[gmx-users] install Gromacs with MPI?

[Wu Xun]

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/Compile.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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