From f72cd79ad1737f44616827c96f3ea32d7ac93738 Mon Sep 17 00:00:00 2001 From: Douglas Duckworth Date: Thu, 18 May 2017 16:37:47 -0400 Subject: [PATCH 01/20] add mpi support to meme (#4265) * added openmpi support to meme * openmpi is a link dependency which leverages r_path * openmpi support now the default - meme does not have configure argument for mpi - if it's found then it's used * added serial option and set mpi to not be default * modified meme --- var/spack/repos/builtin/packages/meme/package.py | 11 +++++++++++ 1 file changed, 11 insertions(+) diff --git a/var/spack/repos/builtin/packages/meme/package.py b/var/spack/repos/builtin/packages/meme/package.py index ca7554c565e..87174c391e9 100644 --- a/var/spack/repos/builtin/packages/meme/package.py +++ b/var/spack/repos/builtin/packages/meme/package.py @@ -35,9 +35,20 @@ class Meme(AutotoolsPackage): version('4.11.4', '371f513f82fa0888205748e333003897') + variant('mpi', default=True, description='Enable MPI support') + depends_on('zlib', type=('link')) depends_on('libxml2', type=('link')) depends_on('libxslt', type=('link')) depends_on('libgcrypt', type=('link')) depends_on('perl', type=('build', 'run')) depends_on('python@2.7:', type=('build', 'run')) + depends_on('mpi', when='+mpi') + + # disable mpi support + def configure_args(self): + spec = self.spec + args = [] + if '~mpi' in spec: + args += ['--enable-serial'] + return args From 153a63de62463e4da630971297b42c19f7efdb4c Mon Sep 17 00:00:00 2001 From: kothah Date: Fri, 19 May 2017 02:01:40 +0200 Subject: [PATCH 02/20] added new version 7.900.1 (#4292) added new md5 --- var/spack/repos/builtin/packages/armadillo/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/armadillo/package.py b/var/spack/repos/builtin/packages/armadillo/package.py index 7bf28efc0dc..0729afd8c87 100644 --- a/var/spack/repos/builtin/packages/armadillo/package.py +++ b/var/spack/repos/builtin/packages/armadillo/package.py @@ -33,6 +33,7 @@ class Armadillo(Package): homepage = "http://arma.sourceforge.net/" url = "http://sourceforge.net/projects/arma/files/armadillo-7.200.1.tar.xz" + version('7.900.1', '5ef71763bd429a3d481499878351f3be') version('7.500.0', '7d316fdf3c3c7ea92b64704180ae315d') version('7.200.2', 'b21585372d67a8876117fd515d8cf0a2') version('7.200.1', 'ed86d6df0058979e107502e1fe3e469e') From be356cf707f37d172a73141f1d1c163e9028b08c Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Thu, 18 May 2017 17:02:03 -0700 Subject: [PATCH 03/20] Add info for libxml2@2.7.8 (#4290) bcl2fastq2 needs this older version. --- var/spack/repos/builtin/packages/libxml2/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/libxml2/package.py b/var/spack/repos/builtin/packages/libxml2/package.py index 4324b1dcd39..6a9e6e65100 100644 --- a/var/spack/repos/builtin/packages/libxml2/package.py +++ b/var/spack/repos/builtin/packages/libxml2/package.py @@ -34,6 +34,7 @@ class Libxml2(AutotoolsPackage): version('2.9.4', 'ae249165c173b1ff386ee8ad676815f5') version('2.9.2', '9e6a9aca9d155737868b3dc5fd82f788') + version('2.7.8', '8127a65e8c3b08856093099b52599c86') variant('python', default=False, description='Enable Python support') From 0bff9c1eb1b99484e077a5cd18dc52a16057feb0 Mon Sep 17 00:00:00 2001 From: Tom Merrick Date: Fri, 19 May 2017 09:59:35 -0500 Subject: [PATCH 04/20] Add r-rmpfr and r-gmp to R (#4287) * Add mpi support to R * Add multiple precision math routines to R * Updated the URL to match the version * Remove duplicate packages --- .../repos/builtin/packages/r-gmp/package.py | 39 +++++++++++++++++ .../repos/builtin/packages/r-rmpfr/package.py | 42 +++++++++++++++++++ 2 files changed, 81 insertions(+) create mode 100644 var/spack/repos/builtin/packages/r-gmp/package.py create mode 100644 var/spack/repos/builtin/packages/r-rmpfr/package.py diff --git a/var/spack/repos/builtin/packages/r-gmp/package.py b/var/spack/repos/builtin/packages/r-gmp/package.py new file mode 100644 index 00000000000..13b890220d6 --- /dev/null +++ b/var/spack/repos/builtin/packages/r-gmp/package.py @@ -0,0 +1,39 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RGmp(RPackage): + """Multiple Precision Arithmetic (big integers and rationals, prime + number tests, matrix computation), "arithmetic without limitations" + using the C library GMP (GNU Multiple Precision Arithmetic).""" + + homepage = "http://mulcyber.toulouse.inra.fr/projects/gmp" + url = "https://cran.r-project.org/src/contrib/gmp_0.5-13.1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/gmp" + + version('0.5-13.1', '4a45d45e53bf7140720bd44f10b075ed') + + depends_on('gmp@4.2.3:') diff --git a/var/spack/repos/builtin/packages/r-rmpfr/package.py b/var/spack/repos/builtin/packages/r-rmpfr/package.py new file mode 100644 index 00000000000..cbf9b3d3c2d --- /dev/null +++ b/var/spack/repos/builtin/packages/r-rmpfr/package.py @@ -0,0 +1,42 @@ +############################################################################## +# Copyright (c) 2013-2016, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class RRmpfr(RPackage): + """Arithmetic (via S4 classes and methods) for arbitrary precision + floating point numbers, including transcendental ("special") + functions. To this end, Rmpfr interfaces to the LGPL'ed MPFR + (Multiple Precision Floating-Point Reliable) Library which itself + is based on the GMP (GNU Multiple Precision) Library.""" + + homepage = "http://rmpfr.r-forge.r-project.org" + url = "https://cran.r-project.org/src/contrib/Rmpfr_0.6-1.tar.gz" + list_url = "https://cran.r-project.org/src/contrib/Archive/Rmpfr" + + version('0.6-1', '55d4ec257bd2a9233bafee9e444d0265') + + depends_on('r-gmp@0.5-8:') + depends_on('mpfr@3.0.0:') From 18c7e9662437081e4d283abf656e1604228af045 Mon Sep 17 00:00:00 2001 From: George Hartzell Date: Fri, 19 May 2017 09:55:21 -0700 Subject: [PATCH 05/20] Fix boost@:1.56.0%gcc@:5 (#4295) I need boost@1.54.0 for bcl2fastq2. I tested bcl2fastq2 using the system compiler (gcc@4.8.5). My full build uses a spack-build gcc@5.4.0. boost@1.54.0 won't build. I found the answer [here](https://github.com/hashdist/hashstack/issues/802) with the details in [this upstream/boost ticket](https://svn.boost.org/trac/boost/ticket/10125). I've confirmed that these combo's build: boost version| compiler ------------ | ------------------ boost@1.54.0 | gcc@4.8.5 (system) boost@1.54.0 | gcc@5.4.0 (Spack) boost@1.64.0 | gcc@5.5.0 (system) --- .../packages/boost/call_once_variadic.patch | 57 +++++++++++++++++++ .../repos/builtin/packages/boost/package.py | 2 + 2 files changed, 59 insertions(+) create mode 100644 var/spack/repos/builtin/packages/boost/call_once_variadic.patch diff --git a/var/spack/repos/builtin/packages/boost/call_once_variadic.patch b/var/spack/repos/builtin/packages/boost/call_once_variadic.patch new file mode 100644 index 00000000000..f143644a70c --- /dev/null +++ b/var/spack/repos/builtin/packages/boost/call_once_variadic.patch @@ -0,0 +1,57 @@ +diff --git a/boost/thread/pthread/once.hpp b/boost/thread/pthread/once.hpp +index ccfb051..0bef038 100644 +--- a/boost/thread/pthread/once.hpp ++++ b/boost/thread/pthread/once.hpp +@@ -42,7 +42,7 @@ namespace boost + } + + #ifdef BOOST_THREAD_PROVIDES_ONCE_CXX11 +-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES ++#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES) + template + inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args); + #else +@@ -65,7 +65,7 @@ namespace boost + private: + volatile thread_detail::uintmax_atomic_t epoch; + +-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES ++#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES) + template + friend void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args); + #else +@@ -118,7 +118,7 @@ namespace boost + // http://www.open-std.org/jtc1/sc22/wg21/docs/papers/2007/n2444.html + + +-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES ++#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES) + + + template +diff --git a/boost/thread/pthread/once_atomic.hpp b/boost/thread/pthread/once_atomic.hpp +index 9e2f876..923f07b 100644 +--- a/boost/thread/pthread/once_atomic.hpp ++++ b/boost/thread/pthread/once_atomic.hpp +@@ -115,7 +115,7 @@ namespace boost + #endif + + +-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES ++#if !defined(BOOST_NO_CXX11_VARIADIC_TEMPLATES) && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES) + + template + inline void call_once(once_flag& flag, BOOST_THREAD_RV_REF(Function) f, BOOST_THREAD_RV_REF(ArgTypes)... args) +diff --git a/boost/thread/win32/once.hpp b/boost/thread/win32/once.hpp +index cafcfd4..9b37b31 100644 +--- a/boost/thread/win32/once.hpp ++++ b/boost/thread/win32/once.hpp +@@ -227,7 +227,7 @@ namespace boost + } + } + +-#ifndef BOOST_NO_CXX11_VARIADIC_TEMPLATES ++#if !defined BOOST_NO_CXX11_VARIADIC_TEMPLATES && !defined(BOOST_NO_CXX11_RVALUE_REFERENCES) + //#if defined(BOOST_THREAD_RVALUE_REFERENCES_DONT_MATCH_FUNTION_PTR) + inline void call_once(once_flag& flag, void (*f)()) + { diff --git a/var/spack/repos/builtin/packages/boost/package.py b/var/spack/repos/builtin/packages/boost/package.py index c0aa582d72d..9ac2d7e2ab0 100644 --- a/var/spack/repos/builtin/packages/boost/package.py +++ b/var/spack/repos/builtin/packages/boost/package.py @@ -148,6 +148,8 @@ class Boost(Package): patch('xl_1_62_0_le.patch', when='@1.62.0%xl_r') patch('xl_1_62_0_le.patch', when='@1.62.0%xl') + patch('call_once_variadic.patch', when='@:1.56.0%gcc@5:') + def url_for_version(self, version): url = "http://downloads.sourceforge.net/project/boost/boost/{0}/boost_{1}.tar.bz2" return url.format(version.dotted, version.underscored) From 8b47fe5a781ba73bd3a5d86e23b6debbd27cf625 Mon Sep 17 00:00:00 2001 From: Douglas Duckworth Date: Fri, 19 May 2017 12:55:48 -0400 Subject: [PATCH 06/20] added R 3.4.0, again (#4260) (#4294) --- var/spack/repos/builtin/packages/r/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/r/package.py b/var/spack/repos/builtin/packages/r/package.py index 948de4340ec..4ae8caab238 100644 --- a/var/spack/repos/builtin/packages/r/package.py +++ b/var/spack/repos/builtin/packages/r/package.py @@ -36,10 +36,11 @@ class R(AutotoolsPackage): Please consult the R project homepage for further information.""" homepage = "https://www.r-project.org" - url = "https://cloud.r-project.org/src/base/R-3/R-3.3.2.tar.gz" + url = "https://cloud.r-project.org/src/base/R-3/R-3.4.0.tar.gz" extendable = True + version('3.4.0', '75083c23d507b9c16d5c6afbd7a827e7') version('3.3.3', '0ac211ec15e813a24f8f4a5a634029a4') version('3.3.2', '2437014ef40641cdc9673e89c040b7a8') version('3.3.1', 'f50a659738b73036e2f5635adbd229c5') From 571a42d6149faf88e5b49fa6d8d9bfa6c2b6c783 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Fri, 19 May 2017 19:03:56 +0200 Subject: [PATCH 07/20] Fix gcc not finding zlib (#4291) --- var/spack/repos/builtin/packages/gcc/package.py | 9 +++++++++ 1 file changed, 9 insertions(+) diff --git a/var/spack/repos/builtin/packages/gcc/package.py b/var/spack/repos/builtin/packages/gcc/package.py index 893b8efce59..1bdee43e831 100644 --- a/var/spack/repos/builtin/packages/gcc/package.py +++ b/var/spack/repos/builtin/packages/gcc/package.py @@ -170,6 +170,15 @@ def patch(self): 'typedef void* dispatch_block_t', new_header) + # Use installed libz + if self.version >= Version('6'): + filter_file('@zlibdir@', + '-L{0}'.format(spec['zlib'].prefix.lib), + 'gcc/Makefile.in') + filter_file('@zlibinc@', + '-I{0}'.format(spec['zlib'].prefix.include), + 'gcc/Makefile.in') + def configure_args(self): spec = self.spec From efbcdafd30d0df8b2317f772d00c31df08fe57d8 Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Fri, 19 May 2017 15:09:21 -0700 Subject: [PATCH 08/20] Mpifileutils (#4283) * adding mpifileutils * mpifileutils: add +lustre variant * mpifileutils: add variant for xattr * mpifileutils: update to AutotoolsPackage * mpifileutils: simplify and eliminate redundant make * mpifileutils: drop unnecessary comments --- .../builtin/packages/mpifileutils/package.py | 81 +++++++++++++++++++ 1 file changed, 81 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mpifileutils/package.py diff --git a/var/spack/repos/builtin/packages/mpifileutils/package.py b/var/spack/repos/builtin/packages/mpifileutils/package.py new file mode 100644 index 00000000000..102a1e9ff99 --- /dev/null +++ b/var/spack/repos/builtin/packages/mpifileutils/package.py @@ -0,0 +1,81 @@ +############################################################################## +# Copyright (c) 2013-2017, Lawrence Livermore National Security, LLC. +# Produced at the Lawrence Livermore National Laboratory. +# +# This file is part of Spack. +# Created by Todd Gamblin, tgamblin@llnl.gov, All rights reserved. +# LLNL-CODE-647188 +# +# For details, see https://github.com/llnl/spack +# Please also see the LICENSE file for our notice and the LGPL. +# +# This program is free software; you can redistribute it and/or modify +# it under the terms of the GNU Lesser General Public License (as +# published by the Free Software Foundation) version 2.1, February 1999. +# +# This program is distributed in the hope that it will be useful, but +# WITHOUT ANY WARRANTY; without even the IMPLIED WARRANTY OF +# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the terms and +# conditions of the GNU Lesser General Public License for more details. +# +# You should have received a copy of the GNU Lesser General Public +# License along with this program; if not, write to the Free Software +# Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA +############################################################################## +from spack import * + + +class Mpifileutils(AutotoolsPackage): + """mpiFileUtils is a suite of MPI-based tools to manage large datasets, + which may vary from large directory trees to large files. + High-performance computing users often generate large datasets with + parallel applications that run with many processes (millions in some + cases). However those users are then stuck with single-process tools + like cp and rm to manage their datasets. This suite provides + MPI-based tools to handle typical jobs like copy, remove, and compare + for such datasets, providing speedups of up to 20-30x.""" + + homepage = "https://github.com/hpc/mpifileutils" + url = "https://github.com/hpc/mpifileutils/releases/download/v0.6/mpifileutils-0.6.tar.gz" + + version('0.6', '620bcc4966907481f1b1a965b28fc9bf') + + depends_on('mpi') + depends_on('libcircle') + depends_on('lwgrp') + depends_on('dtcmp') + depends_on('libarchive') + + variant('xattr', default=True, + description="Enable code for extended attributes") + + variant('lustre', default=False, + description="Enable optimizations and features for Lustre") + + # install experimental tools + # (coming with v0.7) + # variant('experimental', default=False, + # description="Install experimental tools") + + def configure_args(self): + args = [] + + if '+lustre' in self.spec: + args.append('--enable-lustre') + else: + args.append('--disable-lustre') + + # coming with v0.7 + # if '+experimental' in self.spec: + # args.append('--enable-experimental') + # else: + # args.append('--disable-experimental') + + return args + + @property + def build_targets(self): + targets = [] + if '+xattr' in self.spec: + targets.append('CFLAGS=-DDCOPY_USE_XATTRS') + return targets From a62bbb6ed89024499d4c6e3fe41bd0a69d94c5ca Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sat, 20 May 2017 00:30:54 +0200 Subject: [PATCH 09/20] gobject-introspection depends on pkg-build (#4301) --- .../repos/builtin/packages/gobject-introspection/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/gobject-introspection/package.py b/var/spack/repos/builtin/packages/gobject-introspection/package.py index 5f147cccfca..55ea0369a4f 100644 --- a/var/spack/repos/builtin/packages/gobject-introspection/package.py +++ b/var/spack/repos/builtin/packages/gobject-introspection/package.py @@ -44,6 +44,7 @@ class GobjectIntrospection(Package): depends_on("cairo") depends_on("bison", type="build") depends_on("flex", type="build") + depends_on("pkg-config@0.9.0:", type="build") # This package creates several scripts from # toosl/g-ir-tool-template.in. In their original form these From ff6ebe30e07aa105e9b5eb36bb24d1339ec9e476 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 19 May 2017 18:31:20 -0400 Subject: [PATCH 10/20] cmake: new version (#4274) --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 7642df9f198..70d6c14351a 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -33,6 +33,7 @@ class Cmake(Package): list_url = 'https://cmake.org/files/' list_depth = 1 + version('3.8.1', 'e8ef820ddf7a650845252bca846696e7') version('3.8.0', 'f28cba717ba38ad82a488daed8f45b5b') version('3.7.2', '79bd7e65cd81ea3aa2619484ad6ff25a') version('3.7.1', 'd031d5a06e9f1c5367cdfc56fbd2a1c8') From eb001e4d5dc4b7bde6592a8d903f28f2545041bd Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 19 May 2017 18:31:53 -0400 Subject: [PATCH 11/20] hpx5: new version (#4273) --- var/spack/repos/builtin/packages/hpx5/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/hpx5/package.py b/var/spack/repos/builtin/packages/hpx5/package.py index a1b1b0fc6b6..55f253f4672 100644 --- a/var/spack/repos/builtin/packages/hpx5/package.py +++ b/var/spack/repos/builtin/packages/hpx5/package.py @@ -39,6 +39,7 @@ class Hpx5(AutotoolsPackage): homepage = "http://hpx.crest.iu.edu" url = "http://hpx.crest.iu.edu/release/hpx-3.1.0.tar.gz" + version('4.1.0', '43cb78758506f77416b95276a472f84f') version('4.0.0', 'b40dc03449ae1039cbb48ee149952b22') version('3.1.0', '9e90b8ac46788c009079632828c77628') version('2.0.0', '3d2ff3aab6c46481f9ec65c5b2bfe7a6') From 4b075de9de5847a5104ef008f24117a62e7e4f7a Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 19 May 2017 18:32:16 -0400 Subject: [PATCH 12/20] hwloc: new version (#4272) --- var/spack/repos/builtin/packages/hwloc/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/hwloc/package.py b/var/spack/repos/builtin/packages/hwloc/package.py index 6efa2dfbd93..b2db0b3b38c 100644 --- a/var/spack/repos/builtin/packages/hwloc/package.py +++ b/var/spack/repos/builtin/packages/hwloc/package.py @@ -44,6 +44,7 @@ class Hwloc(AutotoolsPackage): list_url = "http://www.open-mpi.org/software/hwloc/" list_depth = 2 + version('1.11.7', '867a5266675e5bf1ef4ab66c459653f8') version('1.11.6', 'b4e95eadd2fbdb6d40bbd96be6f03c84') version('1.11.5', '8f5fe6a9be2eb478409ad5e640b2d3ba') version('1.11.4', 'b6f23eb59074fd09fdd84905d50b103d') From a32f8c33b045f8bcb70ad0cb5b00d4e0b0c373e0 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 19 May 2017 18:32:40 -0400 Subject: [PATCH 13/20] julia: New version 0.5.2 (#4259) --- var/spack/repos/builtin/packages/julia/package.py | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 007a384f10e..ad44d026192 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -37,7 +37,8 @@ class Julia(Package): git='https://github.com/JuliaLang/julia.git', branch='master') version('release-0.5', git='https://github.com/JuliaLang/julia.git', branch='release-0.5') - version('0.5.1', 'bce119b98f274e0f07ce01498c463ad5', preferred=True) + version('0.5.2', '8c3fff150a6f96cf0536fb3b4eaa5cbb', preferred=True) + version('0.5.1', 'bce119b98f274e0f07ce01498c463ad5') version('0.5.0', 'b61385671ba74767ab452363c43131fb') version('release-0.4', git='https://github.com/JuliaLang/julia.git', branch='release-0.4') From c741cd900b81e65d3a2b959bb3744de745ffaac4 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sat, 20 May 2017 16:40:10 +0200 Subject: [PATCH 14/20] magics fixes for versions > 2.29.x (#4302) --- var/spack/repos/builtin/packages/magics/package.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py index f7df6ce2feb..22fb6a73c36 100644 --- a/var/spack/repos/builtin/packages/magics/package.py +++ b/var/spack/repos/builtin/packages/magics/package.py @@ -42,7 +42,7 @@ class Magics(Package): # The patch changes the hardcoded path to python in shebang to enable the # usage of the first python installation that appears in $PATH - patch('no_hardcoded_python.patch') + patch('no_hardcoded_python.patch', when='@:2.29.6') # The patch reorders includes and adds namespaces where necessary to # resolve ambiguity of invocations of isnan and isinf functions. The @@ -63,7 +63,8 @@ class Magics(Package): depends_on('python', type='build') depends_on('perl', type='build') depends_on('perl-xml-parser', type='build') - depends_on('grib-api') + depends_on('eccodes', when='@2.30.0:') + depends_on('grib-api', when='@:2.29.6') depends_on('proj') depends_on('boost') depends_on('expat') @@ -72,6 +73,7 @@ class Magics(Package): depends_on('libemos', when='+bufr') depends_on('qt', when='+metview+qt') + @when('@:2.29.6') def patch(self): filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', 'tools/xml2cc_new.pl') @@ -83,9 +85,13 @@ def install(self, spec, prefix): options.append('-DENABLE_PYTHON=OFF') options.append('-DBOOST_ROOT=%s' % spec['boost'].prefix) options.append('-DPROJ4_PATH=%s' % spec['proj'].prefix) - options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix) options.append('-DENABLE_TESTS=OFF') + if self.version >= Version('2.30.0'): + options.append('-DECCODES_PATH=%s' % spec['eccodes'].prefix) + else: + options.append('-DGRIB_API_PATH=%s' % spec['grib-api'].prefix) + if '+bufr' in spec: options.append('-DENABLE_BUFR=ON') options.append('-DLIBEMOS_PATH=%s' % spec['libemos'].prefix) From 17b2db0bd215bbd77319484b76bc8d950fa7564d Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sun, 21 May 2017 03:59:15 +0200 Subject: [PATCH 15/20] Fix ncview with netcdf+mpi (#4305) ncview has to be compiled using the same compiler as netcdf. --- var/spack/repos/builtin/packages/ncview/package.py | 10 ++++++++++ 1 file changed, 10 insertions(+) diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py index 6f83aa9139e..ecd733ccea2 100644 --- a/var/spack/repos/builtin/packages/ncview/package.py +++ b/var/spack/repos/builtin/packages/ncview/package.py @@ -36,3 +36,13 @@ class Ncview(AutotoolsPackage): depends_on('udunits2') depends_on('libpng') depends_on('libxaw') + + def configure_args(self): + spec = self.spec + + config_args = [] + + if spec.satisfies('^netcdf+mpi'): + config_args.append('CC={0}'.format(spec['mpi'].mpicc)) + + return config_args From e4a3295c37f3bc68a659f7400ef3315d75b6e2ca Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Sun, 21 May 2017 06:40:59 +0200 Subject: [PATCH 16/20] spark: remove whitespaces from run_env variable (#4210) --- var/spack/repos/builtin/packages/spark/package.py | 9 +++++++-- 1 file changed, 7 insertions(+), 2 deletions(-) diff --git a/var/spack/repos/builtin/packages/spark/package.py b/var/spack/repos/builtin/packages/spark/package.py index 3bc6abd234c..e955a759852 100644 --- a/var/spack/repos/builtin/packages/spark/package.py +++ b/var/spack/repos/builtin/packages/spark/package.py @@ -22,10 +22,11 @@ # License along with this program; if not, write to the Free Software # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## -from spack import * - +import re import shutil +from spack import * + class Spark(Package): """Apache Spark is a fast and general engine @@ -72,4 +73,8 @@ def setup_environment(self, spack_env, run_env): hadoop = self.spec['hadoop'].command hadoop_classpath = hadoop('classpath', return_output=True) + # Remove whitespaces, as they can compromise syntax in + # module files + hadoop_classpath = re.sub('[\s+]', '', hadoop_classpath) + run_env.set('SPARK_DIST_CLASSPATH', hadoop_classpath) From ca2755d53268756f8c1c004f4f9e96f78765d8a8 Mon Sep 17 00:00:00 2001 From: Milton Woods Date: Sun, 21 May 2017 23:33:34 +1000 Subject: [PATCH 17/20] flex: create variant +lex that creates symlinks for lex and libl.{a,so} (#3894) * flex: create variant +lex that creates symlinks for lex and libl.{a,so} * flex: enable variant +lex by default * flex: use dso_suffix for portability; replace repetitive code with a loop --- .../repos/builtin/packages/flex/package.py | 17 +++++++++++++++++ 1 file changed, 17 insertions(+) diff --git a/var/spack/repos/builtin/packages/flex/package.py b/var/spack/repos/builtin/packages/flex/package.py index 8f0c46bc56e..73d08d98e0e 100644 --- a/var/spack/repos/builtin/packages/flex/package.py +++ b/var/spack/repos/builtin/packages/flex/package.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import os class Flex(AutotoolsPackage): @@ -39,6 +40,9 @@ class Flex(AutotoolsPackage): version('2.6.0', '760be2ee9433e822b6eb65318311c19d') version('2.5.39', '5865e76ac69c05699f476515592750d7') + variant('lex', default=True, + description="Provide symlinks for lex and libl") + depends_on('bison', type='build') depends_on('gettext@0.19:', type='build') depends_on('help2man', type='build') @@ -61,3 +65,16 @@ def url_for_version(self, version): url += "/archive/flex-{0}.tar.gz".format(version.dashed) return url + + @run_after('install') + def symlink_lex(self): + if self.spec.satisfies('+lex'): + dso = dso_suffix + for dir, flex, lex in \ + ((self.prefix.bin, 'flex', 'lex'), + (self.prefix.lib, 'libfl.a', 'libl.a'), + (self.prefix.lib, 'libfl.' + dso, 'libl.' + dso)): + with working_dir(dir): + if (os.path.isfile(flex) and not + os.path.lexists(lex)): + symlink(flex, lex) From f9203d42812261b22417f1f8129416a825414301 Mon Sep 17 00:00:00 2001 From: Michael Kuhn Date: Sun, 21 May 2017 20:34:16 +0200 Subject: [PATCH 18/20] libdrm depends on pkg-config (#4308) --- var/spack/repos/builtin/packages/libdrm/package.py | 1 + 1 file changed, 1 insertion(+) diff --git a/var/spack/repos/builtin/packages/libdrm/package.py b/var/spack/repos/builtin/packages/libdrm/package.py index bebc20f089a..750d3361d96 100644 --- a/var/spack/repos/builtin/packages/libdrm/package.py +++ b/var/spack/repos/builtin/packages/libdrm/package.py @@ -38,6 +38,7 @@ class Libdrm(Package): version('2.4.59', '105ac7af1afcd742d402ca7b4eb168b6') version('2.4.33', '86e4e3debe7087d5404461e0032231c8') + depends_on('pkg-config@0.9.0:', type='build') depends_on('libpciaccess@0.10:', when=(sys.platform != 'darwin')) depends_on('libpthread-stubs') From 132b3c56bc09e3cafef1355024d7efdee0e13744 Mon Sep 17 00:00:00 2001 From: Milton Woods Date: Mon, 22 May 2017 09:01:26 +1000 Subject: [PATCH 19/20] qt: patch JavaScriptCore to favour internal pcre headers (#4270) --- .../repos/builtin/packages/qt/package.py | 3 ++ .../repos/builtin/packages/qt/qt5-pcre.patch | 33 +++++++++++++++++++ 2 files changed, 36 insertions(+) create mode 100644 var/spack/repos/builtin/packages/qt/qt5-pcre.patch diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 3737c70f5ac..c0b08d86f1f 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -73,6 +73,9 @@ class Qt(Package): # https://github.com/xboxdrv/xboxdrv/issues/188 patch('btn_trigger_happy.patch', when='@5.7.0:') + # https://github.com/LLNL/spack/issues/1517 + patch('qt5-pcre.patch', when='@5:') + patch('qt4-corewlan-new-osx.patch', when='@4') patch('qt4-pcre-include-conflict.patch', when='@4') patch('qt4-el-capitan.patch', when='@4') diff --git a/var/spack/repos/builtin/packages/qt/qt5-pcre.patch b/var/spack/repos/builtin/packages/qt/qt5-pcre.patch new file mode 100644 index 00000000000..8fdf25661c6 --- /dev/null +++ b/var/spack/repos/builtin/packages/qt/qt5-pcre.patch @@ -0,0 +1,33 @@ +--- a/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/runtime/RegExp.cpp 2016-09-17 20:55:14.000000000 +0000 ++++ b/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/runtime/RegExp.cpp 2017-05-17 01:55:10.000000000 +0000 +@@ -44,7 +44,7 @@ + #include "JIT.h" + #include "WRECGenerator.h" + #endif +-#include ++#include "../pcre/pcre.h" + + #endif + +--- a/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.cpp 2016-09-17 20:55:14.000000000 +0000 ++++ b/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.cpp 2017-05-17 01:55:51.000000000 +0000 +@@ -32,7 +32,7 @@ + #include "MacroAssembler.h" + #include "RegexCompiler.h" + +-#include "pcre.h" // temporary, remove when fallback is removed. ++#include "../pcre/pcre.h" // temporary, remove when fallback is removed. + + #if ENABLE(YARR_JIT) + +--- a/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h 2016-09-17 20:55:14.000000000 +0000 ++++ b/qtscript/src/3rdparty/javascriptcore/JavaScriptCore/yarr/RegexJIT.h 2017-05-17 01:55:36.000000000 +0000 +@@ -34,7 +34,7 @@ + #include "RegexPattern.h" + #include + +-#include ++#include "../pcre/pcre.h" + struct JSRegExp; // temporary, remove when fallback is removed. + + #if CPU(X86) && !COMPILER(MSVC) From 8ab845939780d1dfcc9a405d9dafff0ed0f2b26d Mon Sep 17 00:00:00 2001 From: Milton Woods Date: Mon, 22 May 2017 21:45:24 +1000 Subject: [PATCH 20/20] magics: use spack perl instead of system perl (#4310) --- var/spack/repos/builtin/packages/magics/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/var/spack/repos/builtin/packages/magics/package.py b/var/spack/repos/builtin/packages/magics/package.py index 22fb6a73c36..fca92d69d44 100644 --- a/var/spack/repos/builtin/packages/magics/package.py +++ b/var/spack/repos/builtin/packages/magics/package.py @@ -23,6 +23,7 @@ # Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA ############################################################################## from spack import * +import glob class Magics(Package): @@ -73,10 +74,9 @@ class Magics(Package): depends_on('libemos', when='+bufr') depends_on('qt', when='+metview+qt') - @when('@:2.29.6') def patch(self): - filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', - 'tools/xml2cc_new.pl') + for plfile in glob.glob('*/*.pl'): + filter_file('#!/usr/bin/perl', '#!/usr/bin/env perl', plfile) def install(self, spec, prefix): options = []