[gmx-users] a installation problem of gromacs4.5.4 using mpi

[Justin A. Lemkul]

mircial at sjtu.edu.cn wrote:
> Dear All:
> 
> I encountered a problem when installing gromacs4.5.4 by using mpi. When 
> 
> I finished the installation successfully, I submit a job by assigning 8 processes. However, the job was not run by 8 processes, by generate 8 same jobs each use only 1 process (I have encountered the same problem before, but it is solved by using the same mpirun path during the installation and the simulation. However, this time i am sure the path of mpirun assigned during the installation is the same of that assigned in the simulation command and this problem occures again.). The followings are the commonds used in my installation:
> 
> ########################install fftw#######
> ./configure --prefix=my_path --enable-thread --disable-float --enable-shared
> make 
> make install
> 
> #######################install gromacs#####
> 
> export CPPFLAGS=-I/my_path/
> export LDFFLAGS=-L/my_path/
> 
> ./configure --prefix=my_path --enable-shared --disable-float --enable-mpi=the_path_of_mpirun

The --enable-mpi flag does not take any argument. It is also advisable to append 
a suffix (e.g. _mpi) to the mdrun executable so you can unambiguously use the 
commands.

> make
> make install

There is no need to try to compile the entire Gromacs package with MPI support; 
only mdrun is MPI-aware.  Instead, use:

make mdrun
make install-mdrun

-Justin

> ###########################################
> 
> then I used the following command to do the simulations
> 
> /the_path_of_mpirun/mpirun -np 8 mdrun -s myfile.tpr
> 
> I am sure the path of mpirun assigned during the installation is the same of that assigned in the simulation command.
> 
> Could anyone tell me how to solve this problem?
> 
> Thanks in advance!!
> 
> R-X Gu
> 

-- 
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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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