[gmx-users] 1replica/1cpu problem

[Mark Abraham]

On 19/07/2012 6:24 PM, francesco oteri wrote:
> Sorry for the multiple emails but everytime I tried to send the mail I
> obtained a message like this:
>
> "The message's content type was not explicitly allowed. Please send
> your messages as plain text only. See
> http://www.gromacs.org/Support/Mailing_Lists"
>
> So I tried as long as no message has been replied to me.
>
>
> Concerning the bug fixes, I did the following steps
>
> git clone git://git.gromacs.org/gromacs.git  gromacs-4.5.5-patches
> cd gromacs-4.5.5-patches
> git checkout --track -b release-4-5-patches origin/release-4-5-patches
> git pull
> ./bootstrap
> ./configure --prefix=/ibpc/etna/oteri/PKG/gromacs/4.5.5/patched
> --without-x --enable-mpi --program-suffix=_mpi --enable-all-static
> CFLAGS="-I/ibpc/etna/oteri/PKG/openmpi/1.4.5/include
> -I/ibpc/etna/oteri/PKG/fftw/3.3.1/gcc/include"
> "LDFLAGS=-L/ibpc/etna/oteri/PKG/fftw/3.3.1/gcc/lib
> -L/ibpc/etna/oteri/PKG/openmpi/1.4.5/lib"   LIBSUFFIX=_mpi
> make mdrun
> make install-mdrun

Well, that shouldn't happen. You want to be sure your grompp version 
matches your mdrun version. If so, please open a Redmine issue here 
http://redmine.gromacs.org <http://redmine.gromacs.org/>, upload your 
.tpr set, give the command line that will reproduce the problem and flag 
it for my attention.

Mark

>
> 2012/7/19 Mark Abraham<Mark.Abraham at anu.edu.au>:
>> On 19/07/2012 12:32 AM, francesco oteri wrote:
>>> Dear gromacs users,
>>> I am trying to run a replica exchange simulation using the files you find
>>> inhttp://dl.dropbox.com  /u/40545409/gmx_mailinglist/inputs.tgz
>>>
>>> The 4 replicas have been generated, as following:
>>> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_0  -f rest2_0.mdp
>>> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_1  -f rest2_1.mdp
>>> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_2  -f rest2_2.mdp
>>> grompp -p rest2.top -c 03md.gro -n index.ndx -o rest2_3  -f rest2_3.mdp
>>>
>>> The simulation was started with command, using gromacs 4.5.5  with the
>>> latest bug fix:
>> Which bug fix? How did you apply it?
>>
>> Mark
>>
>>
>>> mpirun -np 4  mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out1
>>>
>>> giving the following error:
>>>
>>> [etna:10799] *** An error occurred in MPI_comm_size
>>> [etna:10799] *** on communicator MPI_COMM_WORLD
>>> [etna:10799] *** MPI_ERR_COMM: invalid communicator
>>> [etna:10799] *** MPI_ERRORS_ARE_FATAL (your MPI job will now abort)
>>> --------------------------------------------------------------------------
>>> mpirun has exited due to process rank 0 with PID 10796 on
>>> node etna exiting without calling "finalize". This may
>>> have caused other processes in the application to be
>>> terminated by signals sent by mpirun (as reported here).
>>> --------------------------------------------------------------------------
>>> [etna:10795] 3 more processes have sent help message
>>> help-mpi-errors.txt / mpi_errors_are_fatal
>>> [etna:10795] Set MCA parameter "orte_base_help_aggregate" to 0 to see
>>> all help / error messages
>>>
>>>
>>> The nice thing is that the same error doesn't appear either if I use
>>> the 4.5.5 without applying tha patches!!!
>>>
>>> mpirun -np 4  mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out2
>>>
>>> or the bug fixed with multiple processors per replica:
>>>
>>> mpirun -np 8  mdrun_mpi -s rest2_.tpr -multi 4 -replex 1000 >& out3
>>>
>>> Since I have to use more then 4 replicas, I need to run 1cpu/replica.
>>>
>>> Has someone any idea of the probem?
>>>
>>> Francesco
>>
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