[gmx-users] gromacs on glacier

[Justin A. Lemkul]

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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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