ChimeraX: chashes in no-gui execution
Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script. Here is an example of my script that calculates hbonds and contacts between protein and ligand open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico
Hi Enrico, A "wait" command with no arguments waits for any ongoing motions (such as from a "move" command with a "frames" argument) to finish. Your script has no ongoing motions and therefore the wait commands should do nothing. I tried your script (without the waits) 100 times with the NMR structure ensemble 1a2i (which has a ligand) and got no crashes. Are you using the 1.4 release? What kind of error messages or output do you get when these crashes occur? --Eric Eric Pettersen UCSF Computer Graphics Lab
On Jun 16, 2022, at 6:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script.
Here is an example of my script that calculates hbonds and contacts between protein and ligand
open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit
as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
i've just check, I am using chimeraX 1.3, so.. the error message can be seen directly in the bash terminal it is something like segmentation fault and then the command associated with the execution of the chimerax with the script чт, 16 июн. 2022 г. в 19:35, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Enrico, A "wait" command with no arguments waits for any ongoing motions (such as from a "move" command with a "frames" argument) to finish. Your script has no ongoing motions and therefore the wait commands should do nothing. I tried your script (without the waits) 100 times with the NMR structure ensemble 1a2i (which has a ligand) and got no crashes. Are you using the 1.4 release? What kind of error messages or output do you get when these crashes occur?
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 16, 2022, at 6:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script.
Here is an example of my script that calculates hbonds and contacts between protein and ligand
open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit
as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
p.s. just one question regarding chimera-x 14 I've noticed that the start-up is very slow compared to the previous version (takes 2-3 minutes both from terminal or from the application menu with the following lag reason): Startup Messages notes available bundle cache has not been initialized yet Updating list of available bundles failed: [Errno 60] Operation timed out how may I desablel this updating list? Thanks in advance! пт, 17 июн. 2022 г. в 09:23, Enrico Martinez <jmsstarlight@gmail.com>:
i've just check, I am using chimeraX 1.3, so.. the error message can be seen directly in the bash terminal it is something like segmentation fault and then the command associated with the execution of the chimerax with the script
чт, 16 июн. 2022 г. в 19:35, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Enrico, A "wait" command with no arguments waits for any ongoing motions (such as from a "move" command with a "frames" argument) to finish. Your script has no ongoing motions and therefore the wait commands should do nothing. I tried your script (without the waits) 100 times with the NMR structure ensemble 1a2i (which has a ligand) and got no crashes. Are you using the 1.4 release? What kind of error messages or output do you get when these crashes occur?
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 16, 2022, at 6:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script.
Here is an example of my script that calculates hbonds and contacts between protein and ligand
open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit
as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
That check should be done asynchronously and not affect the startup time. We will take a look. -- Greg On 6/17/2022 12:42 AM, Enrico Martinez via ChimeraX-users wrote:
p.s. just one question regarding chimera-x 14 I've noticed that the start-up is very slow compared to the previous version (takes 2-3 minutes both from terminal or from the application menu with the following lag reason):
Startup Messages notes available bundle cache has not been initialized yet Updating list of available bundles failed: [Errno 60] Operation timed out
how may I desablel this updating list? Thanks in advance!
пт, 17 июн. 2022 г. в 09:23, Enrico Martinez <jmsstarlight@gmail.com>:
i've just check, I am using chimeraX 1.3, so.. the error message can be seen directly in the bash terminal it is something like segmentation fault and then the command associated with the execution of the chimerax with the script
чт, 16 июн. 2022 г. в 19:35, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Enrico, A "wait" command with no arguments waits for any ongoing motions (such as from a "move" command with a "frames" argument) to finish. Your script has no ongoing motions and therefore the wait commands should do nothing. I tried your script (without the waits) 100 times with the NMR structure ensemble 1a2i (which has a ligand) and got no crashes. Are you using the 1.4 release? What kind of error messages or output do you get when these crashes occur?
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 16, 2022, at 6:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script.
Here is an example of my script that calculates hbonds and contacts between protein and ligand
open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit
as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thanks! I've just checked, there is the same issue with the chimeraX-daily (I am using macOSX Big Sur ) This what I see from the bash terminal NOTE: available bundle cache has not been initialized yet NOTE: Updating list of available bundles failed: [Errno 60] Operation timed out executed make_muto.cxc Otherwise ChimeraX-13 works pretty well on the same configuration! пт, 17 июн. 2022 г. в 09:44, Greg Couch <gregc@cgl.ucsf.edu>:
That check should be done asynchronously and not affect the startup time. We will take a look.
-- Greg
On 6/17/2022 12:42 AM, Enrico Martinez via ChimeraX-users wrote:
p.s. just one question regarding chimera-x 14 I've noticed that the start-up is very slow compared to the previous version (takes 2-3 minutes both from terminal or from the application menu with the following lag reason):
Startup Messages notes available bundle cache has not been initialized yet Updating list of available bundles failed: [Errno 60] Operation timed out
how may I desablel this updating list? Thanks in advance!
пт, 17 июн. 2022 г. в 09:23, Enrico Martinez <jmsstarlight@gmail.com>:
i've just check, I am using chimeraX 1.3, so.. the error message can be seen directly in the bash terminal it is something like segmentation fault and then the command associated with the execution of the chimerax with the script
чт, 16 июн. 2022 г. в 19:35, Eric Pettersen <pett@cgl.ucsf.edu>:
Hi Enrico, A "wait" command with no arguments waits for any ongoing motions (such as from a "move" command with a "frames" argument) to finish. Your script has no ongoing motions and therefore the wait commands should do nothing. I tried your script (without the waits) 100 times with the NMR structure ensemble 1a2i (which has a ligand) and got no crashes. Are you using the 1.4 release? What kind of error messages or output do you get when these crashes occur?
--Eric
Eric Pettersen UCSF Computer Graphics Lab
On Jun 16, 2022, at 6:09 AM, Enrico Martinez via ChimeraX-users <chimerax-users@cgl.ucsf.edu> wrote:
Dear ChimeraX users! I noticed that sometimes ChimeraX crashes while being executed in batch mode using bash script.
Here is an example of my script that calculates hbonds and contacts between protein and ligand
open mypdb.pdb #calculate h-bonds and contacts in each frame hbonds #1.1-24&protein restrict #1.1-24&ligand coordsets false interModel false makePseudobonds false log true distSlop 0.5 angleSlop 20 intraRes false saveFile hbondsALL_rep1.log clashes #1.1-24&protein& :41,49 restrict #1.1-24&ligand overlapCutoff 0.3 interModel false makePseudobonds false log true intraRes false saveFile contactsALL_rep1.log wait wait exit
as you may see I added two times wait in the end of the script that could reduce the frequency of crashes. May you specify what is the default value for each wait (in seconds??) and how I could use just one wait command to set up the pause in the proper way? Many thanks in advance! Cheers Enrico _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Enrico Martinez -
Eric Pettersen -
Greg Couch