DKIM-Filter: OpenDKIM Filter v2.11.0 delorie.com 46NF9SPX3068933 Authentication-Results: delorie.com; dkim=pass (1024-bit key, unprotected) header.d=cygwin.com header.i=@cygwin.com header.a=rsa-sha256 header.s=default header.b=bwEp3Cfl X-Recipient: archive-cygwin AT delorie DOT com DKIM-Filter: OpenDKIM Filter v2.11.0 sourceware.org 7B2943860757 DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=cygwin.com; s=default; t=1721747366; bh=EwYct4nir3rBt+dxZiJqeajUrgThiFHRdEBpuFKTaf8=; h=Date:Subject:To:List-Id:List-Unsubscribe:List-Archive:List-Post: List-Help:List-Subscribe:From:Reply-To:From; b=bwEp3CflZvSZHWZPyhIB+rkpssabJfM7VhZGPpmZdPTGAEvzJwzeDHkEX+XkBgDEv 8fpEGMG+LFWJYlFcHhfwjZ6PynuGa4YMThbXLeNL5h0JcybkNCLnvjBW0lWHp2jx8F lCBGX3yKKGIE/cne7YdWCkgPp+rPcicTJM21mqu0= X-Original-To: cygwin AT cygwin DOT com Delivered-To: cygwin AT cygwin DOT com DMARC-Filter: OpenDMARC Filter v1.4.2 sourceware.org 86905385840A ARC-Filter: OpenARC Filter v1.0.0 sourceware.org 86905385840A ARC-Seal: i=1; a=rsa-sha256; d=sourceware.org; s=key; t=1721747345; cv=none; b=u+qNWrqgOiLFeR7GWAm4hi0zT/k6fusJ++iTq+vQAJ+OJyaZ6dluW1lX9HNGnMcbcMAYzVwXRNIbeizWl+Rdi5wRAqHD7p+vaN+vAoEs5M/RW3tIaSGRsrRHeNZQ4Ul/BG6s1OEXCEp30dcKhRFB2Hy0KfgDf8iF3CTjsunHfZY= ARC-Message-Signature: i=1; a=rsa-sha256; d=sourceware.org; s=key; t=1721747345; c=relaxed/simple; bh=PVZTCc8/BEVxhUhpH/eDIu9JDEHAMzwzP45G55nrS1Q=; h=DKIM-Signature:MIME-Version:From:Date:Message-ID:Subject:To; b=ET5viOQsxPksRqMqV3bm8r5ZXNVo2XgiHzC2YMtOFK6r2lB4k9SmhJSDMtk6wSPMS1p1bUMf0hUg5dDztF7GBrZeByoBVhwCk207yFrPyeXEyCjlzhX1fUdSWTmiobd+sI9Lk87frkxh67/l+nbqAEczlfz7opx1O2E1ICztui8= ARC-Authentication-Results: i=1; server2.sourceware.org X-Google-DKIM-Signature: v=1; a=rsa-sha256; c=relaxed/relaxed; d=1e100.net; s=20230601; t=1721747342; x=1722352142; h=to:subject:message-id:date:from:mime-version:x-gm-message-state :from:to:cc:subject:date:message-id:reply-to; bh=PVZTCc8/BEVxhUhpH/eDIu9JDEHAMzwzP45G55nrS1Q=; b=MkjGNXmjCENoXeIsAHyc34MPB8C4eC+ABFlI4WpHP50o2t2JPJdk3cc9ZHWx39FvAI okvtOiDtE6xePr9BENnFJ/9w5d486sg+63Uujod7OhIGsHPcXrTmj4NW3IivUSGBk3bi QOnlxzcMfafSqCb7huPJ5DbOeCSgzydIhXoDdkP80K+phtV8aFqYKxxER0nK+xcME/4a mpu067+JpBorlX4ZTHYMDwpe8PCT1WF0DZsV1IHqwE0gQ1dbnjfDxi2CKqqei8S2mcba BZvhTdghZWhDTyD5bYxuyKQdvkU8tUA7+EImfuJIDxVdnXgnsMnr8mVOeBMO9uLbvPG1 YVqg== X-Gm-Message-State: AOJu0YwZ1nTBUr7eKTHMgSDHtRJmyYZ/vE5qKlO2leYJUnvGOYzy9MFD OxccgQaU2o1PWxyKl+sJubVFX+UBL8uvK2hx5iwOz01xmf8lk+yRpCRSZqByJ6/qiuimKmJeA0y 1CBQlAfSu5Bj07zvZ35p45l4aIDRAyMW+LH94oSXHwBmJPMoFSfRuxA== X-Google-Smtp-Source: AGHT+IEKRYdcxbfBywpxtPPw2+ruNvM9+gKo/q7DxoY0sG9oKplNp38lntGrdx1IOEwqm1NUbUp6uX3nqf30UiPVlBk= X-Received: by 2002:a17:90a:708f:b0:2cb:58e1:abc8 with SMTP id 98e67ed59e1d1-2cd8d134fc7mr3639773a91.21.1721747341935; Tue, 23 Jul 2024 08:09:01 -0700 (PDT) MIME-Version: 1.0 Date: Wed, 24 Jul 2024 00:08:45 +0900 Message-ID: Subject: GCC 12.4.0-2 causing OpenMP issues within MMseqs2 To: cygwin AT cygwin DOT com X-Spam-Status: No, score=-0.6 required=5.0 tests=BAYES_00, DKIM_SIGNED, DKIM_VALID, DKIM_VALID_AU, DKIM_VALID_EF, HTML_MESSAGE, KAM_NUMSUBJECT, RCVD_IN_DNSWL_NONE, SPF_HELO_NONE, SPF_PASS, TXREP autolearn=no autolearn_force=no version=3.4.6 X-Spam-Checker-Version: SpamAssassin 3.4.6 (2021-04-09) on server2.sourceware.org X-Content-Filtered-By: Mailman/MimeDel 2.1.30 X-BeenThere: cygwin AT cygwin DOT com X-Mailman-Version: 2.1.30 List-Id: General Cygwin discussions and problem reports List-Archive: List-Post: List-Help: List-Subscribe: , From: Milot Mirdita via Cygwin Reply-To: Milot Mirdita Content-Type: text/plain; charset="us-ascii" Content-Transfer-Encoding: 7bit Sender: "Cygwin" Hi! I am the maintainer for the bioinformatics tool suite MMseqs2. We build Windows binaries for our windows users with Cygwin for many years without major issues. Thanks a lot! This weeks' GCC 12.4 update seems to have introduced issues with OpenMP. Every command line invocation that uses OpenMP now fails with: libgomp: Out of memory allocating 1504 bytes We build the binaries and run integration tests within Azure Pipelines, so it should be straightforward to reproduce: https://github.com/soedinglab/MMseqs2/blob/a14688744081c15439fa3092eec9dfd8be40440b/azure-pipelines.yml#L210-L244 The previous CI build ~2 weeks ago ran successfully: https://github.com/soedinglab/MMseqs2/runs/27320996112 Any help would be appreciated! Best regards, Milot Mirdita -- Problem reports: https://cygwin.com/problems.html FAQ: https://cygwin.com/faq/ Documentation: https://cygwin.com/docs.html Unsubscribe info: https://cygwin.com/ml/#unsubscribe-simple