Re: [PyMOL] High Resolution Ray Tracing

[Stephen Kerry]

Hi Thomas,

Thank you for letting me know that this is a genuine limitation of the code as 
it stands. The strange thing is that despite the vast memory usage, the final 
PNG images are rarely over 10 MB, unless there are many lines from a CCP4 map 
for example. Making the scene from scratch rather than from a session file 
helped reduce memory usage during ray tracing, but still gave me the same 
segmentation fault.

Do you know a workaround to divide a scene into halves or quarters and process 
the individual segments separately? I could then combine the PNG images 
afterwards. However, I fear this might be harder to achieve than it sounds, as 
the lighting and ray shadows would have to match up across the segments to 
produce a seamless final image.

Cheers,

Stephen


From: Thomas Holder <thomas.hol...@schrodinger.com>
Sent: 12 May 2016 17:56:02
To: Stephen Kerry
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing

Hi Stephen,

This is not an artificial Open Source PyMOL limitation.

PyMOL's ray tracing code was written at a time when probably nobody had a 
computer with 64GB of RAM, or at least didn't attempt to ray trace images that 
size. The code is pretty hard to read and understand, and currently there is 
nobody who's familiar with it and could easily fix such a limitation. I assume 
the code makes an assumption which is only true up to a certain memory address 
range.

Cheers,
  Thomas

On 12 May 2016, at 10:20, Stephen Kerry <stephen.kerr...@outlook.com> wrote:

> So the images are back from the printers and I can easily tell the difference 
> between 180 and 300 dpi. You have to look closely to tell the difference 
> between 300 and 600 dpi. I am unable to distinguish between 600 and 1200 dpi.
>
> My image size is still limited to 7500 x 6000, which at 600 dpi gives a 12.5 
> x 10 inch image. Is this an artificial Open Source PyMOL software limitation 
> or a genuine bug/memory leak? The segmentation faults also seems to happen 
> even with 128 GB and 256 GB of RAM!
>
> On my system with 32 GB of RAM, I see PyMOL reserves more virtual RAM than 
> the amount of physical RAM, which might be why it crashes when trying to 
> write the PNG at the end of ray tracing? It does not appear to use this 
> virtual RAM or even compress any RAM, according to activity monitor on OSX 
> 10.10. Disabling memory compression and/or swap makes no difference.
>
> Is there anything else I can try to successfully output such a large image?
>
> 
> From: Thomas Holder <thomas.hol...@schrodinger.com>
> Sent: 10 May 2016 20:34:44
> To: harold steinberg
> Cc: Stephen Kerry; pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] High Resolution Ray Tracing
>
> Hi Adam et al.,
>
> This is a super interesting and helpful discussion!
>
> Just wanted to throw in the following shortcut for creating the 6" test 
> images:
>
> png image1.png, 6in, ray=1, dpi=180
> png image2.png, 6in, ray=1, dpi=300
> png image3.png, 6in, ray=1, dpi=600
> png image4.png, 6in, ray=1, dpi=1200
>
> Cheers,
>  Thomas
>
> On 10 May 2016, at 14:27, harold steinberg <h.adam.steinb...@gmail.com> wrote:
>
>> The 9600 x 4800 is a very common poster printer spec. Most print shops use 
>> 180 dpi images on their poster printers (for best print speed) and customers 
>> cannot tell the difference between that and a higher resolution.
>>
>> As a test, render a small image (say 6” x 6”) in PyMOL at four different 
>> dpi, 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi 
>> (ray 7200). Then use Photoshop or GIMP to make them all 6” x 6”.
>>
>> Put them together side-by-side in a layout program and print them on one 
>> sheet to compare. I bet you will have an extremely difficult time telling 
>> them apart.
>>
>>> On May 10, 2016, at 12:40 PM, Stephen Kerry <stephen.kerr...@outlook.com> 
>>> wrote:
>>>
>>> Harold, I agree 2400 dpi might be wasted, but the professional printer 
>>> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
>>> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
>>> four passes from each CMYK component apparently increases the vertical dpi 
>>> by four.
>>
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM

Re: [PyMOL] High Resolution Ray Tracing

[Thomas Holder]

Hi Stephen,

This is not an artificial Open Source PyMOL limitation.

PyMOL's ray tracing code was written at a time when probably nobody had a 
computer with 64GB of RAM, or at least didn't attempt to ray trace images that 
size. The code is pretty hard to read and understand, and currently there is 
nobody who's familiar with it and could easily fix such a limitation. I assume 
the code makes an assumption which is only true up to a certain memory address 
range.

Cheers,
  Thomas

On 12 May 2016, at 10:20, Stephen Kerry <stephen.kerr...@outlook.com> wrote:

> So the images are back from the printers and I can easily tell the difference 
> between 180 and 300 dpi. You have to look closely to tell the difference 
> between 300 and 600 dpi. I am unable to distinguish between 600 and 1200 dpi.
> 
> My image size is still limited to 7500 x 6000, which at 600 dpi gives a 12.5 
> x 10 inch image. Is this an artificial Open Source PyMOL software limitation 
> or a genuine bug/memory leak? The segmentation faults also seems to happen 
> even with 128 GB and 256 GB of RAM!
> 
> On my system with 32 GB of RAM, I see PyMOL reserves more virtual RAM than 
> the amount of physical RAM, which might be why it crashes when trying to 
> write the PNG at the end of ray tracing? It does not appear to use this 
> virtual RAM or even compress any RAM, according to activity monitor on OSX 
> 10.10. Disabling memory compression and/or swap makes no difference.
> 
> Is there anything else I can try to successfully output such a large image?
> 
> 
> From: Thomas Holder <thomas.hol...@schrodinger.com>
> Sent: 10 May 2016 20:34:44
> To: harold steinberg
> Cc: Stephen Kerry; pymol-users@lists.sourceforge.net
> Subject: Re: [PyMOL] High Resolution Ray Tracing
> 
> Hi Adam et al.,
> 
> This is a super interesting and helpful discussion!
> 
> Just wanted to throw in the following shortcut for creating the 6" test 
> images:
> 
> png image1.png, 6in, ray=1, dpi=180
> png image2.png, 6in, ray=1, dpi=300
> png image3.png, 6in, ray=1, dpi=600
> png image4.png, 6in, ray=1, dpi=1200
> 
> Cheers,
>  Thomas
> 
> On 10 May 2016, at 14:27, harold steinberg <h.adam.steinb...@gmail.com> wrote:
> 
>> The 9600 x 4800 is a very common poster printer spec. Most print shops use 
>> 180 dpi images on their poster printers (for best print speed) and customers 
>> cannot tell the difference between that and a higher resolution.
>> 
>> As a test, render a small image (say 6” x 6”) in PyMOL at four different 
>> dpi, 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi 
>> (ray 7200). Then use Photoshop or GIMP to make them all 6” x 6”.
>> 
>> Put them together side-by-side in a layout program and print them on one 
>> sheet to compare. I bet you will have an extremely difficult time telling 
>> them apart.
>> 
>>> On May 10, 2016, at 12:40 PM, Stephen Kerry <stephen.kerr...@outlook.com> 
>>> wrote:
>>> 
>>> Harold, I agree 2400 dpi might be wasted, but the professional printer 
>>> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
>>> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
>>> four passes from each CMYK component apparently increases the vertical dpi 
>>> by four.
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
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Re: [PyMOL] High Resolution Ray Tracing

[Stephen Kerry]

So the images are back from the printers and I can easily tell the difference 
between 180 and 300 dpi. You have to look closely to tell the difference 
between 300 and 600 dpi. I am unable to distinguish between 600 and 1200 dpi.

My image size is still limited to 7500 x 6000, which at 600 dpi gives a 12.5 x 
10 inch image. Is this an artificial Open Source PyMOL software limitation or a 
genuine bug/memory leak? The segmentation faults also seems to happen even with 
128 GB and 256 GB of RAM!

On my system with 32 GB of RAM, I see PyMOL reserves more virtual RAM than the 
amount of physical RAM, which might be why it crashes when trying to write the 
PNG at the end of ray tracing? It does not appear to use this virtual RAM or 
even compress any RAM, according to activity monitor on OSX 10.10. Disabling 
memory compression and/or swap makes no difference.

Is there anything else I can try to successfully output such a large image?


From: Thomas Holder <thomas.hol...@schrodinger.com>
Sent: 10 May 2016 20:34:44
To: harold steinberg
Cc: Stephen Kerry; pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing

Hi Adam et al.,

This is a super interesting and helpful discussion!

Just wanted to throw in the following shortcut for creating the 6" test images:

png image1.png, 6in, ray=1, dpi=180
png image2.png, 6in, ray=1, dpi=300
png image3.png, 6in, ray=1, dpi=600
png image4.png, 6in, ray=1, dpi=1200

Cheers,
  Thomas

On 10 May 2016, at 14:27, harold steinberg <h.adam.steinb...@gmail.com> wrote:

> The 9600 x 4800 is a very common poster printer spec. Most print shops use 
> 180 dpi images on their poster printers (for best print speed) and customers 
> cannot tell the difference between that and a higher resolution.
>
> As a test, render a small image (say 6” x 6”) in PyMOL at four different dpi, 
> 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi (ray 
> 7200). Then use Photoshop or GIMP to make them all 6” x 6”.
>
> Put them together side-by-side in a layout program and print them on one 
> sheet to compare. I bet you will have an extremely difficult time telling 
> them apart.
>
>> On May 10, 2016, at 12:40 PM, Stephen Kerry <stephen.kerr...@outlook.com> 
>> wrote:
>>
>> Harold, I agree 2400 dpi might be wasted, but the professional printer 
>> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
>> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
>> four passes from each CMYK component apparently increases the vertical dpi 
>> by four.
>
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366

--
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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Re: [PyMOL] High Resolution Ray Tracing

[harold steinberg]

There is Sooo much I need to learn about PyMOL… :)


> On May 10, 2016, at 2:34 PM, Thomas Holder  
> wrote:
> 
> Hi Adam et al.,
> 
> This is a super interesting and helpful discussion!
> 
> Just wanted to throw in the following shortcut for creating the 6" test 
> images:
> 
> png image1.png, 6in, ray=1, dpi=180
> png image2.png, 6in, ray=1, dpi=300
> png image3.png, 6in, ray=1, dpi=600
> png image4.png, 6in, ray=1, dpi=1200
> 
> Cheers,
>  Thomas
> 
> On 10 May 2016, at 14:27, harold steinberg  wrote:
> 
>> The 9600 x 4800 is a very common poster printer spec. Most print shops use 
>> 180 dpi images on their poster printers (for best print speed) and customers 
>> cannot tell the difference between that and a higher resolution.
>> 
>> As a test, render a small image (say 6” x 6”) in PyMOL at four different 
>> dpi, 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi 
>> (ray 7200). Then use Photoshop or GIMP to make them all 6” x 6”. 
>> 
>> Put them together side-by-side in a layout program and print them on one 
>> sheet to compare. I bet you will have an extremely difficult time telling 
>> them apart.
>> 
>>> On May 10, 2016, at 12:40 PM, Stephen Kerry  
>>> wrote:
>>> 
>>> Harold, I agree 2400 dpi might be wasted, but the professional printer 
>>> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
>>> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
>>> four passes from each CMYK component apparently increases the vertical dpi 
>>> by four.
>> 
>> H. Adam Steinberg
>> 7904 Bowman Rd
>> Lodi, WI 53555
>> 608/592-2366
> 
> -- 
> Thomas Holder
> PyMOL Principal Developer
> Schrödinger, Inc.
> 

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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Re: [PyMOL] High Resolution Ray Tracing

[Thomas Holder]

Hi Adam et al.,

This is a super interesting and helpful discussion!

Just wanted to throw in the following shortcut for creating the 6" test images:

png image1.png, 6in, ray=1, dpi=180
png image2.png, 6in, ray=1, dpi=300
png image3.png, 6in, ray=1, dpi=600
png image4.png, 6in, ray=1, dpi=1200

Cheers,
  Thomas

On 10 May 2016, at 14:27, harold steinberg  wrote:

> The 9600 x 4800 is a very common poster printer spec. Most print shops use 
> 180 dpi images on their poster printers (for best print speed) and customers 
> cannot tell the difference between that and a higher resolution.
> 
> As a test, render a small image (say 6” x 6”) in PyMOL at four different dpi, 
> 180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi (ray 
> 7200). Then use Photoshop or GIMP to make them all 6” x 6”. 
> 
> Put them together side-by-side in a layout program and print them on one 
> sheet to compare. I bet you will have an extremely difficult time telling 
> them apart.
> 
>> On May 10, 2016, at 12:40 PM, Stephen Kerry  
>> wrote:
>> 
>> Harold, I agree 2400 dpi might be wasted, but the professional printer 
>> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
>> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
>> four passes from each CMYK component apparently increases the vertical dpi 
>> by four.
> 
> H. Adam Steinberg
> 7904 Bowman Rd
> Lodi, WI 53555
> 608/592-2366

-- 
Thomas Holder
PyMOL Principal Developer
Schrödinger, Inc.


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
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Re: [PyMOL] High Resolution Ray Tracing

[harold steinberg]

The 9600 x 4800 is a very common poster printer spec. Most print shops use 180 
dpi images on their poster printers (for best print speed) and customers cannot 
tell the difference between that and a higher resolution.

As a test, render a small image (say 6” x 6”) in PyMOL at four different dpi, 
180 dpi (ray 1080), 300 dpi (ray 1800), 600 dpi (ray 3600) and 1200 dpi (ray 
7200). Then use Photoshop or GIMP to make them all 6” x 6”. 

Put them together side-by-side in a layout program and print them on one sheet 
to compare. I bet you will have an extremely difficult time telling them apart.


> On May 10, 2016, at 12:40 PM, Stephen Kerry  
> wrote:
> 
> Harold, I agree 2400 dpi might be wasted, but the professional printer 
> supports up to 9600 horizontal dpi x 4800 vertical dpi, so a source image 
> with 1200 dpi would be a nice step up from 600 dpi. The lpi is 1200 as the 
> four passes from each CMYK component apparently increases the vertical dpi by 
> four.

H. Adam Steinberg
7904 Bowman Rd
Lodi, WI 53555
608/592-2366


--
Mobile security can be enabling, not merely restricting. Employees who
bring their own devices (BYOD) to work are irked by the imposition of MDM
restrictions. Mobile Device Manager Plus allows you to control only the
apps on BYO-devices by containerizing them, leaving personal data untouched!
https://ad.doubleclick.net/ddm/clk/304595813;131938128;j
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Re: [PyMOL] High Resolution Ray Tracing

[Stephen Kerry]

Thank you for all of the suggestions so far.

James, I have tried POV-Ray but am unable to emulate PyMOLs internal ray tracer 
to match my other images, which have smaller actual dimensions at the same dpi.

Harold, I agree 2400 dpi might be wasted, but the professional printer supports 
up to 9600 horizontal dpi x 4800 vertical dpi, so a source image with 1200 dpi 
would be a nice step up from 600 dpi. The lpi is 1200 as the four passes from 
each CMYK component apparently increases the vertical dpi by four.

Takanori, your idea of dividing a scene into sections and rendering them 
individually sounds ideal, but I have no idea how to go about that properly, in 
order to get the lighting and shadows to match up when the images are joined.

From: Takanori Nakane <takanori.nak...@bs.s.u-tokyo.ac.jp>
Sent: 10 May 2016 01:58:09
To: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing

Hi,

By tweaking the projection matrix, we can divide a big scene into
several sub-images and render them separately. Thus, we can reduce
the memory consumption. I think this is scriptable, although I
don't have time to implement myself.

 > I was wondering if the developers have come across this upper limit too?
 > I have a 2400 dpi printer, so I want to go with the highest dpi possible
 > for the best quality.

"2400 dpi" for a printer does not have the same meaning as 2400
dpi (or better, ppi, pixel per inch) for a screen.
Printers use many dots to represent an image pixel.
Did you take that into the account? Probably you don't need 2400 dpi
or 1200 dpi.

https://en.wikipedia.org/wiki/Dots_per_inch#/media/File:DPI_and_PPI.png

Best regards,

Takanori Nakane

Am 2016年05月10日 um 09:34 schrieb Stephen Kerry:
> Thank you for trying this out on a workstation with 128 GB and then 256
> GB of RAM. It is much appreciated as I do not have easy access to that
> kind of computational power. The fact that you also get these segfaults
> with all of your RAM, suggests that this might be a PyMOL limitation,
> rather than a hardware issue.
>
> I have come to the conclusion that it is impossible to ray trace an
> image with an output resolution greater than 45 megapixels (7500 x
> 6000). Halving the dpi from 1200 to 600 gives a 11.25 megapixel (3750 x
> 3000) resolution.
>
> I was wondering if the developers have come across this upper limit too?
> I have a 2400 dpi printer, so I want to go with the highest dpi possible
> for the best quality.
>
> 
> *From:* David Hall <li...@cowsandmilk.net>
> *Sent:* 06 May 2016 19:17:38
> *To:* Stephen Kerry
> *Cc:* pymol-users@lists.sourceforge.net
> *Subject:* Re: [PyMOL] High Resolution Ray Tracing
> Feel free to send me the files off list.
>
> -David Hall
>
>> On May 6, 2016, at 1:54 PM, Stephen Kerry <stephen.kerr...@outlook.com
>> <mailto:stephen.kerr...@outlook.com>> wrote:
>>
>> Dear All,
>>
>> I have a protein complex scene that I need to create a large, high
>> resolution (1200 dpi) ray traced image of, but am unable to do so as I
>> always run out of memory at the end of the ray tracing process, with
>> the following error:
>>
>> python2.7(972,0x7fff7397f300) malloc: ***
>> mach_vm_map(size=18446744068907188224) failed (error code=3)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>>
>> This is with PyMOL 1.81 from Fink on OSX 10.10 with
>> ani7-4790Kprocessor and 32 GB of DDR3. Python2.7 expands up to 15 GB
>> of RAM, with more than twice this reserved for virtual memory, but no
>> swap is actually used.
>>
>> Decreasing hash_max just increases the ray tracing time until the
>> error at the end. Sometimes PyMOL will be terminated with this error,
>> whilst at other times a transparent PNG is all that is produced.
>>
>> Is there a way to force PyMOL to use virtual memory to avoid these
>> errors/crashes at the expense of processing time?
>>
>> If not, is there anyone who has PyMOL 1.8x installed on a system with
>> 64 GB or more RAM, who would be able to render this ray traced image
>> if I send the, the .pse file and .pml script off list? Takes about 10
>> mins to process.
>>
>> Cheers,
>>
>> Stephen
>>
>> --
>> Find and fix application performance issues faster with Applications
>> Manager
>> Applications Manager provides deep performance insights into multiple
>> tiers of
>> your business applications. It resolves application problems quickly and
>> re

Re: [PyMOL] High Resolution Ray Tracing

[James Kress]

Did you try using POV-Ray with PyMOL to do the ray tracing?

renderer = 1 uses PovRay's renderer. This is Unix-only and you must have
"povray" in your path. It utilizes two temporary files: "tmp_pymol.pov" and
"tmp_pymol.png". Also works on Mac via Povray37UnofficialMacCmd but it needs
to be in your path as "povray".

 

Jim

 

James Kress Ph.D., President

The KressWorksR Foundation 

An IRS Approved 501 (c)(3) Charitable, Nonprofit Organization

"Engineering The Cure" C

(248) 573-5499

 

Learn More and Donate At:

Website:  <http://www.kressworks.org/> http://www.kressworks.org

Facebook: https://www.facebook.com/KressWorks.Foundation/

Twitter: @KressWorksFnd

 

Confidentiality Notice | This e-mail message, including any attachments, is
for the sole use of the intended recipient(s) and may contain confidential
or proprietary information. Any unauthorized review, use, disclosure or
distribution is prohibited. If you are not the intended recipient,
immediately contact the sender by reply e-mail and destroy all copies of the
original message.

 

From: Stephen Kerry [mailto:stephen.kerr...@outlook.com] 
Sent: Monday, May 09, 2016 8:35 PM
To: David Hall <li...@cowsandmilk.net>
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing

 

Thank you for trying this out on a workstation with 128 GB and then 256 GB
of RAM. It is much appreciated as I do not have easy access to that kind of
computational power. The fact that you also get these segfaults with all of
your RAM, suggests that this might be a PyMOL limitation, rather than a
hardware issue. 

 

I have come to the conclusion that it is impossible to ray trace an image
with an output resolution greater than 45 megapixels (7500 x 6000). Halving
the dpi from 1200 to 600 gives a 11.25 megapixel (3750 x 3000) resolution. 

 

I was wondering if the developers have come across this upper limit too? I
have a 2400 dpi printer, so I want to go with the highest dpi possible for
the best quality. 

  _  

From: David Hall <li...@cowsandmilk.net <mailto:li...@cowsandmilk.net> >
Sent: 06 May 2016 19:17:38
To: Stephen Kerry
Cc: pymol-users@lists.sourceforge.net
<mailto:pymol-users@lists.sourceforge.net> 
Subject: Re: [PyMOL] High Resolution Ray Tracing 

 

Feel free to send me the files off list.

 

-David Hall

 

On May 6, 2016, at 1:54 PM, Stephen Kerry <stephen.kerr...@outlook.com
<mailto:stephen.kerr...@outlook.com> > wrote:

 

Dear All,

 

I have a protein complex scene that I need to create a large, high
resolution (1200 dpi) ray traced image of, but am unable to do so as I
always run out of memory at the end of the ray tracing process, with the
following error:

 

python2.7(972,0x7fff7397f300) malloc: ***
mach_vm_map(size=18446744068907188224) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor
and 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than
twice this reserved for virtual memory, but no swap is actually used.

Decreasing hash_max just increases the ray tracing time until the error at
the end. Sometimes PyMOL will be terminated with this error, whilst at other
times a transparent PNG is all that is produced.

Is there a way to force PyMOL to use virtual memory to avoid these
errors/crashes at the expense of processing time?

If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB
or more RAM, who would be able to render this ray traced image if I send
the, the .pse file and .pml script off list? Takes about 10 mins to process.

Cheers,

Stephen

 


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Re: [PyMOL] High Resolution Ray Tracing

[harold steinberg]

I can try to address the 2400 dpi printer resolution.

Printer manufactures specify their printer's resolution in the number of pixels 
per inch (ppi) in the horizontal plane because it’s higher, and looks better in 
advertising. But all printers also have a vertical printing resolution that is 
much lower, and therefore is the true limit on the resolution that a printer 
can print high quality images.

Printed magazines are screened at 133 lines per inch in the vertical dimension 
and so twice that resolution is all you need in ppi to get the best possible 
print. Magazines typically print at 2400 dpi in the horizontal plane. 266 dpi 
is all you’d really need, but people generally use 300 dpi because they don’t 
understand how offset printing presses work. Coffee table books (high end) 
print at 200 lines per inch.

Poster printers, which can print extremely high resolution in the horizontal 
plane generally only need 180 dpi in files because of the lower resolution in 
the vertical plane. And the fact that throwing a huge 2400 dpi file at a poster 
printer will generally slow it’s print speed to a crawl… and that make printing 
multiple posters in a limited amount of time hard to do.

All printers are pretty similar but you should check yours for it’s specific 
details. All printers have multiple settings and options that will effect print 
speed and quality but check yours for the lpi (lines per inch) and then double 
that number to figure out how much dpi you need.

Most people do not understand how this all works, I can try and give a primer 
on it. Using the information above as the example, if you want to have a final 
image size of four inches in a magazine, then you’d need to ray trace your file 
at 4" x 300 dpi = 1200 dpi in width.

So once you figure out the size of the image you want the final image to be, 
multiple that by twice your printer's vertical printing limitation, to get the 
ray trace image width.



> On May 9, 2016, at 7:34 PM, Stephen Kerry <stephen.kerr...@outlook.com> wrote:
> 
> Thank you for trying this out on a workstation with 128 GB and then 256 GB of 
> RAM. It is much appreciated as I do not have easy access to that kind of 
> computational power. The fact that you also get these segfaults with all of 
> your RAM, suggests that this might be a PyMOL limitation, rather than a 
> hardware issue.
>  
> I have come to the conclusion that it is impossible to ray trace an image 
> with an output resolution greater than 45 megapixels (7500 x 6000). Halving 
> the dpi from 1200 to 600 gives a 11.25 megapixel (3750 x 3000) resolution.
>  
> I was wondering if the developers have come across this upper limit too? I 
> have a 2400 dpi printer, so I want to go with the highest dpi possible for 
> the best quality.
> From: David Hall <li...@cowsandmilk.net <mailto:li...@cowsandmilk.net>>
> Sent: 06 May 2016 19:17:38
> To: Stephen Kerry
> Cc: pymol-users@lists.sourceforge.net 
> <mailto:pymol-users@lists.sourceforge.net>
> Subject: Re: [PyMOL] High Resolution Ray Tracing
>  
> Feel free to send me the files off list.
> 
> -David Hall
> 
>> On May 6, 2016, at 1:54 PM, Stephen Kerry <stephen.kerr...@outlook.com 
>> <mailto:stephen.kerr...@outlook.com>> wrote:
>> 
>> Dear All,
>> 
>> I have a protein complex scene that I need to create a large, high 
>> resolution (1200 dpi) ray traced image of, but am unable to do so as I 
>> always run out of memory at the end of the ray tracing process, with the 
>> following error:
>> 
>> python2.7(972,0x7fff7397f300) malloc: *** 
>> mach_vm_map(size=18446744068907188224) failed (error code=3)
>> *** error: can't allocate region
>> *** set a breakpoint in malloc_error_break to debug
>> 
>> This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor 
>> and 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than 
>> twice this reserved for virtual memory, but no swap is actually used.
>> 
>> Decreasing hash_max just increases the ray tracing time until the error at 
>> the end. Sometimes PyMOL will be terminated with this error, whilst at other 
>> times a transparent PNG is all that is produced.
>> 
>> Is there a way to force PyMOL to use virtual memory to avoid these 
>> errors/crashes at the expense of processing time?
>> 
>> If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB 
>> or more RAM, who would be able to render this ray traced image if I send 
>> the, the .pse file and .pml script off list? Takes about 10 mins to process.
>> 
>> Cheers,
>> 
>> Stephen
>> 
>> --
>> Find

Re: [PyMOL] High Resolution Ray Tracing

[Stephen Kerry]

Thank you for trying this out on a workstation with 128 GB and then 256 GB of 
RAM. It is much appreciated as I do not have easy access to that kind of 
computational power. The fact that you also get these segfaults with all of 
your RAM, suggests that this might be a PyMOL limitation, rather than a 
hardware issue.



I have come to the conclusion that it is impossible to ray trace an image with 
an output resolution greater than 45 megapixels (7500 x 6000). Halving the dpi 
from 1200 to 600 gives a 11.25 megapixel (3750 x 3000) resolution.



I was wondering if the developers have come across this upper limit too? I have 
a 2400 dpi printer, so I want to go with the highest dpi possible for the best 
quality.


From: David Hall <li...@cowsandmilk.net>
Sent: 06 May 2016 19:17:38
To: Stephen Kerry
Cc: pymol-users@lists.sourceforge.net
Subject: Re: [PyMOL] High Resolution Ray Tracing

Feel free to send me the files off list.

-David Hall

On May 6, 2016, at 1:54 PM, Stephen Kerry 
<stephen.kerr...@outlook.com<mailto:stephen.kerr...@outlook.com>> wrote:


Dear All,

I have a protein complex scene that I need to create a large, high resolution 
(1200 dpi) ray traced image of, but am unable to do so as I always run out of 
memory at the end of the ray tracing process, with the following error:


python2.7(972,0x7fff7397f300) malloc: *** 
mach_vm_map(size=18446744068907188224) failed (error code=3)
*** error: can't allocate region
*** set a breakpoint in malloc_error_break to debug

This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor and 
32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than twice this 
reserved for virtual memory, but no swap is actually used.

Decreasing hash_max just increases the ray tracing time until the error at the 
end. Sometimes PyMOL will be terminated with this error, whilst at other times 
a transparent PNG is all that is produced.

Is there a way to force PyMOL to use virtual memory to avoid these 
errors/crashes at the expense of processing time?

If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB or 
more RAM, who would be able to render this ray traced image if I send the, the 
.pse file and .pml script off list? Takes about 10 mins to process.

Cheers,

Stephen


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Re: [PyMOL] High Resolution Ray Tracing

[David Hall]

Feel free to send me the files off list.

-David Hall

> On May 6, 2016, at 1:54 PM, Stephen Kerry  wrote:
> 
> Dear All,
> 
> I have a protein complex scene that I need to create a large, high resolution 
> (1200 dpi) ray traced image of, but am unable to do so as I always run out of 
> memory at the end of the ray tracing process, with the following error:
> 
> python2.7(972,0x7fff7397f300) malloc: *** 
> mach_vm_map(size=18446744068907188224) failed (error code=3)
> *** error: can't allocate region
> *** set a breakpoint in malloc_error_break to debug
> 
> This is with PyMOL 1.81 from Fink on OSX 10.10 with an i7-4790K processor and 
> 32 GB of DDR3. Python2.7 expands up to 15 GB of RAM, with more than twice 
> this reserved for virtual memory, but no swap is actually used.
> 
> Decreasing hash_max just increases the ray tracing time until the error at 
> the end. Sometimes PyMOL will be terminated with this error, whilst at other 
> times a transparent PNG is all that is produced.
> 
> Is there a way to force PyMOL to use virtual memory to avoid these 
> errors/crashes at the expense of processing time?
> 
> If not, is there anyone who has PyMOL 1.8x installed on a system with 64 GB 
> or more RAM, who would be able to render this ray traced image if I send the, 
> the .pse file and .pml script off list? Takes about 10 mins to process.
> 
> Cheers,
> 
> Stephen
> 
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> Applications Manager provides deep performance insights into multiple tiers of
> your business applications. It resolves application problems quickly and
> reduces your MTTR. Get your free trial!
> https://ad.doubleclick.net/ddm/clk/302982198;130105516;z___
>  
> 
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> 
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