Discussion group for the ARIA software

[Brian Smith <Brian.Smith AT glasgow.ac.uk>]

Here's how to fix the FPEPS issue

https://sites.google.com/site/ccpnwiki/Home/documentation/ccpnmr-analysis/howtos-1/centos-7-x-standard-installation#TOC-ARIA-2.3.1

Centos 7.x standard installation - Biomolecular NMR Wiki

Analysis 2.4.x I prefer to install from source code, because this should always work once you've got it started. I also prefer to use the system libraries (because that should be the right thing to do) rather than tacking on alternative versions of software which can complicate installation and the operation of other programs. I've not yet had serious problems with this methodology.

sites.google.com

Dr. Brian O. Smith --------------------------- Brian Smith at glasgow ac uk
Institute of Molecular, Cell and Systems Biology & School of Life Sciences,
          College of Medical, Veterinary & Life Sciences,
  Joseph Black Building, University of Glasgow, Glasgow G12 8QQ, UK.
Tel: 0141 330 5167/6459/3089

https://www.gla.ac.uk/researchinstitutes/biology/research/structuralbiologybiophysicalcharacterisationfacility/

----------------------------------------------------------------------
The University of Glasgow, charity number SC004401

---

From: aria-discuss-request AT services.cnrs.fr <aria-discuss-request AT services.cnrs.fr> on behalf of Julien CAPPELE <julien.cappele AT univ-lorraine.fr>
Sent: 01 October 2020 12:47
To: Benjamin Bardiaux <bardiaux AT pasteur.fr>
Cc: aria-discuss AT services.cnrs.fr <aria-discuss AT services.cnrs.fr>
Subject: Re: [aria-discuss] Error during PSF-file generation

 

Hi Benjamin, thanks for your answer.

I forgot to mention that the error about ARIA Gui is specific to CcpNmr. I can launch it from the terminal (aria -g) but when I click on the "Launch Aria gui" in CcpNmr, it says Tix cannot be imported. I assume this error is more on the CcpNmr side. The check.py says it's all OK, especially :

"""

Tkinter and Tix modules...
Tkinter imported (Tk version 8.600)

Tix imported.

"""

On the actual generation problem:

I tried to generate the PSF-file myself just to see if it was related to rights or something, and it produced the exact same output which is :

"""

 %SETFPEPS increase value of MXFPEPS2 and recompile
 %SETFPEPS error encountered: Could not determine machine epsilon
   (CNS is in mode: SET ABORT=NORMal END)
 *****************************************************
 ABORT mode will terminate program execution.
 *****************************************************
 Program will stop immediately.
          ============================================================
           Maximum dynamic memory allocation:           0 bytes
           Maximum dynamic memory overhead:             0 bytes
           Program started at: \00\00\00\00\00\00\00\00 on \00\00\00\00\00\00\00\00\00\00\00
           Program stopped at: 13:25:55 on 01-Oct-2020
           CPU time used:       0.0017 seconds
          ============================================================

"""

I really do not know how to fix that epsilon thingy. I tried to google it, but I have no idea how to force CNS to use one.

The CPU in the laptop i'm using is a quad-core Intel i7-4710MQ

Thanks again,

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

Julien Cappèle

Doctorant - 2ème année - ED C2MP

Université de Lorraine

CRM² - UMR CNRS 7036

julien.cappele@univ-lorraine.fr

Tel: (+33)6 99 18 59 03

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

Le jeu. 1 oct. 2020 à 11:35, Benjamin Bardiaux <bardiaux AT pasteur.fr> a écrit :

Hi Julien,

On 01/10/2020 11:11, julien.cappele AT univ-lorraine.fr wrote:
> Good morning/afternoon everyone,
>
> I am a PhD student and I am currently trying to locally calculate some NMR
> structures with Aria, on a Ubuntu 20.04 LTS plateform.
> To be honest, I've been trying for a week now and I finally installed
> "correctly" all the softwares (Aria2.3, CNS1.2) and I am using CcpNmr 2.5.0.

What does the check.py script tells you about Tix being installed ?

>
> I'm doing the tutorial dedicated to structure calculation of CcpNmr.
> However, now that the project is finally set up, I get an error when i'm
> starting the calculation with Aria.
> Using this command: $ aria2 /path/to/my/project/project.xml, I get a strange
> error that I cannot understand.
>
> "IOError: USER ERROR <aria.cns.CNS> File "/some/path/to/aria2.3.2_05.08.2019/
> aria2.3/src/py/aria/cns.py", line 2038 in prepare
> An error occurered during creation of the PSF-file: "/some/path/to/Tutorials/
> CcpnCourse3a/run1/cns/begin/CcpnCourse3a.psf" could not be found."

check the run1/cns/begin/generate.out for ERROR, this should tell you more about the issue.

Best,

Benjamin

>
> Also, I cannot use the GUI interface with Aria because I get a strange error
> about Tix package being not installed and I didn't find any solution to it.
>
> Does someone have a solution to this problem ?
> Thanks a lot for your time.
>
> JC
>


--
---------------------------------------------
Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
---------------------------------------------

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

Julien Cappèle

Doctorant - 2ème année - ED C2MP

Université de Lorraine

CRM² - UMR CNRS 7036

julien.cappele@univ-lorraine.fr

Tel: (+33)6 99 18 59 03

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

Le jeu. 1 oct. 2020 à 11:35, Benjamin Bardiaux <bardiaux AT pasteur.fr> a écrit :

Hi Julien,

On 01/10/2020 11:11, julien.cappele AT univ-lorraine.fr wrote:
> Good morning/afternoon everyone,
>
> I am a PhD student and I am currently trying to locally calculate some NMR
> structures with Aria, on a Ubuntu 20.04 LTS plateform.
> To be honest, I've been trying for a week now and I finally installed
> "correctly" all the softwares (Aria2.3, CNS1.2) and I am using CcpNmr 2.5.0.

What does the check.py script tells you about Tix being installed ?

>
> I'm doing the tutorial dedicated to structure calculation of CcpNmr.
> However, now that the project is finally set up, I get an error when i'm
> starting the calculation with Aria.
> Using this command: $ aria2 /path/to/my/project/project.xml, I get a strange
> error that I cannot understand.
>
> "IOError: USER ERROR <aria.cns.CNS> File "/some/path/to/aria2.3.2_05.08.2019/
> aria2.3/src/py/aria/cns.py", line 2038 in prepare
> An error occurered during creation of the PSF-file: "/some/path/to/Tutorials/
> CcpnCourse3a/run1/cns/begin/CcpnCourse3a.psf" could not be found."

check the run1/cns/begin/generate.out for ERROR, this should tell you more about the issue.

Best,

Benjamin

>
> Also, I cannot use the GUI interface with Aria because I get a strange error
> about Tix package being not installed and I didn't find any solution to it.
>
> Does someone have a solution to this problem ?
> Thanks a lot for your time.
>
> JC
>


--
---------------------------------------------
Dr Benjamin Bardiaux      bardiaux AT pasteur.fr
Unité de Bioinformatique Structurale
CNRS UMR3528 - Institut Pasteur
25,28 rue du Docteur Roux 75015 Paris, France
---------------------------------------------