[gmx-users] Re: MPI problem——Cannot compile and link MPI code with cc

[Justin A. Lemkul]

DreamCatcher wrote:
> Hello guys,
>         Me again.After a reinstallation with a root previlege the 
> compile problem with MPI is solved now. But I am still confused about 
> the difference with or without MPI in a dual-core system.Can anybody 
> spark me?
>    

MPI allows the two processors to communicate with one another.  Without MPI 
(serial installation), you can only use one of your two processors.  With MPI 
(parallel installation), you can use both to speed up your calculations.

-Justin
 

> celeste
>                                                                                               
> 2010-3-29
> 
> 
> On Mon, Mar 29, 2010 at 7:24 AM, DreamCatcher 
> <huangshuping1987 at gmail.com <mailto:huangshuping1987 at gmail.com>> wrote:
> 
>     Hello gmx-users,
>            I am trying to install a MPI version of Gromacs that I come
>     across some problems as follows:
>     [celeste at celeste gromacs-4.0.7]$ sudo ./configure
>     --prefix=/home/programmes/gromacs --disable-float --enable-mpi
>     checking build system type... i686-pc-linux-gnu
>     checking host system type... i686-pc-linux-gnu
>     checking for a BSD-compatible install... /usr/bin/install -c
>     checking whether build environment is sane... yes
>     checking for a thread-safe mkdir -p... /bin/mkdir -p
>     checking for gawk... gawk
>     checking whether make sets $(MAKE)... yes
>     checking how to create a ustar tar archive... gnutar
>     checking for cc... cc
>     checking for C compiler default output file name... a.out
>     checking whether the C compiler works... yes
>     checking whether we are cross compiling... no
>     checking for suffix of executables...
>     checking for suffix of object files... o
>     checking whether we are using the GNU C compiler... yes
>     checking whether cc accepts -g... yes
>     checking for cc option to accept ISO C89... none needed
>     checking for style of include used by make... GNU
>     checking dependency style of cc... gcc3
>     checking dependency style of cc... gcc3
>     checking for mpxlc... no
>     checking for mpicc... no
>     checking for mpcc... no
>     checking for hcc... no
>     checking whether the MPI cc command works... configure: error:
>     Cannot compile and link MPI code with cc
> 
>            I have installed MPICH2 in my PC and export the PATH where
>     the mpicc is.Yet,as a matter of fact,the prompts above indicates
>     that there isn't an mpicc in my PC.Could anybody tell me what the
>     hell the problem is. How can I fix it?
> 
>          Another question, I am use a PC with dual-CPU, is it neccissary
>     to install an MPI version? Will the difference between a gmx with or
>     without a MPI in such a system be big enough to save our CPU time
>     when implement a molecular dynamics? My system may contains about
>     10000 or more atoms.
>          Thanks in advance.
>                                                                                                                                                                           
>     celeste
>                                                                                                                                                                          
>     2010-03-29
> 
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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