[gmx-users] install Gromacs with MPI?

[Chng Choon Peng]

Hi Weihua,

   Rest assured that MPICH-VMI works with Gromacs :)
I tried that before on our IA32 cluster and
However, MPICH-VMI was compiled using GCC and so we
compiled FFTw and Gromacs with GCC as well.
As long as MPICH-VMI installation works with other MPI codes,
GROMACS should work too.

Unfortunately, I can't seem to find my installation notes.
And I think it's still best to contact the NCSA folks directly.


Regards,
Choon-Peng
-- 
Mr. Choon-Peng CHNG
Research Associate
BioInformatics Institute, BMSI, A*STAR
30 Biopolis Street
#07-01 Matrix Building
Singapore 138671
Tel (O): +65 64788301 Fax (O): +65 64789047
www.bii.a-star.edu.sg/~cpchng


On 2/11/04 7:43 AM, "Wu Xun" <wxun2000 at yahoo.com> wrote:

> Hi,
> 
> I was trying to install Gromacs on the IA-32
> ("platinum") cluster in NCSA with MPI, but could not
> get through. I contacted their consultant but it was
> not of much help. I would really appreciate it if
> someone here can help me out.
> 
> First I found the information about MPI on platinum
> here:
> http://www.ncsa.uiuc.edu/UserInfo/Resources/Hardware/IA32LinuxCluster/Doc/Comp
> ile.html#vmi
> 
> *********** Here is the description about MPI
> ***********
> The VMI Application Interface consists of the VMI
> library, to which applications are required to link.
> The VMI device interface mediates between the VMI
> library and the underlying VMI drivers. ......
> The layering of MPI on top of VMI is accomplished by
> means of a ch_vmi MPI device running on the Argonne
> National Laboratory MPICH distribution.
> 3.1 Platinum
> The following libraries are required for MPI codes:
> -lmpich -lvmi -ldl -lpthread
> 
> For Fortran MPI codes, use: -lmpich -lfmpich -lvmi
> -ldl -lpthread
> 
> Note that OpenMP/MPI hybrid programming models are
> currently not supported.
> Compiling MPI code using the Intel compilers:
> 
> The Intel compiler suite includes Fortran 77/90 (ifc),
> C (icc), and C++ (icpc).. The mpich, vmi, dl, and
> pthread libraries built using the Intel compilers are
> located in /usr/local/vmi/mpich/lib/icc.
> 
> Examples:
> 
> icc -I/usr/local/vmi/mpich/include mpicode.c -o
> mpicode \
>   -L/usr/local/vmi/mpich/lib/icc -lmpich -lvmi -ldl
> -lpthread
> 
> ifc -I/usr/local/vmi/mpich/include mpicode.f -o
> mpicode \
>   -L/usr/local/vmi/mpich/lib/icc -lmpich -lfmpich
> -lvmi -ldl -lpthread
> 
> Compiling MPI code using the PGI compilers:
> 
> The PGI compiler suite includes Fortran 90 (pgf90),
> Fortran 77 (pgf77), C (pgcc), and C++ (pgCC). The
> mpich, vmi, dl, and pthread libraries built using the
> PGI compilers are located in
> /usr/local/vmi/mpich/lib/pgi.
> 
> Example:
> 
> pgf77 -I/usr/local/vmi/mpich/include mpicode.f -o
> mpicode \
>     -L/usr/local/vmi/mpich/lib/pgi -lmpich -lfmpich
> -lvmi -ldl -lpthread
> 
> Compiling MPI code using the GNU compilers:
> 
> The GNU compilers are Fortran 77 (g77), C (gcc), and
> C++ (g++). The libraries are located under
> /usr/local/vmi/mpich/lib/gcc.
> 
> Example:
> 
> gcc -I/usr/local/vmi/mpich/include mpicode.c -o
> mpicode \
>   -L/usr/local/vmi/mpich/lib/gcc -lmpich -lvmi -ldl
> -lpthread
> 
> The gcc (and g77) compilers are particular about the
> order of arguments--the order shown above works well,
> other arrangements may not.
> 
> ****************** end about MPI ******************
> 
> Here is what I tried:
> 
> setenv CPPFLAGS
> -I/usr/apps/math/fftw/fftw-2.1.5/icc7/lib
> setenv LDFLAGS
> -L/usr/apps/math/fftw/fftw-2.1.5/icc7/include
> set CC icc
> set MPICC 'icc -I/usr/local/vmi/mpich/include
> -L/usr/local/vmi/mpich/lib/icc -lmpich -lfmpich -lvmi
> -ldl -lpthread'
> ./configure --enable-mpi
> --prefix=/u/ncsa/weihua/Gromacs/gromacs_mpi
> 
> ******************
> 
> Here is the last line of the configure output:
> 
> checking whether the MPI cc command works...
> configure: error: Cannot compile and link MPI code
> with icc -I/usr/local/vmi/mpich/include
> -L/usr/local/vmi/mpich/lib/icc -lmpich -lvmi -ldl
> -lpthread
> 
> And in config.log it gives:
> /u/ncsa/weihua/Gromacs/gromacs-3.1.4/configure:3350:
> undefined reference to `MPI_Init'
> configure:3360: $? = 1
> configure: failed program was:
> #line 3345 "configure"
> #include "confdefs.h"
> #include <mpi.h>
> int
> main ()
> {
> int argc; char **argv; MPI_Init(&argc,&argv);
> ;
> return 0;
> }
> configure:3373: error: Cannot compile and link MPI
> code with icc -I/usr/local/vmi/mpich/include
> -L/usr/local/vmi/mpich/lib/icc -lmpich -lv
> mi -ldl -lpthread
> 
> *******************************
> 
> So it looks that it did not find the mpi compiler at
> all. Could someone tell me the commands that I should
> run step by step? Or is this a system-specific problem
> for VMI?
> 
> Thanks a lot. sorry this email is long, I just hope
> you can find all the info needed.
> 
> Weihua Guo
> 
> 
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