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Author Topic: Turn of Auxiliary File Creation (x3dna-dssr)  (Read 2688 times)

Offline saladi

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Turn of Auxiliary File Creation (x3dna-dssr)
« on: August 14, 2015, 06:02:08 am »
Dear DSSR Community,

Is is possible to turn of the generation of the auxiliary files by x3dna-dssr? I am interested in the output given in the command line only at this time as I analyze the frames of a MD trajectory.

Alternatively, does x3dna-dssr use these auxiliary files created in the process of calculating the parameters printed?

Thanks,
Shyam

Offline xiangjun

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Re: Turn of Auxiliary File Creation (x3dna-dssr)
« Reply #1 on: August 14, 2015, 10:18:14 am »
Hi Shyam,

It'd certainly be possible to turn off the various auxiliary files generatd with DSSR -- there are actually more than you see by default. However, I do not see the point of why bother of doing so. For one thing, the files have fixed file names, and thus would be overwritten each time. Second, the auxiliary files are created in parallel to the main output file, and have been proven to be of general use. Third, along the same line, the main DSSR ouput itself is likely to contain more parameters than you'd be interested in, especially with the --more option turned on. Why not simply select the portion that are relevent to your project, and ignore the rest?

If there is sufficient interest, I'd consider to add a new option so users can control whether to produce the auxiliary files. Does anyone else have such a need?

HTH,

Xiang-Jun
« Last Edit: August 14, 2015, 03:03:42 pm by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline chemikeris

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Re: Turn of Auxiliary File Creation (x3dna-dssr)
« Reply #2 on: March 15, 2018, 11:19:00 am »
I have a also a question related to auxiliary files created by DSSR.

In current version (I use v1.7.4-2018jan30) creation of these files may be regulated by '--prefix' option which is useful if you are interested only in the main output file. However, we have noticed that DSSR also creates a file named 'x3dna-dssr.log' in the directory from which it is run. It causes problems when running multiple instances of DSSR in parallel (for example, on a high-performance cluster), because for some processes we get an error message like this:

Code: [Select]
remove_file failed: x3dna-dssr.log

I do not know what is happening but probably some other DSSR process has already removed the file in the cases when this message appears?

Now I solved this problem by changing the working directory before calling DSSR in my script, but in general the problem persists, so I think that you should know it :-) Please contact me, if you need some additional information.

Regards,
Justas

Offline xiangjun

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Re: Turn of Auxiliary File Creation (x3dna-dssr)
« Reply #3 on: March 15, 2018, 04:41:29 pm »
Hi Justas,

Thanks for reporting the issue when running DSSR in parallel. Please try the following DSSR options in your script, and report back it does the trick.

Code: [Select]
--auxfile=no --parallel
Best regards,

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline chemikeris

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Re: Turn of Auxiliary File Creation (x3dna-dssr)
« Reply #4 on: March 16, 2018, 05:48:31 am »
Hello.
I see that  using "--auxfile=no"  does not create any auxiliary files. When using "--parallel" , the x3dna-dssr.log file is created but not deleted. Probably it works as the authors expected :-)

Maybe the real problem is that this behavior and the command line options are not described in the manual of the software? The options were available in the DSSR version I had in my computer, update was not necessary, but I did not find any information about that in the PDF manual.

Regards,
Justas

Offline xiangjun

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Re: Turn of Auxiliary File Creation (x3dna-dssr)
« Reply #5 on: March 16, 2018, 08:43:18 am »
DSSR has many undocummented options. Even for the documented options, there are many undocumented variations thereof. As already mentioned several times in this Forum, there are two reasons: one is to keep the manual not too long, another is some featues are experimental (including using “--parallel”).

DSSR already has many documented features, probably far too many for a typical user would normally care. I’ve tried hard to ensure the accuracy of the documented features, and using this Forms as a means to promptly address users’ questions, and requests for ‘new’ functionality. Afterall, it is impossible to made DSSR (or any tool) perfectly fit to ever imaginable use case. As the author of DSSR, I’ve just made it work the way that makes sense to me, while listening carefully to users’ feedback.

Did the suggested options solve your problems?

Regards,

Xiang-Jun
« Last Edit: March 16, 2018, 09:04:10 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline chemikeris

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Re: Turn of Auxiliary File Creation (x3dna-dssr)
« Reply #6 on: March 16, 2018, 09:30:39 am »
Thank you very much for the explanations. I will check not only the manual, but also the forum for the solutions in the future.

And yes, the suggested options solved my problems now, thank you very much for the fast answer.

Regards,
Justas

Offline xiangjun

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Re: Turn of Auxiliary File Creation (x3dna-dssr)
« Reply #7 on: March 16, 2018, 09:35:51 am »
Glad to hear your confirmation the suggested options did the trick.

In a future release of DSSR, the code/option for the log file will be revised (no x3dna-dssr.log file will be generated by default). I may also add an FAQ on running DSSR in parallel (as in GNU Parallel). Do not be surprised if the "--parallel" option is gone, or is replaced by another name with similar functionality. That's what an experimental option means, and why it is not documented.

Best regards,

Xiang-Jun


PS. Do not be shy in pointing out areas of DSSR that do not work as you expect (from a user's perspective). I'm always keen to improve DSSR in ways that make sense to me while incorporating users' feedback.
« Last Edit: March 19, 2018, 12:06:20 am by xiangjun »
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

Offline xiangjun

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Re: Turn of Auxiliary File Creation (x3dna-dssr)
« Reply #8 on: March 21, 2018, 11:53:35 pm »
As a followup, DSSR v1.7.6-2018mar22 is released. The "--parallel" option is gone and the "--auxfile=no" is documented in the manual. The log-file is no longer generated by default.

Xiang-Jun
Dr. Xiang-Jun Lu [律祥俊]
Email: xiangjun@x3dna.org
Homepage: http://x3dna.org/
Forum: http://forum.x3dna.org/

 

Created and maintained by Dr. Xiang-Jun Lu [律祥俊], Principal Investigator of the NIH grant R01GM096889
Dr. Lu is currently affiliated with the Bussemaker Laboratory at the Department of Biological Sciences, Columbia University.