Spyder: Segmentation fault (core dumped) when trying to start conda-installed spyder 3.2.8

[MattJEM]

Developer Note: *This issue is now resolved in Spyder >=3.3.0. Therefore, to fix the problem, just run conda update spyder from the command line (Anaconda Prompt if on Windows) to get the latest version, or pip install -U spyder if you don't have Anaconda.

If this doesn't work, then you are experiencing a different issue; try conda install pyqt=5.9 and conda install pyqt=5.6 to see if it fixes it.*

Problem Description

I have Spyder 3.2.8 installed through conda. Two days ago it worked, today I am getting a segmentation fault:

$ spyder
Segmentation fault (core dumped)

What steps will reproduce the problem?

1. Type in "spyder" at the command line.

What is the expected output? What do you see instead?

I expect Spyder to start. Instead I get Segmentation fault (core dumped)

Paste Traceback/Error Below (if applicable)

There's no traceback or error, just Segmentation fault (core dumped)

Package Versions

• Spyder: 3.2.8 (installed with conda)
• Python: 2.7.14
• Qt: 5.6.2
• PyQt: 5.6.0
• Operating System: Ubuntu 16.04 LTS

Dependencies

I can't start Spyder.

---

I've gone through the troubleshooting document and have tried the various suggestions within including uninstalling and reinstalling through conda. I haven't tried installing via source, I'm hoping there is something else going on that won't require that.

---

Update: aaaaaand ten minutes later it's working. I did absolutely nothing different since posting this question, I could not tell you what changed.

[ccordoba12]

Update: aaaaaand ten minutes later it's working. I did absolutely nothing different since posting this question, I could not tell you what changed.

Good to know! Please let us know if you are able to reproduce the conditions that generated the initial segfault in this same issue.

I'm closing it for now because we can't really do something about this.

[CAM-Gerlach]

Thanks for reporting. If it re-occurs, please try the steps listed in the Spyder Troubleshooting Guide, specifically the Basic First Aid and Emergency CPR sections, which resolve the great majority of Spyder installation issues.

If it does happen again and you can isolate why, please describe in detail the circumstances in which the error occurred, and post the information listed in relevant subsection of the Calling for Help section as a comment to this issue, and we'll try to help if we can.

[lawpdas]

I have same problem. Just update qt&pyqt 5.6-->5.9 .

[MattJEM]

Unfortunately RStudio runs in 5.6. The problem has not recurred, but just in case I went ahead and created a separate environment with 5.9.

[ccordoba12]

This problem will be solved in our 3.3 version. In the meantime, please downgrade to Qt/PyQt 5.6

[addyblue]

same problem with me after downloading first time it never launched.

[CAM-Gerlach]

@addyblue Try conda install pyopengl

[deciomoritz]

@CAM-Gerlach solution worked for me.

[akriti22]

@addyblue I have tried this command "conda install pyopengl" but nothing happened...
again and again spyder crashed....

[CAM-Gerlach]

@akriti22 Make sure you've first activated the environment in which Spyder is installed (if its not the base one), and that you are running the install command in a system console (specifically, the Anaconda Prompt if on Windows).

Other than that, you'll need to be way more specific if we're to be able to help you. What operating system and version? What Spyder version? How did you install it? What versions of qt, pyqt, and python do you have (you can read these off conda list <insert-package-name-here>)? What do you mean by

but nothing happened...

You should have gotten some message when you tried to install pyopengl, positive or negative.

Also, please try the steps listed in the Spyder Troubleshooting Guide, specifically the Basic First Aid and Emergency CPR sections, which resolve the great majority of Spyder installation issues.

[Samarth-Tripathi3]

Having the same issue. Fresh install of ubuntu and conda. Spyder: Segmentation fault, core dumped

[ccordoba12]

@Samarth-Tripathi3, this should be solved by doing

conda install pyopengl

EDIT: Now that Spyder >= 3.3.0 is released with the built-in fix for this, the current solution that should fix this is now just conda update spyder.

[Prosimio]

conda install pyopengl works for me too

[mostafaGwely]

conda install pyopengl works for me too

[rajendraarora16]

conda install pyopengl worked for me too.

[yangzhaonan18]

conda install pyopengl worked for me too.

[CAM-Gerlach]

Thanks all for your reports and your patience. Just FYI, we are well aware that's the solution and its fixed with Spyder 3.3.0 now, so no need to keep posting it further.

[Ovesta]

For me worked #conda install pyqt
(Use conda install pyqt to get these #Python bindings for the Qt framework.)

[CAM-Gerlach]

@Ovesta If you didn't have PyQt in your environment, that's another issue entirely...it should have been automatically installed along with Spyder if following one of our recommended install methods (particularly Anaconda, as you've apparently used). Glad you've got Spyder working though.

For the record, the fix for the pyopengl issue discussed here is now released to the broader public with Spyder 3.3.0.

[kamrankh068]

conda install pyopengl
it is not work for me in ubuntu 18.04

[CAM-Gerlach]

@kamrankh068 Install the new version of Spyder (3.3.0) if you haven't already, preferably in a new/clean environment to isolate other potential causes with conda install spyder . If that doesn't help, please try the steps listed in the Spyder Troubleshooting Guide, specifically the Basic First Aid and Emergency CPR sections, which resolve the great majority of Spyder installation issues. Thanks, and best of luck!

[hammad97]

conda install pyopengl
worked for me.
Thankss.

[wtrungvu]

Thank you!
worked for me
conda install pyopengl

[Ceasar9]

it does not work on ubuntu 18.04.1:
conda install pyopengl

[CAM-Gerlach]

@Ceasar9 You shouldn't need to install pyopengl, as Spyder has included the fixes built in since 3.3.0 (the current version is 3.3.1). You can update with conda update spyder. Also, you could try downgrading Qt with conda install pyqt=5.6, as well as the other fixes suggested in the Spyder Troubleshooting Guide, specifically the Basic First Aid and Emergency CPR sections,

[Ceasar9]

@CAM-Gerlach Fantastic!! downgrading Qt works very well. thx!
conda install pyqt=5.6

[SatishTelaprolu]

it worked for me on Ubuntu 18.04 LTS
conda install pyopengl

[CAM-Gerlach]

@SatishTelaprolu As we've said several times, the real fix is to just update to Spyder >=3.3.0 (the current version is 3.3.1), which resolves the issue as well as patches other bugs and adds a number of enhancements, without the need for this workaround. Thanks.

[kamrankh068]

yes it does not work so what i do

On Fri, 24 Aug 2018 at 04:41, Behzad Sezari [e-mail]
wrote:

it does not work on ubuntu 18.04.1:
conda install pyopengl

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/spyder-ide/spyder/issues/6908#issuecomment-415601866,
or mute the thread
https://github.com/notifications/unsubscribe-auth/Ak_2DM2FernlWbV3qg6YWOvco6DtfSnTks5uTzajgaJpZM4TLQyv
.

[kamrankh068]

see this picture and please tell me what i do

On Fri, 3 Aug 2018 at 12:50, C.A.M. Gerlach [e-mail]
wrote:

@kamrankh068 https://github.com/kamrankh068 Install the new version of
Spyder (3.3.0) if you haven't already, preferably in a new/clean
environment to isolate other potential causes with conda install spyder .
If that doesn't help, please try the steps listed in the Spyder
Troubleshooting Guide
https://github.com/spyder-ide/spyder/wiki/Troubleshooting-Guide-and-FAQ,
specifically the Basic First Aid
https://github.com/spyder-ide/spyder/wiki/Troubleshooting-Guide-and-FAQ#basic-first-aid-general-troubleshooting
and Emergency CPR
https://github.com/spyder-ide/spyder/wiki/Troubleshooting-Guide-and-FAQ#emergency-cpr-spyder-wont-launch
sections, which resolve the great majority of Spyder installation issues.
Thanks, and best of luck!

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/spyder-ide/spyder/issues/6908#issuecomment-410167821,
or mute the thread
https://github.com/notifications/unsubscribe-auth/Ak_2DD5tCiu1t7vXAlWZXVbYKZh5_z02ks5uM_mwgaJpZM4TLQyv
.

[Ceasar9]

@kamrankh068

how about downgrading Qt :
conda install pyqt=5.6

[kamrankh068]

thanx it work😊

On Sat, Sep 8, 2018, 6:50 PM Behzad Sezari [e-mail] wrote:

@kamrankh068 https://github.com/kamrankh068

how about downgrading Qt :
conda install pyqt=5.6

—
You are receiving this because you were mentioned.
Reply to this email directly, view it on GitHub
https://github.com/spyder-ide/spyder/issues/6908#issuecomment-419641631,
or mute the thread
https://github.com/notifications/unsubscribe-auth/Ak_2DIKKWEKOl7xJDajsA7K8OpNywstwks5uY8QjgaJpZM4TLQyv
.

[aliabavi]

I have the same issue (segment fault when try running spyder). I don't use conda. Do you have suggestions?

[CAM-Gerlach]

@aliabavi We recommend you use Anaconda, since pip is for expert users only who are able to solve the resulting install problems on their own. In any case, if its the same issue, updating Spyder should fix it. Other than that, please try the steps listed in the Spyder Troubleshooting Guide, specifically the Basic First Aid and Emergency CPR sections, which resolve the great majority of Spyder installation issues.

[jupiterjosh]

Fyi same issue as of 2018-01-10 -- installing pyopengl fixed it.

Fresh install of Linux Mint 19.
Fresh install of Anaconda 4.5.11. (all default parms/locations; did not sudo install)
Run spyder, seg fault.

[CAM-Gerlach]

@jupiterjosh As we've mentioned previously, this was fixed many months ago in Spyder 3.3.0, and so to fix it you should simply update Spyder (e.g. conda update spyder). I added a prominent note to the top of the OP to try to make sure its much harder to miss, since its a fairly long thread.

Fresh install of Anaconda 4.5.11. (all default parms/locations; did not sudo install)

FYI, this must be substantially older than the current, which would naturally contain a quite old version of Spyder; the most recent version of Anaconda is 5.2.0 released several months ago by now.

[jupiterjosh]

@CAM-Gerlach conda update spyder only updates Spyder to version 3.2.8 as of Anaconda version 5.3 for Python 3.7 (which Continuum packaged on 9/27). I had incorrectly reported my anaconda version in the previous post (4.5.11 was my conda version).

Since Spyder recommends not using pip to update spyder (as per the "New Update is Available!" gui window) for Anaconda installations, the only recourse is to pip install pyopengl.

[CAM-Gerlach]

conda update spyder only updates Spyder to version 3.2.8 as of Anaconda version 5.3 for Python 3.7

Okay, thanks for the additional information @jupiterjosh . Something weird's going on with your install, as this certainly shouldn't be the case. On Windows (8.1 x64), I created a fresh Python 3.7 environment and ran conda install spyder, and got 3.3.1 (as I have several times before); I also tried a full anaconda install (conda install anaconda) and that gave me Spyder 3.3.1 as well; as this is the same Anaconda and Python version and the build number is zero, it must be the same build you downloaded. Therefore, if you installed 5.3.0 fresh, Spyder 3.3.1 should have been installed be default; if you did conda update spyder or conda update anaconda from a 5.2.0 install, I'm not sure why it wouldn't have updated Spyder to 3.3.1 since it is hard-pinned to that version and the install would fail otherwise, unless there is a bug, inconsistency or pinning issue on your particular platform.

Are you sure you have Spyder 3.2.8 still in the environment you're trying to update? Are you sure you're running Spyder from that environment? What OS and bitness are you on? What were the exact commands/steps you used to update anaconda and spyder? Can you try creating a fresh environment just for Spyder (conda create -n your-env-name-here python=3.7, activate it then conda install spyder)?

[ccordoba12]

@CAM-Gerlach, I think @jupiterjosh means that the default Spyder version that comes with Anaconda 5.3 is 3.2.8, not 3.3.1.

[CAM-Gerlach]

@ccordoba12 , I don't think that's the case. since @jupiterjosh explicitly ran conda update spyder as stated above, and Anaconda 5.3 does come with 3.3.1 (as confirmed by both downloading the requires file in the tar package, and by test installing anaconda 5.3.0 in a fresh Python 3.7 environment). That's why I'm not sure what's preventing Spyder from being updated to 3.3.1, unless there's something user-specific going on.

[jupiterjosh]

@CAM-Gerlach, @ccordoba12, sorry -- I messed up. I thought I installed Anaconda 5.3 but I only had 5.2 installed. The package timestamp for Anaconda 5.3 on Continuum's repo website is 09/27 and since I downloaded Anaconda on 09/30, I thought that was the version I had. I pulled my installer out of the Trash and realized it was version 5.2 (Anaconda3-5.2.0-Linux-x86_64.sh).

So when I had originally tried to update Spyder I was actually running a fresh Anaconda 5.2 install. I executed (conda update conda, conda update spyder) and conda reported that I already had the latest version of Spyder which was version 3.2.8. I was able to verify the version by opening Spyder and going to Help->About.

I didn't realize that I didn't have Anaconda 5.3 till I started writing this post, so I went ahead and updated anaconda (conda update anaconda) and it upgraded Spyder to 3.3.1 as indicated.

Thanks -- sorry about the run-around -- I was sure I had version 5.3 running.

[CAM-Gerlach]

@jupiterjosh Perhaps Spyder is being pinned to the version specified in the anaconda metapackage. If so, you could uninstall it with conda uninstall anaconda (which would basically just remove the pinning), or you could create a fresh environment just for Spyder with the commands specified at the end of my first post to you above, and use spyder from there (launching via Anaconda Navigator or the command line spyder rather than the shortcut to make sure it launches from the correct environment).

[JoaoGF21]

For me worked #conda install pyqt
(Use conda install pyqt to get these #Python bindings for the Qt framework.)

It worked for my too.
Spyder was working in the base of conda, but it was not working in the environment.

[Paritosh535]

conda install pyopengl
it is working :)

[CAM-Gerlach]

conda install pyopengl

@Paritosh535 As we've stated numerous times in this thread and in large, bold type at the top of this thread, you should no longer need to install pyopengl, and instead the proper solution is to simply update Spyder, e.g. with conda update spyder. I've edited the one developer comment from several months ago that stated the fix as conda install pyopengl to reflect this current situation; otherwise I'm not sure how people are still getting the out of date solution. Thanks.

[resperic]

So many times above it's been stated "simply update Spyder 3.3.0", but I'm getting the segmentation fault error with Spyder 3.3.2 (in Ubuntu 18.04).

[CAM-Gerlach]

@resperic Then its likely a different issue, then. Try (in order; assuming you're using conda as we recommend):

1. conda update pyqt qt qtpy
2. conda install pyopengl
3. spyder --opengl=OPENGL_IMPLELENTATION with each of software, desktop and gles
4. conda install pyqt=5.6 and try the different --opengl implemenations

5. Create a new clean environment for Spyder, with

   conda create -n spyder-env python=3.6
   source activate spyder-env
   spyder
   

   and if that doesn't work, you can retry the above steps.

6. Do a clean uninstall/reinstall of Anaconda/Miniconda

[resperic]

I tried what CAM-Gerlach suggested.

1. & 2. both resulted in "All requested packages already installed".

2. spyder --opengl=software
   This one resulted in "Segmentation fault", interestingly.

Perhaps I should jump to 6., uninstall/reinstall...

[CAM-Gerlach]

Did you try spyder --opengl=desktop and spyder --opengl=gles? If neither of those do it, there is a good chance conda install pyqt=5.6 will fix it. Failing that, creating a clean environment for Spyder is almost as good as reinstalling, but far faster.

Perhaps I should jump to 6., uninstall/reinstall...

I ordered the steps that way for a reason, putting those with the highest probability of fixing the problem relative to their time taken and impact on your environment first; therefore, you should complete them in order. Furthermore, reinstalling might not fix it, while one of the other ones might. You should rule out all of them before reinstalling.

[resperic]

Thanks CAM-Gerlach, for helping!

OK I got "Segmentation fault" for spyder --opengl=desktop and spyder --opengl=gles both. When I tried conda install pyqt=5.6, "All requested packages already installed".

5 worked - I was able to fun Spyder; however, there are lots of things I need to conda install. The question is, will it still run after I load the entire environment?

We'll see...

[CAM-Gerlach]

When I tried conda install pyqt=5.6, "All requested packages already installed".

@resperic Oh, I assumed you had 5.9 since I had you run conda update pyqt qt qtpy, correct? Go back to your previous environment (not the new one you created) and try conda install pyqt=5.9. Most likely, your new environment using that latest version is the reason why its working.

Its possible you may have been mixing packages from conda-forge and defaults, which is not supported and can cause segfaults like that. If the above still doesn't work, please post the output of conda list in your previous/main environment (not the new one) inside a <details> block, like this:

<details>
YOUR CONDA LIST OUTPUT
</details>

[resperic]

When I ran conda instrall pyqt=5.9 the resulting error message seemed relevant to my problem:

`Solving environment: failed

UnsatisfiableError: The following specifications were found to be in conflict:

• defaults/linux-64::qt==5.6.3=h8bf5577_3
• pyqt=5.9 -> qt[version='5.9.*,>=5.9.6,<5.10.0a0']
  Use "conda info " to see the dependencies for each package.`

[CAM-Gerlach]

It looks like something is pinning your Qt version to 5.6.x. In your freshly created Spyder environment, try running conda list qt and pasting the results here. Also, in your old environment, try conda install -c defaults pyqt=5.9 qt=5.9 and report the results. Finally, make sure to paste your conda list output of your old environment in a <details> block as described above.

If things work fine in your new environment, you can just install the basics there (numpy, pandas, matplotlib, and scipy, as well as cython and sympy if you use either), and then set your Python interpreter under Preferences > Python interpreter > Use the following Python interpreter in your working copy of Spyder to the python.exe of your previous work environment with all your packages, e.g. under Anaconda3/envs/base/python.exe (replace base with whatever your environment is named). Then, new Consoles will open in that environment, and you will be able to use it just as if you'd launched Spyder from there.

You can change it at any time and have Consoles open from multiple environments simultaniously and tab between them at will, and you can do the same thing to work in other Python installations, virtualenvs/venvs, conda environments, system Python, other Python installs and more, so long as they have the spyder-kernels package installed so Spyder can talk to them.

[kalkidanRas]

"conda install pyopengl " worked for me too on Ubuntu 18.04 LTS.

[CAM-Gerlach]

@kalkidanRas Did you read my comment in large bold type at the very top of the first post in this thread?

[buzonjl]

pyqt work for me too

[faraday702]

Update pyqt.
Happened to me with spyder 4 update as well.

[mahdipoori]

conda install pyqt=5.6
It is work for me
thanks