HyPhy message board - basic starting problem

Beckett

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basic starting problem
Feb 26^th, 2009 at 6:31am

Hi Sergei. since you helped me with the viewing of the GUI I have been able to run all the tutorial examples and others in the graphic interfase, but now I want to learn the basics of the HBL folowing again the tutorial and I can´t. My problem is basic: I don´t know how to run the program from the shell... is it needed to run it?? Or I have to type the HyPhy comands in the Linux shell itself?? I´ve tried both but nothing worked. I´m just learning to use the Linux shell and I´m still very newbie at this.
The _GTK files are only for an X interfase and cannot be run in Comand Line Mode (shell) , right?
Well, I apologise again for bothering you with such simple issues, I hope my questions won´t take much of your time. Thank you!

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Danny

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Re: basic starting problem
Reply #1 - Feb 26^th, 2009 at 1:19pm

Beckett wrote on Feb 26^th, 2009 at 6:31am:

Hi Sergei. since you helped me with the viewing of the GUI I have been able to run all the tutorial examples and others in the graphic interfase, but now I want to learn the basics of the HBL folowing again the tutorial and I can´t. My problem is basic: I don´t know how to run the program from the shell... is it needed to run it?? Or I have to type the HyPhy comands in the Linux shell itself?? I´ve tried both but nothing worked. I´m just learning to use the Linux shell and I´m still very newbie at this.
The _GTK files are only for an X interfase and cannot be run in Comand Line Mode (shell) , right?
Well, I apologise again for bothering you with such simple issues, I hope my questions won´t take much of your time. Thank you!

What is the command you are using to start the command line version? The command line version is a different program. The graphical version will be called something like HYPHY_GTK and the command line version will be called something like HYPHY. If you don't have a hyphy executable without the GTK you need to compile it with something like ./build.sh SP

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Sergei

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Re: basic starting problem
Reply #2 - Feb 26^th, 2009 at 10:22pm

Hi Beckett,

Like Danny says, HyPhy can be compiled to run in command line mode (use the 'bash build.sh MP2' command to compile a multithreaded HyPhy executable), but you can also use the GUI version to execute batch files directly -- just use File->Open->Open Batch File menu option.

If you compile HYPHYMP, then you can call it in terminal simply by typing

Code:

$/path/to/HYPHYMP CPU=x BASEPATH=/path/to/installation_directory

where you would replace 'x' with the number of processors you want HyPhy to keep busy if possible (the default is 1) and /path/to with the unix paths to directories where the binary and the installation directory are (probably /home/beckett/HYPHY or something along those lines).

Cheers,
Sergei

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Division of Biomedical Informatics
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University of California San Diego

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Beckett

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Re: basic starting problem
Reply #3 - Feb 27^th, 2009 at 10:29am

Thank you very much!! I could compile it and execute it from the Linux shell. I also found that I can execute it going to the directory and typing ./HYPHYM Is it the same to run it this way? What happens with the number of processors? (does it run with the default number = 1? )

Thanks for the advise of how to execute the batch files from the GUI, but I´m trying to avoid the X interface to archive better procecing times. Some analysis are taking realy too much time... a lot more than it shold be expected. For example, the optimization of the LF in an example in the tutorial (p51.nex MG94xHKY85x3_4x2_Rates model with RateHet) that shold take "up to an hour, depending on the speed of the computer", takes 5hs or more in my computer! Someone told me the graphical interfaces of Linux consume a lot of memory, so now I´m trying with the shell.

Thanks Danny for your help, and as always thanks Sergei.

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Danny YaBB Newbies Offline Posts: 31	Re: basic starting problem Reply #4 - Feb 27^th, 2009 at 10:46am Type cat /proc/cpuinfo \| grep process This should show you how many cpu's your computer is using. If only one line shows up like processor : 0 you have a single cpu processor : 0 processor : 1 means 2 cpus, etc. If you have 2 cpus, as Sergei said above, you can add CPU=2 as an argument to the hyphy command.
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Beckett

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Re: basic starting problem
Reply #5 - Mar 2^nd, 2009 at 5:52am

Thanks for the tip Danny, in fact I already know how many processors my computer has. I just want to know if

$/path/to/HYPHYMP CPU=x BASEPATH=/path/to/installation_directory

is the only way of making al the processors work or it can be setted from another place, executing ./HYPHYMP for exmple? Anyway, my biggest problem is the computation time, tests are taking too long. Can a linux graphic interface like Gnome take such a quantity of memory to make my test last like this?? Anyway, now I will try it with the shell and using all the processors.

Thank you! =)

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: basic starting problem Reply #6 - Mar 2^nd, 2009 at 8:15am Dear Beckett, Code: ./HYPHYMP CPU=x from the installation directory will work just fine. I am not sure why the execution takes so long. Can you execute the attached file and tell me how long that takes on your machine? Cheers, Sergei
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Beckett YaBB Newbies Offline Posts: 10 Bs As - Argentina Gender:	Re: basic starting problem Reply #7 - Mar 2^nd, 2009 at 11:25am Thanks for the shorter code Sergei. The computation times are better now that I use HyPhy from the Linux shell and not just with one processor. The file you attached me takes 14 seconds in the GUI (it´s ok, right?), but I couldn´t run it the comand line mode, it gives: Error Empty File Encountered By ReadDataSet
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