RAM and local disk run full when stitching gigapixel panorama

[Daniel Hertrich]

Hi all,

using 

- PTGui Pro Trial 11.6 on a 

- Mac Pro from 2013 with 64GB of RAM, 1TB SSD and 6-core Xeon E5 3.5GHz processor with

- macOS Sierra 10.12.6:

As a current user of Kolor's "Autopano Giga" stitching solution, after Kolor's closing I'm now in search for a good alternative. PTGui seems to be one, however, I have some issues that I hope to find solutions for here.

I wanted, for testing purposes, to let PTGui stitch my so far largest panorama, consisting of 1.200 individual JPEG images with 42 Megapixel each as input and the output being 24 Gigapixels in size.

However, even though I have set PTGui to use at most 35GB of RAM (64GB are installed  in my Mac Pro), RAM seems to be running full and macOS stops PTGui and other applications.

When I still had RAM limit set to "Automatic", which was the default, RAM overload, even while "Aligning images" already, could directly be observed in the activity monitor of macOS. The "RAM pressure" graph turned to yellow and then to red, before applications were stopped by the OS.

Now that I have RAM limit manually set to 35GB, RAM pressure doesn't seem to go too high anymore, however, applications are stopped anyway. Not whilt "Aligning images", but when stitching.

Also, the local disk runs full (before stitching process, 30GB were free). And that, although I have set temporary directories AND the stitching output directory to be located on external drives. 

Maybe those two issues are related, I don't know.

One more data point:
After I killed the PTGui process and revived all other applications, the system is in a state where it reacts very slowly (only in certain regular intervals, a few seconds each) to mouse input and shows the color ball in the meantime. Very annoying. I need to restart macOS in such a case to get back normal system behavior,

Screenshots with explaining markers are attached.

Questions:

- Why does RAM run full, even though I have limited RAM usage ["automatically" | "manually" to 35GB]?

- Why does the local disk run full, even though I have set temporary and output folders to external drives?

- How can I avoid either issue?

- Does the memory limit set in Preferences affect the RAM occupation (second column in activity monitor's RAM usage tab) or the "Compressed RAM" occupation (third column in activity monitor's RAM usage tab)?

- If PTGui has problems with stitching a 24GP panorama, does that mean I cannot even think of stitching my soon planned 60GP panorama on that machine without upgrading RAM or disk?

Thank you very much,

Daniel

[PTGui Support]

Hi Daniel,

There's something strange going on, you sent me a screenshot earlier on
showing a kernel_task occupying nearly 40 GB of RAM. I will do some
investigations to see if I can reproduce this behavior.

What kind of external drives have you configured in PTGui for temporary
files? Are those USB3 drives? SSD or spinning disks? And are they
formatted in APFS or something else?

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

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[Daniel Hertrich]

Hi Joost,

Am Montag, 17. September 2018 15:23:41 UTC+2 schrieb PTGui Support:

There's something strange going on, you sent me a screenshot earlier on
showing a kernel_task occupying nearly 40 GB of RAM. I will do some
investigations to see if I can reproduce this behavior.

What kind of external drives have you configured in PTGui for temporary
files? Are those USB3 drives? SSD or spinning disks? And are they
formatted in APFS or something else?

 

The main external drive, which is configured for the output and as a temporary drive, is a Thunderbolt RAID system (Promise Pegasus2 R8) with 8 spinning disks 4TB each, 6 of them configured for a 16GB RAID (I believe this is RAID 5 or 6? Not sure at the moment, but shouldn't matter for the software, macOS transparently shows this as a normal large drive, as far as I can tell).

It is formatted with Journaled HFS+.

The second external drive is one of the two remaining disks in that Thundebolt housing, configured as a standalone disk formatted with ExFAT. I have added that just to let the software have a choice. It's not important to have that in the setup.

Should I rather remove it from the Preferences to avoid one possible source of failure?

Daniel

 

[Daniel Hertrich]

...I'm still on macOS Sierra, so no APFS support yet. I'm still on HFS+ for all my drives. As far as I know, the Kolor products were not able to cope with APFS yet (or was it some other software I use?), hence I didn't upgrade yet.

[PTGui Support]

Hi Daniel,

I did some tests but couldn't reproduce any problem here. First of all
the kernel_task occupying many gigabytes seems to be normal. I see it
too but it doesn't seem to cause any problems. Eventually it's the
Compressed Mem column that counts, this is raw physical memory, and this
is 0 bytes for kernel_task.

PTGui writes temp data to uncached files. This ensures that data is
written directly to disk; if it would be cached then more RAM would be
used by the OS. It's a bit of a guess but in your case it seems as if
there's still some caching being done in the underlying macos layers.
This would also explain why swap on your main drive runs full (there's
not enough ram available for caching).

You might try testing both temp drives separately (restart PTGui after
changing the temp file settings). Perhaps the problem occurs with just
one of them.

And it's better to use an SSD for temp space in PTGui, probably even
compared to an 6 disk RAID, because of lower seek times.

APFS is not a requirement (but I wouldn't use FAT for temp files). PTGui
should run fine on any OS since 10.7.

If you have any new information please let me know.

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

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[Daniel Hertrich]

Hi Joost,

thanks for answering. 

I have some new data:

I have changed three things yesterday:
1. Removed the ExFat temp space, so only the HFS+ space on RAID is left for temp files

2. I made more space available on the internal SSD, not about 80GB are free

3. I limited PTGui memory usage to 25GB

Then I started a stitching process again.

Result:
It ran over night without any flaw. However:

1. In the morning I needed to start some programs (Mail, Lightroom), and that let the RAM overload again and macOS paused PTGui. (25GB RAM limit should leave plenty of RAM for all the other applications that I regularly use!)

2. I was able to resume PTGui operation, it stll runs

3. PTGui stitching progress bar seems to be stuck at a value it reached far earlier than I started Mail and Lightroom (so this memory overload doesn't seem to be the cause for the stuck progress bar).

4. Activitiy monitor reports occupied RAM by PTGUI most of the times within the set limit, but sometimes way beyond (why?)

The progress bar has the same value now for about 8 hours (since abt 4:30am).

Should I continue to wait? Or is PTGui really stuck here now, so should I kill it? The CPU load still indicates some work, although not too much by PTGUI (84% CPU load; 1200% would be the max with all cores fully loaded).

Screenshots attached - you can see the point of time the screenshot was taken in its file name. I have also added comments to the file names.

Note: The moment when the progress bar reaches its final(?) position, that it still has, memory occupation of PTGui reached the 25GB limit for the first time. Coincidence? Shortly after, the limit was even exceeded.

If caching was the reason for exceeding the limit, would that really add to the causing processes name (i.e. PTGUI) and not instead to some OS-related process?

At 5:54am, memory occupation of PTGui reached 50GB (!), and from then on, compressed memory began to be used. Constantly increasing from a few kB at 5:55 up to 16GB at 6:39am. Then eventually it would decrease again a bit, then increase again and then move in a range from 10GB to 25GB. 

And this (screenshot of 9:30am) is still the current state. Slightly changing CPU and memory values, stuck progress bar, no visible change in the GUI.

What to do now?

Would it help if I try to capture RAM values over a long time and create a graph from them? Or let PTGui write some debug logging?

With the next try, I can replace the RAID temp space by a USB3 SSD drive per your suggestion. However, I'd prefer if that does not need to be a permanent solution.

Daniel

[PTGui Support]

Hi Daniel,

Not sure what is going on, but the 50+ GB of memory usage looks suspect.

Could you send me the project file (just the .pts file, not the images)?

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

On 18/09/2018 13:13, Daniel Hertrich wrote:
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[Daniel Hertrich]

Hi Joost,

A few hours ago, I started over to stitch that panorama, this time with a USB3 SSD drive as temporary drive, as you suggested. No other settings changed.

Result: When progress bar was at about 80%, I suddenly get an error message and the error log opens. See screenshot.

Log output:

...errrr... why is the error log dialog content not copyable? Okay, you can see a part of it in the screenshot, too.

Seems as if the temp file size on the temp SSD drive got too large? However, when I look into the drive, there are almost 650GB free on it. The temp file hat 270GB, says the error message.

I don't really understand the behavior of PTGui here.

Do you know what's going on here?

Is it normal that PTGui needs so much temp space? about 270GB?

Why does it report that error, although on the SSD there must be plenty of additional space?

The error occurred before in prior runs the memory and SSD ran full, so I cannot say, if the temp location change to USB3 SSD did any good to avoid that issue.

Will start another test overnight with an empty USB3 1TB hard disk as temporary file location.

After closing PTGui now, I copy the pts file and send it to you via email (don't want to make it public).

I hope this helps so you can help me. :)

Daniel

[Daniel Hertrich]

Another question:

Is it normal that PTGui occupies so much CPU resources in that state for such a long time (about 2 minutes)?

Panorama creation wasn't started yet!

See screenshots: First during high CPU load, second directly after.

Daniel

[PTGui Support]

Hi Daniel,

Thanks for sending the project file. I will need to investigate, this is
going to take some time. I'll get back to you.

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

On 18/09/2018 23:51, Daniel Hertrich wrote:
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[PTGui Support]

Yes, it was probably busy loading the images and generating thumbnails
and previews. It's actually very good to see 1200% CPU utilization, it
means you have a fast enough disk and PTGui's multi threading works well.

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

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[Daniel Hertrich]

Am Mittwoch, 19. September 2018 09:05:05 UTC+2 schrieb PTGui Support:

Yes, it was probably busy loading the images and generating thumbnails
and previews. It's actually very good to see 1200% CPU utilization, it
means you have a fast enough disk and PTGui's multi threading works well.

Good to know!

News from my side. I gave the stitching process another go, this time with a 1TB USB3 HDD (HFS+ freshly formatted, so definitely empty) as temporary storage.

Results:
- Stitching went significantly slower than with the USB3 SSD (expected?)

- CPU usage was very low all the time compared to the run with the SSD (expected, since HDD is bottleneck?)

- Until progress bar was again at approx. 90%, memory usage was moderate, as with the SSD. and below the limit I set. 10 to 20 GB (and 0 compressed memory).

- When progress bar reached approx. 90%, memory usage went up again and progress bar didn't move anymore, as always. At last, macOS paused PTGui doe to too much memory consumption. See screenshots. THe pause did only happen when I used Safari for a short time (see red area in memory pressure bar). If I hadn't used Safari, maybe this would not have happened, or it would have happened later. 

- On the USB3 HDD PTGui allocated a significant amount of storage. Only 174GB were reported free. Is this normal? Does PTGui really need that much temporary space? Then it's clear that the SSD didn't work, since it only had about 600GB free. 

Questions:
#1 - If for a 24GP stitch, PTGui needs 840GB of temporary storage, how much temporary storage will it need to allocate for a 60GP / 100GP panorama? I'll need to know that, because I plan on creating such panoramas.

#2 - On the temporary HDD / SSD, I never see any files created by PTGui. This is irritating: The drive is almost empty (except Trash and Spotlight index files), but is it reported only 174GB free. I have enabled visiblity of hidden files. But none is there. How does PTGui allocate the space, if not via files? 

#3 - What does PTGui do in the last 10% of the stitching process? Maybe knowing this helps to understand why it works so well until 90%, but when reaching 90%, memory consumption exceeds all set limits and makes PTGui halt. Is this something I can influence, e.g. by a setting in preferences? Is this an issue with a specific image in my pile of source images? Or with some specific control points? 

#4 - Would it make a difference if I send the stitching job to the batch stitched and let that do the stitching? Is there a chance this will work better?

I would try things instead of asking some of the questions, however, the last run with the HDD temp space ran about 2 days, so it's a huge waste of time, if I do test runs that won't lead to anything. Hence I hope you can answer the questions.

In case you may need the source image files for reproduction of the issue, let me know in time please. That's 23GB of data. Upload of them will take probably about 2 days..

I could recode them to be significantly smaller, of course, but I don't know, if the issue is reproducible then. Should I try?

Thanks,

Daniel

[PTGui Support]

Hi Daniel,

I'll be running some tests with your project and will get back to you.

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

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[Daniel Hertrich]

Thanks.

News from me in the meantime:

I did another run with USB3 HDD over night. This time with much smaller images (I re-exported them from Lightroom with lower quality setting. Same resolution as before, but around 4MB instead of around 20MB each file, so I can upload the footage for you, if you need it.

I simply exchanged footage but used the same project file in PTGui that you have. I thought this should work, as control points would be the same, since image content is basically the same, just with more artifacts.

Is that supposed to lead to issues?

--> This run only worked for a few hours. Then there was an error (see attachments).

Seems it wanted to write a really HUGE temp file (2TB, if I am not mistaken reading that number?), which of course would not fit onto the 1TB USB3 HDD.

Do you have an explanation for that?

Another pecularity: In the moment when the error is shown, macOS begins to compress PTGui's memory (see activity monitor in the screenshots).

What is the cause and what the result? May PTGui have a problem surviving the moment when macOS begins to compress memory?

Or did memory compression happen, because the error occurred?

I'll now start over with the smaller footage and create a new project, trying if that one will run though.

I'll save the old project file for further tests, if needed.

Daniel

[PTGui Support]

Hi Daniel,

I can reproduce the problems here using your project file. There seems
to be a bug in PTGui's virtual memory management. No need to do more
testing.

One thing to note though: you've enabled tone mapping on a 30 gigapixel
panorama. Tone mapping is a extremely resource intensive process. You
might be able to finish stitching if you disable tone mapping (see
Panroama Editor sidebar). It certainly will finish much faster.

Nevertheless it should eventually work, even with tone mapping enabled.
Will be fixed.

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

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[Daniel Hertrich]

Hi Joost,

great, thanks for letting me know.

I never used tone mapping in my tests so far, so switching that off won't work as a workaround.

I'll wait for the bugfix and try again.

If the bug is within virtual memory management, will the bugfix allow me again to use the (maybe cached) Thunderbolt RAID as temporary storage, or will I need to use a USB3 drive? Will it be possible to use a USB3 drive that only has a few 100 GB free on it?

If you don't mind, answers to the questions I asked in my prior mails would be interesting to me anyway, as I always like to understand what software does. That builds a lot of trust and it also gives the user capabilities to find workaround for issues by himself instead of asking the support so much ;-)

Thanks,

Daniel

[PTGui Support]

Hi Daniel,

The project file you sent me definitely has tone mapping enabled. See
the Tone Mapping side bar in the panorama editor.

Yes by design (any bugs like these aside) PTGui allows you to use any
kind of drive for temporary storage. Performance will vary of course.

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

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[Daniel Hertrich]

Hi Joost,

Am Freitag, 21. September 2018 13:36:57 UTC+2 schrieb PTGui Support:

The project file you sent me definitely has tone mapping enabled. See
the Tone Mapping side bar in the panorama editor.

Indeed. *blush*

Well, I didn't realize that basic exposure correction is part of the tone mapping feature. 

Good to know, that this feature would slow down a lot. I deactivated it, and then stitching went through in just several hours.

With further tests I'll wait for the bugfix version.

Do you have an idea when it will be ready?

Thanks!

Daniel

 

[Daniel Hertrich]

Hi Joost, 

any news about the virtual memory bugfix? 

I am eager to test stitching my panorama, but I can't yet. ;-)

Daniel

[PTGui Support]

Hi Daniel,

The bug was fixed that caused PTGui to attempt to create 2 TB size temp
files. Do you mean it still doesn't work?

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

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[Daniel Hertrich]

Hi Joost, 

oops, I didn't realize that 11.7 is already out. Sorry.

Will try it now. :-)

Will it still make a difference, if I use a USB2 HDD; USB3 SSD or Thunderbolt RAID (HDDs) as temporary space? 

Of course I'd prefer the RAID...

Daniel

[PTGui Support]

Hi Daniel,

Definitely the USB3 SSD, it will be much faster than the othe two options.

Kind regards,

Joost Nieuwenhuijse
www.ptgui.com

On 8-11-2018 14:29, Daniel Hertrich wrote:
> Hi Joost,
>

> oops, I didn't realize that 11.7 is already out. Sorry.
> Will try it now. :-)
>
> Will it still make a difference, if I use a USB2 HDD; USB3 SSD or
> Thunderbolt RAID (HDDs) as temporary space?
> Of course I'd prefer the RAID...
>
> Daniel
>
>
>
> Am Donnerstag, 8. November 2018 12:57:15 UTC+1 schrieb PTGui Support:
>
> Hi Daniel,
>
> The bug was fixed that caused PTGui to attempt to create 2 TB size temp
> files. Do you mean it still doesn't work?
>
> Kind regards,
>
> Joost Nieuwenhuijse

> www.ptgui.com <http://www.ptgui.com>

>
> On 8-11-2018 11:25, Daniel Hertrich wrote:
> > Hi Joost,
> > any news about the virtual memory bugfix?
> > I am eager to test stitching my panorama, but I can't yet. ;-)
> > Daniel
> >
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[Daniel Hertrich]

Hi Joost,

great. The configured RAM usage limit seems to work now. No overflow anymore. And so far no out-of-space of the 1TB USB3 SSD. PTGui is currently stitching a 175(!) Gigapixel panorama, for about 12 hours now. Status bar indicates a progress of about 15-20% now. So far not a single issue.

Daniel