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runtime error for google colab code

Open lalalalala-ai opened this issue 9 months ago • 4 comments

dear sir,

I run your colab code but i was given the errors like below at install dependency step.i also ran your colab code one week ago and at that time everything looks fine. i wonder whether you did some updates or do you have some suggestions to fix it?

Found existing installation: jax 0.5.2 Uninstalling jax-0.5.2: Successfully uninstalled jax-0.5.2 Found existing installation: jaxlib 0.5.1 Uninstalling jaxlib-0.5.1: Successfully uninstalled jaxlib-0.5.1 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 87.3/87.3 MB 8.1 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.2/2.2 MB 17.3 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 86.1/86.1 MB 8.0 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 15.5/15.5 MB 2.1 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100.8/100.8 MB 1.2 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 77.9/77.9 kB 2.0 MB/s eta 0:00:00 Preparing metadata (setup.py) ... done Building wheel for ml-collections (setup.py) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 371.0/371.0 kB 8.3 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 2.4/2.4 MB 39.8 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 105.1/105.1 MB 8.0 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 4.7/4.7 MB 31.5 MB/s eta 0:00:00 Installing build dependencies ... done Getting requirements to build wheel ... done Preparing metadata (pyproject.toml) ... done Building wheel for pandas (pyproject.toml) ... done ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 3.1/3.1 MB 7.9 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 85.3/85.3 kB 2.1 MB/s eta 0:00:00 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 152.8/152.8 kB 2.7 MB/s eta 0:00:00 ERROR: Ignored the following yanked versions: 1.11.0, 1.14.0rc1 ERROR: Ignored the following versions that require a different python version: 1.6.2 Requires-Python >=3.7,<3.10; 1.6.3 Requires-Python >=3.7,<3.10; 1.7.0 Requires-Python >=3.7,<3.10; 1.7.1 Requires-Python >=3.7,<3.10; 1.7.2 Requires-Python >=3.7,<3.11; 1.7.3 Requires-Python >=3.7,<3.11; 1.8.0 Requires-Python >=3.8,<3.11; 1.8.0rc1 Requires-Python >=3.8,<3.11; 1.8.0rc2 Requires-Python >=3.8,<3.11; 1.8.0rc3 Requires-Python >=3.8,<3.11; 1.8.0rc4 Requires-Python >=3.8,<3.11; 1.8.1 Requires-Python >=3.8,<3.11 ERROR: Could not find a version that satisfies the requirement scipy==1.7.3 (from versions: 0.8.0, 0.9.0, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4, 1.6.0, 1.6.1, 1.9.0rc1, 1.9.0rc2, 1.9.0rc3, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.10.0rc1, 1.10.0rc2, 1.10.0, 1.10.1, 1.11.0rc1, 1.11.0rc2, 1.11.1, 1.11.2, 1.11.3, 1.11.4, 1.12.0rc1, 1.12.0rc2, 1.12.0, 1.13.0rc1, 1.13.0, 1.13.1, 1.14.0rc2, 1.14.0, 1.14.1, 1.15.0rc1, 1.15.0rc2, 1.15.0, 1.15.1, 1.15.2) ERROR: No matching distribution found for scipy==1.7.3 ERROR: Could not find a version that satisfies the requirement tensorflow==2.11.0 (from versions: 2.12.0rc0, 2.12.0rc1, 2.12.0, 2.12.1, 2.13.0rc0, 2.13.0rc1, 2.13.0rc2, 2.13.0, 2.13.1, 2.14.0rc0, 2.14.0rc1, 2.14.0, 2.14.1, 2.15.0rc0, 2.15.0rc1, 2.15.0, 2.15.0.post1, 2.15.1, 2.16.0rc0, 2.16.1, 2.16.2, 2.17.0rc0, 2.17.0rc1, 2.17.0, 2.17.1, 2.18.0rc0, 2.18.0rc1, 2.18.0rc2, 2.18.0, 2.18.1, 2.19.0rc0, 2.19.0) ERROR: No matching distribution found for tensorflow==2.11.0 ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 29.4/29.4 MB 42.9 MB/s eta 0:00:00

lalalalala-ai avatar Mar 15 '25 15:03 lalalalala-ai

Hi,

I don't think this should prevent the run? Do you not get any output?

patrickbryant1 avatar Mar 16 '25 16:03 patrickbryant1

No. Firstly, the installation could not be done correctly. It said the couldn’t find spicy and tensorflow at the required version. After I removed the version require, they are giving error messages when I run your prediction code part. Saying the jax version problems. So no output. But the thing wired me most is that I run your colab code like one week ago. I am pretty sure the code is fine at that time. Could you try to run it again?

More details:

if i remove the version requirement for tensorflow and scipy as below. i got error message like below. i also tried a few different jax versions. but i didnt got anyone working .


AttributeError Traceback (most recent call last) in <cell line: 0>() 25 26 ---> 27 from mc_design_colab import main 28 MAX_RECYCLES=8 #max_recycles (default=3) 29 MODEL_NAME='model_1' #model_1_ptm

8 frames /usr/local/lib/python3.11/dist-packages/jax/_src/deprecations.py in getattr(name) 52 message, fn = deprecations[name] 53 if fn is None: # Is the deprecation accelerated? ---> 54 raise AttributeError(message) 55 warnings.warn(message, DeprecationWarning, stacklevel=2) 56 return fn

AttributeError: jax.interpreters.xla.xe was removed in JAX v0.4.36. Use jax.lib.xla_extension instead. On Sun, Mar 16, 2025 at 12:56 PM Patrick Bryant @.***> wrote:

Hi,

I don't think this should prevent the run? Do you not get any output?

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Hi,

I don't think this should prevent the run? Do you not get any output?

— Reply to this email directly, view it on GitHub https://github.com/patrickbryant1/EvoBind/issues/34#issuecomment-2727541350, or unsubscribe https://github.com/notifications/unsubscribe-auth/BKRIM5RFTVNN4SPAOXL3ODD2UWULRAVCNFSM6AAAAABZCR4XW6VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDOMRXGU2DCMZVGA . You are receiving this because you authored the thread.Message ID: @.***>

lalalalala-ai avatar Mar 16 '25 17:03 lalalalala-ai

Hi,

I think there are some updates from Google. We will look into it and provide a fix in the coming weeks.

Best,

Patrick

patrickbryant1 avatar Mar 22 '25 15:03 patrickbryant1

Hi,

It should work now - please try.

Best,

Patrick

patrickbryant1 avatar Apr 14 '25 11:04 patrickbryant1

Hi,

I think there are some updates from Google. We will look into it and provide a fix in the coming weeks.

Best,

Patrick

I just tried it again, but it's still not working. The issue seems to be unresolved. Could you please check it again? Thanks for your help!

puzhongji-enzymedesign avatar Jun 13 '25 02:06 puzhongji-enzymedesign

I checked - it works. I think that maybe you are not restarting the runtime after installation? I have added a note about this. "After it finishes (the play button wheel stops spinning) do: Runtime > Restart session (above)."

patrickbryant1 avatar Jun 13 '25 08:06 patrickbryant1

This seems to be back

utimcraig avatar Oct 22 '25 11:10 utimcraig

There was a problem with fetching the example structure from the PDB. It should be fixed now, please try again.

Best,

Patrick

patrickbryant1 avatar Oct 22 '25 13:10 patrickbryant1