[maker-devel] some suggestion

[Carson Holt]

The system we commonly use with MAKER is Lustre and we get no issues. We also commonly run MAKER on TACC which uses Lustre for all it’s file systems. So there is no Lustre limitation. MAKER does require that each node also have a local temporary directory for some operations which can generate high IOPS or require that traditional flock support (cannot be guaranteed on some NFS systems). These operations occur in the location specified by TMP= in the control file. Perhaps you are attempting to set your TMP value in the control files to a Lustre space which can overload the MDS (metadata server) used by Lustre. Make sure you do not set TMP to a shared location. Your working directory can be a shared Lustre space and result files will be stored there, but IO operations that are not safe for shared spaces will occur in TMP, and TMP must be set to a local storage location (usually /tmp).

--Carson



> On Jul 12, 2017, at 12:19 AM, zhushilin at frasergen.com wrote:
> 
> Dear developer,
> 
> It seems that MAKER can only run in the general hard disk which support structrued data, as SQLite was used.
> When running in lustre filesystem, we got  I/O error and nothing was written to .db file which saves the gff information.
> 
> Maybe the best way is to check the filesystem automatically and give the different strategy to store the information in gff files.
> 
> Best wishes
> Shilin Zhu   R&D director
> DEPT. of Bioinformatics
> Wuhan Frasergen Bioinformatics Co., Ltd
> B8 building│Biolake│666 Gaoxin Road│Wuhan East Lake High-tech Zone│Wuhan 430075│China
> T: 027-87224705│M: +86 18502745140 
> F: 027-87224785│E: service at frasergen.com <mailto:service at frasergen.com>
> W: http://www.frasergen.com <x-msg://93/www.frasergen.com>
> Disclaimer
> This e-mail is intended to be used only by persons entitled to receive such information and may contain information that is confidential, proprietary, and/or legally privileged. If you are not the intended recipient, you are hereby  notified that any use, retention, disclosure, dissemination, copying, or taking any other action in reliance on contents of this e-mail is prohibited. If you have received this e-mail in error, please immediately contact the sender and delete the e-mail from your mailbox or any other storage mechanism. Thank you!
> _______________________________________________
> maker-devel mailing list
> maker-devel at box290.bluehost.com <mailto:maker-devel at box290.bluehost.com>
> http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org <http://box290.bluehost.com/mailman/listinfo/maker-devel_yandell-lab.org>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://yandell-lab.org/pipermail/maker-devel_yandell-lab.org/attachments/20170717/ddac2be0/attachment-0003.html>