Re: [structure-group] Issues with the 2.3.4 graphical front end for Linux

[Vikram Chhatre]

Hi Maria,

A similar problem was reported very recently and I believe a solution
was proposed also. Please search the list archive.

V



On Fri, Oct 12, 2012 at 7:34 AM, Maria <mtde...@gmail.com> wrote:
> Hi!
> I was running Structure on a very fast Windows7 personal PC (413 samples and 4500 SNPs) and it took more than 3 days for each K. So I decided to have a try on our IBM machine (2 Xeon processors)running Fedora I think 14, with Java 1.7. at 64 bits It is the machine we use for running CLC.
> We downloaded Structure 2.3.4.with graphical front end, the guy who can understand something of Linux had some problem, but at the end Structure was installed. It looks the same as the windows version, but when I run a Job, for example 100000-100000 K=1 to 8, 3 repetitions it seems to work but in reality nothing appears in the data screen. After few minutes it says the job is finished, but, obviously, there are not results. The same happens directly running a K whatsoever. Ideas?
>
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[Maria]

Hi!
Thanks for answering, but I already did it before posting my question, going back to last February, (before the 2.3.4 version), and I could not find an answer. There were posts with similar problems, like "Open SUSE Linux issue with 2.3.4" or "Result files not created but the job is finished "correctly""  and an older
"No results after a run 2.3.3" but I do not believe they were solved. Am I missing something?

PS I'm accessing the Linux machine as root, so there should not be administrative privilege problems

Maria

[Vikram Chhatre]

Hi Maria,

This doesn't solve your problem, but you should never run regular
programs as 'root' user. Have you tried running it as 'user'?

V

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[Pall Melsted]

Hi Maria

On the linux can you try running

java -cp ???/class/Structure.jar RunStructure

where ??? is the location where Structure is installed, either a local
directory or /usr/local/Structure/ by default.

Do you get any error messages when you run it this way?

Second point, since Structure is not multithreaded it won't run that
much faster on a Xeon processor than on your desktop, assuming the
processors have similar speeds.

- Pall

[Maria]

Root issue: it was temporary just to be sure to have all the permissions.

First point:
we followed your suggestion and, in fact, we have some problems with java
Here is the error message:
Java.io.IOException: Cannot run program "bin/structure": Java.io.IOException:error=2, No such file or directory
Second Point:
that's really a very bad new; perhaps I would better divede the work between more PCs and then unite the results in a single folder and feed harvester with it?
Thanks a lot

[Pall Melsted]

The issue is that the java program cannot find the structure
executable, it expects to find it in the bin/ folder relative to where
you start the java program. Check that the program is there and that
you can run it, just type

./bin/structure

from the base folder and start java from the base folder as before.

- Pall

On Wed, Oct 31, 2012 at 10:20 AM, Clément <goubert...@gmail.com> wrote:
> Dear all,
>
> I think this issue is still not fixed, and I have excactly the same problem that Maria have. When I start my run in structure using the Front End, it doesn't run and display this in the console :
>
> java.io.IOException: Cannot run program "bin/structure": java.io.IOException: error=2, Aucun fichier ou dossier de ce type ("no file or folder of this kind")
>
> is it a problem related to my version of Java ?
>
> Thanks for your help,
>
> C.

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[Yohannes Besufekad]

Oh sorry structure harvester did not perform for structure out put analysis.

so what can I do?

[Clément]

Ok thank you for your quick response,
so I tried to run structure from ./bin/strucuture
it prompts :
bash: ./bin/structure: No such file or directory

when I ask : ls in /usr/bin it displays well "strucutre", so I guess the program is there but I can't run it.

[Vikram Chhatre]

The correct syntax is

/usr/bin/./structure

Dot slash should immediately precede the binary. 

---------------------------------------

Vikram Chhatre

Graduate Program in Genetics

Texas A&M University

cryptic...@gmail.com

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[Pall Melsted]

Hi Clément

what I meant is that you should run this from the path where the frontend is installed, the default for the install script is 

/usr/local/Structure/

so right there should be a bin directory etc. The code in the frontend expects there to be a bin directory in the same place so it will call bin/structure. Even if you have the installed the command line version in your path, it will not use it.

If you have just downloaded the front end version and not installed it, you can run structure from that location as before. 

- Pall

[Yohannes Besufekad]

Go again and use the following link to run the program. First the program set up will appear as coulored picture or structure_start directory chose one by one to use the program

http://pritch.bsd.uchicago.edu/software/structure2_1.html

[Clément]

 @Pall  So, what happened is that : I first tryed to run structure with frontend without installing. So I launched ./structure from the unzipped folder. It runs the frontend but when I try to begin a run it says it can't find the strucure file in the /bin directory (I guess it refers to the /bin directory inside the unziped directory, called "frontend"), but there is actually a structure file inthere, but looks like it can't find it.
Second thing, I then installed structure, so it is present in my usr/local/Structure directory. Here, when I prompt ./structure nothing appen.

as you could have guessed, I am not really experienced with linux and the console working

@john I downloaded it, but unlike the latest version I downloaded, the "frontend" folder is missing. When I try to start the structure program (./structure, in the directory I downloaded, nothing happen). And, sorry, I don't know what you mean by "First the program set up will appear as coulored picture or structure_start directory chose one by one to use the program"

Thank you for your help, I am a bit lost...

[Nite Loser]

Hi Maria and Clement,

In the event you still have not fixed the problem, are you by any chance running Linux 64bit? I know I had the same issue, and it was because of that.

The way I fixed it was to use:

"sudo apt-get install ia32-libs"

which installs libraries necessary to run 32 bit programs on 64 bit systems. Then I ran structure as per instructions and it worked fine.

,Andrei

[Markus]

Hi Andrei, hi Maria, hi Clement,

you can find out if you have the wrong version of structure by trying to start the binary: <installation folder>/bin/structure
If you get a complaint about a wrong ELF interpreter you probably try to start a 32bit structure in a 64bit environment.

The Andrei suggested won't be of use to you if you're using a Fedora machine. Redhat-based systems don't have a metapackage like ia32-libs on Debian/Ubuntu. You'll have to find out which libs you need and install their compat-versions, which can become quite cumbersome.

It might be easier to compile the structure binary on the 64 bit machine from source. You can probably just exchange it for the 32 bit one.

As for the multi-threading problem: Try creating the options files with the frontend and using them on the binaries "manually". You can then start multiple instances with different Ks in parallel, even on more than one machine, which makes the analysis considerably faster.

Best,
Markus

[Adii_ (Institute of Genetics and Animal Breeding)]

For multithread You can use the script for console version of STRUCTURE. It's very simple to use. Check the Group for it. 

[Sunny Song]

Dear Sir/Madame,

      I guess I met the most strange bug: I can find the structure in bin folder, but when I trying to ./structure in the terminal, it can't find that. Is that the problem of Java?

     Sunny

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[Zsjit Ngiam]

Dear Sunny,

nice to meet you here :) I've got the same problem.

"sudo apt-get install ia32-libs"

This will help if you are running Structure on 64bit Linux.