[gmx-users] Problem Compiling mdrun parallel version for GROMACS 4.5.6

[Johnny Lu]

By the way, have you tried gromacs 4.6.7? I think that only needs a c
compiler.
Or 5.0.1 ?

On Fri, Sep 12, 2014 at 8:38 PM, Johnny Lu <johnny.lu128 at gmail.com> wrote:

> Hi.
>
> google "undefined reference to `_intel_fast_memset'"
> gives:
>
> https://software.intel.com/en-us/forums/topic/310493
>
>
> 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?
>
> p.s.
> 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>
> wrote:
>
>> 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
>> cluster
>>
>> 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 :-
>>
>> /home/agosai/GROMACS/gromacs-
>> 4.5.6/src/mdlib/.libs/libmd_mpi_d.so: undefined reference to
>> `__libm_sse2_sincos'
>> /home/agosai/GROMACS/gromacs-4.5.6/src/mdlib/.libs/libmd_mpi_d.so:
>> undefined reference to `_intel_fast_memset'
>> /home/agosai/GROMACS/gromacs-4.5.6/src/mdlib/.libs/libmd_mpi_d.so:
>> undefined reference to `_intel_fast_memcpy'
>> /home/agosai/GROMACS/gromacs-4.5.6/src/mdlib/.libs/libmd_mpi_d.so:
>> undefined reference to `__svml_sincos2'
>> collect2: ld returned 1 exit status
>> make[1]: *** [mdrun] Error 1
>> make[1]: 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
>> Agnivo
>> Ames,Iowa
>> --
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>
>