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Wed, 4 Jan 2023 01:37:35 +0000 From: Zacchaeus Scheffer To: "bug-guix@gnu.org" Subject: Keras h5py Version Mismatch Thread-Topic: Keras h5py Version Mismatch Thread-Index: AQHZH9Wh0MLpLigzvEqp8wKBTEZluA== Date: Wed, 4 Jan 2023 01:37:34 +0000 Message-ID: Accept-Language: en-US Content-Language: en-US X-MS-Has-Attach: X-MS-TNEF-Correlator: msip_labels: authentication-results: dkim=none (message not signed) header.d=none;dmarc=none action=none header.from=synaptics.com; x-ms-publictraffictype: Email x-ms-traffictypediagnostic: CY4PR03MB2759:EE_|BY5PR03MB4966:EE_ x-ms-office365-filtering-correlation-id: 8ec937f6-907f-4354-f109-08daedf4412a x-ms-exchange-senderadcheck: 1 x-ms-exchange-antispam-relay: 0 x-microsoft-antispam: BCL:0; x-microsoft-antispam-message-info: 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 x-forefront-antispam-report: CIP:255.255.255.255; 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charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable Hi Guix! It would seem that the current keras version expects an earlier h5py versio= n for loading models. Specifically, running: from tensorflow.keras.models import load_model model =3D load_model("model.h5") fails with: File "/gnu/store/idfn4l2kxil9id21v1yci4jcw6103fah-profile/lib/python3.9/s= ite-packages/tensorflow/python/keras/engine/saving.py", line 228, in load_m= odel model_config =3D json.loads(model_config.decode('utf-8')) AttributeError: 'str' object has no attribute 'decode' The above works fine in my local pip environment (see below). A quick sear= ch online indicates that this can be fixed by downgrading h5py to version 2= .10. The current h5py version in guix is 3.6. My assumption is that this could also be fixed with an upgrade to keras, bu= t upgrading keras sounds much more involved. For a short-term fix, would i= t be possible to add back a package definition for an earlier h5py in addit= ion to the current version? I'm sure an appropriate version exists somewhe= re in guix's git history, though my git-foo is too weak for me to check. Thanks, Zacchae P.S. working (pip): keras 2.10.0, h5py 3.7.0 not working (current guix): keras 2.2.4, h5py 3.6.0 --_000_CY4PR03MB27591E805538BEE2A385256098F59CY4PR03MB2759namp_ Content-Type: text/html; charset="iso-8859-1" Content-Transfer-Encoding: quoted-printable
Hi Guix!


It would seem that the current keras version expect= s an earlier h5py version for loading models.  Specifically, running:

from tensorflow.keras.models import load_model
model =3D load_model("model.h5")

fails with:

  File "/gnu/store/idfn4l2kxil9id21v1yci4jcw6103fah-profile/lib/p= ython3.9/site-packages/tensorflow/python/keras/engine/saving.py", line= 228, in load_model
    model_config = =3D json.loads(model_config.decode('utf-8'))
AttributeError: 'str' object = has no attribute 'decode'

The above works fine in my local pip environment (see below).  A quick= search online indicates that this can be fixed by downgrading h5py to vers= ion 2.10.  The current h5py version in guix is 3.6.

My assumption is that this could also be fixed with an upgrade to keras, bu= t upgrading keras sounds much more involved.  For a short-term fix, wo= uld it be possible to add back a package definition for an earlier h5py in = addition to the current version?  I'm sure an appropriate version exists somewhere in guix's git history, though= my git-foo is too weak for me to check.


Thanks,
Zacchae


P.S.
working (pip): keras 2.10.0, h5py 3.7.0
not working (current guix): keras 2.2.4, h5py 3.6.0
--_000_CY4PR03MB27591E805538BEE2A385256098F59CY4PR03MB2759namp_-- From debbugs-submit-bounces@debbugs.gnu.org Fri Jan 06 11:30:18 2023 Received: (at 60545) by debbugs.gnu.org; 6 Jan 2023 16:30:19 +0000 Received: from localhost ([127.0.0.1]:55672 helo=debbugs.gnu.org) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pDpbm-0001uN-Jb for submit@debbugs.gnu.org; Fri, 06 Jan 2023 11:30:18 -0500 Received: from mail-wm1-f50.google.com ([209.85.128.50]:43736) by debbugs.gnu.org with esmtp (Exim 4.84_2) (envelope-from ) id 1pDpbj-0001u4-TX for 60545@debbugs.gnu.org; Fri, 06 Jan 2023 11:30:17 -0500 Received: by mail-wm1-f50.google.com with SMTP id k22-20020a05600c1c9600b003d1ee3a6289so1440311wms.2 for <60545@debbugs.gnu.org>; Fri, 06 Jan 2023 08:30:15 -0800 (PST) DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=gmail.com; s=20210112; h=mime-version:message-id:date:references:in-reply-to:subject:to:from :from:to:cc:subject:date:message-id:reply-to; bh=19ptH7oWU8GeTJM336u0ODhPhxKUmBshEo3V3+fs4ic=; b=ALmI6L6bsVrMMmM9/lLZ1e/dwLuQxS2qcjKT8u/6UpC/XUAOJa1etSOom3cJp1VEY+ tZ2WvIZO52yfIUVqucZGjxepU1kffULdgsPFGbscAnSUGjL8AvidWubOu5LgLFchdK4b hfZj5tqIivTiPD6xbnfA4r0goyPLQq7CpHl+WmlgXrQyuvoX8ixj03bh5TzPAVbsF5du 8YV8FInnrQDyBEx/QoOtvzKld4A5uvwMzs8ooVfdD2A3j+UsjmErZaotUUMlKj/6PUX9 UzmAyrpXvjracuM79G2uK3FJ821MEDKnKx/BPFLiz/8ybjaUoV/26vA/HR2HzVFUOD67 1IdA== X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20210112; h=mime-version:message-id:date:references:in-reply-to:subject:to:from :x-gm-message-state:from:to:cc:subject:date:message-id:reply-to; bh=19ptH7oWU8GeTJM336u0ODhPhxKUmBshEo3V3+fs4ic=; b=VhPZUDbw+0En5FWlI6epRDxfQhS2wGZ5aYR52tLNcfzg6ZkPgoKJ/IJChBLGClLyMC f5Tnmyvw45zOBuW363Yxklb0eFor6Xx7DVJhGijzDQVOmBxxWYF7x4u4eTw+2177VAj6 48McuQ2idPd8u4D743gfxeYeOspXhsxqRkobJ0SxrZ0I1tbKv1KhSMwPJz9ZKFB5UOeP 1lMyMPiBGuRrMZZ0A84drg1biov05MEQzBwQxbYf21I21hbYEL9YbL1W01lID6elPCHf fC31xGWc2D1NWvmSE+yLnrT/jbivlpaHRlcZ2ojJU41zDQwW7crvMzd9O/9ddbK5bchc sNoQ== X-Gm-Message-State: AFqh2kqHQjAJnKmcv1/Rt0WTGngwnTaV1eRpNWeN7MASxTFm6fx92MyE rxbUdnUd+wQsILXTYhAO4A+ePbc/S2w= X-Google-Smtp-Source: AMrXdXtHT8ubdXV4QJ0dCRE3ghUz0cdc0u30sFHodkFJTeJujGFSi+KKPu9nLYdaJylekiX96h7tuQ== X-Received: by 2002:a05:600c:1d15:b0:3d5:b45a:d792 with SMTP id l21-20020a05600c1d1500b003d5b45ad792mr10913576wms.0.1673022609846; Fri, 06 Jan 2023 08:30:09 -0800 (PST) Received: from pfiuh07 ([193.48.40.241]) by smtp.gmail.com with ESMTPSA id t12-20020a05600c198c00b003d9de0c39fasm2475265wmq.36.2023.01.06.08.30.09 (version=TLS1_3 cipher=TLS_AES_256_GCM_SHA384 bits=256/256); Fri, 06 Jan 2023 08:30:09 -0800 (PST) From: zimoun To: Zacchaeus Scheffer , 60545@debbugs.gnu.org Subject: Re: bug#60545: Keras h5py Version Mismatch In-Reply-To: References: Date: Fri, 06 Jan 2023 15:40:41 +0100 Message-ID: <87o7rbiv4m.fsf@gmail.com> MIME-Version: 1.0 Content-Type: text/plain X-Spam-Score: 0.0 (/) X-Debbugs-Envelope-To: 60545 X-BeenThere: debbugs-submit@debbugs.gnu.org X-Mailman-Version: 2.1.18 Precedence: list List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: debbugs-submit-bounces@debbugs.gnu.org Sender: "Debbugs-submit" X-Spam-Score: -1.0 (-) Hi, On Wed, 04 Jan 2023 at 01:37, Zacchaeus Scheffer wrote: > working (pip): keras 2.10.0, h5py 3.7.0 > not working (current guix): keras 2.2.4, h5py 3.6.0 Indeed, it is collateral to ea403bf290f4bf8c7bae314e32dbb90653f92996 --8<---------------cut here---------------start------------->8--- gnu: python-h5py: Update to 3.6.0. * gnu/packages/python-xyz.scm (python-h5py): Update to 3.6.0. [arguments]: Set HDF5_DIR variable instead of patching files. --8<---------------cut here---------------end--------------->8--- Well, the update of Keras to 2.11.0 (the current latest) requires some work. First, fetch from Github instead of PyPI because the sources are not available after v2.6.0; e.g., https://pypi.org/project/keras/2.11.0/#files Then, second adapt the recipe. Do you want to give a try? 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charset="us-ascii" Content-Transfer-Encoding: quoted-printable Hi, I should probably mention that I am not looking into this. I want to learn= more guix, but keras and the additional dependencies required for later ve= rsions is kind of a monster to me at the moment. Thanks, Zacchae ________________________________ From: zimoun Sent: Friday, January 6, 2023 6:40 AM To: Zacchaeus Scheffer ; 60545@debbugs.gn= u.org <60545@debbugs.gnu.org> Subject: Re: bug#60545: Keras h5py Version Mismatch CAUTION: Email originated externally, do not click links or open attachment= s unless you recognize the sender and know the content is safe. Hi, On Wed, 04 Jan 2023 at 01:37, Zacchaeus Scheffer wrote: > working (pip): keras 2.10.0, h5py 3.7.0 > not working (current guix): keras 2.2.4, h5py 3.6.0 Indeed, it is collateral to ea403bf290f4bf8c7bae314e32dbb90653f92996 --8<---------------cut here---------------start------------->8--- gnu: python-h5py: Update to 3.6.0. * gnu/packages/python-xyz.scm (python-h5py): Update to 3.6.0. [arguments]: Set HDF5_DIR variable instead of patching files. --8<---------------cut here---------------end--------------->8--- Well, the update of Keras to 2.11.0 (the current latest) requires some work. First, fetch from Github instead of PyPI because the sources are not available after v2.6.0; e.g., https://urldefense.proofpoint.com/v2/url?u=3Dhttps-3A__pypi.org_project= _keras_2.11.0_-23files&d=3DDwIBAg&c=3D7dfBJ8cXbWjhc0BhImu8wVIoUFmBzj1s88r8E= GyM0UY&r=3D1moyBSYvgSFmdTYHNEHEwakZGFkPl3pixLezH1qWWXFZPpSXOvpoeGr4XIg6G8V0= &m=3DNqD4egq46utBpoyT-8Gr6A3lESGvdg2j7CIMrB0r_y4I-pFRV2Gxn2-Lb7s7tsyD&s=3DR= o23h-Sd5x7VKOXeIYl4j5KGqDMAyZprruKUgdacbCo&e=3D Then, second adapt the recipe. Do you want to give a try? Cheers, simon --_000_CY4PR03MB27599F8ABE114B8822E4ABFF98D09CY4PR03MB2759namp_ Content-Type: text/html; charset="us-ascii" Content-Transfer-Encoding: quoted-printable
Hi,

I should probably mention that I am not looking into this.  I want to = learn more guix, but keras and the additional dependencies required for lat= er versions is kind of a monster to me at the moment.

Thanks,
Zacchae
From: zimoun <zimon.tout= oune@gmail.com>
Sent: Friday, January 6, 2023 6:40 AM
To: Zacchaeus Scheffer <Zacchaeus.Scheffer@synaptics.com>; 605= 45@debbugs.gnu.org <60545@debbugs.gnu.org>
Subject: Re: bug#60545: Keras h5py Version Mismatch
 
CAUTION: Email originated externally, do not click= links or open attachments unless you recognize the sender and know the con= tent is safe.


Hi,

On Wed, 04 Jan 2023 at 01:37, Zacchaeus Scheffer <Zacchaeus.Scheffer@syn= aptics.com> wrote:

> working (pip): keras 2.10.0, h5py 3.7.0
> not working (current guix): keras 2.2.4, h5py 3.6.0

Indeed, it is collateral to ea403bf290f4bf8c7bae314e32dbb90653f92996

--8<---------------cut here---------------start------------->8---
gnu: python-h5py: Update to 3.6.0.

* gnu/packages/python-xyz.scm (python-h5py): Update to 3.6.0.
[arguments]: Set HDF5_DIR variable instead of patching files.
--8<---------------cut here---------------end--------------->8---

Well, the update of Keras to 2.11.0 (the current latest) requires some
work.  First, fetch from Github instead of PyPI because the sources ar= e
not available after v2.6.0; e.g.,

    https://urldefense.proofpoint.com/v2/url?u=3Dhttps-3A__pypi.org_project_ker= as_2.11.0_-23files&d=3DDwIBAg&c=3D7dfBJ8cXbWjhc0BhImu8wVIoUFmBzj1s8= 8r8EGyM0UY&r=3D1moyBSYvgSFmdTYHNEHEwakZGFkPl3pixLezH1qWWXFZPpSXOvpoeGr4= XIg6G8V0&m=3DNqD4egq46utBpoyT-8Gr6A3lESGvdg2j7CIMrB0r_y4I-pFRV2Gxn2-Lb7= s7tsyD&s=3DRo23h-Sd5x7VKOXeIYl4j5KGqDMAyZprruKUgdacbCo&e=3D

Then, second adapt the recipe.  Do you want to give a try?


Cheers,
simon

--_000_CY4PR03MB27599F8ABE114B8822E4ABFF98D09CY4PR03MB2759namp_--