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paintstone

macrumors newbie
Original poster
Jul 19, 2019
26
2
Seattle
Years ago I wanted to run a specific analysis for a client but the home office for the brokerage I worked for said they don't do that and any analysis they are offering takes a few weeks.

Fast forward a few years and I've taught myself a little python, a deeper understanding of Unix, git and likely burned through the CPU on too many MacbookPro's and one iMac.

So I've purchased a MacPro 5,1 as a new home system to handle my ever-growing iTunes collection of movies, music and the first Geforce 1060 which does support 1280 Cuda cores. Eventually, I'll run two of these.

I've done some reading on StackExchange with this post.

[https://ai.stackexchange.com/questions/6855/thoughts-on-apple-mac-pro-vs-gcp-aws-for-deep-learning][1]

and this one

[enter link description here][2]

These two builds ( I believe ) are going in the right direction using the wrong hardware. Since I can't afford to pay Uncle Bezos crazy cash for AWS (nor do I have time to learn it) as I am an undergrad... plus I have some experience in building computers.

Yes, I understand that Google now offers GPU's and I plan to use them. There is also a need to have a local Postgresql server running for my own needs and like I said the iMac has been cooked while I learn how to train hyperparameters of Neural nets. There have been many mistakes. =(

So with the 5,1 that I've purchased, it came with Mojave but I need to wind it back to high sierra which is where the Nvidia drivers do work (yet deprecated in further versions of MacOS)

I have created one problem, now the machine gets to a boot screen and it won't restart, even though the screen says click here to shutdown. Nothing happens.

I figure I would post the screenshot and ask for help.

  1. 1. How can I move forward to install high sierra? From having a Mojave install when I keep getting this screen and it just loops back around to it. To clarify, when I click the triangle in the circle it does nothing, my wifi is connected but I can click the restart or shutdown under the apple icon in the top right of the screen. [![enter image description here][3]][3]
  2. Eventually, I will expand this machine to the 12 core 24 thread 3.42Ghz processor system with 96 gigs of ram, but what is a checklist of things to set up a new Mac? For reference: My shell will likely be bash, Anaconda, using GitHub as version control, Postgresql as backend server and python3 for a scripting language which I am still learning. This might get broken up into other posts but I figure post here as I can't be the only person wanting to get into a medium-sized home system for GPU deep learning. So I figure open-source my concept and share it with the SE community. Edit: There is a boot USB drive that is used to get the machine to this point, many of the how-to MacPro tutorials talk about using keystrokes on the Mac keyboard which I don't have, just an old but reliable Microsoft keyboard. So if you know how to do a firmware update on 2010 MacPro I would appreciate your advice.
Thanks again to the whole group here and for these two links that have been fantastic in researching the issues coming from a Deep Learning cMP - Main Issue. I was able to get high sierra working on a USB to SATA cable to an external HDD. I'm building this thread as a place to store the data for myself and figure there are others who might want to do this build so I'm going to share full transparency on my build.

cMP (classic MacPro) Compatability List
cMP upgrade Sticky, now a Wiki

I'm liking the idea of having my build notes in one location, is it ok if I paste my todo list here and work through it, once complete I will edit the font to be something like strikethrough?
  1. First Challenge - Uninstall Mojave and move back to 10.13.6. COMPLETED
  2. Second Things - As this build evolves I'll likely edit this and welcome recommendations to expand this for others like the two links that this forum has been building. It will be easier to post everything to one place and I guess I could create sub links to others like the compatibility list and the upgrade wiki which are awesome and thanks to each author and contributors for making those.
  3. Third Challenge - I've been able to get the high sierra running after using a USB SATA cable to create a bootable drive in an old 2.5 500 gig drive. The challenge is now my Boot drive is externally USB plugged and I need to move it inside.
  4. Fourth Challenge - The new(ish) mac GPU arrives next week but before then I need to figure out how to share (centralize) data among my 2tb MBP 13", my 1tb iMac 27" and my 2tb cMP 5,1. I have an a1254 airport extreme that I can use where I could use the time machine to back up the other computers but there is a ton of it I want to be migrated to the cMP. Would the migration assistant be a good candidate for that? Or what is a way to have maximum access to the data I have on each machine, in a central location
    1. Airport Challenge - Have any great tutorials or progressive steps about these to see if I can create an ssh connection for data access? Is that even a good idea? Something like this is what I've found but not sure if it best practice, course it all depends right? NAS vs Airport
    2. I have access to the internet currently via wifi and my cMP (classic MacPro) is connecting via wifi board on the machine but should I connect the airport extreme to the wall socket for ethernet about the same speed as wifi. I'm wanting to get firewalls and secure access to the airport but enable access to it for me only via these three machines the MPB, iMac, and cMP respectively.
    3. Each of the three machines is connected to the airport extreme via ethernet and this coming black Friday I'll get a few 10Tb drives or maybe some 4tbsshd that WD has been talking about to expand the capacity but at what point does the Airport extreme need to be migrated or linked to a NAS in terms of size or functionality. This is part of a large question so I am looking for links and advice.
  5. Fifth Challenge - CUDA GPU is my (first of many GPUs) Quadro 4000 arrives from eBay next week so that is Cuda capable, but not as fast as the GTX 1060 but small steps first. I need to get Pycharm setup with anaconda and git version control, then once we have a few tests setup I need to get Concourse to help with integrating the stack and docker will be added into that.
  6. Six Challenge - Are there any links someone can recommend for a checklist of things to set up on a new mac or ubuntu machine for data science work? There is the list of 12 things that Joel recommends for level 10 software developers but I am talking strictly "Setting up a new mac" Things like
    1. Create an admin account and subsequent user accounts.
    2. Create a log of your PATH and use virtual machines with requirements.txt files to set up the machine. I know this is moving into software but I'm hoping I can keep this focused on the build I am doing, is it also ok to link between here and the StackOverflow account as they are more purely focused on the code vs hardware like you guys/girls?
    3. The long term goal of this is to create a somewhat automated list of things that get set up on any subsequent machines so this doesn't have to get recreated ever new machine or ubuntu server we add for the project.
  7. Seventh Challenge - security. How to secure the ports of my computer with some sort of monitoring software like Datadog, Wireshark and or a python based system. This next chunk was sourced at fullstackpython.com which is a great source for best practices in scaling efficient python projects.
    1. Monitoring Layers - There are several important resources to monitor the operating system and network level of a web stack.
      1. CPU utilization
      2. Memory utilization
      3. Persistence storage consumed versus free
      4. Network bandwidth and latency
    2. Application-level monitoring - encompasses several aspects; server time, server timecost, resources dedicated to each aspect will vary based on whether an application is read-heavy, write-heavy, or subject to rapid swings in traffic.
      1. Application warnings and errors (500-level HTTP errors)
      2. Application code performance
      3. Template rendering time
      4. Browser rendering time for the application
      5. Database querying performance


[1]: https://ai.stackexchange.com/questions/6855/thoughts-on-apple-mac-pro-vs-gcp-aws-for-deep-learning
[2]: https://datascience.stackexchange.c...card-to-make-deep-learning-with-a-macbook-pro
[3]:
 

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Your problem is a deprecated BootROM version. Fully read the first post of the thread MP5,1: What you have to do to upgrade to Mojave (BootROM upgrade instructions thread) to learn what you need to upgrade your BootROM, there are a lot of pitfalls.

macOS installer only has drivers for NVIDIA Kepler GPUs and won't work with Maxwell or Pascal. Install an Apple OEM GPU, upgrade your BootROM to MP51.0089.B00 then install the NVIDIA web drivers and finally the 1060.

The last macOS version that works with Maxwell and Pascal GPUs is 10.13.6, Mojave only supports Kepler.
 
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This is probably not the answer you want to hear. But, trying to do deep learning using Nvidia on MacOS it's a waste of time. All training is done on Linux, it's king. From large corporations to tiny startups. If they need Nvidia they are on Linux. Even Apple internally uses Linux/Nvidia for training...

If you want to just do inference. You can convert models to CoreML and thats reasonable to do. But you should either dual boot Linux or just build a dedicated DL machine for training.
 
I agree with teagls. It would be better and easier to just use Linux. For example, with the right distro, you can automatically get the latest Nvidia drivers. (Also, frankly, a 5,1 or any Mac Pro of that era is a terribly-inefficient way to play music.)

If you are going deep into deep learning, consider building a decent dedicated Linux box instead of upgrading an obsolete, highly inefficient and relatively slow computer. It would be far better supported and, with a reasonable budget, worlds faster. That speed is really needed.
 
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I am a virologist and use an Oxford Nanopore MinION to sequence the genomes of organisms. The software required to convert the signal from the MinION into DNA/RNA sequences leverages CUDA. I recently spent quite a bit of time getting a 12 core 5,1 Mac Pro to play nice with an Nvidia 1080 GTX. I have ended up using Ubuntu 16 and honestly, it was a bit of a pain in the ass. I currently only have a Ubuntu SATA drive installed as there are issues with anything else installed in the machine when it comes time to booting Ubuntu.

The Mac Pro EPI and requirement for an EFI flashed GPU makes things tricker and a bit more cumbersome than it should. I would have saved a few hours of hair pulling if I had simply started with a generic PC and built things from there.

My rig was a proof of concept that I could get CUDA working, so I used what I had with me at the time (I have 2 x Mac Pro's). Moving forward, a PC that doesn't have the PITA EFI of the Mac Pro is the way to go.
 
I agree with teagls. It would be better and easier to just use Linux. For example, with the right distro, you can automatically get the latest Nvidia drivers. (Also, frankly, a 5,1 or any Mac Pro of that era is a terribly-inefficient way to play music.)

If you are going deep into deep learning, consider building a decent dedicated Linux box instead of upgrading an obsolete, highly inefficient and relatively slow computer. It would be far better supported and, with a reasonable budget, worlds faster. That speed is really needed.

The collection is in excess of 34,000 songs and I'm not even touching a POS windows system after losing hundreds of hours a few years ago on their version. We totaled up all the lost hours, patching bugs and fixing memory leaks that we lost over 1,600 billable hours troubleshooting windows machines before we switched all to Macs. Fast forward six years running 100% mac, and we are down 19 hours total for issues. 11 of those hours are working on this mac pro, trying to figure out how to go back to high sierra.

I appreciate your comments, however... there doesn't seem to be much of an alternative for large music collections though. Can you provide an example of an alternative setup for a collection as large as mine?
Your problem is a deprecated BootROM version. Fully read the first post of the thread MP5,1: What you have to do to upgrade to Mojave (BootROM upgrade instructions thread) to learn what you need to upgrade your BootROM, there are a lot of pitfalls.

macOS installer only has drivers for NVIDIA Kepler GPUs and won't work with Maxwell or Pascal. Install an Apple OEM GPU, upgrade your BootROM to MP51.0089.B00 then install the NVIDIA web drivers and finally the 1060.

The last macOS version that works with Maxwell and Pascal GPUs is 10.13.6, Mojave only supports Kepler.


Thank you for the details, so what I am reading you say is that my build is possible... I just need to install them in the order you mentioned?
 
I am a virologist and use an Oxford Nanopore MinION to sequence the genomes of organisms. The software required to convert the signal from the MinION into DNA/RNA sequences leverages CUDA. I recently spent quite a bit of time getting a 12 core 5,1 Mac Pro to play nice with an Nvidia 1080 GTX. I have ended up using Ubuntu 16 and honestly, it was a bit of a pain in the ass. I currently only have a Ubuntu SATA drive installed as there are issues with anything else installed in the machine when it comes time to boot Ubuntu.

The Mac Pro EPI and requirement for an EFI flashed GPU makes things tricker and a bit more cumbersome than it should. I would have saved a few hours of hair-pulling if I had simply started with a generic PC and built things from there.

My rig was a proof of concept that I could get CUDA working, so I used what I had with me at the time (I have 2 x Mac Pro's). Moving forward, a PC that doesn't have the PITA EFI of the Mac Pro is the way to go.

Thanks, leon771, a chunk of the solutions we found came from research I did on gene expression and a machine learning algorithm we found to create a similar number like a SwissProt. It was quite a bit more verbose in diagnostics than Biopython so we are expanding upon that.

Would you be so kind as to share some of your notes for the 5,1 Ubuntu setup?

You are correct ubuntu is where most servers are set up for cloud storage so this will move me down the line towards creating the environment we will have online.
 
Your problem is a deprecated BootROM version. Fully read the first post of the thread MP5,1: What you have to do to upgrade to Mojave (BootROM upgrade instructions thread) to learn what you need to upgrade your BootROM, there are a lot of pitfalls.

macOS installer only has drivers for NVIDIA Kepler GPUs and won't work with Maxwell or Pascal. Install an Apple OEM GPU, upgrade your BootROM to MP51.0089.B00 then install the NVIDIA web drivers and finally the 1060.

The last macOS version that works with Maxwell and Pascal GPUs is 10.13.6, Mojave only supports Kepler.

So I've read through your post which is helpful and now I need to start it but my os install is corrupted I guess and the only way it loads is to that screen.

I'm quite confused as to how this happened but my goal is to just get a high sierra OS loaded and not sure how to do that. A new USB drive is coming tomorrow but I do have a 2.5" HD I can load stuff onto from my iMac.

Can you shed light or point to which step I should start first, seeing that mine is in a loop... again I'm lost in the trees?
 
Definitely - you don't find any problems with "Boot screens" in the PC world. That's a problem that Apple created for its users.

Hi Guys, The concept of using a pc sounds great until I load Windows and it can't function when I put 14 terabytes of data onto a program that has anything connected to windows. I'm in the reality of actual BIG DATA and this doesn't seem to be an arena that windows can support.

Can anybody point me to a tutorial or link to a "how to set up Linux on high sierra" that you recommend does a thorough job?
 
Hi Guys, The concept of using a pc sounds great until I load Windows and it can't function when I put 14 terabytes of data onto a program that has anything connected to windows.
I have Windows systems with multiple 96 TB disk arrays, and it works much better than Linux with far less data. (Put 20 million files in a directory on an NTFS filesystem, and it's sluggish but works. Do the same on an EXT4 filesystem and figure a week to do anything that touches that directory.)

(And much of this thread is about using Linux, not Windows. I use Windows for my clients to access my Linux systems running CUDA. Use the right tools for the job.)

And, by the way, 14 TB isn't big data - it easily fits on a single spinner. "Big data" is petabytes.
Can anybody point me to a tutorial or link to a "how to set up Linux on high sierra"
A nonsensical post. You don't run Linux on any version of Apple OSX.
 
A nonsensical post. You don't run Linux on any version of Apple OSX.

Ok let me clarify, I would agree that running Linux inside macOS is not good... I worded that wrong, what I meant was dual boot.

I am saying how can I dual boot macOS or Linux with ubuntu, I'm not even sure where to start but since I can do windows, mac dual boot I'm guessing a mac/Linux dual is possible... where can I find that? You seem to know Linux better than I so I'm asking for help.
 
Ok let me clarify, I would agree that running Linux inside macOS is not good... I worded that wrong, what I meant was dual boot.

I am saying how can I dual boot macOS or Linux with ubuntu, I'm not even sure where to start but since I can do windows, mac dual boot I'm guessing a mac/Linux dual is possible... where can I find that? You seem to know Linux better than I so I'm asking for help.

Dual boot without an EFI flashed GPU doesn’t really work.
Hence why I went with single Ubuntu boot on my 5,1 with a 1080 GTX.

I couldn’t get grub or rEFInd to function properly on my system.
I also found that when something went screwy with the nvidia drivers I had to reinstalll Ubuntu as the Mac didn’t allow me to enter any of the Linux recovery modes. I think this was likely for to not having a functional EFI GPU.
All the traditional key commands to get in to Ubuntu recovery modes didn’t work. Likewise getting to a basic CLI without nvidia drivers installed for troubleshooting.

Hence why I recommended going a cheap PC route. If you’re looking for an environment that is robust and you won’t spend a lot of time trouble shooting, then Linux on a Mac Pro isn’t for you.

Once it works, it works well. But if something software wise falls over it’s a world more pain than a PC would be.
 
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So I've read through your post which is helpful and now I need to start it but my os install is corrupted I guess and the only way it loads is to that screen.

I'm quite confused as to how this happened but my goal is to just get a high sierra OS loaded and not sure how to do that. A new USB drive is coming tomorrow but I do have a 2.5" HD I can load stuff onto from my iMac.

Can you shed light or point to which step I should start first, seeing that mine is in a loop... again I'm lost in the trees?
Read the first post again MP5,1: What you have to do to upgrade to Mojave (BootROM upgrade instructions thread), use the links there to download El Capitan or Sierra Mac App Store installers (don't need firmware upgrade to install, unlike High Sierra), make a createinstallmedia USB key, install a GPU with pre-boot configuration support on your Mac Pro, boot from the createinstallmedia USB key and install macOS.

After that you upgrade it to High Sierra, upgrading first to MP51.0089.B00 BootROM using the MAS High Sierra installer to do it.
 
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what deep learning library are you going to use?

We have evolved into an ensemble approach, but it includes the obvious choice of TensorFlow, PyTorch, Apache and then going homebrew from my training data set with a hybrid RNN.
 
I did a little digging after reading your comments and found this site that details, what I think you were referring to. Is this a decent representation of the process you are speaking of for a 5,1 Linux system?

Linux on 5,1 Mac

There is the other option as some of you mentioned which is using an old pc for the GPU but I'm way out of date of Windows, can any of you provide a link as a starter for Linux on pc? @leon771 @AidenShaw @Ph.D. @teagls
 
I did a little digging after reading your comments and found this site that details, what I think you were referring to. Is this a decent representation of the process you are speaking of for a 5,1 Linux system?

Linux on 5,1 Mac

There is the other option as some of you mentioned which is using an old pc for the GPU but I'm way out of date of Windows, can any of you provide a link as a starter for Linux on pc? @leon771 @AidenShaw @Ph.D. @teagls

I use Ubuntu 18.04, but thats just my preference. There are lots of other flavors of Linux. It's very easy to install. Just download the image file. Burn it to a USB using Etcher or any other imaging tool and then plug it in and boot from it.

 
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I use Ubuntu 18.04, but thats just my preference.
IMO Ubuntu is the best supported for ML - features and library updates appear first for Ubuntu. There are lots of differences between flavors of Linux, and that can lead to incompatibilities.

I always disable the builtin Nvidia driver and download the latest of both CUDA and the kernel device driver from Ubuntu.
 
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IMO Ubuntu is the best supported for ML - features and library updates appear first for Ubuntu. There are lots of differences between flavors of Linux, and that can lead to incompatibilities.

I always disable the builtin Nvidia driver and download the latest of both CUDA and the kernel device driver from Ubuntu.

I've had no luck getting the nVidia drivers installed under Ubuntu on a Mac Pro 5.1. YMMV.
 
I've had no luck getting the nVidia drivers installed under Ubuntu on a Mac Pro 5.1. YMMV.

I managed to get 410 installed and CUDA 10.1 on my 5,1

Lots of trial and error, reinstalling Ubuntu and constantly deactivating the Nouveau driver.
If the nvidia drivers update on my machine then I just get black screens that are not recoverable from.
 
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