I really appreciate this list.
What you both said makes much more sense for me than what the
administrator of the cluster replied (He just said restart.sh should
be binary...).
However the directory I was running indeed didnt allow me to write
anything. So you're both right! And I was two times wrong....
Thank you one more time.
On 5/25/11, Jason Swails <jason.swails.gmail.com> wrote:
> Ah, Ross raises a good point. I hadn't thought enough about what was
> happening here.
>
> What you did was simply start 2 copies of restart.sh, each of which is
> launching a 'sander.MPI' executable. Thus, you have 2 sander.MPI
> executables each using 1 thread, and each one is trying to write to exactly
> the same files. This is why you get the "cannot open for read" and "cannot
> open for write", because you have 2 processes clashing with each other
> simultaneously. Thus, it's not a permissions issue. See Ross's mail for
> suggestions/fixes (I was simply explaining your error messages).
>
> HTH,
> Jason
>
> On Wed, May 25, 2011 at 12:42 PM, Ross Walker <ross.rosswalker.co.uk> wrote:
>
>> Hi Bruno,
>>
>> > The cluster administrator claimed that my ./restart.sh should be a
>> > BINARY
>> > file because mpirun only accepts binaries.
>>
>> This is not strictly true in the real sense of the word BUT you should NOT
>> be passing a script as an argument to mpirun. From your comment above I
>> would conclude that you are trying something like:
>>
>> mpirun -np 2 ./restart.sh
>>
>> This will definitely NOT work. The mpirun needs to be inside your
>> restart.sh
>> script in front of the pmemd.MPI or sander.MPI call.
>>
>> > I guess it's not the case as it recognizes the commands inside. Do you
>> > have
>> > any clue about the input files for mpirun? I read the man from mpirun
>>
>> Sure it recognizes the commands inside but you should probably read up a
>> bit
>> on what MPI actually is and you will realize what is going on here and why
>> this does not make sense. If you just do mpirun -np 2 ./restart.sh it will
>> simply run 2 copies of your restart.sh script and this will just end in a
>> big steaming pile of FAIL!
>>
>> Edit your restart.sh and put the mpirun command in front of the sander.MPI
>> or pmemd.MPI executable and then run the restart script with ./restart.sh.
>>
>> All the best
>> Ross
>>
>> /\
>> \/
>> |\oss Walker
>>
>> ---------------------------------------------------------
>> | Assistant Research Professor |
>> | San Diego Supercomputer Center |
>> | Adjunct Assistant Professor |
>> | Dept. of Chemistry and Biochemistry |
>> | University of California San Diego |
>> | NVIDIA Fellow |
>> | http://www.rosswalker.co.uk | http://www.wmd-lab.org/ |
>> | Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
>> ---------------------------------------------------------
>>
>> Note: Electronic Mail is not secure, has no guarantee of delivery, may not
>> be read every day, and should not be used for urgent or sensitive issues.
>>
>>
>>
>>
>>
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>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
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>
--
--
Bruno Barbosa Rodrigues
PhD Student - Physics Department
Universidade Federal de Minas Gerais - UFMG
Belo Horizonte - Brazil
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Received on Wed May 25 2011 - 12:30:02 PDT
