ERROR EX13 (Solution)
Diego Restrepo
Greetings to all,
I am new is USPEX, after installing USPEX 9.4.4 and trying to run with Octave 3.8.1 in Ubuntu 14.04 (32 bits), I obtained the following:
warning: addpath: -e /home/diego/USPEX/src/FunctionFolder: No such file or directory
warning: addpath: -e /home/diego/USPEX/src/FunctionFolder/sys: No such file or directory
warning: addpath: -e /home/diego/USPEX/src/FunctionFolder/AbinitCode: No such file or directory
warning: addpath: -e /home/diego/USPEX/src/FunctionFolder/Symope: No such file or directory
error: ‘python_uspex’ indefined near line 1 column 11
To correct these files, I followed a suggestion from the forum that was to delete the -e from the file USPEX.m
One of the solutions given was to run USPEX with an octave version earlier or equal to 4, but I had the same problem so I decided to edit the files.
1) USPEX.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
After making these modifications, when executing the EX13 again, appears:
Warning: /home/diego/USPEX/src/FunctionFolder/USPEX/src/createORGStruc.m: posible Matlab-style short-circuit operator at line 90, column 29
Warning: /home/diego/USPEX/src/FunctionFolder/USPEX/src/createORGStruc.m: posible Matlab-style short-circuit operator at line 107, column 30
Warning: /home/diego/USPEX/src/FunctionFolder/USPEX/src/createORGStruc.m: posible Matlab-style short-circuit operator at line 133, column 53
Warning: /home/diego/USPEX/src/FunctionFolder/USPEX/src/createORGStruc.m: posible Matlab-style short-circuit operator at line 133, column 27
Warning: /home/diego/USPEX/src/FunctionFolder/USPEX/src/createORGStruc.m: posible Matlab-style short-circuit operator at line 138, column 52
Warning: /home/diego/USPEX/src/FunctionFolder/USPEX/src/createORGStruc.m: posible Matlab-style short-circuit operator at line 138, column 27
Warning: /home/diego/USPEX/src/FunctionFolder/USPEX/src/createORGStruc.m: posible Matlab-style short-circuit operator at line 146, column 25
error: fgets: invalid stream number = -1
error: evaluating argument list elemt number 1
error: called from:
error: /home/diego/USPEX/src/FunctionFolder/sys/createHeader.m at line 6, column 10
error: /home/diego/USPEX/src/FunctionFolder/USPEX/src/createORGStruc.m at line 58, column 16
error: /home/diego/USPEX/src/FunctionFolder/USPEX/Start.m at line 55, column 1
The warnings are corrected by modifying the logical statements, that is, they must be replaced | By || Y & for && in the createORGStruc.m file
On the other hand, the error occurs because an -e is added to the path, for example:
-e /home/diego/USPEX/Function/Folder/getInput.py
To correct this problem, try two options.
First, measure the length of the string and make a sentence if to remove the characters belonging to the -e in order that the path looks like this:
/home/diego/USPEX/Function/Folder/getInput.py
Example:
longitudORG = length (ORG_STRUC.USPEXPath);
if longitudORG ~ = 21
ORG_STRUC.USPEXPath = ORG_STRUC.USPEXPath (4: end);
End
In my case the desired length is 21.
The disadvantage of this option is that if one wants to take files modified to run USPEX on another computer and does not have the same user should modify the length to compare in several files.
Second option and I recommend it is to delete the -e of several file that it lists in the following list:
2) Start.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);;
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
3) callAWK.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
4) Initialize.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);;
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
5) createORGDefault.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);;
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
6) META_Start.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
7) META_CreateORGStruc.m
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, pathtemp] = unix(‘echo –e $USPEXPATH’);;
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, pathtemp] = unix(‘echo $USPEXPATH’);
8) META_Initialize.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);;
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
9) Initialize_PSO.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);;
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
10) NEB_Start.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);;
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
11) Start_PSO.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo –e $USPEXPATH’);
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, USPEXPath] = unix(‘echo $USPEXPATH’);
12) NEB_creatORGDefault.m:
Original:
[nothing, uspexmode] = unix(‘echo –e $UsPeXmOdE’);
[nothing, pathtemp] = unix(‘echo –e $USPEXPATH’);
Modified:
[nothing, uspexmode] = unix(‘echo $UsPeXmOdE’);
[nothing, pathtemp] = unix(‘echo $USPEXPATH’);
After making these modifications, Example 13 ran.
Now I'm trying to run USPEX and Quantum ESPRESSO.
Greetings from Santa Marta (Colombia)
Andrés Sicard-Ramírez
Following your instructions below (the second option) I could run EX13 with Octave. Thanks!
When using Octave (but no Matlab) I got the following errors:
$ USPEX -r -o
cp: cannot stat './Specific/*': No such file or directory
rm: cannot remove 'Energy_vs_N.pdf': No such file or directory
rm: cannot remove 'Fitness_vs_N.pdf': No such file or directory
rm: cannot remove 'E_series.pdf': No such file or directory
rm: cannot remove 'Variation-Operators.pdf': No such file or directory
Did you get the same errors?
All the best,
Andrés
Diego Restrepo
These messages appear when you run Example 13, they do not interfere with your calculations.
I recommend that you run the calculations with USPEX in Ubuntu 16.04 since in this operating system PDF files are generated corresponding to the graphs like convex hull, energy vs volume, among others. In previous versions of Ubuntu are not generated and in Debian 8 either, I guess it's because of the octave version.
Attached image with output files.
Greetings from Santa Marta, Colombia
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