Re: "ALRM" isn't numeric in exit - MAKER warning message

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Re: "ALRM" isn't numeric in exit - MAKER warning message

Carson Holt-2
Hi Marivi,

The only time MAKER uses the ALRM signal is during exit. Sometimes MPI_Finalize can freeze (it has to do with the fact it is being called from Perl). So we set an alarm just in case. Then if it takes to long we assume it is frozen and let things exit in a less than graceful way rather than let it block forever (it is already finished after all). The complaint you get may be because your system doesn’t support the alarm signal or forks.pm (which tries to intercept signals) is having an issue. Or it may just be ugliness related to parts of the process being killed with other parts still being active (it is an ungraceful exit after all). Or it may be another source of the ALRM all together (but I assume it is the MAKER ALRM given that it happens right after MAKER says it is finished). 

Thanks,
Carson



On Oct 27, 2017, at 1:03 PM, Marivi Colle <[hidden email]> wrote:

Hi Carson,

After running MAKER, I checked my std output and here's the message at the end of the file. I was wondering what this warning message means?


Start_time: 1508465182
End_time:   1508950543
Elapsed:    485361


Maker is now finished!!!

Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm line 2184.
Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm line 2184.
Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm line 2184.
Argument "ALRM" isn't numeric in exit at /opt/software/BioPerl/1.6.924--GCC-4.4.7/lib64/perl5/forks.pm line 2184


Thank you.
Marivi


--
Marivi G. Colle
Research Associate
Department of Horticulture
Michigan State University
1066 Bogue St., East Lansing
Michigan 48824-1325, USA


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