAGS) -mcmodel=large )
Thanks for any suggestions,Kris
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Received on Wed Apr 06 2016 - 08:00:04 PDT
