From mboxrd@z Thu Jan 1 00:00:00 1970 Received: from eggs.gnu.org ([2001:470:142:3::10]:40030) by lists.gnu.org with esmtp (Exim 4.90_1) (envelope-from ) id 1jRbaE-0004oi-Ou for guix-patches@gnu.org; Thu, 23 Apr 2020 09:08:03 -0400 Received: from Debian-exim by eggs.gnu.org with spam-scanned (Exim 4.90_1) (envelope-from ) id 1jRbaE-0002TI-5e for guix-patches@gnu.org; Thu, 23 Apr 2020 09:08:02 -0400 Received: from debbugs.gnu.org ([209.51.188.43]:42690) by eggs.gnu.org with esmtps (TLS1.2:ECDHE_RSA_AES_128_GCM_SHA256:128) (Exim 4.90_1) (envelope-from ) id 1jRbaD-0002Sw-PM for guix-patches@gnu.org; Thu, 23 Apr 2020 09:08:01 -0400 Received: from Debian-debbugs by debbugs.gnu.org with local (Exim 4.84_2) (envelope-from ) id 1jRbaD-0003BA-It for guix-patches@gnu.org; Thu, 23 Apr 2020 09:08:01 -0400 Subject: [bug#40691] [PATCH v3 1/1] gnu: Add gromacs. Resent-Message-ID: References: <87k12b15ki.fsf@gnu.org> <36e8a145-1ca8-c380-9864-dbf8b1fd53cb@gmail.com> <87y2qnv8da.fsf@gnu.org> From: Vincent Legoll Message-ID: Date: Thu, 23 Apr 2020 15:07:42 +0200 MIME-Version: 1.0 In-Reply-To: <87y2qnv8da.fsf@gnu.org> Content-Type: multipart/mixed; boundary="------------2486E0B001B304112530357A" Content-Language: en-US List-Id: List-Unsubscribe: , List-Archive: List-Post: List-Help: List-Subscribe: , Errors-To: guix-patches-bounces+kyle=kyleam.com@gnu.org Sender: "Guix-patches" To: Ludovic =?UTF-8?Q?Court=C3=A8s?= Cc: 40691@debbugs.gnu.org This is a multi-part message in MIME format. --------------2486E0B001B304112530357A Content-Type: text/plain; charset=utf-8; format=flowed Content-Transfer-Encoding: 8bit On 22/04/2020 17:38, Ludovic Courtès wrote: > This v2 looks alright to me, but I got this test failure on x86_64: > > --8<---------------cut here---------------start------------->8--- > Start 13: HardwareUnitTests > 13/52 Test #13: HardwareUnitTests ...................***Failed 0.04 sec > [==========] Running 5 tests from 2 test cases. > [----------] Global test environment set-up. > [----------] 1 test from CpuInfoTest > [ RUN ] CpuInfoTest.SupportLevel > [ OK ] CpuInfoTest.SupportLevel (0 ms) > [----------] 1 test from CpuInfoTest (0 ms total) > > [----------] 4 tests from HardwareTopologyTest > [ RUN ] HardwareTopologyTest.Execute > [ OK ] HardwareTopologyTest.Execute (6 ms) > [ RUN ] HardwareTopologyTest.HwlocExecute > /tmp/guix-build-gromacs-2020.1.drv-0/gromacs-2020.1/src/gromacs/hardware/tests/hardwaretopology.cpp:88: Failure > Expected: (hwTop.supportLevel()) >= (gmx::HardwareTopology::SupportLevel::Basic), actual: 4-byte object <01-00 00-00> vs 4-byte object <02-00 00-00> > Cannot determine basic hardware topology from hwloc. GROMACS will still > > work, but it might affect your performance for large nodes. > Please mail gmx-developers@gromacs.org so we can try to fix it. > [ FAILED ] HardwareTopologyTest.HwlocExecute (5 ms) > [ RUN ] HardwareTopologyTest.ProcessorSelfconsistency > [ OK ] HardwareTopologyTest.ProcessorSelfconsistency (6 ms) > [ RUN ] HardwareTopologyTest.NumaCacheSelfconsistency > [ OK ] HardwareTopologyTest.NumaCacheSelfconsistency (5 ms) > [----------] 4 tests from HardwareTopologyTest (22 ms total) > > [----------] Global test environment tear-down > [==========] 5 tests from 2 test cases ran. (22 ms total) > [ PASSED ] 4 tests. > [ FAILED ] 1 test, listed below: > [ FAILED ] HardwareTopologyTest.HwlocExecute > > 1 FAILED TEST > > […] > > The following tests FAILED: > 13 - HardwareUnitTests (Failed) > Errors while running CTest > make: *** [Makefile:99: test] Error 8 > --8<---------------cut here---------------end--------------->8--- > > Could you check what the test is doing? I think it tries to get CPU topology from the linux kernel, which is not particularly useful to test on a build server, the package may run on completely different hardware. > It may be reasonable to just skip it. Hope you don't mind trading a test suite failure for a (harmless) test suite build warning... How's the crude disabling in the attached patch v3 look to you ? And does it fix the failure ? This test is not failing here (kvm on ryzen). -- Vincent Legoll --------------2486E0B001B304112530357A Content-Type: text/x-patch; charset=UTF-8; name="0001-gnu-Add-gromacs.v3.patch" Content-Transfer-Encoding: 8bit Content-Disposition: attachment; filename="0001-gnu-Add-gromacs.v3.patch" >From 660371d5a3e7c7c763fc123357ddd6c31f730553 Mon Sep 17 00:00:00 2001 From: Vincent Legoll Date: Sat, 18 Apr 2020 00:14:56 +0200 Subject: [PATCH] gnu: Add gromacs. * gnu/packages/bioinformatics.scm (gromacs): New variable. --- gnu/packages/bioinformatics.scm | 56 +++++++++++++++++++++++++++++++++ 1 file changed, 56 insertions(+) diff --git a/gnu/packages/bioinformatics.scm b/gnu/packages/bioinformatics.scm index b9be0c1918..62647d6146 100644 --- a/gnu/packages/bioinformatics.scm +++ b/gnu/packages/bioinformatics.scm @@ -17,6 +17,7 @@ ;;; Copyright © 2019 Brett Gilio ;;; Copyright © 2020 Björn Höfling ;;; Copyright © 2020 Jakub Kądziołka +;;; Copyright © 2020 Vincent Legoll ;;; ;;; This file is part of GNU Guix. ;;; @@ -79,6 +80,7 @@ #:use-module (gnu packages golang) #:use-module (gnu packages glib) #:use-module (gnu packages graph) + #:use-module (gnu packages graphviz) #:use-module (gnu packages groff) #:use-module (gnu packages gtk) #:use-module (gnu packages guile) @@ -785,6 +787,60 @@ input/output delimiter. When the new functionality is not used, bioawk is intended to behave exactly the same as the original BWK awk.") (license license:x11))) +(define-public gromacs + (package + (name "gromacs") + (version "2020.1") + (source (origin + (method url-fetch) + (uri (string-append "http://ftp.gromacs.org/pub/gromacs/gromacs-" + version ".tar.gz")) + (sha256 + (base32 + "1kwrk3i1dxp8abhqqsl049lh361n4910h0415g052f8shdc6arp1")))) + (build-system cmake-build-system) + (arguments + `(#:configure-flags + (list "-DGMX_DEVELOPER_BUILD=on" ; Needed to run tests + ;; Workaround for cmake/FindSphinx.cmake version parsing that does + ;; not understand the guix-wrapped `sphinx-build --version' answer + (string-append "-DSPHINX_EXECUTABLE_VERSION=" + ,(package-version python-sphinx))) + #:phases + (modify-phases %standard-phases + (add-after 'unpack 'disable-hwloc-test + (lambda _ + ;; This test warns about the build host hardware + (substitute* "src/gromacs/hardware/tests/hardwaretopology.cpp" + (("TEST\\(HardwareTopologyTest, HwlocExecute\\)") + "void __guix_disabled()")) + #t))))) + (native-inputs + `(("doxygen" ,doxygen) + ("graphviz" ,graphviz) + ("python" ,python) + ("python-pygments" ,python-pygments) + ("python-sphinx" ,python-sphinx))) + (inputs + `(("fftwf" ,fftwf) + ("hwloc" ,hwloc-2 "lib") + ("imagemagick" ,imagemagick) + ("lapack" ,lapack) + ("openblas" ,openblas) + ("openmpi" ,openmpi) + ("perl" ,perl))) + (home-page "http://www.gromacs.org/") + (synopsis "Molecular dynamics software package") + (description "GROMACS is a versatile package to perform molecular dynamics, +i.e. simulate the Newtonian equations of motion for systems with hundreds to +millions of particles. It is primarily designed for biochemical molecules like +proteins, lipids and nucleic acids that have a lot of complicated bonded +interactions, but since GROMACS is extremely fast at calculating the nonbonded +interactions (that usually dominate simulations) many groups are also using it +for research on non-biological systems, e.g. polymers. GROMACS supports all the +usual algorithms you expect from a modern molecular dynamics implementation.") + (license license:lgpl2.1+))) + (define-public python-pybedtools (package (name "python-pybedtools") -- 2.26.0 --------------2486E0B001B304112530357A--