[gmx-users] Can not open file: topol.tpr

[Jochen Hub]

Guillem Plasencia wrote:

> Hello listers,
>
> this is my first try with Gromacs (3.3.1). I've installed LAM-MPI 
> (7.1.2) and FFTW3 in my two Dual Intel P4 CPU machines (4 physical 
> CPUs, 8 with hyperthreading on, i've already read in the mailing list 
> archive that i should turn off hyperthreading until Gromacs 4 release 
> to improve performance) running Fedora Core 4 (kernel 2.6).
>
> Just to test the parallel processing, i downloaded and tried to run 
> one of the benchmark tests (d.lzm).
>
> I prepared it with:
>
> grompp -f cutoff.mdp -c conf.gro -p topol.top -np 2
>
> (here i had to read the archives to avoid temptation to include -nt 2, 
> which even including --enable-threads in configure options gave me an 
> error).
>
>
> But when tried to run it in my two-nodes as a parallel task with:
>
> mpirun n0,1 mdrun -s topol.tpr -np 2
>
> i got the following output from mdrun:
>
> NNODES=2, MYRANK=1, HOSTNAME=lead8
> NNODES=2, MYRANK=0, HOSTNAME=lead7
> NODEID=1 argc=5
> NODEID=0 argc=5
>
>>>> CUT SOME MDRUN HELP INFO >>>
>>>
> -------------------------------------------------------
> Program mdrun, VERSION 3.3.1
> Source code file: gmxfio.c, line: 706
>
> Can not open file:
> topol.tpr
> ------------------------------------------------------- 


Are you sure that your topol.tpr was your present working diretory?

>
>
> "I'm a Jerk" (F. Black)
>
> Error on node 0, will try to stop all the nodes
> Halting parallel program mdrun on CPU 0 out of 2
>
> gcq#171: "I'm a Jerk" (F. Black)
>
> ----------------------------------------------------------------------------- 
>
> One of the processes started by mpirun has exited with a nonzero exit
> code.  This typically indicates that the process finished in error.
> If your process did not finish in error, be sure to include a "return
> 0" or "exit(0)" in your C code before exiting the application.
>
> PID 27859 failed on node n1 (192.168.1.9) with exit status 1.
> ----------------------------------------------------------------------------- 
>
>
> You can see from lamnodes that node n1 is the originating node
>
>> lamnodes
>
> n0      lead7:2:
> n1      192.168.1.9:2:origin,this_node
>
> and from ps -leaf | grep mdrun i can see that both processes have been 
> started, but neither uses CPU at all. So far, i guess this is because 
> if the originating node (n1) can't read topol.tpr file, it can't 
> distribute tasks amongst nodes (which would be causing the unknown 
> error in node 0, the other node).
>
> Any ideas on what's happening? How do i solve it?
>
> Thank you very much !
>
> Guillem Plasencia
> Spain.
>
> P.D. I've read on the archives that there was some interest in knowing 
> if hyperthreading is still doing wrong balancing in linux kernel 2.6, 
> which happens to be the kernel i'm running. I'd be pleased to test 
> both HT on and off on my nodes, of course as soon as i solve this 
> problem with topol.tpr file.
>
>
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-- 
************************************************
Jochen Hub
Max Planck Institute for Biophysical Chemistry
Computational biomolecular dynamics group
Am Fassberg 11
D-37077 Goettingen, Germany
Email: jhub[at]gwdg.de
************************************************