[gmx-users] gromacs on glacier

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 8 19:56:23 CEST 2009

Payman Pirzadeh wrote:
> Hi Justin,
> Since the manual itself was not sufficient, I asked some other people who
> are running GROMACS in our group (but they run only on 2 CPUs). Here are the
> steps I took to compile the parallel version (I have included my notes that
> they told me as well):
> Installation
> 1.	./configure --prefix=/global/home/pirzadeh/gromacs-4.0.4
> This line specifies the installation path
> 2.	Make
> 3.	Make install
> These two commands will make 'grompp' and analysis functions of GROMACS.
> 4.	Make clean
> This command will clean some files generated during installation which are
> not needed anymore.
> 5.	./configure --enable-mpi --disable-nice
> --prefix=/global/home/pirzadeh/gromacs-4.0.4
> Here we compile the code for parallel version of GROMACS
> 6.	make mdrun
> 7.	 make install-mdrun
> Now the parallel version of mdrun is built. The analysis functions are found
> in 'bin' folder accompanied by 'GMXRC'.
> 8.	Before running 'grompp' to produce the topology file for simulation,
> we should use the command  source
> /global/home/pirzadeh/gromacs-4.0.4/bin/GMXRC to specify the path for the
> current code.

This is pretty much the standard installation procedure.  What we also need to 
know are the compilers used, etc. for the installation.  The error you're 
getting is from MPICH.  Which version is installed on the cluster?  It may be 
old and buggy.  In any case, you can try to install something newer, like a 
recent version of OpenMPI (which we have on our cluster); it may be more 
reliable.  Only a random thought, means nothing unless we know what you have 
installed :)

What about the contents of your system, as I asked before?  Do you really have a 
100% virtual site system?


> Sorry for tons of e-mails.
> Payman
> -----Original Message-----
> From: gmx-users-bounces at gromacs.org [mailto:gmx-users-bounces at gromacs.org]
> On Behalf Of Justin A. Lemkul
> Sent: June 8, 2009 11:12 AM
> To: Discussion list for GROMACS users
> Subject: Re: [gmx-users] gromacs on glacier
> Payman Pirzadeh wrote:
>> Hi,
>> I had the chance to run the GROMACS 4.0.4 on another cluster. Same 
>> problem still persists. But what I found is that it can be run on a node 
>> with 2 CPUs, but as soon as the number of nodes are increased to 2, 3, . 
>> it will crash. Following are the last lines reported in different files:
>> "In the log file of the code":
>> There are: 1611 Atoms
>> There are: 1611 VSites
> All of your atoms are virtual sites?  If so, I would try a simpler test
> case, to 
> rule out stumbling across some obscure bug.
> Also:
>> p2_22627:  p4_error: Timeout in establishing connection to remote process:
> 0
> This is an error message from MPICH, not Gromacs.  See, for example:
> http://www.mail-archive.com/gmx-users@gromacs.org/msg10968.html
> <snip>
>> To me, it seems that code can not communicate through more than one 
>> node. I am suspicious of doing sth wrong during installation! I tried 
>> wiki, but I can not find the documents as before, and I eally do not 
>> know in which step I might have gone wrong.
> If you suspect you have done something wrong, then post the details of the 
> system configuration (hardware, compilers, OS, etc.) as well as a
> step-by-step 
> record of what you did to compile the software.  If your procedure is sound,
> then it helps rule out the possibility that you messed something up.
> -Justin
>> Payman
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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