X2Go Bug report logs - #1496
PyMOL crashes x2goagent

version graph

Package: x2goagent; Maintainer for x2goagent is X2Go Developers <x2go-dev@lists.x2go.org>; Source for x2goagent is src:nx-libs.

Reported by: Craig Morton <craig.morton@unimelb.edu.au>

Date: Mon, 14 Sep 2020 02:55:02 UTC

Severity: normal

Found in version 3.5.99.24

Full log


🔗 View this message in rfc822 format

X-Loop: owner@bugs.x2go.org
Subject: Bug#1496: PyMOL crashes x2goagent
Reply-To: Craig Morton <craig.morton@unimelb.edu.au>, 1496@bugs.x2go.org
Resent-From: Craig Morton <craig.morton@unimelb.edu.au>
Resent-To: x2go-dev@lists.x2go.org
Resent-CC: X2Go Developers <x2go-dev@lists.x2go.org>
X-Loop: owner@bugs.x2go.org
Resent-Date: Mon, 14 Sep 2020 02:55:02 +0000
Resent-Message-ID: <handler.1496.B.160005181420836@bugs.x2go.org>
Resent-Sender: owner@bugs.x2go.org
X-X2Go-PR-Message: report 1496
X-X2Go-PR-Package: x2goagent
X-X2Go-PR-Keywords: 
Received: via spool by submit@bugs.x2go.org id=B.160005181420836
          (code B); Mon, 14 Sep 2020 02:55:02 +0000
Received: (at submit) by bugs.x2go.org; 14 Sep 2020 02:50:14 +0000
X-Spam-Checker-Version: SpamAssassin 3.4.2 (2018-09-13) on
	ymir.das-netzwerkteam.de
X-Spam-Level: 
X-Spam-Status: No, score=-0.6 required=3.0 tests=BAYES_05,DKIM_SIGNED,
	DKIM_VALID,DKIM_VALID_AU,HTML_MESSAGE,RCVD_IN_MSPIKE_H4,
	RCVD_IN_MSPIKE_WL,SPF_HELO_NONE,URIBL_BLOCKED autolearn=ham
	autolearn_force=no version=3.4.2
Received: from au-smtp-delivery-108.mimecast.com (au-smtp-delivery-108.mimecast.com [180.189.28.108])
	by ymir.das-netzwerkteam.de (Postfix) with ESMTP id 015805DAEB
	for <submit@bugs.x2go.org>; Mon, 14 Sep 2020 04:50:09 +0200 (CEST)
DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=unimelb.edu.au;
	s=mimecast20161020; t=1600051747;
	h=from:from:reply-to:subject:subject:date:date:message-id:message-id:
	 to:to:cc:mime-version:mime-version:content-type:content-type;
	bh=CnsHC1GkOZHi4zRT9zGxMzE2Jp+vepvIjAifHo7LNCk=;
	b=jctZAnUarCF6S+nBU7T1SCfv56e7v7/Qvn4N2SnO4FssGf0OtoNOQ+NHjKBPHoyxnAcHHU
	s6GvYGvYxdMIsxN+xWMzojTi4feLMkE+4589D8tHjmZjoQrEy7AB7q6mspDN99K6NMc/+V
	qFkw01046Gnpos7zeHu8o9bWWLvU8ws=
Received: from AUS01-ME1-obe.outbound.protection.outlook.com
 (mail-me1aus01lp2057.outbound.protection.outlook.com [104.47.116.57])
 (Using TLS) by relay.mimecast.com with ESMTP id
 au-mta-53-MJW_eo5nOkmJDblKwPenpQ-1; Mon, 14 Sep 2020 12:48:58 +1000
X-MC-Unique: MJW_eo5nOkmJDblKwPenpQ-1
Received: from ME2PR01MB5124.ausprd01.prod.outlook.com (2603:10c6:220:1f::23)
 by ME2PR01MB4546.ausprd01.prod.outlook.com (2603:10c6:220:1a::14) with
 Microsoft SMTP Server (version=TLS1_2,
 cipher=TLS_ECDHE_RSA_WITH_AES_256_GCM_SHA384) id 15.20.3370.17; Mon, 14 Sep
 2020 02:48:57 +0000
Received: from ME2PR01MB5124.ausprd01.prod.outlook.com
 ([fe80::25bf:8bc1:a971:8240]) by ME2PR01MB5124.ausprd01.prod.outlook.com
 ([fe80::25bf:8bc1:a971:8240%6]) with mapi id 15.20.3370.019; Mon, 14 Sep 2020
 02:48:57 +0000
From: Craig Morton <craig.morton@unimelb.edu.au>
To: "submit@bugs.x2go.org" <submit@bugs.x2go.org>
Thread-Topic: PyMOL crashes x2goagent
Thread-Index: AQHWikBF3da4+MD2gE6pd5bUy16P5A==
Date: Mon, 14 Sep 2020 02:48:57 +0000
Message-ID: 
 <ME2PR01MB5124E9AE48D012398C57EA01BB230@ME2PR01MB5124.ausprd01.prod.outlook.com>
Accept-Language: en-GB, en-US
X-MS-Has-Attach: 
X-MS-TNEF-Correlator: 
x-originating-ip: [128.250.28.201]
x-ms-publictraffictype: Email
x-ms-office365-filtering-correlation-id: d0cfb70e-0d03-4f97-7661-08d85858ba24
x-ms-traffictypediagnostic: ME2PR01MB4546:
x-microsoft-antispam-prvs: 
 <ME2PR01MB4546F3EF487F32188C19265DBB230@ME2PR01MB4546.ausprd01.prod.outlook.com>
x-ms-oob-tlc-oobclassifiers: OLM:8273;
x-ms-exchange-senderadcheck: 1
x-microsoft-antispam: BCL:0;
x-microsoft-antispam-message-info: 
 ViCb1dV3pWsEHqt11cOUFMs5Qa7wxh7viMrZcEzD75Xq2gWxqBEBk2VVla3mtVCHP4t6SuGvBGQ5SiR5NS6Uwiio92IPc4uTvkPtDYmCWz+6IEbPlyBvOBOzhPQmdM4RBN5WeqF1idAGr4/ntNO/5A2V4b1x4ZPEPL8p84Bg1pBgY4bY7R6AODNP5p5Vi/vlANvnahbvDdtjlXR8FJn8d0gzXCjOi2MrXhDOR11XwR3F7Fm4C69RfqUI++QbZJwYGCYvbQCGTyPLymgOsnwPNWyXmvzXLQPyO+L7O11MAmd0y+J/7NOYB+xRU0AwvsuUYQVknb6B+9N8c61FUyAqN23RSK8loxZBj94iqaI4N0677X2O9POes61Viyj7JqrzsWSBOTkKCocI2QhYGNfT6w==
x-forefront-antispam-report: 
 CIP:255.255.255.255;CTRY:;LANG:en;SCL:1;SRV:;IPV:NLI;SFV:NSPM;H:ME2PR01MB5124.ausprd01.prod.outlook.com;PTR:;CAT:NONE;SFS:(346002)(396003)(136003)(376002)(39860400002)(366004)(4744005)(316002)(786003)(76116006)(66946007)(8676002)(44832011)(86362001)(66446008)(66476007)(33656002)(66556008)(64756008)(8936002)(2906002)(71200400001)(186003)(26005)(7116003)(6916009)(19627405001)(6506007)(7696005)(55016002)(52536014)(5660300002)(478600001)(83380400001)(9686003);DIR:OUT;SFP:1101;
x-ms-exchange-antispam-messagedata: 
 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
x-ms-exchange-transport-forked: True
MIME-Version: 1.0
X-OriginatorOrg: unimelb.edu.au
X-MS-Exchange-CrossTenant-AuthAs: Internal
X-MS-Exchange-CrossTenant-AuthSource: ME2PR01MB5124.ausprd01.prod.outlook.com
X-MS-Exchange-CrossTenant-Network-Message-Id: d0cfb70e-0d03-4f97-7661-08d85858ba24
X-MS-Exchange-CrossTenant-originalarrivaltime: 14 Sep 2020 02:48:57.2505
 (UTC)
X-MS-Exchange-CrossTenant-fromentityheader: Hosted
X-MS-Exchange-CrossTenant-id: 0e5bf3cf-1ff4-46b7-9176-52c538c22a4d
X-MS-Exchange-CrossTenant-mailboxtype: HOSTED
X-MS-Exchange-CrossTenant-userprincipalname: 2lLX6gJhcPKMHvMeKaVC1u/M7xTIUQ0cjeX8V+gatXjCWBD6TY7FFHJ2eNJ30w4JgPmsAjdluMb+VQL6r4Bz0E9ah6jqstSy8hlv0wBQxGg=
X-MS-Exchange-Transport-CrossTenantHeadersStamped: ME2PR01MB4546
Authentication-Results: relay.mimecast.com;
	auth=pass smtp.auth=CAU8A14 smtp.mailfrom=craig.morton@unimelb.edu.au
X-Mimecast-Spam-Score: 0.002
X-Mimecast-Originator: unimelb.edu.au
Content-Type: multipart/alternative;
	boundary="_000_ME2PR01MB5124E9AE48D012398C57EA01BB230ME2PR01MB5124ausp_"
Content-Language: en-GB
[Message part 1 (text/plain, inline)]
Package: x2goagent
Version: 3.5.99.24

Starting the PyMOL molecular modelling program (www.pymol.org) opens the PyMOL window then immediately crashes the x2go session. The session can't be restarted.

Dumped core on crash is from x2goagent and has the following information:

Using host libthread_db library "/lib64/libthread_db.so.1".
Core was generated by `x2goagent -nolisten tcp -nolisten tcp -dpi 96 -D -auth /home/craig/.'.
Program terminated with signal 11, Segmentation fault.
#0  0x000055fb9673da3d in _mesa_update_framebuffer_visual ()

PyMOL runs just fine sitting at the computer, the crash only occurs with x2go. Tried under KDE and MATE in case it was a KDE issue, same result, same error.

Running on Centos7, kernel 3.10.0-1127.18.2.el7.x86_64

Craig.
[Message part 2 (text/html, inline)]

Send a report that this bug log contains spam.


X2Go Developers <owner@bugs.x2go.org>. Last modified: Thu Nov 21 15:37:45 2024; Machine Name: ymir.das-netzwerkteam.de

X2Go Bug tracking system

Debbugs is free software and licensed under the terms of the GNU Public License version 2. The current version can be obtained from https://bugs.debian.org/debbugs-source/.

Copyright © 1999 Darren O. Benham, 1997,2003 nCipher Corporation Ltd, 1994-97 Ian Jackson, 2005-2017 Don Armstrong, and many other contributors.