[gmx-users] Problem Compiling mdrun parallel version for GROMACS 4.5.6
johnny.lu128 at gmail.com
Sat Sep 13 02:38:39 CEST 2014
google "undefined reference to `_intel_fast_memset'"
are you using intel compiler with gnu linker?
if you are using intel compiler, I think they have something like
setcompilervar.sh (or something like that... i don't remember now). should
run that first to set some environmental variable.
By the way, what kind of cluster, operating system, compiler, and linker
are you using?
Several weeks ago, I was compiling mixed precision gromacs on AIX, which
was a nightmare that gave 3 ns/day with 24 cpu.
On Fri, Sep 12, 2014 at 6:10 PM, Agnivo Gosai <agnivogromacs14 at gmail.com>
> Dr. Lemkul
> Thanks for your valuable suggestion. I used make distclean and could
> successfully install the serial version of GROMACS 4.5.6 in my university
> After that I used "make distclean" again and proceeded with compiling the
> parallel version of mdrun in a separate directory
> However when I tried to install the parallel version using the following
> command :-
> *./configure --enable-mpi
> --prefix=/home/agosai/GROMACS/gromacs-4.5.6-double-mpi --disable-float
> --program-suffix=-4.5.6-double-mpi --with-fft=fftw3*
> followed by
> *make mdrun*
> I get the below mentioned error message :-
> 4.5.6/src/mdlib/.libs/libmd_mpi_d.so: undefined reference to
> undefined reference to `_intel_fast_memset'
> undefined reference to `_intel_fast_memcpy'
> undefined reference to `__svml_sincos2'
> collect2: ld returned 1 exit status
> make: *** [mdrun] Error 1
> make: Leaving directory `/home/agosai/GROMACS/gromacs-4.5.6/src/kernel'
> Kindly advise on any further corrections for installing the parallel
> version. I have checked the official GROMACS site suggested in your last
> reply but could not find the mistake in my approach.
> Best Regards
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