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kushalkolar / MESmerize

Platform for Calcium Imaging analysis. DEPRECATED.
GNU General Public License v3.0
58 stars 14 forks source link

Help with VM installation #65

Closed AyusoAa closed 2 years ago

AyusoAa commented 2 years ago

System information

  1. OS - Windowa 10
  2. CPU - Intel(R) Xeon (R) X 5650 - 12 cores and 24 logical processors
  3. RAM - 96GB
  4. HDD

Hi all, I am trying to use mesmerize in the VM provided in the repository. I installed Oracle Virtual box, and downloaded the file containing the mesmerize VM. I could import and launch the VM, which has the venv corresponding to mesmerize, as well as the test data (see screenshots). image However, when double clicking in the mesmerize desktop icon, it does not launch. It does not launch either when I try to call it from the terminal. A terminal window pops up, but then it closes and the program does not launch. image I tried installing the VM again, and encountered the same issue. This is the configuration of the VM I installed: image image image image image image image

Please let me know if you'd like to see some more of the settings. Thank you in advance!

kushalkolar commented 2 years ago

@AyusoAa thanks for providing details!

  1. Can you make sure that you downloaded mesmerize-v060-2-vm.ova and not the older version?
  2. What output do you get when you just call mesmerize in the terminal?
  3. What output do you get if you call /home/user/bin/mesmerize in the terminal?
AyusoAa commented 2 years ago

I downloaded the correct version. This is the output: image

kushalkolar commented 2 years ago

Can you make sure that all virtualization features are enabled in your BIOS?

kushalkolar commented 2 years ago

@AyusoAa Looked into this a bit more and my best guess is that your CPU is too old, it was released in 2010 and doesn't support newer instruction sets. An i7 which is a few years old, even with just 4 or 6 cores, will probably be faster than a 10 year old Xeon.

AyusoAa commented 2 years ago

Alright. Thanks for looking it up. Do you think Mesmerize installed through a conda environment will give problems in such a computer?

kushalkolar commented 2 years ago

Probably, many of the underlying math libraries will use instructions available on more modern hardware for speed. I wouldn't use a 10 year old computer for it anyways. A newer computer with fewer cores will be much faster.

kushalkolar commented 2 years ago

Closing, open a new issue if you have problems with an installation on a different computer.

Dong0716 commented 2 years ago

I just ran into the same problem, but my GPU is i9, is there a way to fix this issue?

kushalkolar commented 2 years ago

Can you please supply all your system info

On Fri, Feb 11, 2022, 07:32 Clay @.***> wrote:

I just ran into the same problem, but my GPU is i9, is there a way to fix this issue?

— Reply to this email directly, view it on GitHub https://github.com/kushalkolar/MESmerize/issues/65#issuecomment-1036166720, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRCP7RD2IEEV27P6I7DU2T6WFANCNFSM5FANU6ZA . You are receiving this because you modified the open/close state.Message ID: @.***>

Dong0716 commented 2 years ago

Windows 10 11th Gen Intel(R) Core(TM) i9-11950H @ 2.60GHz 2.61 GHz 32GB RAM 64x

Thank you!

kushalkolar commented 2 years ago

Can you please follow these steps:

  1. What output do you get when you just call mesmerize in the terminal?
  2. What output do you get if you call /home/user/bin/mesmerize in the terminal?

Can you give me the output of lscpu in the VM terminal.

Can you also post your VM configuration.

Dong0716 commented 2 years ago

Hi, Here is the output of the terminal: image

VM configuration: image image image image image image image image image

Much appreciated for help!

kushalkolar commented 2 years ago

So the issue is that avx isn't showing up in your CPU flags (as shown by lscpu).

Can you use CPU-Z on your Windows host and see what's under "Instructions", (post a screenshot) it should look something like this for an i9-11950H and AVX should be listed. If it's not listed it's probably disabled in the BIOS.

image

Dong0716 commented 2 years ago

image So it looks like this, with AVX being listed. What should I do next?

kushalkolar commented 2 years ago

For some reason the VM isn't seeing the avx features of the CPU, this might help: https://stackoverflow.com/questions/65780506/how-to-enable-avx-avx2-in-virtualbox-6-1-16-with-ubuntu-20-04-64bit

Might be easier to install it on your host machine.

On Mon, Feb 14, 2022, 07:57 Clay @.***> wrote:

[image: image] https://user-images.githubusercontent.com/87111861/153863096-7c26d0fe-1b76-4805-befa-a08980248f4e.png So it looks like this, with AVX being listed. What should I do next?

— Reply to this email directly, view it on GitHub https://github.com/kushalkolar/MESmerize/issues/65#issuecomment-1039021822, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACHXXRARLK2N7NRGWPX66MLU3DXPXANCNFSM5FANU6ZA . You are receiving this because you modified the open/close state.Message ID: @.***>