[gmx-users] mdrun_mpi executable not found

[Justin A. Lemkul]

Justin Kat wrote:
> Dear gmx users,
> 
> 
> I have installed the parallel version 4.0.7 of gromacs on one of the 
> nodes of my cluster. Here is the steps I've done through root:
> 
> 
> first, the normal installation:
> 
> ./configure
> 
> make
> 
> 
> make install
> 
> make links
> 
>  
> 
> then issued commands below for the mpi build:
> 
> ./configure |--enable-mpi|
> 
> make mdrun
> 
> make install-mdrun
> 
> make links
> 
> 
> I dont see any errors and everything seems to install fine.
> 
> 
> 
> I then switch to a normal user to do my work and then after issuing the grompp_md command as usual, I entered the command below:
> 
> 
> mpirun -np 8 mdrun_mpi -s *.tpr -o *.tpr -c *_after_md -v >& output.mdrun_md
> 
> 
> 
> however, output.mdrun_md gives: 
> 
> 
> 
> mpirun was unable to launch the specified application as it could not find an executable:
> 
> 
> 
> 
> Executable: mdrun_mpi
> Node: node3.reyclus.loc
> 
> 
> 
> 
> while attempting to start process rank 0.
> 
> 
> Was the installation procedure incorrect? Or do I need to go through a 
> separate installation for the mdrun_mpi executable? Please guide me on 
> what is wrong.
> 

No, the commands you gave should have built mdrun_mpi, as long as they finished 
successfully.  Were there errors in the installation?

With "make links" you should have links to all the Gromacs executables in 
/usr/local/bin - are they there?  You don't need to make links, instead you can 
follow the steps here:

http://www.gromacs.org/Downloads/Installation_Instructions#Getting_access_to_GROMACS_after_installation

-Justin

> Thanks,
> Justin
> 

-- 
========================================

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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