Re: [AMBER] AmberTools19/AMBER18 - FFTW3 and MKL compiling issues

From: viktor drobot <>
Date: Sat, 17 Aug 2019 13:29:38 +0300

Just tried with gmake -j1 and got the same results:

(cd rism && gmake yes )
gmake[2]: Entering directory
[RISM]  AR librism
[RISM] FC rism1d.F90
[RISM]  FC rism1d
[RISM] FC rism3d.thermo.F90
[RISM]  FC rism3d.thermo
[RISM] FC rism3d.orave.F90
[RISM]  FC rism3d.orave
[RISM] FC volslice.F90
[RISM]  FC volslice
/home/linux776_2091/build/amber18-intel/lib/libfftw3.a(malloc.o): In
function `fftw_free':
malloc.c:(.text+0x0): multiple definition of `fftw_free'
first defined here
gmake[2]: *** [volslice] Error 1
gmake[2]: Leaving directory
gmake[1]: *** [serial] Error 2
gmake[1]: Leaving directory
gmake: *** [install] Error 2

Possibly volslice source have some problems with FFTW/MKL hybrid linking.

17.08.2019 02:54, Tyler Luchko (Lists) пишет:
>> On Aug 16, 2019, at 1:54 PM, David Case <> wrote:
>> On Fri, Aug 16, 2019, viktor drobot wrote:
>>> Seems like the problem persists even with Intel 15.0.3 compilers:
>> Are you using the "-j" option for make? If so, it might help to leave that
>> out (or use "-j1") to get better error messages.
>> [Tyler: it kind of looks like this error is related to volslice, but it's hard
>> to tell.]
>> If you just want to see if you get some performance boost for QM/MM, try
>> commenting out the build of rism in AMBERHOME/AmberTools/src/Makefile.
> I’m not sure why this is happening as I compile with MKL and Intel all the time without issue.
> To get a better idea, I suggest building with
> make -j 1 VB=''
> This should give a better idea of which file is causing this problem and the compiler command used.
> Otherwise, if you are not using RISM, then commenting it out of the makefile may work.
> Tyler
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Received on Sat Aug 17 2019 - 04:00:02 PDT
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