[maker-devel] MAKER Commercial User -- Install and run issues

[Carson Holt]

Once you install MPICH or OpenMPI you must launch MAKER through mpiexec and speciffy the CPU count to MPI. On a single instance you just give the CPU count off that instance, but you can also go across instances using Amazon’s Parallel Cluster. 

Here is an example —> https://efish.integrativebiology.msu.edu/2015/02/10/annotate.html
That example uses StarCluster which is now deprecated, but the MPI install and MAKER run still apply.

Here is another example of using MPi —> https://weatherby.genetics.utah.edu/MAKER/wiki/index.php/MAKER_Tutorial_for_WGS_Assembly_and_Annotation_Winter_School_2018#MPI_Support

Note that for OpenMPI you have to set the LD_PRELOAD environmental variable before launch.
export LD_PRELOAD=/usr/lib64/openmpi-1.10/lib/libmpi.so

—Carson


> On Aug 18, 2023, at 2:53 PM, Hayley Mangelson <hayley at phasegenomics.com> wrote:
> 
> I am working on an AWS EC2 instance that runs Amazon Linux, and I have tried a couple of installs (MPICH and Open MPI), neither of which worked. I don't have any installed on my current instance.
> 
> On Tue, Aug 15, 2023 at 5:08 PM Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>> Do you already have MPI installed on your system, and if so which MPI and what version (i.e. MPICH, MVAPICH2, Intel MPI, Open MPI, etc)?
>> 
>> —Carson
>> 
>> 
>>> On Aug 15, 2023, at 9:34 AM, Hayley Mangelson <hayley at phasegenomics.com <mailto:hayley at phasegenomics.com>> wrote:
>>> 
>>> Hi Carson,
>>> 
>>> Excellent, thanks so much! I have that part working. The multithreading is still eluding me. Do you have a recommended method of installing a compatible version of MPI?
>>> 
>>> Thanks,
>>> 
>>> Hayley
>>> 
>>> On Fri, Aug 11, 2023 at 4:04 PM Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>>>> The error is coming from Augustus. There is a problem with the species file you selected. Or you put it in the wrong place.
>>>> 
>>>> This is the error —> 
>>>> Could not find the config file /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/BUSCO_evans_trout_hap1/BUSCO_evans_trout_hap1_parameters.cfg
>>>> 
>>>> The species info must exist under this base directory by default (it’s where you let MAKER install Augustus) —>  /home/ec2-user/MAKERTOOLS/maker/exe/augustus/config/species/
>>>> 
>>>> You can also place the species files somewhere else but you need to set the AUGUSTUS_CONFIG_PATH so Augustus knows where to look.
>>>> 
>>>> Example (in your ~/.bash_profile):
>>>> export AUGUSTUS_CONFIG_PATH=$HOME/muy_augustus_species
>>>> 
>>>> Thanks,
>>>> Carson
>>>> 
>>>> 
>>>> 
>>>>> On Aug 11, 2023, at 7:20 AM, Hayley Mangelson <hayley at phasegenomics.com <mailto:hayley at phasegenomics.com>> wrote:
>>>>> 
>>>>> Hi Carson,
>>>>> 
>>>>> Sure thing! Sorry for the delay, I was on vacation. I reran with just a single scaffold. Here is the STDERR.
>>>>> 
>>>>> On Mon, Jul 31, 2023 at 12:06 PM Carson Holt <carsonhh at gmail.com <mailto:carsonhh at gmail.com>> wrote:
>>>>>> Can you send me the STDERR from the maker run? If you don’t have it, run maker again with the output from the screen redirected to a file. Example —> maker &> all_output.txt
>>>>>> 
>>>>>> --Carson
>>>>>> 
>>>>>> Sent from my iPhone
>>>>>> 
>>>>>>> On Jul 31, 2023, at 10:04 AM, Hayley Mangelson <hayley at phasegenomics.com <mailto:hayley at phasegenomics.com>> wrote:
>>>>>>> 
>>>>>>> 
>>>>>>> Hi!
>>>>>>> 
>>>>>>> I am trying to get a fresh install of MAKER to work for me and am having a few issues. 
>>>>>>> 
>>>>>>> 1. I got MAKER installed (I thought) and now the log is saying all contigs failed. See attached log.
>>>>>>> 2. Having tried several versions and methods of installation, I cannot get multithreading to work.
>>>>>>> 
>>>>>>> Could you help me work through these issues?
>>>>>>> Thanks,
>>>>>>> 
>>>>>>> Hayley
>>>>>>> -- 
>>>>>>> Hayley Mangelson
>>>>>>> Senior Bioinformatics Lead
>>>>>>> Phase Genomics, Inc
>>>>>>> www.phasegenomics.com <http://www.phasegenomics.com/>
>>>>>>> 
>>>>>>> <PGA_assembly_hap1_master_datastore_index.log>
>>>>>>> _______________________________________________
>>>>>>> maker-devel mailing list
>>>>>>> maker-devel at yandell-lab.org <mailto:maker-devel at yandell-lab.org>
>>>>>>> http://yandell-lab.org/mailman/listinfo/maker-devel_yandell-lab.org
>>>>> 
>>>>> 
>>>>> -- 
>>>>> Hayley Mangelson
>>>>> Senior Bioinformatics Lead
>>>>> Phase Genomics, Inc
>>>>> www.phasegenomics.com <http://www.phasegenomics.com/>
>>>>> 
>>>>> <all_output.txt>
>>>> 
>>> 
>>> 
>>> -- 
>>> Hayley Mangelson
>>> Senior Bioinformatics Lead
>>> Phase Genomics, Inc
>>> www.phasegenomics.com <http://www.phasegenomics.com/>
>>> 
>> 
> 
> 
> -- 
> Hayley Mangelson
> Senior Bioinformatics Lead
> Phase Genomics, Inc
> www.phasegenomics.com <http://www.phasegenomics.com/>
> 

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