[maker-devel] (no subject)

Tue Jul 15 08:03:12 MDT 2014

Carson, many thanks for the info!

I haven't installed Maker with MPI support. Is this segfault only occurring
when you install it with MPI support?

On Tue, Jul 15, 2014 at 3:58 PM, Carson Holt <carsonhh at gmail.com> wrote:

> If you are getting a segfault.  It is more likely an MPI error especially
> if you are using OpenMPI or MVAPICH2.  They both use OpenFabrics libraries
> that have bugs on forks and system calls.
>
> If it is OpenMPI, run the following command before launching MAKER -->
> export LD_PRELOAD=Š/openmpi_location/lib/libmpi.so
>
> Make sure to set replace openmpi_location with the location of your
> OpenMPI.
>
> Also add the following to your MPI command before running MAKER.
> --> -mca btl ^openib
> Example --> mpiexec -mca btl ^openib -n 40 maker
>
>
> If you are using MVAPICH2, then you need to switch to OpenMPI.
>
> --Carson
>
>
>
>
> From: Panos Ioannidis <panos.ioannidis at gmail.com>
> Date: Tuesday, July 15, 2014 at 12:59 AM
> To: Carson Holt <carsonhh at gmail.com>
> Cc: Daniel Ence <dence at genetics.utah.edu>, maker-devel <
> maker-devel at yandell-lab.org>
>
> Subject: Re: [maker-devel] (no subject)
>
> I didn't know there are more than one forks.pm files! We'll give it
> another try later today.
>
> As for the error, it's just "Segmentation fault"! And we know this
> segfault is because of forks.pm, because if you remove the "use forks;"
> line script execution continues without segfault (till it crashes later for
> another reason, of course). In fact, even if you create a script with just
> the line "use forks;" and try to run it, you'll get a segfault. So it looks
> like it's something pretty general and serious, and I'm really surprised I
> can't find anything by googling (except your fix!)...
>
>
> On Mon, Jul 14, 2014 at 4:49 PM, Carson Holt <carsonhh at gmail.com> wrote:
>
>> Also one more question.  What is the exact error text you get for the
>> forks error?  Is it a forks.pm error or is it an MPI warn on fork error
>> (which are actually very different).
>>
>> --Carson
>>
>>
>> From: Carson Holt <carsonhh at gmail.com>
>> Date: Monday, July 14, 2014 at 8:46 AM
>> To: Panos Ioannidis <panos.ioannidis at gmail.com>, Daniel Ence <
>> dence at genetics.utah.edu>
>>
>> Cc: maker-devel <maker-devel at yandell-lab.org>
>> Subject: Re: [maker-devel] (no subject)
>>
>> If you do the BLAST's yourself the results could be dramatically worse.
>>  The filtering and polishing done by MAKER is rather significant (direct
>> BLAST is actually worse with homology searches than many people realize).
>>
>> With respect to forks.pm, your admin most likely edited the wrong
>> forks.pm.  There may be more than one on your system. If you let maker
>> install some prerequisites for you (because it requires a specific version
>> of forks.pm), it may be in .../maker/perl/lib/forks.pm.  Otherwise you
>> have to identify the exact location of the forks.pm being used. Or if he
>> is editing it as part of the install tarball, his edits may actually be
>> undone during the installation procedure.
>>
>> Use this command line to identify the location of the forks.pm module
>> that would have to be edited -->
>> maker --debug 2>&1 | grep "forks.pm"
>>
>> You can even send me a copy of the file once it has been edited, and I
>> can tell you if it was done correctly.
>>
>> --Carson
>>
>>
>>
>>
>> From: Panos Ioannidis <panos.ioannidis at gmail.com>
>> Date: Monday, July 14, 2014 at 1:20 AM
>> To: Daniel Ence <dence at genetics.utah.edu>
>> Cc: maker-devel <maker-devel at yandell-lab.org>
>> Subject: Re: [maker-devel] (no subject)
>>
>> Daniel, thanks for the info.
>>
>> Regarding (3), the only reason I think of running BLASTs separately is
>> because I'm currently not able to run Maker on our cluster due to a problem
>> in the Perl "forks" library. And it looks like there isn't much I can do
>> about it; I tried Perlbrew but it doesn't work when I try to install
>> versions <5.18 (the problem in forks occurs on 5.18 and later versions).
>> Our admin also tried to change the code in the forks.pm file as per
>> Carson's suggestion in another thread, but that didn't work either... As a
>> result I'm running Maker on my workstation (really slooow) till a solution
>> is found and since BLAST is a time-consuming step I was thinking of running
>> it separately.
>>
>>
>> On Fri, Jul 11, 2014 at 4:08 PM, Daniel Ence <dence at genetics.utah.edu>
>> wrote:
>>
>>> Hi Panos,
>>>
>>> 1) You'll only use est2genome and protein2genome for creating models
>>> that will be used for training the ab-initio predictors (like SNAP).
>>> Sometimes that means one run of MAKER for training; sometimes that means
>>> two runs of MAKER. You usually don't gain any accuracy after the second
>>> round of training. It's ok to use both EST and protein data for this
>>> training step.
>>>
>>> 2) If you're using both ESTs and protein sequence to train your
>>> ab-initio predictors, then both est2genome and protein2genome should be set
>>> to 1.
>>>
>>> 3) If you want to pass Blast results to MAKER, you'll need to pass those
>>> results as GFF3, but MAKER will install and run blast for you, and does a
>>> good job of keeping track of all those results and making them accessible
>>> to you in the end, so it's going to be a lot of work to do those blasts on
>>> your own outside of MAKER. I seriously suggest that you use blast internal
>>> to maker.
>>>
>>> Daniel Ence
>>> Graduate Student
>>> Eccles Institute of Human Genetics
>>> University of Utah
>>> 15 North 2030 East, Room 2100
>>> Salt Lake City, UT 84112-5330
>>> ------------------------------
>>> *From:* maker-devel [maker-devel-bounces at yandell-lab.org] on behalf of
>>> Panos Ioannidis [panos.ioannidis at gmail.com]
>>> *Sent:* Friday, July 11, 2014 5:56 AM
>>> *To:* maker-devel
>>> *Subject:* [maker-devel] (no subject)
>>>
>>> I got back to my annotations this past week and have a couple of
>>> questions!
>>>
>>> 1) Since my organism isn't closely related with any other that's already
>>> sequenced, I will have to run maker twice (according to the tutorial). So
>>> for the first run I see that some people use only the ESTs and some others
>>> use ESTs and a protein database (CEGMA, Uniref50, Swiss-Prot, etc). I guess
>>> that the ESTs will give better models, but for the cases where genes aren't
>>> covered by an EST, it's okay to have a protein database to detect them as
>>> well. Am I right? What do you think?
>>>
>>> 2) In case I use both ESTs and a protein database how should I set the
>>> est2genome and protein2genome parameters in the maker_opts.ctl file?
>>> Should they both equal to "1"?
>>>
>>> 3) I've been thinking of running the BLAST searches separately and
>>> giving Maker directly the results. I guess that in this case, I'll have to
>>> first convert the BLAST output to a gff3 file and give it to the
>>> protein_gff parameter, right?
>>>
>>> Thanks,
>>> Panos
>>>
>>
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>
>
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