Discussion group for the ARIA software

[Julien CAPPELE <julien.cappele AT univ-lorraine.fr>]

Hi Benjamin,

Thanks for your answer,

Indeed, I completely forgot to copy the aria2-cns binary into cns directory before compiling, when I started with a fresh CNS directory after the first round of errors last time week.

I recompiled CNS with Aria2 files yesterday evening, and now the calculation works. Thank you, again!

Though, using ocamlfuse for the data I noticed some latency with Aria2. I just put the working directory out of the google drive folder so it can work faster and now it seems to do fine.

Thanks again,

Have a nice day,

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

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 lun. 5 oct. 2020 à 12:57, Benjamin Bardiaux <bardiaux AT pasteur.fr> a écrit :

 From your cns ouput file I can tell that cns1.2 wasn't compiled with the specific aria sources (see aria2.3/README for
installation details).
When the CNS binary is ran from the command line, the header should say:
           ============================================================
           |                                                          |
           |            Crystallography & NMR System (CNS)            |
           |                         CNSsolve                         |
           |                                                          |
           ============================================================
            Version: 1.2 at patch level 1
            Status: General release with ARIA enhancements

Again, according to your refine.out file, the run1/cns/begin/ directory exists (or existed ?) because cns could read the
.psf file from there (same for the run1/cns/data/ directory that you didn't list has being present in the run1/cns/ folder)

Best advice, start from fresh on a local or NFS mounted disk with an ARIA compliant cns binary.

Best,

Benjamin

On 05/10/2020 16:20, Julien CAPPELE wrote:
> Hi Benjamin,
>
> Thanks for both your answer,
>
> Regarding the run1 folder, the path /run/cns does exist, it is the /begin/ folder that doesn't. There are only 2 other
> folders called "protocols" and "toppar" in /run1/cns
>
> I checked in the temporary folder that was generated, and I did find a file called refine.out, i'm sending it in
> attached files.
>  From what I'm seeing, the final error message is "%PARSER error encountered: Encountered too many parsing errors." at
> line 25 534.
> Also, beginning at line 25 414, there are a bunch of unrecognized commands like "%CNSsolve-ERR: unrecognized command:"
> Maybe those commands were not compiled correctly ? Would another fortran compiler than gfortran work better for CNS ?
>
> Thanks again for your help,
> ---------------------------------------------
> Julien Cappèle
> Doctorant - 3ème année - ED C2MP
> Université de Lorraine
> CRM² - UMR CNRS 7036
> julien.cappele@ <mailto:juliencappele AT gmail.com>univ-lorraine.fr
> <https://urldefense.com/v3/__http://univ-lorraine.fr__;!!JFdNOqOXpB6UZW0!7Q3aEmzKowGsMop2AnJGOdUZbbpB6f6nK_8YdLMCSjQ7aXUfWxil-HpwH7a_TBoXQg$>*
> *
> Tel: (+33)6 99 18 59 03
> ---------------------------------------------
>
>
> Le lun. 5 oct. 2020 à 12:02, Benjamin Bardiaux <bardiaux AT pasteur.fr <mailto:bardiaux AT pasteur.fr>> a écrit :
>
>
>      > However, I don't have a run1/cns/begin folder, which could indicate that CNS is still not fully functional on my
>     computer...
>
>     According to your previous screenshot, it should be in /home/jcappele/google-drive/Doctorat/RMN/
>
>      > I still don't know what is wrong with it though...
>      >
>      > Have a nice day,
>      > ---------------------------------------------
>      > Julien Cappèle
>      > Doctorant - 2ème année - ED C2MP
>      > Université de Lorraine
>      > CRM² - UMR CNRS 7036
>      > julien.cappele@ <mailto:juliencappele AT gmail.com <mailto:juliencappele AT gmail.com>>univ-lorraine.fr
>     <https://urldefense.com/v3/__http://univ-lorraine.fr__;!!JFdNOqOXpB6UZW0!7Q3aEmzKowGsMop2AnJGOdUZbbpB6f6nK_8YdLMCSjQ7aXUfWxil-HpwH7a_TBoXQg$>
>
>      >
>     <https://urldefense.com/v3/__http://univ-lorraine.fr__;!!JFdNOqOXpB6UZW0!4Heqt6us5iYyKK-SYUQf7ND6UFqKisi5xjiHyAfQGFN70H0wfOWKEqrjtTkp2Awbng$>*
>      > *
>      > Tel: (+33)6 99 18 59 03
>      > ---------------------------------------------
>      >
>      >
>      > Le lun. 5 oct. 2020 à 10:30, Xiao Wang <xiao.wang AT etu.parisdescartes.fr <mailto:xiao.wang AT etu.parisdescartes.fr>
>     <mailto:xiao.wang AT etu.parisdescartes.fr <mailto:xiao.wang AT etu.parisdescartes.fr>>> a écrit :
>      >
>      >     Hi, Julien
>      >
>      >     I have met this. Remove any previous psf and template in run1/cns/begin/ before trying again.
>      >
>      >     Hopt it will help u. Good luck.
>      >
>      >
>      >
>      >
>      >
>      >
>      >
>      >
>      >
>      >     WANG Xiao
>      >
>      >     Ph.D. Student
>      >
>      >     Paris Descartes University, Faculty of Pharmacy Therapeutic Targets and Drug Design -CiTCoM-UMR 8038
>      >
>      >     75270 Paris CEDEX 06
>      >
>      >
>      >   
>       ------------------------------------------------------------------------------------------------------------------------
>      >     *De :* aria-discuss-request AT services.cnrs.fr <mailto:aria-discuss-request AT services.cnrs.fr>
>     <mailto:aria-discuss-request AT services.cnrs.fr <mailto:aria-discuss-request AT services.cnrs.fr>>
>      >     <aria-discuss-request AT services.cnrs.fr <mailto:aria-discuss-request AT services.cnrs.fr>
>     <mailto:aria-discuss-request AT services.cnrs.fr <mailto:aria-discuss-request AT services.cnrs.fr>>> de la part de Julien
>     CAPPELE
>      >     <julien.cappele AT univ-lorraine.fr <mailto:julien.cappele AT univ-lorraine.fr>
>     <mailto:julien.cappele AT univ-lorraine.fr <mailto:julien.cappele AT univ-lorraine.fr>>>
>      >     *Envoyé :* lundi 5 octobre 2020 14:08
>      >     *À :* aria-discuss AT services.cnrs.fr <mailto:aria-discuss AT services.cnrs.fr>
>     <mailto:aria-discuss AT services.cnrs.fr <mailto:aria-discuss AT services.cnrs.fr>> <aria-discuss AT services.cnrs.fr
>     <mailto:aria-discuss AT services.cnrs.fr>
>      >     <mailto:aria-discuss AT services.cnrs.fr <mailto:aria-discuss AT services.cnrs.fr>>>
>      >     *Objet :* [aria-discuss] Structure calculation failing
>      >     Hello everyone,
>      >
>      >     I am sorry to disturb again, as I encountered another error, and again I can't understand what is wrong. I didn't
>      >     find anything using google yet.
>      >
>      >     I have been able to compile CNS 1.2 and now it can be launched correctly from the terminal. On my project
>     this time
>      >     (not the tutorial of CcpNmr), I have set up an XML file for aria to work. Using the GUI, the project was
>     completed
>      >     and then I used :
>      >     $ aria2 -s test_aria.xml   # test_aria.xml is the name of the xml file that I used
>      >     $ aria2 test_aria.xml
>      >     Everything started and the structure calculation began. However, a few minutes later, I received some messages
>      >     saying that the whole 20 structure calculation failed, and that I should check CNS output for errors. (I joined a
>      >     screenshot in png format for you to see the output).
>      >
>      >     The thing is, the path to CNS output is empty. There are no cns files there. And I didn't find any files of
>     use yet.
>      >     Has anyone encountered a similar error?
>      >
>      >     There are multiple options that I can already consider :
>      >
>      >     1. I'm using google-drive ocamlfuse to work with my cloud, and maybe it is a problem for whatever reason. I can
>      >     allocate more space to my ubuntu partition and do copy all the files to a local space. But i'm skeptical
>     about that,
>      >     it shouldn't be a problem.
>      >
>      >     2. CNS compiled without visible errors, but is not functional yet. I really don't know how to do better than I
>      >     already did with my last question.
>      >
>      >     3. I could stop using local Aria and try AriaWeb but as I am new to NMR structure calculation, I do not know
>     how to
>      >     set up the parameters correctly. The jobs I tried to launch did not produce anything decent yet. My NMR
>     supervisor
>      >     also tried with one of her older projects that resulted with a publishable structure on Aria2 locally, but with
>      >     AriaWeb she didn't get a good result either with the default parameters.
>      >
>      >     I have been struggling with these NMR structure calculations for over a month now, and starting to lose faith.
>      >     Please help me, I don't really want to deal with bad x-ray diffraction nightmares again!
>      >
>      >     Thanks again,
>      >     ---------------------------------------------
>      >     Julien Cappèle
>      >     Doctorant - 3ème année - ED C2MP
>      >     Université de Lorraine
>      >     CRM² - UMR CNRS 7036
>      >     julien.cappele@ <mailto:juliencappele AT gmail.com <mailto:juliencappele AT gmail.com>>univ-lorraine.fr
>     <https://urldefense.com/v3/__http://univ-lorraine.fr__;!!JFdNOqOXpB6UZW0!7Q3aEmzKowGsMop2AnJGOdUZbbpB6f6nK_8YdLMCSjQ7aXUfWxil-HpwH7a_TBoXQg$>
>      >   
>       <https://urldefense.com/v3/__http://univ-lorraine.fr__;!!JFdNOqOXpB6UZW0!4Heqt6us5iYyKK-SYUQf7ND6UFqKisi5xjiHyAfQGFN70H0wfOWKEqrjtTkp2Awbng$>*
>      >     *
>      >     Tel: (+33)6 99 18 59 03
>      >     ---------------------------------------------
>      >
>
>
>     --
>     ---------------------------------------------
>     Dr Benjamin Bardiaux bardiaux AT pasteur.fr <mailto:bardiaux AT pasteur.fr>
>     Unité de Bioinformatique Structurale
>     CNRS UMR3528 - Institut Pasteur
>     25,28 rue du Docteur Roux 75015 Paris, France
>     ---------------------------------------------
>


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