[gmx-users] gromacs on glacier

Justin A. Lemkul jalemkul at vt.edu
Mon Jun 8 19:12:05 CEST 2009

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.


> p2_22627:  p4_error: Timeout in establishing connection to remote process: 0

This is an error message from MPICH, not Gromacs.  See, for example:



> 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.


> 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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