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mrirecon / bart

BART: Toolbox for Computational Magnetic Resonance Imaging
https://mrirecon.github.io/bart/
BSD 3-Clause "New" or "Revised" License
294 stars 163 forks source link

Issues with making bart v 0.8.00 #302

Closed natalia-dubljevic closed 1 year ago

natalia-dubljevic commented 1 year ago

I thought it would be an easier installation this time since I am now using WSL instead of Windows, but there still seems to be many issues. For reference, I am using WSL2 with Ubuntu 22.04.02

I followed the commands verbatim on this page: https://mrirecon.github.io/bart/installation.html. I have been trying to install v0.8.00

The issues began when I got around to the make command.

Error #1:
image Seems that the bart file can't find fftw3.h. I looked around and, well, I couldn't find it anywhere either. So I commented out that line in the bart file and tried again.

Error #2: Lots of warnings showed up about some inconsistencies in the code, and then I got this: image I wasn't able to find this either when I looked around. I figured since I was this far, let's not include cblas.h in the blas file

Error #3: A long list of errors regarding no cblas came about that I assume are due to my removal of the line that led to error #2.

I've run out of ideas to make this installation work, and I don't know where the issue stems from. This has been an incredibly difficult package to make!

jtamir commented 1 year ago

Hi, could you please try these instructions? https://drive.google.com/file/d/1A64wD-lemHWLyT8C8m4KSXTnyKgRJ8Fp/view?usp=drivesdk

Let us know if you still run into issues.

Thanks

Jon www.jtsense.com

From: Natalia @.> Sent: Tuesday, March 14, 2023 1:07:40 PM To: mrirecon/bart @.> Cc: Subscribed @.***> Subject: [mrirecon/bart] Issues with making bart v 0.8.00 (Issue #302)

I thought it would be an easier installation this time since I am now using WSL instead of Windows, but there still seems to be many issues. For reference, I am using WSL2 with Ubuntu 22.04.02

I followed the commands verbatim on this page: https://mrirecon.github.io/bart/installation.htmlhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fmrirecon.github.io%2Fbart%2Finstallation.html&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=dbPwSyeJcUmy6lFfi9FBFFJ4Msr4XGdUOw4aPJmPbRU%3D&reserved=0. I have been trying to install v0.8.00

The issues began when I got around to the make command.

Error #1https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmrirecon%2Fbart%2Fpull%2F1&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=VRid7otg%2BWysuj7Sw8Pe0VlmtMqjmMrmhIpXUB9dnIM%3D&reserved=0: [image]https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F59702377%2F225095939-5b9076aa-f874-4b2e-8cc3-253e2f6a05fa.png&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=4yCfYba6vtYcUyUAe35JIl4bDC7OjS9rrShAHr23j9E%3D&reserved=0 Seems that the bart file can't find fftw3.h. I looked around and, well, I couldn't find it anywhere either. So I commented out that line in the bart file and tried again.

Error #2https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmrirecon%2Fbart%2Fpull%2F2&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RQxSVZiQ%2BQAsB%2BEC4mO9QHIcxVqRWSNQTsNLzDKxUNg%3D&reserved=0: Lots of warnings showed up about some inconsistencies in the code, and then I got this: [image]https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fuser-images.githubusercontent.com%2F59702377%2F225096923-42eeba1f-e01b-4718-a9f5-c7f92a0cf195.png&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=liqZQ%2B%2Bi1yvSKv%2BMU3g4AVqIZs1ahMzXOyJj3hcPMoE%3D&reserved=0 I wasn't able to find this either when I looked around. I figured since I was this far, let's not include cblas.h in the blas file

Error #3https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmrirecon%2Fbart%2Fissues%2F3&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=CIGDbN5m%2BikL5IuIc%2FWIuuh%2BU6MMm2S97elm5P%2FBfLI%3D&reserved=0: A long list of errors regarding no cblas came about that I assume are due to my removal of the line that led to error #2https://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmrirecon%2Fbart%2Fpull%2F2&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=RQxSVZiQ%2BQAsB%2BEC4mO9QHIcxVqRWSNQTsNLzDKxUNg%3D&reserved=0.

I've run out of ideas to make this installation work, and I don't know where the issue stems from. This has been an incredibly difficult package to make!

— Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmrirecon%2Fbart%2Fissues%2F302&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=ZrtWmjAAAm0IN3cikAl1VBEcdscf69NM6Dcqh7QcWkI%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACCQC2Y6OHVSY3PXZBIZIODW4CXWZANCNFSM6AAAAAAV2ZIGOE&data=05%7C01%7C%7Ce6f8ae6a60564b8fbdcd08db24b701cc%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144140665641460%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=aQeFX6j4RbrFjiTlDPGGU8kOoTGIjIxcjLhyAZMuLDk%3D&reserved=0. You are receiving this because you are subscribed to this thread.Message ID: @.***>

natalia-dubljevic commented 1 year ago

Hi Jon,

That seems to have worked! Is there any way these instructions could be made public or more easily found? They don't appear in the README file or elsewhere on the site from what I can tell.

jtamir commented 1 year ago

Yes we are in the process of updating it. Apologies that it wasn’t more clear.

Sincerely

Jon www.jtsense.com

From: Natalia @.> Sent: Tuesday, March 14, 2023 3:45:07 PM To: mrirecon/bart @.> Cc: Jon Tamir @.>; Comment @.> Subject: Re: [mrirecon/bart] Issues with making bart v 0.8.00 (Issue #302)

Hi Jon,

That seems to have worked! Is there any way these instructions could be made public or more easily found? They don't appear in the README file or elsewhere on the site from what I can tell.

— Reply to this email directly, view it on GitHubhttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fmrirecon%2Fbart%2Fissues%2F302%23issuecomment-1468816346&data=05%7C01%7C%7C8f85b8793247414a521108db24ccffd1%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144235155796410%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=lKJou9HH29fFbnzfAr5MqWw8%2B3x8IUnA5gzFEhUciQk%3D&reserved=0, or unsubscribehttps://nam12.safelinks.protection.outlook.com/?url=https%3A%2F%2Fgithub.com%2Fnotifications%2Funsubscribe-auth%2FACCQC2373KW75P5NCFVO3PLW4DKFHANCNFSM6AAAAAAV2ZIGOE&data=05%7C01%7C%7C8f85b8793247414a521108db24ccffd1%7C31d7e2a5bdd8414e9e97bea998ebdfe1%7C0%7C0%7C638144235155796410%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000%7C%7C%7C&sdata=uugR99emieOr3bTE%2F1tqF9tanHnmyH8yZOdhCcEyB7k%3D&reserved=0. You are receiving this because you commented.Message ID: @.***>

uecker commented 1 year ago

I wonder why the original instructions did not work? They include the commands for installing fftw3 and blas. Was there an error before? For Ubuntu there is also a pre-compiled package distributed with Ubuntu you can just install.

natalia-dubljevic commented 1 year ago

I'm not sure...when I installed fftw3 and blas, some warnings came up, but it didn't appear to be anything serious. Unfortunately, I don't remember what the warnings were, and can't seem to recreate them on my current device. I didn't notice the pre-compiled package-- I'll try it out if I need to install bart on another Linux system!