Problem in EX13 run on local mechine with octave

[novice]

Dear USPEX Members

Greetings from a Novice user of USPEX!!

I installed USPEX with Octave in Ubuntu16. My octave was found by USPEX whithout any error.

I wanted to run an example i.e. EX13 (for Co Ti O).

What I did is
1. mkdir EX13
2. cd EX13
3. USPEX -c 13  (files were copied in cwd)
4. USPEX -o

Nothing happened, i kept FunctionFolder and USPEX.m in current directory.


Seeking your help.

[novice]

I tried just like trial and error. Including my previous post (mentioned below).

I just copied /src in the cwd and modified "EX13-3D_special_quasirandom_structure_TiCoO.job" files by these contents:

#!/bin/sh
source $HOME/.bashrc
date >> log
USPEX -o >> log

and issued the below command on terminal:
nohup: redirecting stderr to stdout

xxx@Lenovo-B570:~/uspex_test/EX13$ ls
AntiSeeds        
 CalcFoldTemp
Current_POP.mat.backup                                   
INPUT.txt  results2  still_running
ANTISEEDS.mat        
Current_ORG.mat        
EX13-3D_special_quasirandom_structure_TiCoO.job          
log      
Seeds    
Submission                              >> I created this DIR as I met an warning that no Submission file exists.
ANTISEEDS.mat.backup 
Current_ORG.mat.backup  
reference 
Specific 
USPEX.m
CalcFold1           
Current_POP.mat        
results1  
src                                >>> I copied this as I got warning that no src dir exists

The contents of "still_running" file are as below:

This file is present for two possible reasons
1, MATLAB is still running
2, MATLAB exits with error
If it stays for long time when numParallel is on
Matlab is either in dead loop or exits with error.
please do check it  
xxx@Lenovo-B570:~/uspex_test/EX13$

It seems the job is still running as I am getting this line on terminal:
kcbhamu@Lenovo-B570:~/uspex_test/EX13$ nohup: redirecting stderr to stdout


I have QE but I dont know how to configure it with USPEX.

Please help me to overcome my problem.

Kind regards
Chandra

[novice]

contents of log file:

chmod: cannot access 'clean': No such file or directory
rm: cannot remove 'Specific/get*': No such file or directory
 
 
Read Seeds ...
 
seed number 1 has been successfully added
 
End of pickup Seeds
Read AntiSeeds ...
cp: cannot stat './Specific/*': No such file or directory
Structure1 step1 at CalcFold1
error: 'checkStatusC' undefined near line 13 column 10
error: called from
    ReadJobs_300 at line 13 column 8
    EA_300 at line 12 column 1
    Start at line 77 column 1

[Артём Самцевич]

Hello!!!

It seems that you install USPEX in wrong way. Because, after successful installation, you won't see src folder.
Please, download the latest version of USPEX - 9.4.4 and carefully follow instructions during installation.

But, first, I think, you can try to run it like 
octave < USPEX.m

if it works and you won't get an error - that means that you installed USPEX in wrong way.

Best,
Artem


среда, 26 октября 2016 г., 17:39:24 UTC+3 пользователь novice написал:

[novice]

I downloaded the recent version of USPEX and what I followed is:
untar and then:
novice@Lenovo:~/USPEX-9.4.4$ bash ./install.sh

*------------------------------------------------------------------------------*
|                                                                              |
|             _|    _|     _|_|_|   _|_|_|     _|_|_|_|   _|      _|           |
|             _|    _|   _|         _|    _|   _|           _|  _|             |
|             _|    _|     _|_|     _|_|_|     _|_|_|         _|               |
|             _|    _|         _|   _|         _|           _|  _|             |
|               _|_|     _|_|_|     _|         _|_|_|_|   _|      _|           |
|                                                                              |
|                          Version 9.4.4 (04/10/2015)                          |
|                                                                              |
|             Evolutionary Algorithm Code for Structure Prediction             |
|                   more info at http://uspex.stonybrook.edu                   |
|                                                                              |
*------------------------------------------------------------------------------*

==========================
 Installing USPEX code ...
==========================



====================================================

....
  Octave found at :  /usr/bin/octave
....
====================================================




Please enter the USPEX install path :  /home/novice/uspex_test                                               >>> changed the cwd to this dir

Do you want to install USPEX at /home/novice/uspex_test ? (y/n) y
 
======================================================
The USPEX install directory:
     /home/novice/uspex_test
is found. Do you want to install USPEX there? (y/n) y


===========================================================================
    Copying files, please  wait ...............                      
===========================================================================


==========================
    Install finished.
==========================


1) You can edit the file to change the install path of MATLAB or Octave:

   /home/novice/uspex_test/CODEPATH

2) Please Set the Shell Environment Variables to enable USPEX code!

   For Bash shell system, add these lines to ~/.bashrc or ~/.profile or /etc/profile:
     export PATH=/home/novice/uspex_test:$PATH
     export USPEXPATH=/home/novice/uspex_test/src

   For C shell system, add these lines to ~/.cshrc or ~/.profile or /etc/profile:
     setenv PATH "/home/novice/uspex_test:$PATH"
     setenv USPEXPATH "/home/novice/uspex_test/src"

3) For tests running, please go to the tests folder and run the following command for more details:

   python /home/novice/uspex_test/tests/USPEX_test.py -h


==========================
    Have fun with USPEX!  
==========================
novice@Lenovo:~/USPEX-9.4.4$ gedit ~/.bashrc

added     
export PATH=/home/novice/uspex_test:$PATH
export USPEXPATH=/home/novice/uspex_test/src    to the ~/.bashrc

novice@Lenovo:~/USPEX-9.4.4$ cd ../uspex_test/
novice@Lenovo:~/uspex_test$ ls
CODEPATH  doc  examples  lib  src  tests  USPEX                                    >>>> src is still here
novice@Lenovo:~/uspex_test$

I have Quantum espresso installed. May you suggest any example how to run USPEX using QE?

I am struggling since last three days but could not get success.
Thanks in advance.

Kind regards


Chandra

[Diego Restrepo]

FunctionFoGreetings to all.

I'm new using Uspex, I downloaded version 9.4.4 and 3.8.1 have Octavian in 32-bit ubuntu 14.04.

The same message he left me to remove warnings change the conditional Logics | and & by || and && since MATLAB supports | and & but octave not therefore to use || Y &&.

To eliminate errors must be eliminated -e links, for example, in the createORG_System file says:

getPy = [ORG_STRUC.USPEXPath, '/ FunctionFolder / getInput.y'];

when impleme shown: getPy = -e /home/user/USPEX/Function/Folder/getInput.py

For Octave can run the -e must be eliminated, then the link should be:

getPy = -e /home/user/USPEX/Function/Folder/getInput.py

To perform this done

getPy = [ORG_STRUC.USPEXPath, '/ FunctionFolder / getInput.y'];

longitud_getPy = length (getPy); % 4 characters should be removed from "-e"

% For my case:

if longitud_getPy ~ = 48

     getPy = getPy (4: end);

end

===========================

At the previous alplicar in multiple files as CreateCalcFolder, you can run the EX13 smoothly.

Thank you very much for your attention.

Greetings from Santa Marta (Colombia)

Since I do not write very well English I will leave the same message in Spanish.

Thank you very much for your attention.

=======================================================================

Saludos a todos.

Soy nuevo usando USPEX , descargué la versión 9.4.4 y tengo Octave 3.8.1 en ubuntu 14.04 de 32 bits.

El mismo mensaje me salia a mí, para eliminar las advertencias cambie los condicionales lógics | y & por || y &&, ya que MATLAB admite | y & pero octave no, por lo tanto se debe usar || y &&.

Para eliminar los errores hay que eliminar de los enlaces el -e, por ejemplo, En el archivo createORG_System dice:

getPy = [ORG_STRUC.USPEXPath,'/FunctionFolder/getInput.y'];

cuando se impleme se muestra:  getPy = -e  /home/user/USPEX/Function/Folder/getInput.py

Para que Octave pueda correr la -e debe ser eliminada, entonces el enlace debe ser así:

getPy = -e  /home/user/USPEX/Function/Folder/getInput.py

Para realizar esto se hace: 

getPy = [ORG_STRUC.USPEXPath,'/FunctionFolder/getInput.y'];

longitud_getPy = length(getPy); % Se deben quitar 4 caracteres de "  -e  " 

%Para mi caso:

if longitud_getPy ~= 48

     getPy = getPy(4:end);

end

===========================

Al aplicar los anterior en varios archivos como es CreateCalcFolder, puede ejecutar el EX13 sin problemas. 

Muchas gracias por su atención.

[Diego Restrepo]

Hi.

I had the same error,

I did siquiente to correct.

I entered the CreateCalcFolder.m file

And after instruction: cd (ORG_STRUC.homePath)

I wrote siquiente:

================================================

longitudORG = length (ORG_STRUC.USPEXPath);

if longitudORG ~ = 21

        ORG_STRUC.USPEXPath = ORG_STRUC.USPEXPath (4: end);

end

================================================== =======

21 for me, the rest of the code and has left it just me well corriedo Example 13

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

Hola.

Yo tenia el mismo error,

Para corregirlo hice lo siquiente.

Ingresé al archivo CreateCalcFolder.m

Y despues de la instrucción: cd(ORG_STRUC.homePath)

escribí lo siquiente:

================================================

longitudORG = length(ORG_STRUC.USPEXPath);

if longitudORG ~= 21

       ORG_STRUC.USPEXPath =        ORG_STRUC.USPEXPath(4:end);

end

=========================================================

21 para mi caso, el resto del código lo dejé igual y me ha corriedo bien el ejemplo 13