[maker-devel] master_datastore_index.log file shrinks.

[Carson Holt]

Great news.  I'm glad it's working.  If you have more questions, just let
me know.

--Carson


On 13-03-25 8:18 AM, "mnuhn" <mnuhn at ebi.ac.uk> wrote:

>Thanks, this works and mpi maker is running now.
>
>Cheers,
>Michael.
>
>P.S.:
>
>If anyone is trying to reproduce this, I only had one directory in
>LD_PRELOAD and it didn't like the trailing colon, so I removed it to
>make it work:
>
>export LD_PRELOAD=/software/openmpi-1.4.3/lib/libmpi.so
>
>On 2013-03-19 15:22, 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
>