Gajoe on external pool error

Linear (OLIGOMER), and non-linear (MIXTURE) analysis, singular value decomposition (SVDPLOT), addition of missing fragments (BUNCH, CORAL), analysis of flexible systems (EOM/RANCH & GAJOE), flexible refinement of high-resolution models (SREFLEX)
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Tiago Gomes
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Posts: 3
Joined: 2015.01.20 13:21

Gajoe on external pool error

#1 Post by Tiago Gomes » 2015.01.20 13:29

I´m currently trying to run Gajoe on a external pdb pool. It only lets me run around 4000 models. If i try 10000 or 20000 models it gives me this error:
Don´t know if its a computer specific error or a program limitation.
I currently have mac osx 10.6.8.
Thank you,
Tiago

bash-3.2$ /Applications/ATSAS/bin/gajoe -p
******* ------------------------------------------------------ *******
******* GAJOE - version 2.1 - (r4556) *******
******* Copyright (c) ATSAS Team *******
******* EMBL, Hamburg Outstation, 2007 - 2014 *******
******* *******
******* For doubts/questions please visit SAXIER forum: *******
******* http://www.saxier.org/forum/viewforum.php?f=10 *******
******* *******
******* In case of bugs please refer to: *******
******* G. Tria, D.I. Svergun, EMBL BioSAXS group *******
******* atsas@embl-hamburg.de *******
******* ------------------------------------------------------ *******
---------------------------- ATTENTION ------------------------------
Using a pool of PDBs could take a while due to the CRYSOL computation
---------------------------------------------------------------------
Number of experimental curves to fit? (default: 1) ................... :
Experimental data file name 1? (*.dat) .............................. : SF_BF\subtraction\1.0_mgml_sf_002_sub.dat
Directory containing the PDB files? (default: .) ..................... : pdbs
Number of harmonics (min. 10, max. 50)? (default: 15) ................ :
Maximum s value (min. 0.1, max. 0.5)? (default: 0.500) ............... :
Number of points (min. 10, max. 201)? (default: 51) .................. :
Number of generations (min. 10) (default: 1000) ...................... : 20
Number of ensembles (min. 10) (default: 50) .......................... : 25
Ensemble size fixed? (default: no) ................................... :
Maximum number of curves per ensemble (min. 1, max. 50) (default: 20) :
Minimum number of curves per ensemble (min. 1) (default: 5) .......... :
Curve repetition in the ensemble allowed? (default: yes) ............. :
Constant subtraction allowed? (default: yes) ......................... :
Number of times you want the genetic algorithm repeated (min. 1)
(default: 100) ....................................................... : 150
Curve: SF_BF\subtraction\1.0_mgml_sf_002_sub.dat - Loading values and configuration ...
... Theoretical scattering computation (CRYSOL time) ...
sh: /bin/ls: Argument list too long
[ 1%]
... CRYSOL time completed!
Number of theoretical curves : 0
Starting the Genetic Algorithm ...

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:

Program received signal SIGABRT: Process abort signal.

Backtrace for this error:

Program received signal SIGABRT: Process abort signal.

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Hayds
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Location: EMBL, Hamburg

Re: Gajoe on external pool error

#2 Post by Hayds » 2015.01.20 14:25

Hi Tiago,

could you please PM me the intensities file for your pool and the data (I will keep it confidential) and I will try and reproduce the error.

Cheers,

Haydyn

Tiago Gomes
Member
Posts: 3
Joined: 2015.01.20 13:21

Re: Gajoe on external pool error

#3 Post by Tiago Gomes » 2015.01.20 15:36

Hi Hayds,

The problem is that i get back an empty intensity file (junXXX.int), for a 10000 pdb pool.

At the log it says: sh: /bin/ls: Argument list too long. Maybe some osx unix general problem with the ls command.

thank you,
regards

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Hayds
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Posts: 101
Joined: 2008.05.21 19:01
Location: EMBL, Hamburg

Re: Gajoe on external pool error

#4 Post by Hayds » 2015.01.20 16:59

Ah I see,

so you can run it successfully on a subset of this pool? Does GAJOE crash on a particular PDB file?

Haydyn

Tiago Gomes
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Posts: 3
Joined: 2015.01.20 13:21

Re: Gajoe on external pool error

#5 Post by Tiago Gomes » 2015.01.20 18:09

Exactly.
I divided the pool into subsets and all ran ok. I think that problem could be that on a mac the ARG_MAX is limited to around 250k. In linux around 2mb.
Gajoe uses ls command to list the pdbs i think, thus the error. I´m not an expert....don´t no if this makes sense. I think that find command or the C std lib for listing are not subject to this.
Once again sorry if this is not correct.

thanks

Kiofor
Member
Posts: 4
Joined: 2016.06.02 12:59

Re: Gajoe on external pool error

#6 Post by Kiofor » 2016.06.02 13:22

Hi!

Could you solve the problem above? I encounter a similar error when running GAJOE on an external pool. Although, in my case GAJOE always throws this error, no matter how many pdb-files in the pool-folder. It seems to not even touch the first pdb-file..

GAJOE runs perfectly fine on an "internal" pool. I use Windows 7, SP1.

Thanks in advance,
Nico


******* ------------------------------------------------------ *******
******* GAJOE - version 2.1 - (r6669) *******
******* Copyright (c) ATSAS Team *******
******* EMBL, Hamburg Outstation, 2007 - 2015 *******
******* *******
******* For doubts/questions please visit SAXIER forum: *******
******* http://www.saxier.org/forum/viewforum.php?f=10 *******
******* *******
******* In case of bugs please refer to: *******
******* G. Tria, D.I. Svergun, EMBL BioSAXS group *******
******* atsas@embl-hamburg.de *******
******* ------------------------------------------------------ *******
---------------------------- ATTENTION ------------------------------
Using a pool of PDBs could take a while due to the CRYSOL computation
---------------------------------------------------------------------
Number of experimental curves to fit? (default: 1) ................... :
Experimental data file name 1? (*.dat) .............................. : IgG2_fi
nal.dat
Directory containing the PDB files? (default: .) ..................... : pdbs
Number of harmonics (min. 10, max. 50)? (default: 15) ................ :
Maximum s value (min. 0.1, max. 0.5)? (default: 0.500) ............... : 0.3
Number of points (min. 10, max. 201)? (default: 51) .................. : 100
Number of generations (min. 10) (default: 1000) ...................... :
Number of ensembles (min. 10) (default: 50) .......................... :
Ensemble size fixed? (default: no) ................................... :
Maximum number of curves per ensemble (min. 1, max. 50) (default: 20) :
Minimum number of curves per ensemble (min. 1) (default: 5) .......... :
Curve repetition in the ensemble allowed? (default: yes) ............. :
Constant subtraction allowed? (default: yes) ......................... :
Number of times you want the genetic algorithm repeated (min. 1)
(default: 100) ....................................................... :
Random number generator has not been initialised; using current time
Random seed is: 1464866219
Curve: IgG2_final.dat - Loading values and configuration ...
... Theoretical scattering computation (CRYSOL time) ...
[ 1%]
... CRYSOL time completed!
Number of theoretical curves : -22297415
Starting the Genetic Algorithm ...

Program received signal SIGSEGV: Segmentation fault - invalid memory reference.

Backtrace for this error:
#0 ffffffffffffffff

Alex
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Posts: 692
Joined: 2007.08.09 21:10
Location: Planet Earth

Re: Gajoe on external pool error

#7 Post by Alex » 2016.06.02 13:32

recently there were few reports on GAJOE not working on external pool.
You can run CRYSOL yourself and create master files from *.log and *.int files. This never had failed for me.
Alex

Kiofor
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Posts: 4
Joined: 2016.06.02 12:59

Re: Gajoe on external pool error

#8 Post by Kiofor » 2016.06.02 13:42

Ok, thanks. So I just append the individual CRYSOL data, one after another, to mimic the RANCH files?
However, any idea what might be going wrong?
Nico

Alex
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Posts: 692
Joined: 2007.08.09 21:10
Location: Planet Earth

Re: Gajoe on external pool error

#9 Post by Alex » 2016.06.02 13:47

Ok, thanks. So I just append the individual CRYSOL data, one after another, to mimic the RANCH files?
in a way - you need to extract Rg/Dmax from *.log file and final intensity from *.int files
However, any idea what might be going wrong?
bug(s).

Kiofor
Member
Posts: 4
Joined: 2016.06.02 12:59

Re: Gajoe on external pool error

#10 Post by Kiofor » 2016.06.02 14:29

Thanks!

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