With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay?
~jacob
Hi Jacob,
I would not expect any delay rotating the surface. Maybe you are clipping with a near clip plane and it is constantly recomputing the clipping plane cap on every motion. In that case you could turn off clip plane caps ("surface cap false"). Even if you do that if you are using Full or Soft lighting with near clipping then the ambient shadowing of those lighting mode will update on every motion since the clipped away part constantly changes. That casts shadows from 64 directions basically equivalent to rendering 64 frames and will slow down even the fastest graphics card. To remedy that switch to simple lighting (Toolbar button, or command "light simple") which does not cast shadows. If you are not using clipping then I bet something else is updating on the CPU and you will have to provide more details of what exact ChimeraX features you are using (what kind of coloring, what other models are shown, what tools are you using, ...).
Tom
On Nov 24, 2020, at 7:05 PM, Anderson, Jacob jacob_r_anderson@hms.harvard.edu wrote:
With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay?
~jacob _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Dear Tom,
I did not realize the clipping cap was running on one CPU at max. Turning that off eliminated any delay. Thanks for your quick reply. I will also switch to simple light, taking your advice.
~jacob ________________________________ From: Tom Goddard goddard@sonic.net Sent: Tuesday, November 24, 2020 10:19 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
I would not expect any delay rotating the surface. Maybe you are clipping with a near clip plane and it is constantly recomputing the clipping plane cap on every motion. In that case you could turn off clip plane caps ("surface cap false"). Even if you do that if you are using Full or Soft lighting with near clipping then the ambient shadowing of those lighting mode will update on every motion since the clipped away part constantly changes. That casts shadows from 64 directions basically equivalent to rendering 64 frames and will slow down even the fastest graphics card. To remedy that switch to simple lighting (Toolbar button, or command "light simple") which does not cast shadows. If you are not using clipping then I bet something else is updating on the CPU and you will have to provide more details of what exact ChimeraX features you are using (what kind of coloring, what other models are shown, what tools are you using, ...).
Tom
On Nov 24, 2020, at 7:05 PM, Anderson, Jacob <jacob_r_anderson@hms.harvard.edumailto:jacob_r_anderson@hms.harvard.edu> wrote:
With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay?
~jacob _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-usershttps://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=4trpeUI99BIsNu4qjm3wtfP3QglOdtMSEn0cM4gLavk&s=6tAMU78zrOpkbJcOBY7YiFPDZJEIMw0EX7ozXtQFuYM&e=
Hi Jacob,
ChimeraX only uses multiple threads for a few calculations, such as computing solvent excluded molecular surfaces or Coulombic electrostatic potential. Calculations like computing the clip cap surface which is spending most of its time trying to triangulate the polygonal path where the surface intersects the plane would be tricky to divide into multiple threads. Actually it could also be spending a fraction of a second computing the intersections of say a 50 million triangles with the plane -- it does not have any fancy oct-tree decomposition to accelerate that computation so it has to check every single triangle on every move.
Tom
On Nov 24, 2020, at 7:25 PM, Anderson, Jacob jacob_r_anderson@hms.harvard.edu wrote:
Dear Tom,
I did not realize the clipping cap was running on one CPU at max. Turning that off eliminated any delay. Thanks for your quick reply. I will also switch to simple light, taking your advice.
~jacob From: Tom Goddard goddard@sonic.net Sent: Tuesday, November 24, 2020 10:19 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
I would not expect any delay rotating the surface. Maybe you are clipping with a near clip plane and it is constantly recomputing the clipping plane cap on every motion. In that case you could turn off clip plane caps ("surface cap false"). Even if you do that if you are using Full or Soft lighting with near clipping then the ambient shadowing of those lighting mode will update on every motion since the clipped away part constantly changes. That casts shadows from 64 directions basically equivalent to rendering 64 frames and will slow down even the fastest graphics card. To remedy that switch to simple lighting (Toolbar button, or command "light simple") which does not cast shadows. If you are not using clipping then I bet something else is updating on the CPU and you will have to provide more details of what exact ChimeraX features you are using (what kind of coloring, what other models are shown, what tools are you using, ...).
Tom
On Nov 24, 2020, at 7:05 PM, Anderson, Jacob <jacob_r_anderson@hms.harvard.edu mailto:jacob_r_anderson@hms.harvard.edu> wrote:
With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay?
~jacob _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=4trpeUI99BIsNu4qjm3wtfP3QglOdtMSEn0cM4gLavk&s=6tAMU78zrOpkbJcOBY7YiFPDZJEIMw0EX7ozXtQFuYM&e=
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu mailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you for the intuition - it makes the limit make more sense.
Thanks again,
~jacob ________________________________ From: Tom Goddard goddard@sonic.net Sent: Tuesday, November 24, 2020 10:35 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
ChimeraX only uses multiple threads for a few calculations, such as computing solvent excluded molecular surfaces or Coulombic electrostatic potential. Calculations like computing the clip cap surface which is spending most of its time trying to triangulate the polygonal path where the surface intersects the plane would be tricky to divide into multiple threads. Actually it could also be spending a fraction of a second computing the intersections of say a 50 million triangles with the plane -- it does not have any fancy oct-tree decomposition to accelerate that computation so it has to check every single triangle on every move.
Tom
On Nov 24, 2020, at 7:25 PM, Anderson, Jacob <jacob_r_anderson@hms.harvard.edumailto:jacob_r_anderson@hms.harvard.edu> wrote:
Dear Tom,
I did not realize the clipping cap was running on one CPU at max. Turning that off eliminated any delay. Thanks for your quick reply. I will also switch to simple light, taking your advice.
~jacob ________________________________ From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Sent: Tuesday, November 24, 2020 10:19 PM To: Anderson, Jacob <jacob_r_anderson@hms.harvard.edumailto:jacob_r_anderson@hms.harvard.edu> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
I would not expect any delay rotating the surface. Maybe you are clipping with a near clip plane and it is constantly recomputing the clipping plane cap on every motion. In that case you could turn off clip plane caps ("surface cap false"). Even if you do that if you are using Full or Soft lighting with near clipping then the ambient shadowing of those lighting mode will update on every motion since the clipped away part constantly changes. That casts shadows from 64 directions basically equivalent to rendering 64 frames and will slow down even the fastest graphics card. To remedy that switch to simple lighting (Toolbar button, or command "light simple") which does not cast shadows. If you are not using clipping then I bet something else is updating on the CPU and you will have to provide more details of what exact ChimeraX features you are using (what kind of coloring, what other models are shown, what tools are you using, ...).
Tom
On Nov 24, 2020, at 7:05 PM, Anderson, Jacob <jacob_r_anderson@hms.harvard.edumailto:jacob_r_anderson@hms.harvard.edu> wrote:
With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay?
~jacob _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-usershttps://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=4trpeUI99BIsNu4qjm3wtfP3QglOdtMSEn0cM4gLavk&s=6tAMU78zrOpkbJcOBY7YiFPDZJEIMw0EX7ozXtQFuYM&e=
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-usershttps://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=a4zx6EGVx35lmzrqwFwDFy3uhBWn9smXsiuHlgU3tcQ&s=MDWuDurZF1tp10TBGMTZPbvSJfFRZQE1_tXHyW2N99g&e=
To follow-up on this older thread, is there a way to make the surface caps off by default? I am finding a 10-20s slow down when changing the contour level of a large surface. I believe this is related to the surface cap feature as the following is displayed during the hang-up.
[cid:d9c255e0-fd8d-4a9a-b399-be75ae0cd5c5]
This is after I have run the command
[cid:58a3a9c0-5fc4-4a92-bccd-f3cee2ae9320] ________________________________ From: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Sent: Tuesday, November 24, 2020 11:08 PM To: Tom Goddard goddard@sonic.net Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Thank you for the intuition - it makes the limit make more sense.
Thanks again,
~jacob ________________________________ From: Tom Goddard goddard@sonic.net Sent: Tuesday, November 24, 2020 10:35 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
ChimeraX only uses multiple threads for a few calculations, such as computing solvent excluded molecular surfaces or Coulombic electrostatic potential. Calculations like computing the clip cap surface which is spending most of its time trying to triangulate the polygonal path where the surface intersects the plane would be tricky to divide into multiple threads. Actually it could also be spending a fraction of a second computing the intersections of say a 50 million triangles with the plane -- it does not have any fancy oct-tree decomposition to accelerate that computation so it has to check every single triangle on every move.
Tom
On Nov 24, 2020, at 7:25 PM, Anderson, Jacob <jacob_r_anderson@hms.harvard.edumailto:jacob_r_anderson@hms.harvard.edu> wrote:
Dear Tom,
I did not realize the clipping cap was running on one CPU at max. Turning that off eliminated any delay. Thanks for your quick reply. I will also switch to simple light, taking your advice.
~jacob ________________________________ From: Tom Goddard <goddard@sonic.netmailto:goddard@sonic.net> Sent: Tuesday, November 24, 2020 10:19 PM To: Anderson, Jacob <jacob_r_anderson@hms.harvard.edumailto:jacob_r_anderson@hms.harvard.edu> Cc: chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu <chimerax-users@cgl.ucsf.edumailto:chimerax-users@cgl.ucsf.edu> Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
I would not expect any delay rotating the surface. Maybe you are clipping with a near clip plane and it is constantly recomputing the clipping plane cap on every motion. In that case you could turn off clip plane caps ("surface cap false"). Even if you do that if you are using Full or Soft lighting with near clipping then the ambient shadowing of those lighting mode will update on every motion since the clipped away part constantly changes. That casts shadows from 64 directions basically equivalent to rendering 64 frames and will slow down even the fastest graphics card. To remedy that switch to simple lighting (Toolbar button, or command "light simple") which does not cast shadows. If you are not using clipping then I bet something else is updating on the CPU and you will have to provide more details of what exact ChimeraX features you are using (what kind of coloring, what other models are shown, what tools are you using, ...).
Tom
On Nov 24, 2020, at 7:05 PM, Anderson, Jacob <jacob_r_anderson@hms.harvard.edumailto:jacob_r_anderson@hms.harvard.edu> wrote:
With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay?
~jacob _______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-usershttps://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=4trpeUI99BIsNu4qjm3wtfP3QglOdtMSEn0cM4gLavk&s=6tAMU78zrOpkbJcOBY7YiFPDZJEIMw0EX7ozXtQFuYM&e=
_______________________________________________ ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edumailto:ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-usershttps://urldefense.proofpoint.com/v2/url?u=https-3A__plato.cgl.ucsf.edu_mailman_listinfo_chimerax-2Dusers&d=DwMFAg&c=WO-RGvefibhHBZq3fL85hQ&r=WAfw3qrUG1ShU2YpwE9tWl1TX9X2iVUkDLLxcqiRjEo&m=a4zx6EGVx35lmzrqwFwDFy3uhBWn9smXsiuHlgU3tcQ&s=MDWuDurZF1tp10TBGMTZPbvSJfFRZQE1_tXHyW2N99g&e=
Hi Jacob, In the ChimeraX Settings dialog (aka preferences), the Clipping section, you can set "cap clipped surfaces" to false and save it.
https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#clipping
The ChimeraX Settings dialog is listed in a standard platform-dependent location in the menu (for example, Favorites... Settings on Windows and Linux, UCSF ChimeraX... Preferences on a Mac).
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 2, 2021, at 5:18 PM, Anderson, Jacob jacob_r_anderson@hms.harvard.edu wrote:
To follow-up on this older thread, is there a way to make the surface caps off by default? I am finding a 10-20s slow down when changing the contour level of a large surface. I believe this is related to the surface cap feature as the following is displayed during the hang-up.
<image.png>
This is after I have run the command
<image.png> From: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Sent: Tuesday, November 24, 2020 11:08 PM To: Tom Goddard goddard@sonic.net Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Thank you for the intuition - it makes the limit make more sense.
Thanks again,
~jacob From: Tom Goddard goddard@sonic.net Sent: Tuesday, November 24, 2020 10:35 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
ChimeraX only uses multiple threads for a few calculations, such as computing solvent excluded molecular surfaces or Coulombic electrostatic potential. Calculations like computing the clip cap surface which is spending most of its time trying to triangulate the polygonal path where the surface intersects the plane would be tricky to divide into multiple threads. Actually it could also be spending a fraction of a second computing the intersections of say a 50 million triangles with the plane -- it does not have any fancy oct-tree decomposition to accelerate that computation so it has to check every single triangle on every move.
Tom
On Nov 24, 2020, at 7:25 PM, Anderson, Jacob jacob_r_anderson@hms.harvard.edu wrote:
Dear Tom,
I did not realize the clipping cap was running on one CPU at max. Turning that off eliminated any delay. Thanks for your quick reply. I will also switch to simple light, taking your advice.
~jacob From: Tom Goddard goddard@sonic.net Sent: Tuesday, November 24, 2020 10:19 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
I would not expect any delay rotating the surface. Maybe you are clipping with a near clip plane and it is constantly recomputing the clipping plane cap on every motion. In that case you could turn off clip plane caps ("surface cap false"). Even if you do that if you are using Full or Soft lighting with near clipping then the ambient shadowing of those lighting mode will update on every motion since the clipped away part constantly changes. That casts shadows from 64 directions basically equivalent to rendering 64 frames and will slow down even the fastest graphics card. To remedy that switch to simple lighting (Toolbar button, or command "light simple") which does not cast shadows. If you are not using clipping then I bet something else is updating on the CPU and you will have to provide more details of what exact ChimeraX features you are using (what kind of coloring, what other models are shown, what tools are you using, ...).
Tom
On Nov 24, 2020, at 7:05 PM, Anderson, Jacob jacob_r_anderson@hms.harvard.edu wrote:
With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay?
~jacob _______________________________________________ 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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
Thank you so much for your repy over the weekend. That worked great.
~jacob ________________________________ From: Elaine Meng meng@cgl.ucsf.edu Sent: Sunday, January 3, 2021 12:53 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob, In the ChimeraX Settings dialog (aka preferences), the Clipping section, you can set "cap clipped surfaces" to false and save it.
https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html https://rbvi.ucsf.edu/chimerax/docs/user/preferences.html#clipping
The ChimeraX Settings dialog is listed in a standard platform-dependent location in the menu (for example, Favorites... Settings on Windows and Linux, UCSF ChimeraX... Preferences on a Mac).
I hope this helps, Elaine ----- Elaine C. Meng, Ph.D. UCSF Chimera(X) team Department of Pharmaceutical Chemistry University of California, San Francisco
On Jan 2, 2021, at 5:18 PM, Anderson, Jacob jacob_r_anderson@hms.harvard.edu wrote:
To follow-up on this older thread, is there a way to make the surface caps off by default? I am finding a 10-20s slow down when changing the contour level of a large surface. I believe this is related to the surface cap feature as the following is displayed during the hang-up.
<image.png>
This is after I have run the command
<image.png> From: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Sent: Tuesday, November 24, 2020 11:08 PM To: Tom Goddard goddard@sonic.net Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Thank you for the intuition - it makes the limit make more sense.
Thanks again,
~jacob From: Tom Goddard goddard@sonic.net Sent: Tuesday, November 24, 2020 10:35 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
ChimeraX only uses multiple threads for a few calculations, such as computing solvent excluded molecular surfaces or Coulombic electrostatic potential. Calculations like computing the clip cap surface which is spending most of its time trying to triangulate the polygonal path where the surface intersects the plane would be tricky to divide into multiple threads. Actually it could also be spending a fraction of a second computing the intersections of say a 50 million triangles with the plane -- it does not have any fancy oct-tree decomposition to accelerate that computation so it has to check every single triangle on every move.
Tom
On Nov 24, 2020, at 7:25 PM, Anderson, Jacob jacob_r_anderson@hms.harvard.edu wrote:
Dear Tom,
I did not realize the clipping cap was running on one CPU at max. Turning that off eliminated any delay. Thanks for your quick reply. I will also switch to simple light, taking your advice.
~jacob From: Tom Goddard goddard@sonic.net Sent: Tuesday, November 24, 2020 10:19 PM To: Anderson, Jacob jacob_r_anderson@hms.harvard.edu Cc: chimerax-users@cgl.ucsf.edu chimerax-users@cgl.ucsf.edu Subject: Re: [chimerax-users] Bottleneck Large Surfaces
Hi Jacob,
I would not expect any delay rotating the surface. Maybe you are clipping with a near clip plane and it is constantly recomputing the clipping plane cap on every motion. In that case you could turn off clip plane caps ("surface cap false"). Even if you do that if you are using Full or Soft lighting with near clipping then the ambient shadowing of those lighting mode will update on every motion since the clipped away part constantly changes. That casts shadows from 64 directions basically equivalent to rendering 64 frames and will slow down even the fastest graphics card. To remedy that switch to simple lighting (Toolbar button, or command "light simple") which does not cast shadows. If you are not using clipping then I bet something else is updating on the CPU and you will have to provide more details of what exact ChimeraX features you are using (what kind of coloring, what other models are shown, what tools are you using, ...).
Tom
On Nov 24, 2020, at 7:05 PM, Anderson, Jacob jacob_r_anderson@hms.harvard.edu wrote:
With large colored surfaces of maps ~2.4GB, I experience a lag/delay of several seconds during rotation and translation. Is it obvious where the bottleneck might be that causes the lag? I am running ChimeraX on a 3090 gpu w/ 128gb ram, & 12 core CPU. Might there be ways to change other graphics settings to make the manipulations have a less observable delay?
~jacob _______________________________________________ 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
ChimeraX-users mailing list ChimeraX-users@cgl.ucsf.edu Manage subscription: https://www.rbvi.ucsf.edu/mailman/listinfo/chimerax-users
participants (3)
-
Anderson, Jacob -
Elaine Meng -
Tom Goddard