From ac088bae6a09c8d2ee7f9deac3e701126ca5dfa4 Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Tue, 1 Sep 2015 16:02:14 -0700 Subject: update boost --- var/spack/packages/boost/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/packages/boost/package.py b/var/spack/packages/boost/package.py index 254d1afda1..35824d53a2 100644 --- a/var/spack/packages/boost/package.py +++ b/var/spack/packages/boost/package.py @@ -14,6 +14,10 @@ class Boost(Package): list_url = "http://sourceforge.net/projects/boost/files/boost/" list_depth = 2 + version('1.59.0', '6aa9a5c6a4ca1016edd0ed1178e3cb87') + version('1.58.0', 'b8839650e61e9c1c0a89f371dd475546') + version('1.57.0', '1be49befbdd9a5ce9def2983ba3e7b76') + version('1.56.0', 'a744cf167b05d72335f27c88115f211d') version('1.55.0', 'd6eef4b4cacb2183f2bf265a5a03a354') version('1.54.0', '15cb8c0803064faef0c4ddf5bc5ca279') version('1.53.0', 'a00d22605d5dbcfb4c9936a9b35bc4c2') -- cgit v1.2.3-60-g2f50 From b06117f77a71a5c82a07b2ff063c30cb9a9a25c3 Mon Sep 17 00:00:00 2001 From: Rasmus Wriedt Larsen Date: Thu, 3 Sep 2015 14:19:27 -0700 Subject: Add fish (shell) package --- var/spack/packages/fish/package.py | 18 ++++++++++++++++++ 1 file changed, 18 insertions(+) create mode 100644 var/spack/packages/fish/package.py (limited to 'var') diff --git a/var/spack/packages/fish/package.py b/var/spack/packages/fish/package.py new file mode 100644 index 0000000000..1225558705 --- /dev/null +++ b/var/spack/packages/fish/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Fish(Package): + """fish is a smart and user-friendly command line shell for OS X, Linux, and + the rest of the family. + """ + + homepage = "http://fishshell.com/" + url = "http://fishshell.com/files/2.2.0/fish-2.2.0.tar.gz" + list_url = homepage + + version('2.2.0', 'a76339fd14ce2ec229283c53e805faac48c3e99d9e3ede9d82c0554acfc7b77a') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") -- cgit v1.2.3-60-g2f50 From 99ca0f31531059037a6508aab8ecc62d080f8ce5 Mon Sep 17 00:00:00 2001 From: Justin Too Date: Fri, 11 Sep 2015 20:27:09 +0000 Subject: (Package) Add Doxygen (v1.8.10) --- var/spack/packages/doxygen/package.py | 25 +++++++++++++++++++++++++ 1 file changed, 25 insertions(+) create mode 100644 var/spack/packages/doxygen/package.py (limited to 'var') diff --git a/var/spack/packages/doxygen/package.py b/var/spack/packages/doxygen/package.py new file mode 100644 index 0000000000..3d4a4e47a7 --- /dev/null +++ b/var/spack/packages/doxygen/package.py @@ -0,0 +1,25 @@ +#------------------------------------------------------------------------------ +# Author: Justin Too +# Date: September 11, 2015 +#------------------------------------------------------------------------------ + +from spack import * + +class Doxygen(Package): + """Doxygen is the de facto standard tool for generating documentation + from annotated C++ sources, but it also supports other popular programming + languages such as C, Objective-C, C#, PHP, Java, Python, IDL (Corba, + Microsoft, and UNO/OpenOffice flavors), Fortran, VHDL, Tcl, and to some extent D.. + """ + homepage = "http://www.stack.nl/~dimitri/doxygen/" + url = "http://ftp.stack.nl/pub/users/dimitri/doxygen-1.8.10.src.tar.gz" + + version('1.8.10', '79767ccd986f12a0f949015efb5f058f') + + depends_on("cmake@2.8.12:") + + def install(self, spec, prefix): + cmake('.', *std_cmake_args) + + make() + make("install") -- cgit v1.2.3-60-g2f50 From e4e22ed17ec92a7be2895070e1d720ba4afb3dcb Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Mon, 21 Sep 2015 16:19:50 -0700 Subject: add protobuf package --- var/spack/packages/protobuf/package.py | 16 ++++++++++++++++ 1 file changed, 16 insertions(+) create mode 100644 var/spack/packages/protobuf/package.py (limited to 'var') diff --git a/var/spack/packages/protobuf/package.py b/var/spack/packages/protobuf/package.py new file mode 100644 index 0000000000..34085c7ce9 --- /dev/null +++ b/var/spack/packages/protobuf/package.py @@ -0,0 +1,16 @@ +import os +from spack import * + +class Protobuf(Package): + """Google's data interchange format.""" + + homepage = "https://developers.google.com/protocol-buffers" + url = "https://github.com/google/protobuf/releases/download/v2.5.0/protobuf-2.5.0.tar.bz2" + + version('2.5.0', 'a72001a9067a4c2c4e0e836d0f92ece4') + + def install(self, spec, prefix): + configure("--prefix=" + prefix) + make() + make("check") + make("install") -- cgit v1.2.3-60-g2f50 From b5d7cd55ce197bf4e6d476996ab874083efb86a2 Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Mon, 21 Sep 2015 16:30:11 -0700 Subject: add glog package --- var/spack/packages/glog/package.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 var/spack/packages/glog/package.py (limited to 'var') diff --git a/var/spack/packages/glog/package.py b/var/spack/packages/glog/package.py new file mode 100644 index 0000000000..d73386b394 --- /dev/null +++ b/var/spack/packages/glog/package.py @@ -0,0 +1,15 @@ +import os +from spack import * + +class Glog(Package): + """C++ implementation of the Google logging module.""" + + homepage = "https://github.com/google/glog" + url = "https://github.com/google/glog/archive/v0.3.3.tar.gz" + + version('0.3.3', 'c1f86af27bd9c73186730aa957607ed0') + + def install(self, spec, prefix): + configure("--prefix=" + prefix) + make() + make("install") -- cgit v1.2.3-60-g2f50 From 22ba02b22b50107463928878430dbab2b26c39d1 Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Mon, 21 Sep 2015 16:40:23 -0700 Subject: add gflags package --- var/spack/packages/gflags/package.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/packages/gflags/package.py (limited to 'var') diff --git a/var/spack/packages/gflags/package.py b/var/spack/packages/gflags/package.py new file mode 100644 index 0000000000..62dd80a094 --- /dev/null +++ b/var/spack/packages/gflags/package.py @@ -0,0 +1,21 @@ +import os +from spack import * + +class Gflags(Package): + """The gflags package contains a C++ library that implements + commandline flags processing. It includes built-in support for + standard types such as string and the ability to define flags + in the source file in which they are used. Online documentation + available at: https://gflags.github.io/gflags/""" + + homepage = "https://gflags.github.io/gflags" + url = "https://github.com/gflags/gflags/archive/v2.1.2.tar.gz" + + version('2.1.2', 'ac432de923f9de1e9780b5254884599f') + + def install(self, spec, prefix): + cmake("-DCMAKE_INSTALL_PREFIX=" + prefix, + "-DBUILD_SHARED_LIBS=ON") + make() + make("test") + make("install") -- cgit v1.2.3-60-g2f50 From 30acc6f2f04beb56ef67af385cc8543ceeca82af Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Mon, 21 Sep 2015 16:45:59 -0700 Subject: add snappy package --- var/spack/packages/snappy/package.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 var/spack/packages/snappy/package.py (limited to 'var') diff --git a/var/spack/packages/snappy/package.py b/var/spack/packages/snappy/package.py new file mode 100644 index 0000000000..c8f9ceef7d --- /dev/null +++ b/var/spack/packages/snappy/package.py @@ -0,0 +1,15 @@ +import os +from spack import * + +class Snappy(Package): + """A fast compressor/decompressor: https://code.google.com/p/snappy""" + + homepage = "https://code.google.com/p/snappy" + url = "https://github.com/google/snappy/releases/download/1.1.3/snappy-1.1.3.tar.gz" + + version('1.1.3', '7358c82f133dc77798e4c2062a749b73') + + def install(self, spec, prefix): + configure("--prefix=" + prefix) + make() + make("install") -- cgit v1.2.3-60-g2f50 From 3ade141829bc382cd7d50d02d79967e78d0de147 Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Tue, 22 Sep 2015 11:59:09 -0700 Subject: add leveldb package --- var/spack/packages/leveldb/package.py | 29 +++++++++++++++++++++++++++++ 1 file changed, 29 insertions(+) create mode 100644 var/spack/packages/leveldb/package.py (limited to 'var') diff --git a/var/spack/packages/leveldb/package.py b/var/spack/packages/leveldb/package.py new file mode 100644 index 0000000000..da68a9cbcb --- /dev/null +++ b/var/spack/packages/leveldb/package.py @@ -0,0 +1,29 @@ +import os +import glob +from spack import * + +class Leveldb(Package): + """LevelDB is a fast key-value storage library written at Google + that provides an ordered mapping from string keys to string values.""" + + homepage = "https://github.com/google/leveldb" + url = "https://github.com/google/leveldb/archive/v1.18.tar.gz" + + version('1.18', '73770de34a2a5ab34498d2e05b2b7fa0') + + depends_on("snappy") + + def install(self, spec, prefix): + make() + + mkdirp(prefix.include) + mkdirp(prefix.lib) + + cp = which('cp') + + # cp --preserve=links libleveldb.* prefix/lib + args = glob.glob('libleveldb.*') + args.append(prefix + '/lib') + cp('--preserve=links', *args) + + cp('-r', 'include/leveldb', prefix + '/include') -- cgit v1.2.3-60-g2f50 From 84823ed828599aa03ba9d6cd49488d975652d242 Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Tue, 22 Sep 2015 12:17:01 -0700 Subject: add lmdb package --- var/spack/packages/lmdb/package.py | 39 ++++++++++++++++++++++++++++++++++++++ 1 file changed, 39 insertions(+) create mode 100644 var/spack/packages/lmdb/package.py (limited to 'var') diff --git a/var/spack/packages/lmdb/package.py b/var/spack/packages/lmdb/package.py new file mode 100644 index 0000000000..875b8100c5 --- /dev/null +++ b/var/spack/packages/lmdb/package.py @@ -0,0 +1,39 @@ +import os +from spack import * + +class Lmdb(Package): + """Read-only mirror of official repo on openldap.org. Issues and + pull requests here are ignored. Use OpenLDAP ITS for issues. + http://www.openldap.org/software/repo.html""" + + + homepage = "http://www.openldap.org/software/repo.html" + url = "https://github.com/LMDB/lmdb/archive/LMDB_0.9.16.tar.gz" + + version('0.9.16', '0de89730b8f3f5711c2b3a4ba517b648') + + def install(self, spec, prefix): + os.chdir('libraries/liblmdb') + + make() + + mkdirp(prefix.bin) + mkdirp(prefix + '/man/man1') + mkdirp(prefix.lib) + mkdirp(prefix.include) + + bins = ['mdb_stat', 'mdb_copy', 'mdb_dump', 'mdb_load'] + for f in bins: + install(f, prefix.bin) + + mans = ['mdb_stat.1', 'mdb_copy.1', 'mdb_dump.1', 'mdb_load.1'] + for f in mans: + install(f, prefix + '/man/man1') + + libs = ['liblmdb.a', 'liblmdb.so'] + for f in libs: + install(f, prefix.lib) + + includes = ['lmdb.h'] + for f in includes: + install(f, prefix.include) -- cgit v1.2.3-60-g2f50 From 521632b3dc30c81fe4230ef010b972e65d80c47a Mon Sep 17 00:00:00 2001 From: Mario Melara Date: Wed, 23 Sep 2015 16:30:44 -0700 Subject: Added samtools bioinformatics software --- var/spack/packages/samtools/package.py | 18 ++++++++++++++++++ var/spack/packages/samtools/samtools1.2.patch | 20 ++++++++++++++++++++ 2 files changed, 38 insertions(+) create mode 100644 var/spack/packages/samtools/package.py create mode 100644 var/spack/packages/samtools/samtools1.2.patch (limited to 'var') diff --git a/var/spack/packages/samtools/package.py b/var/spack/packages/samtools/package.py new file mode 100644 index 0000000000..72900398d8 --- /dev/null +++ b/var/spack/packages/samtools/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Samtools(Package): + """SAM Tools provide various utilities for manipulating alignments in the SAM format, + including sorting, merging, indexing and generating + alignments in a per-position format""" + + homepage = "www.htslib.org" + version('1.2','988ec4c3058a6ceda36503eebecd4122',url = "https://github.com/samtools/samtools/releases/download/1.2/samtools-1.2.tar.bz2") + + depends_on("zlib") + depends_on("mpc") + parallel=False + patch("samtools1.2.patch",level=0) + + def install(self, spec, prefix): + make("prefix=%s" % prefix, "install") + diff --git a/var/spack/packages/samtools/samtools1.2.patch b/var/spack/packages/samtools/samtools1.2.patch new file mode 100644 index 0000000000..ead3ab4e2c --- /dev/null +++ b/var/spack/packages/samtools/samtools1.2.patch @@ -0,0 +1,20 @@ +--- Makefile 2015-02-03 08:27:34.000000000 -0800 ++++ Makefile.new 2015-07-21 10:38:27.881406892 -0700 +@@ -26,7 +26,7 @@ + CFLAGS = -g -Wall -O2 + LDFLAGS = + LDLIBS = +-DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=1 ++DFLAGS= -D_FILE_OFFSET_BITS=64 -D_LARGEFILE64_SOURCE -D_CURSES_LIB=0 + LOBJS= bam_aux.o bam.o bam_import.o sam.o \ + sam_header.o bam_plbuf.o + AOBJS= bam_index.o bam_plcmd.o sam_view.o \ +@@ -37,7 +37,7 @@ + faidx.o stats.o stats_isize.o bam_flags.o bam_split.o \ + bam_tview.o bam_tview_curses.o bam_tview_html.o bam_lpileup.o + INCLUDES= -I. -I$(HTSDIR) +-LIBCURSES= -lcurses # -lXCurses ++#LIBCURSES= -lcurses # -lXCurses + + prefix = /usr/local + exec_prefix = $(prefix) -- cgit v1.2.3-60-g2f50 From 13eb461ec31520c75d6d604038e455468d061a61 Mon Sep 17 00:00:00 2001 From: Mario Melara Date: Thu, 24 Sep 2015 11:21:54 -0700 Subject: Adding bowtie2 package along with patch --- var/spack/packages/bowtie2/bowtie2-2.5.patch | 16 ++++++++++++++++ var/spack/packages/bowtie2/package.py | 24 ++++++++++++++++++++++++ 2 files changed, 40 insertions(+) create mode 100644 var/spack/packages/bowtie2/bowtie2-2.5.patch create mode 100644 var/spack/packages/bowtie2/package.py (limited to 'var') diff --git a/var/spack/packages/bowtie2/bowtie2-2.5.patch b/var/spack/packages/bowtie2/bowtie2-2.5.patch new file mode 100644 index 0000000000..290be39c73 --- /dev/null +++ b/var/spack/packages/bowtie2/bowtie2-2.5.patch @@ -0,0 +1,16 @@ +--- Makefile 2015-02-26 10:50:00.000000000 -0800 ++++ Makefile.new 2015-07-29 18:03:59.891357399 -0700 +@@ -22,10 +22,10 @@ + # + + INC = +-GCC_PREFIX = $(shell dirname `which gcc`) ++GCC_PREFIX = + GCC_SUFFIX = +-CC = $(GCC_PREFIX)/gcc$(GCC_SUFFIX) +-CPP = $(GCC_PREFIX)/g++$(GCC_SUFFIX) ++CC = cc ++CPP = c++ + CXX = $(CPP) + HEADERS = $(wildcard *.h) + BOWTIE_MM = 1 diff --git a/var/spack/packages/bowtie2/package.py b/var/spack/packages/bowtie2/package.py new file mode 100644 index 0000000000..339aab6598 --- /dev/null +++ b/var/spack/packages/bowtie2/package.py @@ -0,0 +1,24 @@ +from spack import * +from glob import glob +class Bowtie2(Package): + """Description""" + homepage = "bowtie-bio.sourceforge.net/bowtie2/index.shtml" + version('2.2.5','51fa97a862d248d7ee660efc1147c75f', url = "http://downloads.sourceforge.net/project/bowtie-bio/bowtie2/2.2.5/bowtie2-2.2.5-source.zip") + + patch('bowtie2-2.5.patch',when='@2.2.5', level=0) + + def install(self, spec, prefix): + make() + mkdirp(prefix.bin) + for bow in glob("bowtie2*"): + install(bow, prefix.bin) + # install('bowtie2',prefix.bin) + # install('bowtie2-align-l',prefix.bin) + # install('bowtie2-align-s',prefix.bin) + # install('bowtie2-build',prefix.bin) + # install('bowtie2-build-l',prefix.bin) + # install('bowtie2-build-s',prefix.bin) + # install('bowtie2-inspect',prefix.bin) + # install('bowtie2-inspect-l',prefix.bin) + # install('bowtie2-inspect-s',prefix.bin) + -- cgit v1.2.3-60-g2f50 From 5563c666758f593b311a2de3e47cf617966a4c25 Mon Sep 17 00:00:00 2001 From: Adam Moody Date: Tue, 29 Sep 2015 18:18:34 -0700 Subject: update scr to 1.1.8 --- var/spack/packages/scr/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/packages/scr/package.py b/var/spack/packages/scr/package.py index 74b75a8742..9fb758f072 100644 --- a/var/spack/packages/scr/package.py +++ b/var/spack/packages/scr/package.py @@ -28,12 +28,14 @@ class Scr(Package): """SCR caches checkpoint data in storage on the compute nodes of a Linux cluster to provide a fast, scalable checkpoint/restart capability for MPI codes""" + homepage = "https://computation.llnl.gov/project/scr/" - url = "http://downloads.sourceforge.net/project/scalablecr/releases/scr-1.1-7.tar.gz" depends_on("mpi") +# depends_on("dtcmp") - version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd') + version('1.1-7', 'a5930e9ab27d1b7049447c2fd7734ebd', url='http://downloads.sourceforge.net/project/scalablecr/releases/scr-1.1-7.tar.gz') + version('1.1.8', '6a0f11ad18e27fcfc00a271ff587b06e', url='https://github.com/hpc/scr/releases/download/v1.1.8/scr-1.1.8.tar.gz') def install(self, spec, prefix): configure("--prefix=" + prefix, -- cgit v1.2.3-60-g2f50 From 75d30b08fbf09cbbc587891d0df472327d3669b9 Mon Sep 17 00:00:00 2001 From: Mario Melara Date: Thu, 1 Oct 2015 21:51:55 -0700 Subject: Added current version 3.2 of libffi version 3.1 has a bug that interferes with glib --- var/spack/packages/libffi/package.py | 7 ++++--- 1 file changed, 4 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/packages/libffi/package.py b/var/spack/packages/libffi/package.py index 2c1c4eed4d..acec031717 100644 --- a/var/spack/packages/libffi/package.py +++ b/var/spack/packages/libffi/package.py @@ -6,11 +6,12 @@ class Libffi(Package): to call any function specified by a call interface description at run time.""" homepage = "https://sourceware.org/libffi/" - url = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz" - - version('3.1', 'f5898b29bbfd70502831a212d9249d10') + + version('3.2.1','83b89587607e3eb65c70d361f13bab43',url = "ftp://sourceware.org/pub/libffi/libffi-3.2.1.tar.gz") + #version('3.1', 'f5898b29bbfd70502831a212d9249d10',url = "ftp://sourceware.org/pub/libffi/libffi-3.1.tar.gz") # Has a bug $(lib64) instead of ${lib64} in libffi.pc def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() make("install") + -- cgit v1.2.3-60-g2f50 From 6fcf16b710ef5e8ec8639aa191200661be7be2fd Mon Sep 17 00:00:00 2001 From: "Gregory L. Lee" Date: Mon, 5 Oct 2015 12:59:26 -0700 Subject: added libxcb version 1.11.1 --- var/spack/packages/libxcb/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/packages/libxcb/package.py b/var/spack/packages/libxcb/package.py index 521cd0d475..16a5525c0d 100644 --- a/var/spack/packages/libxcb/package.py +++ b/var/spack/packages/libxcb/package.py @@ -10,7 +10,7 @@ class Libxcb(Package): url = "http://xcb.freedesktop.org/dist/libxcb-1.11.tar.gz" version('1.11', '1698dd837d7e6e94d029dbe8b3a82deb') - + version('1.11.1', '118623c15a96b08622603a71d8789bf3') depends_on("python") depends_on("xcb-proto") -- cgit v1.2.3-60-g2f50 From 5dd39bfca56e984089236f4383d3ad348e1b0a54 Mon Sep 17 00:00:00 2001 From: "Gregory L. Lee" Date: Thu, 8 Oct 2015 08:12:30 -0700 Subject: bug fix for github issue 122 --- var/spack/packages/bzip2/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/packages/bzip2/package.py b/var/spack/packages/bzip2/package.py index fbd5869a53..d88336664d 100644 --- a/var/spack/packages/bzip2/package.py +++ b/var/spack/packages/bzip2/package.py @@ -22,8 +22,10 @@ class Bzip2(Package): bzip2_exe = join_path(prefix.bin, 'bzip2') install('bzip2-shared', bzip2_exe) - for libfile in glob('libbz2.so*'): + for i, libfile in enumerate(glob('libbz2.so*')): install(libfile, prefix.lib) + if i == 0: + symlink(join_path(prefix.lib, libfile), join_path(prefix.lib, 'libbz2.so')) bunzip2 = join_path(prefix.bin, 'bunzip2') remove(bunzip2) -- cgit v1.2.3-60-g2f50 From 9ec4ae83af7f88110e464fca22a9d1377d74b28e Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Thu, 15 Oct 2015 09:20:16 -0400 Subject: netcdf: link to MPI Newer GNU linker refuses to use transitive linking; if netcdf calls MPI_Allreduce, it must link the providing library directly. Also switched to CMake because I don't know autoconf well enough to know how to put MPI stuff into it. --- var/spack/packages/netcdf/netcdf-4.3.3-mpi.patch | 25 ++++++++++++++++++++ var/spack/packages/netcdf/package.py | 29 ++++++++++++------------ 2 files changed, 39 insertions(+), 15 deletions(-) create mode 100644 var/spack/packages/netcdf/netcdf-4.3.3-mpi.patch (limited to 'var') diff --git a/var/spack/packages/netcdf/netcdf-4.3.3-mpi.patch b/var/spack/packages/netcdf/netcdf-4.3.3-mpi.patch new file mode 100644 index 0000000000..46dda5fc9d --- /dev/null +++ b/var/spack/packages/netcdf/netcdf-4.3.3-mpi.patch @@ -0,0 +1,25 @@ +diff -Nur netcdf-4.3.3/CMakeLists.txt netcdf-4.3.3.mpi/CMakeLists.txt +--- netcdf-4.3.3/CMakeLists.txt 2015-02-12 16:44:35.000000000 -0500 ++++ netcdf-4.3.3.mpi/CMakeLists.txt 2015-10-14 16:44:41.176300658 -0400 +@@ -753,6 +753,7 @@ + SET(USE_PARALLEL OFF CACHE BOOL "") + MESSAGE(STATUS "Cannot find HDF5 library built with parallel support. Disabling parallel build.") + ELSE() ++ FIND_PACKAGE(MPI REQUIRED) + SET(USE_PARALLEL ON CACHE BOOL "") + SET(STATUS_PARALLEL "ON") + ENDIF() +diff -Nur netcdf-4.3.3/liblib/CMakeLists.txt netcdf-4.3.3.mpi/liblib/CMakeLists.txt +--- netcdf-4.3.3/liblib/CMakeLists.txt 2015-02-12 16:44:35.000000000 -0500 ++++ netcdf-4.3.3.mpi/liblib/CMakeLists.txt 2015-10-14 16:44:57.757793634 -0400 +@@ -71,6 +71,10 @@ + SET(TLL_LIBS ${TLL_LIBS} ${CURL_LIBRARY}) + ENDIF() + ++IF(USE_PARALLEL) ++ SET(TLL_LIBS ${TLL_LIBS} ${MPI_C_LIBRARIES}) ++ENDIF() ++ + IF(USE_HDF4) + SET(TLL_LIBS ${TLL_LIBS} ${HDF4_LIBRARIES}) + ENDIF() diff --git a/var/spack/packages/netcdf/package.py b/var/spack/packages/netcdf/package.py index 34284ea725..e1e0d836c6 100644 --- a/var/spack/packages/netcdf/package.py +++ b/var/spack/packages/netcdf/package.py @@ -1,28 +1,27 @@ from spack import * class Netcdf(Package): - """NetCDF is a set of software libraries and self-describing, machine-independent - data formats that support the creation, access, and sharing of array-oriented - scientific data.""" + """NetCDF is a set of software libraries and self-describing, machine-independent + data formats that support the creation, access, and sharing of array-oriented + scientific data.""" homepage = "http://www.unidata.ucar.edu/software/netcdf/" url = "ftp://ftp.unidata.ucar.edu/pub/netcdf/netcdf-4.3.3.tar.gz" version('4.3.3', '5fbd0e108a54bd82cb5702a73f56d2ae') + patch('netcdf-4.3.3-mpi.patch') + # Dependencies: - # >HDF5 + # >HDF5 depends_on("hdf5") - def install(self, spec, prefix): - configure( - "--prefix=%s" % prefix, - "--disable-dap", # Disable DAP. - "--disable-shared", # Don't build shared libraries (use static libs). - "CPPFLAGS=-I%s/include" % spec['hdf5'].prefix, # Link HDF5's include dir. - "LDFLAGS=-L%s/lib" % spec['hdf5'].prefix) # Link HDF5's lib dir. - - make("install") + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', + "-DCMAKE_INSTALL_PREFIX:PATH=%s" % prefix, + "-DENABLE_DAP:BOOL=OFF", # Disable DAP. + "-DBUILD_SHARED_LIBS:BOOL=OFF") # Don't build shared libraries (use static libs). - # Check the newly installed netcdf package. Currently disabled. - # make("check") + make() + make("install") -- cgit v1.2.3-60-g2f50 From f39e40664f8415493b2c5e511fdc608e97009186 Mon Sep 17 00:00:00 2001 From: Jeff Squyres Date: Fri, 16 Oct 2015 15:26:58 -0400 Subject: openmpi: add v1.10.0 and update v1.8.2->v1.8.8 --- var/spack/packages/openmpi/package.py | 6 ++++-- 1 file changed, 4 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/packages/openmpi/package.py b/var/spack/packages/openmpi/package.py index 7e84cbaf65..925d390281 100644 --- a/var/spack/packages/openmpi/package.py +++ b/var/spack/packages/openmpi/package.py @@ -11,8 +11,10 @@ class Openmpi(Package): homepage = "http://www.open-mpi.org" - version('1.8.2', 'ab538ed8e328079d566fc797792e016e', - url='http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.2.tar.gz') + version('1.10.0', '280cf952de68369cebaca886c5ce0304', + url = "http://www.open-mpi.org/software/ompi/v1.10/downloads/openmpi-1.10.0.tar.bz2") + version('1.8.8', '0dab8e602372da1425e9242ae37faf8c', + url = 'http://www.open-mpi.org/software/ompi/v1.8/downloads/openmpi-1.8.8.tar.bz2') version('1.6.5', '03aed2a4aa4d0b27196962a2a65fc475', url = "http://www.open-mpi.org/software/ompi/v1.6/downloads/openmpi-1.6.5.tar.bz2") -- cgit v1.2.3-60-g2f50 From 43f58d9f6183725f84c90bdd33a8386a5a9a8a97 Mon Sep 17 00:00:00 2001 From: Jeff Squyres Date: Fri, 16 Oct 2015 15:27:22 -0400 Subject: openmpi: update the MPI conformance for each Open MPI version --- var/spack/packages/openmpi/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/packages/openmpi/package.py b/var/spack/packages/openmpi/package.py index 925d390281..f9d0034878 100644 --- a/var/spack/packages/openmpi/package.py +++ b/var/spack/packages/openmpi/package.py @@ -21,7 +21,9 @@ class Openmpi(Package): patch('ad_lustre_rwcontig_open_source.patch', when="@1.6.5") patch('llnl-platforms.patch', when="@1.6.5") - provides('mpi@:2') + provides('mpi@:2.2', when='@1.6.5') # Open MPI 1.6.5 supports MPI-2.2 + provides('mpi@:3.0', when='@1.8.8') # Open MPI 1.8.8 supports MPI-3.0 + provides('mpi@:3.0', when='@1.10.0') # Open MPI 1.10.0 supports MPI-3.0 def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix] -- cgit v1.2.3-60-g2f50 From 67b94acd42fcb883993d99fc965beae3d0a76a45 Mon Sep 17 00:00:00 2001 From: Jeff Squyres Date: Sat, 17 Oct 2015 07:06:06 -0400 Subject: mpich: add fine-grained MPI conformance versions Similar to the Open MPI and MVAPICH packages. Signed-off-by: Jeff Squyres --- var/spack/packages/mpich/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/packages/mpich/package.py b/var/spack/packages/mpich/package.py index b6b2dfde21..c25c3eed91 100644 --- a/var/spack/packages/mpich/package.py +++ b/var/spack/packages/mpich/package.py @@ -35,8 +35,8 @@ class Mpich(Package): version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') - provides('mpi@:3', when='@3:') - provides('mpi@:1', when='@1:') + provides('mpi@:3.0', when='@3:') + provides('mpi@:1.3', when='@1:') def setup_dependent_environment(self, module, spec, dep_spec): """For dependencies, make mpicc's use spack wrapper.""" -- cgit v1.2.3-60-g2f50 From 44ba16a391d75f97bab9ebf0a8f1b609b18aba1d Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Sat, 17 Oct 2015 17:03:49 -0700 Subject: Add libiberty option to binutils --- var/spack/packages/binutils/package.py | 14 +++++++++++++- var/spack/packages/gcc/package.py | 2 +- 2 files changed, 14 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/packages/binutils/package.py b/var/spack/packages/binutils/package.py index 5a3059bbcf..0c33bf0426 100644 --- a/var/spack/packages/binutils/package.py +++ b/var/spack/packages/binutils/package.py @@ -10,8 +10,20 @@ class Binutils(Package): version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') + variant('libiberty', default=False, description='Also install libiberty.') + def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + configure_args = [ + '--prefix=%s' % prefix, + '--disable-dependency-tracking', + '--enable-interwork', + '--enable-multilib', + '--enable-64-bit-bfd', + '--enable-targets=all'] + + if '+libiberty' in spec: + configure_args.append('--enable-install-libiberty') + configure(*configure_args) make() make("install") diff --git a/var/spack/packages/gcc/package.py b/var/spack/packages/gcc/package.py index 5e3d1a3efa..2fc6794b70 100644 --- a/var/spack/packages/gcc/package.py +++ b/var/spack/packages/gcc/package.py @@ -47,7 +47,7 @@ class Gcc(Package): depends_on("gmp") depends_on("mpc") # when @4.5: depends_on("libelf") - depends_on("binutils") + depends_on("binutils~libiberty") # Save these until we can do optional deps. #depends_on("isl") -- cgit v1.2.3-60-g2f50 From f4460894beea13c2d028338503c9cef5608e05b6 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Fri, 25 Sep 2015 10:44:47 +0200 Subject: hdf5 : updated version mpich : updated version trilinos : created stub --- var/spack/packages/hdf5/package.py | 3 ++- var/spack/packages/mpich/package.py | 5 +++++ var/spack/packages/trilinos/package.py | 40 ++++++++++++++++++++++++++++++++++ 3 files changed, 47 insertions(+), 1 deletion(-) create mode 100644 var/spack/packages/trilinos/package.py (limited to 'var') diff --git a/var/spack/packages/hdf5/package.py b/var/spack/packages/hdf5/package.py index 992dd8ec70..15e0ef9338 100644 --- a/var/spack/packages/hdf5/package.py +++ b/var/spack/packages/hdf5/package.py @@ -10,7 +10,8 @@ class Hdf5(Package): url = "http://www.hdfgroup.org/ftp/HDF5/releases/hdf5-1.8.13/src/hdf5-1.8.13.tar.gz" list_url = "http://www.hdfgroup.org/ftp/HDF5/releases" list_depth = 3 - + + version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') version('1.8.13', 'c03426e9e77d7766944654280b467289') depends_on("mpi") diff --git a/var/spack/packages/mpich/package.py b/var/spack/packages/mpich/package.py index b6b2dfde21..315fc4a5a3 100644 --- a/var/spack/packages/mpich/package.py +++ b/var/spack/packages/mpich/package.py @@ -33,6 +33,11 @@ class Mpich(Package): list_url = "http://www.mpich.org/static/downloads/" list_depth = 2 + version('3.1.4', '2ab544607986486562e076b83937bba2') + version('3.1.3', '93cb17f91ac758cbf9174ecb03563778') + version('3.1.2', '7fbf4b81dcb74b07ae85939d1ceee7f1') + version('3.1.1', '40dc408b1e03cc36d80209baaa2d32b7') + version('3.1', '5643dd176499bfb7d25079aaff25f2ec') version('3.0.4', '9c5d5d4fe1e17dd12153f40bc5b6dbc0') provides('mpi@:3', when='@3:') diff --git a/var/spack/packages/trilinos/package.py b/var/spack/packages/trilinos/package.py new file mode 100644 index 0000000000..2fa4f3cc84 --- /dev/null +++ b/var/spack/packages/trilinos/package.py @@ -0,0 +1,40 @@ +# FIXME: +# This is a template package file for Spack. We've conveniently +# put "FIXME" labels next to all the things you'll want to change. +# +# Once you've edited all the FIXME's, delete this whole message, +# save this file, and test out your package like this: +# +# spack install trilinos +# +# You can always get back here to change things with: +# +# spack edit trilinos +# +# See the spack documentation for more information on building +# packages. +# +from spack import * + +class Trilinos(Package): + """FIXME: put a proper description of your package here.""" + # FIXME: add a proper url for your package's homepage here. + homepage = "http://www.example.com" + url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + + version('12.2.1' , '6161926ea247863c690e927687f83be9') + version('12.0.1' , 'bd99741d047471e127b8296b2ec08017') + version('11.14.3', '2f4f83f8333e4233c57d0f01c4b57426') + version('11.14.2', 'a43590cf896c677890d75bfe75bc6254') + version('11.14.1', '40febc57f76668be8b6a77b7607bb67f') + + # FIXME: Add dependencies if this package requires them. + # depends_on("foo") + + def install(self, spec, prefix): + # FIXME: Modify the configure line to suit your build system here. + cmake('.', *std_cmake_args) + + # FIXME: Add logic to build and install here + make() + make("install") -- cgit v1.2.3-60-g2f50 From ff0d039a1fea0b713455c38ab4df6a5cbe0d4783 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 15 Oct 2015 08:48:39 +0200 Subject: trilinos : prototype for the whole package --- var/spack/packages/trilinos/package.py | 51 +++++++++++++++++++++++++--------- 1 file changed, 38 insertions(+), 13 deletions(-) (limited to 'var') diff --git a/var/spack/packages/trilinos/package.py b/var/spack/packages/trilinos/package.py index 2fa4f3cc84..6f7cc253dd 100644 --- a/var/spack/packages/trilinos/package.py +++ b/var/spack/packages/trilinos/package.py @@ -16,25 +16,50 @@ # from spack import * + class Trilinos(Package): - """FIXME: put a proper description of your package here.""" - # FIXME: add a proper url for your package's homepage here. - homepage = "http://www.example.com" - url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" + """ + The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented + software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. + A unique design feature of Trilinos is its focus on packages. + """ + homepage = "https://trilinos.org/" + url = "http://trilinos.csbsju.edu/download/files/trilinos-12.2.1-Source.tar.gz" - version('12.2.1' , '6161926ea247863c690e927687f83be9') - version('12.0.1' , 'bd99741d047471e127b8296b2ec08017') + version('12.2.1', '6161926ea247863c690e927687f83be9') + version('12.0.1', 'bd99741d047471e127b8296b2ec08017') version('11.14.3', '2f4f83f8333e4233c57d0f01c4b57426') version('11.14.2', 'a43590cf896c677890d75bfe75bc6254') version('11.14.1', '40febc57f76668be8b6a77b7607bb67f') - # FIXME: Add dependencies if this package requires them. - # depends_on("foo") + variant('mpi', default=True, description='Add a dependency on MPI and enables MPI dependent packages') + + # Everything should be compiled with -fpic + depends_on('blas') + depends_on('lapack') + depends_on('boost') + depends_on('netcdf') + depends_on('matio') + depends_on('glm') + depends_on('swig') + depends_on('mpi', when='+mpi') def install(self, spec, prefix): - # FIXME: Modify the configure line to suit your build system here. - cmake('.', *std_cmake_args) - # FIXME: Add logic to build and install here - make() - make("install") + options = [ + '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', + '-DTrilinos_ENABLE_TESTS:BOOL=ON', + '-DBUILD_SHARED_LIBS:BOOL=ON', + '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix, + '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix + ] + if '+mpi' in spec: + mpi_options = ['-DTPL_ENABLE_MPI:BOOL=ON'] + options.extend(mpi_options) + + # -DCMAKE_INSTALL_PREFIX and all the likes... + options.extend(std_cmake_args) + with working_dir('spack-build', create=True): + cmake('..', *options) + make() + make('install') -- cgit v1.2.3-60-g2f50 From 3a4bdf1856685ae63116793e532d45aa2ee7fd28 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Fri, 16 Oct 2015 13:02:27 +0200 Subject: trilinos : first version that compiles on bellatrix --- var/spack/packages/swig/package.py | 2 ++ var/spack/packages/trilinos/package.py | 19 ++----------------- 2 files changed, 4 insertions(+), 17 deletions(-) (limited to 'var') diff --git a/var/spack/packages/swig/package.py b/var/spack/packages/swig/package.py index d7a3d815b9..ee536d7063 100644 --- a/var/spack/packages/swig/package.py +++ b/var/spack/packages/swig/package.py @@ -38,6 +38,8 @@ class Swig(Package): version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') + depends_on('pcre') + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() diff --git a/var/spack/packages/trilinos/package.py b/var/spack/packages/trilinos/package.py index 6f7cc253dd..7c43f796a4 100644 --- a/var/spack/packages/trilinos/package.py +++ b/var/spack/packages/trilinos/package.py @@ -1,19 +1,3 @@ -# FIXME: -# This is a template package file for Spack. We've conveniently -# put "FIXME" labels next to all the things you'll want to change. -# -# Once you've edited all the FIXME's, delete this whole message, -# save this file, and test out your package like this: -# -# spack install trilinos -# -# You can always get back here to change things with: -# -# spack edit trilinos -# -# See the spack documentation for more information on building -# packages. -# from spack import * @@ -48,7 +32,8 @@ class Trilinos(Package): options = [ '-DTrilinos_ENABLE_ALL_PACKAGES:BOOL=ON', - '-DTrilinos_ENABLE_TESTS:BOOL=ON', + '-DTrilinos_ENABLE_TESTS:BOOL=OFF', + '-DTrilinos_ENABLE_EXAMPLES:BOOL=OFF', '-DBUILD_SHARED_LIBS:BOOL=ON', '-DBLAS_LIBRARY_DIRS:PATH=%s' % spec['blas'].prefix, '-DLAPACK_LIBRARY_DIRS:PATH=%s' % spec['lapack'].prefix -- cgit v1.2.3-60-g2f50 From aab7102b9bcf2b35461ef3816f874f53d9eef976 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 14 Oct 2015 15:52:46 +0200 Subject: matio : added basic configuration for the package --- var/spack/packages/matio/package.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 var/spack/packages/matio/package.py (limited to 'var') diff --git a/var/spack/packages/matio/package.py b/var/spack/packages/matio/package.py new file mode 100644 index 0000000000..12cfb80926 --- /dev/null +++ b/var/spack/packages/matio/package.py @@ -0,0 +1,15 @@ +from spack import * + + +class Matio(Package): + """matio is an C library for reading and writing Matlab MAT files""" + homepage = "http://sourceforge.net/projects/matio/" + url = "http://downloads.sourceforge.net/project/matio/matio/1.5.2/matio-1.5.2.tar.gz" + + version('1.5.2', '85b007b99916c63791f28398f6a4c6f1') + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") -- cgit v1.2.3-60-g2f50 From ec5560374c218bfb1f16934259108ebc305cf838 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Wed, 14 Oct 2015 16:13:56 +0200 Subject: glm : added basic configuration for the package --- var/spack/packages/glm/package.py | 19 +++++++++++++++++++ 1 file changed, 19 insertions(+) create mode 100644 var/spack/packages/glm/package.py (limited to 'var') diff --git a/var/spack/packages/glm/package.py b/var/spack/packages/glm/package.py new file mode 100644 index 0000000000..d00c301b4c --- /dev/null +++ b/var/spack/packages/glm/package.py @@ -0,0 +1,19 @@ +from spack import * + + +class Glm(Package): + """ + OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on + the OpenGL Shading Language (GLSL) specification. + """ + + homepage = "https://github.com/g-truc/glm" + url = "https://github.com/g-truc/glm/archive/0.9.7.1.tar.gz" + + version('0.9.7.1', '61af6639cdf652d1cdd7117190afced8') + + def install(self, spec, prefix): + with working_dir('spack-build', create=True): + cmake('..', *std_cmake_args) + make() + make("install") -- cgit v1.2.3-60-g2f50 From 7e2f3cff443dd1ae634eb375fd06ee41df149989 Mon Sep 17 00:00:00 2001 From: David Beckingsale Date: Mon, 19 Oct 2015 15:41:46 -0700 Subject: Added ncdu package --- var/spack/packages/ncdu/package.py | 28 ++++++++++++++++++++++++++++ 1 file changed, 28 insertions(+) create mode 100644 var/spack/packages/ncdu/package.py (limited to 'var') diff --git a/var/spack/packages/ncdu/package.py b/var/spack/packages/ncdu/package.py new file mode 100644 index 0000000000..234f9730d6 --- /dev/null +++ b/var/spack/packages/ncdu/package.py @@ -0,0 +1,28 @@ +from spack import * + +class Ncdu(Package): + """ + Ncdu is a disk usage analyzer with an ncurses interface. It is designed + to find space hogs on a remote server where you don't have an entire + gaphical setup available, but it is a useful tool even on regular desktop + systems. Ncdu aims to be fast, simple and easy to use, and should be able + to run in any minimal POSIX-like environment with ncurses installed. + """ + + homepage = "http://dev.yorhel.nl/ncdu" + url = "http://dev.yorhel.nl/download/ncdu-1.11.tar.gz" + + version('1.11', '9e44240a5356b029f05f0e70a63c4d12') + version('1.10', '7535decc8d54eca811493e82d4bfab2d') + version('1.9' , '93258079db897d28bb8890e2db89b1fb') + version('1.8' , '94d7a821f8a0d7ba8ef3dd926226f7d5') + version('1.7' , '172047c29d232724cc62e773e82e592a') + + depends_on("ncurses") + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix, + '--with-ncurses=%s' % spec['ncurses']) + + make() + make("install") -- cgit v1.2.3-60-g2f50 From e0e79a2cb3cda043bf1fb456c58ceff8d4e9375d Mon Sep 17 00:00:00 2001 From: Kevin Huck Date: Wed, 21 Oct 2015 11:56:01 -0700 Subject: Adding package for activeharmony. --- var/spack/packages/activeharmony/package.py | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 var/spack/packages/activeharmony/package.py (limited to 'var') diff --git a/var/spack/packages/activeharmony/package.py b/var/spack/packages/activeharmony/package.py new file mode 100644 index 0000000000..45dcc7c0e8 --- /dev/null +++ b/var/spack/packages/activeharmony/package.py @@ -0,0 +1,15 @@ +from spack import * + +class Activeharmony(Package): + """Active Harmony: a framework for auto-tuning (the automated search for values to improve the performance of a target application).""" + homepage = "http://www.dyninst.org/harmony" + url = "http://www.dyninst.org/sites/default/files/downloads/harmony/ah-4.5.tar.gz" + + version('4.5', 'caee5b864716d376e2c25d739251b2a9') + + def install(self, spec, prefix): + make("CFLAGS=-O3") + make("install", 'PREFIX=%s' % prefix) + +from spack import * + -- cgit v1.2.3-60-g2f50