[maker-devel] master_datastore_index.log file shrinks.]

[Michael Nuhn]

Hello Carson!

Thanks for the pointers. I'll give mpi another shot.

Cheers,
Michael.

On 03/19/2013 03:22 PM, Carson Holt wrote:
> I have MAKER working under OpemnMPI 1.4.3 (intel compiled).
>
> I had to set a couple of environmental variables prior to setup. You would
> probably need to set these values as well.  If you your OpenMPI path was
> here for example --> /software/openmpi-1.4.3/, run the following commands
> (path set accordingly) before even attempting maker setup.
>
> export OMPI_MCA_mpi_warn_on_fork  0
> export LD_PRELOAD /software/openmpi-1.4.3/lib/libmpi.so:$LD_PRELOAD
>
> These not only need to be set before compilation, but also before any run
> (so add them to you ~.bashrc or ~/.bash_profile or any module load scripts
> thanks).  The LD_PRELOAD statement needs to be set for any program using
> OpenMPI's shared libraries and not just MAKER, so it's normally a good
> idea to have that set system wide for all users.  The detail can be found
> in the OpenMPI documentation.  Note sometimes system library updates can
> break OpenMPI's shared libraries while not breaking OpenMPI itself, so you
> might also need to recompile OpenMPI if it has broken shared libraries.
>
> Once you have those commands in place, run the perl Buil.PL step. Say yes
> to install with MPI. Then run ./Build install
>
> Thanks,
> Carson
>
>
>
> On 13-03-19 11:02 AM, "Carson Holt" <carsonhh at gmail.com> wrote:
>
>> Try it with the no_locks option then.  Make sure to let one instance
>> finish populating the mpi_blastdb directory before running other
>> instances
>> as that is where most initial locking occurs.
>>
>> I'll send you more details on how to install with OpenMPI, so you can
>> give
>> that a shot while your jobs are also running serially (so you don't lose
>> time).  Also instead of 50 serial instances, you could try 10 with -cpus
>> set to 5.
>>
>> Thanks,
>> Carson
>>
>>
>>
>> On 13-03-19 11:19 AM, "Michael Nuhn" <mnuhn at ebi.ac.uk> wrote:
>>
>>> Hello Carson!
>>>
>>> On 03/19/2013 02:27 PM, Carson Holt wrote:
>>>> Yes.  If at all possible use MPI.  It removes the overhead of locks
>>>> which happen per primary instance of MAKER.  So one maker job using
>>>> 1000
>>>> cpus via MPI will have one shared set of locks.  1000 serial instances
>>>> of MAKER on the other hand would have 1000x the locks.
>>>
>>> I don't know a thing about MPI.
>>>
>>> I tried installing maker (2.2.7) with mpich-3.0.2, mpich2-1.4.1 and open
>>> mpi and none of them worked for me. I also tried the automatic
>>> installation that comes with maker, but it didn't work for me either.
>>>
>>> If need be, I could spend time getting to the bottom of this, but there
>>> is no telling how long this would take me so I'd rather not, if there is
>>> an alternative.
>>>
>>> Would the approach I outlined before work? (Treating the split files as
>>> separate genomes to annotate and then combine the gffs afterwards)
>>>
>>> I also like this approach, because I would select a few contigs in the
>>> beginning which I would run on their own. They would complete early and
>>> this way I would get a preview of the results of the run instead of
>>> having to wait for everything to complete.
>>>
>>> It might also be more robust, because file locking issues would be
>>> confined to the instances working on a sequence chunk, but the rest of
>>> the instances could continue working.
>>>
>>> Cheers,
>>> Michael.
>>>
>>>> Alternatively if you do need to continue without MPI for some reason, I
>>>> just finished a devel version of MAKER that has a --no_locks option.
>>>>    You can never start two instances using the same input fasta when
>>>> --no_locks is specified, but the splitting to use different input
>>>> fastas
>>>> I mentioned before in the example will still work fine.
>>>>
>>>> I also have updated the indexing/reindexing, so if indexing failures
>>>> happen, MAKER will switch between the current working directory and the
>>>> TMP= directory from the maker_opts.ctl file so as to try different IO
>>>> locations (I.e. NFS and non-NFS).  Note you should never set TMP= in
>>>> the
>>>> control files to an NFS mounted location (it not only makes things a
>>>> lot
>>>> slower, but berkleydb and sqllite will get frequent errors on NFS).
>>>>    TMP= defaults to /tmp when not specified
>>>>
>>>> I'll send you download information in a separate e-mail.  Try a regular
>>>> MAKER run to see if the indexing/reindexing changes are sufficient
>>>> before attempting the ‹no_locks option.
>>>>
>>>> Thanks,
>>>> Carson
>
>