error in runstructure, No such file or directory

[Sasha Millán]

Hi, I'm hitting a wall as to what's wrong with Strauto.

 strauto_1.py3 works just fine, it reads my data and sets mainparams and extraparams correctly. However, when I use  ./runstructure, it creates the output directories but nothing else happens, no computing going on. 

I tried running ./runstructure again and it says; 

mkdir: cannot create directory ‘results_f’: File exists

mkdir: cannot create directory ‘log’: File exists

mkdir: cannot create directory ‘harvester’: File exists

mkdir: cannot create directory ‘k1’: File exists

mkdir: cannot create directory ‘k2’: File exists

mkdir: cannot create directory ‘k3’: File exists

mkdir: cannot create directory ‘k4’: File exists

mkdir: cannot create directory ‘k5’: File exists

mkdir: cannot create directory ‘k6’: File exists

which is obvious, and also the following, because the run outputs don't exist yet.

cp: cannot stat 'results_f/k*/*_f': No such file or directory

Your structure run has finished.

zip warning: name not matched: harvester_input/*

zip error: Nothing to do! (Sipho8Orden_118_4798_Harvester_Upload.zip)

mv: cannot stat 'Sipho8Orden_118_4798_Harvester_Upload.zip': No such file or directory

I delete all directories and run strauto_1.py3 and ./runstructure and yet again, nothing happens, however if i use ./structure computing does start, but only on a single core, which is not exactly what I want because i'm in a 16-core machine and it would take forever for my run to end. 

I have no idea where the problem is, maybe it's the directories? but i've tried moving everything to different folders (i.e. frontend) but nothing happens.

Any clue is appreciated, since I'm not that familiar with the console.

[Vikram Chhatre]

The error messages themselves aren't indicative of the problems structure is running into. In the next version of StrAuto we will set up a routine to delete existing files/folders upon rerun of the script (which will get rid of these error messages).

The main culprit here however is likely your data file.  Check the log/ directory where there should be a series of .log files which will point you in the right direction.  Plenty of discussions exist on this topic, so be sure to check the archives before posting a formatting related question.

V

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[Sasha Millán]

I checked previous questions but I can't pinpoint the issue as to why it isn't running, yet.

The thing is there are no .log files in the log/ directory, nor anything in results_f or any other directory created, but my data file runs in the Structure gui and with ./structure (but only 1 rep instead of the multiple reps I need), so maybe it's not my input file.

[Vikram Chhatre]

At this point, you will need to provide us with more information.  First, are you running this on a cluster?  If so, you will need to make specific changes to the runstructure file as outlined in the manual section 8.  But in any case, show us your parameter files, and strauto outputted files.  

The fact that you don't have log files suggests that structure isn't even running.

V

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[Sasha Millán]

I've attached every file created of modified given my input. However now that you mention section 8, I'm working on a 16 core computer and I didn't add srun on the runstructure file, so I'll edit that and see if it runs as it should.

S

[Vikram Chhatre]

Sasha,

First, the section#8 of StrAuto manual only applies to usage on HPC clusters.  If you are working on a multi-core personal workstation, that section does not apply.

I just took a look at your files and I see nothing wrong with them.  The scripts 'runstructure' and 'structureCommands' are expecting that (a) GNU parallel is in your path, and (b) structure binary is located in the same directory as these scripts.  If both of these conditions are true, rerun runstructure (after deleting all files/folders created with previous run), then zip the whole folder and email it to me directly (not to the list).

V

To view this discussion on the web visit https://groups.google.com/d/msgid/structure-software/7d8eadf7-dc56-4008-bc50-03915431800bn%40googlegroups.com.