From 837eff1704d26fb654a964ecea91e268d728fff6 Mon Sep 17 00:00:00 2001 From: Massimiliano Culpo Date: Thu, 31 Mar 2016 18:07:44 +0200 Subject: openssl : special treatment for @external (fixes #647) --- .../repos/builtin/packages/openssl/package.py | 45 ++++++++++++++-------- 1 file changed, 28 insertions(+), 17 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index 70afaf4038..db66d1f56e 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -30,26 +30,14 @@ class Openssl(Package): # Same idea, but just to avoid issuing the same message multiple times warnings_given_to_user = getattr(Openssl, '_warnings_given', {}) if openssl_url is None: - latest = 'http://www.openssl.org/source/openssl-{version}.tar.gz' - older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' - # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then - # return the url for older format - version_number = '.'.join([str(x) for x in version[:-1]]) - older_url = older.format(version_number=version_number, version_full=version) - latest_url = latest.format(version=version) - response = urllib.urlopen(latest.format(version=version)) - if response.getcode() == 404: - openssl_url = older_url - # Checks if we already warned the user for this particular version of OpenSSL. - # If not we display a warning message and mark this version + if self.spec.satisfies('@external'): + # The version @external is reserved to system openssl. In that case return a fake url and exit + openssl_url = '@external (reserved version for system openssl)' if not warnings_given_to_user.get(version, False): - tty.warn('This installation depends on an old version of OpenSSL, which may have known security issues. ') - tty.warn('Consider updating to the latest version of this package.') - tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + tty.msg('Using openssl@external : the version @external is reserved for system openssl') warnings_given_to_user[version] = True else: - openssl_url = latest_url - # Store the computed URL + openssl_url = self.check_for_outdated_release(version, warnings_given_to_user) # Store the computed URL openssl_urls[version] = openssl_url # Store the updated dictionary of URLS Openssl._openssl_url = openssl_urls @@ -58,6 +46,29 @@ class Openssl(Package): return openssl_url + def check_for_outdated_release(self, version, warnings_given_to_user): + latest = 'http://www.openssl.org/source/openssl-{version}.tar.gz' + older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' + # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then + # return the url for older format + version_number = '.'.join([str(x) for x in version[:-1]]) + older_url = older.format(version_number=version_number, version_full=version) + latest_url = latest.format(version=version) + response = urllib.urlopen(latest.format(version=version)) + if response.getcode() == 404: + openssl_url = older_url + # Checks if we already warned the user for this particular version of OpenSSL. + # If not we display a warning message and mark this version + if not warnings_given_to_user.get(version, False): + tty.warn( + 'This installation depends on an old version of OpenSSL, which may have known security issues. ') + tty.warn('Consider updating to the latest version of this package.') + tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) + warnings_given_to_user[version] = True + else: + openssl_url = latest_url + return openssl_url + def install(self, spec, prefix): # OpenSSL uses a variable APPS in its Makefile. If it happens to be set # in the environment, then this will override what is set in the -- cgit v1.2.3-70-g09d2 From d375ddadc4d6f253b21e9c982040757bd5a187d3 Mon Sep 17 00:00:00 2001 From: alalazo Date: Mon, 4 Apr 2016 12:25:13 +0200 Subject: openssl : reads newer version from ftp (recommended on openssl web-site) --- var/spack/repos/builtin/packages/openssl/package.py | 16 ++++++++-------- 1 file changed, 8 insertions(+), 8 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openssl/package.py b/var/spack/repos/builtin/packages/openssl/package.py index db66d1f56e..9e3109bfed 100644 --- a/var/spack/repos/builtin/packages/openssl/package.py +++ b/var/spack/repos/builtin/packages/openssl/package.py @@ -3,6 +3,7 @@ import llnl.util.tty as tty from spack import * + class Openssl(Package): """The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source @@ -47,16 +48,16 @@ class Openssl(Package): return openssl_url def check_for_outdated_release(self, version, warnings_given_to_user): - latest = 'http://www.openssl.org/source/openssl-{version}.tar.gz' + latest = 'ftp://ftp.openssl.org/source/openssl-{version}.tar.gz' older = 'http://www.openssl.org/source/old/{version_number}/openssl-{version_full}.tar.gz' # Try to use the url where the latest tarballs are stored. If the url does not exist (404), then # return the url for older format version_number = '.'.join([str(x) for x in version[:-1]]) - older_url = older.format(version_number=version_number, version_full=version) - latest_url = latest.format(version=version) - response = urllib.urlopen(latest.format(version=version)) - if response.getcode() == 404: - openssl_url = older_url + try: + openssl_url = latest.format(version=version) + urllib.urlopen(openssl_url) + except IOError: + openssl_url = older.format(version_number=version_number, version_full=version) # Checks if we already warned the user for this particular version of OpenSSL. # If not we display a warning message and mark this version if not warnings_given_to_user.get(version, False): @@ -65,8 +66,7 @@ class Openssl(Package): tty.warn('Consider updating to the latest version of this package.') tty.warn('More details at {homepage}'.format(homepage=Openssl.homepage)) warnings_given_to_user[version] = True - else: - openssl_url = latest_url + return openssl_url def install(self, spec, prefix): -- cgit v1.2.3-70-g09d2 From 7197f1578335b38eb2037e8d82f15a27d786d5c1 Mon Sep 17 00:00:00 2001 From: Bruno Turcksin Date: Fri, 1 Apr 2016 12:28:46 -0400 Subject: Add version 2.6.7 of py-setuptools --- var/spack/repos/builtin/packages/py-setuptools/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index c6d9be1add..9338a5e157 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -10,6 +10,7 @@ class PySetuptools(Package): version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06') version('19.2', '78353b1f80375ca5e088f4b4627ffe03') version('20.5', 'fadc1e1123ddbe31006e5e43e927362b') + version('20.6.7', '45d6110f3ec14924e44c33411db64fe6') extends('python') -- cgit v1.2.3-70-g09d2 From a87ae5173f5e30aa9d8b3360e67dbc17568342f5 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Mon, 4 Apr 2016 18:16:25 -0400 Subject: Update Julia - allow checking out the master branche - add dependencies requires by important Julia package - add OpenBLAS patch --- .../repos/builtin/packages/julia/openblas.patch | 68 ++++++++++++++++++++++ var/spack/repos/builtin/packages/julia/package.py | 68 ++++++++++++++-------- 2 files changed, 113 insertions(+), 23 deletions(-) create mode 100644 var/spack/repos/builtin/packages/julia/openblas.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/julia/openblas.patch b/var/spack/repos/builtin/packages/julia/openblas.patch new file mode 100644 index 0000000000..f75d7dd04f --- /dev/null +++ b/var/spack/repos/builtin/packages/julia/openblas.patch @@ -0,0 +1,68 @@ +diff --git a/deps/Makefile b/deps/Makefile +index 6cb73be..bcd8520 100644 +--- a/deps/Makefile ++++ b/deps/Makefile +@@ -1049,7 +1049,7 @@ OPENBLAS_BUILD_OPTS += NO_AFFINITY=1 + + # Build for all architectures - required for distribution + ifeq ($(OPENBLAS_DYNAMIC_ARCH), 1) +-OPENBLAS_BUILD_OPTS += DYNAMIC_ARCH=1 ++OPENBLAS_BUILD_OPTS += DYNAMIC_ARCH=1 MAKE_NO_J=1 + endif + + # 64-bit BLAS interface +@@ -1085,6 +1085,7 @@ OPENBLAS_BUILD_OPTS += NO_AVX2=1 + endif + + $(OPENBLAS_SRC_DIR)/config.status: $(OPENBLAS_SRC_DIR)/Makefile ++ cd $(dir $@) && patch -p1 < ../openblas-make.patch + ifeq ($(OS),WINNT) + cd $(dir $@) && patch -p1 < ../openblas-win64.patch + endif +diff --git a/deps/openblas.version b/deps/openblas.version +index 7c97e1b..58b9467 100644 +--- a/deps/openblas.version ++++ b/deps/openblas.version +@@ -1,2 +1,2 @@ +-OPENBLAS_BRANCH=v0.2.15 +-OPENBLAS_SHA1=53e849f4fcae4363a64576de00e982722c7304f9 ++OPENBLAS_BRANCH=v0.2.17 ++OPENBLAS_SHA1=a71e8c82f6a9f73093b631e5deab1e8da716b61f +--- a/deps/openblas-make.patch ++++ b/deps/openblas-make.patch +@@ -0,0 +1,35 @@ ++diff --git a/Makefile.system b/Makefile.system ++index b89f60e..2dbdad0 100644 ++--- a/Makefile.system +++++ b/Makefile.system ++@@ -139,6 +139,10 @@ NO_PARALLEL_MAKE=0 ++ endif ++ GETARCH_FLAGS += -DNO_PARALLEL_MAKE=$(NO_PARALLEL_MAKE) ++ +++ifdef MAKE_NO_J +++GETARCH_FLAGS += -DMAKE_NO_J=$(MAKE_NO_J) +++endif +++ ++ ifdef MAKE_NB_JOBS ++ GETARCH_FLAGS += -DMAKE_NB_JOBS=$(MAKE_NB_JOBS) ++ endif ++diff --git a/getarch.c b/getarch.c ++index f9c49e6..dffad70 100644 ++--- a/getarch.c +++++ b/getarch.c ++@@ -1012,6 +1012,7 @@ int main(int argc, char *argv[]){ ++ #endif ++ #endif ++ +++#ifndef MAKE_NO_J ++ #ifdef MAKE_NB_JOBS ++ printf("MAKE += -j %d\n", MAKE_NB_JOBS); ++ #elif NO_PARALLEL_MAKE==1 ++@@ -1021,6 +1022,7 @@ int main(int argc, char *argv[]){ ++ printf("MAKE += -j %d\n", get_num_cores()); ++ #endif ++ #endif +++#endif ++ ++ break; ++ diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 6900af38e4..b3a523bc45 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -4,43 +4,55 @@ import os class Julia(Package): """The Julia Language: A fresh approach to technical computing""" homepage = "http://julialang.org" - url = "http://github.com/JuliaLang/julia/releases/download/v0.4.2/julia-0.4.2.tar.gz" + url = "https://github.com/JuliaLang/julia/releases/download/v0.4.3/julia-0.4.3-full.tar.gz" - version('0.4.3', '7b9f096798fca4bef262a64674bc2b52') - version('0.4.2', 'ccfeb4f4090c8b31083f5e1ccb03eb06') + version('master', + git='https://github.com/JuliaLang/julia.git', branch='master') + version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6') + version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac') - patch('gc.patch') + patch('gc.patch', when='@:0.5') + patch('openblas.patch') - # Build-time dependencies - depends_on("cmake @2.8:") + # Build-time dependencies: # depends_on("awk") # depends_on("m4") # depends_on("pkg-config") - depends_on("python @2.6:2.9") - # I think that Julia requires the dependencies above, but it builds find (on - # my system) without these. We should enable them as necessary. + # Combined build-time and run-time dependencies: + depends_on("cmake @2.8:") + depends_on("git") + depends_on("openssl") + depends_on("python @2.7:2.999") + + # I think that Julia requires the dependencies above, but it + # builds fine (on my system) without these. We should enable them + # as necessary. - # Run-time dependencies + # Run-time dependencies: # depends_on("arpack") # depends_on("fftw +float") # depends_on("gmp") + # depends_on("libgit") # depends_on("mpfr") + # depends_on("openblas") # depends_on("pcre2") - # ARPACK: Requires BLAS and LAPACK; needs to use the same version as Julia. + # ARPACK: Requires BLAS and LAPACK; needs to use the same version + # as Julia. - # BLAS and LAPACK: Julia prefers 64-bit versions on 64-bit systems. OpenBLAS - # has an option for this; make it available as variant. + # BLAS and LAPACK: Julia prefers 64-bit versions on 64-bit + # systems. OpenBLAS has an option for this; make it available as + # variant. - # FFTW: Something doesn't work when using a pre-installed FFTW library; need - # to investigate. + # FFTW: Something doesn't work when using a pre-installed FFTW + # library; need to investigate. - # GMP, MPFR: Something doesn't work when using a pre-installed FFTW library; - # need to investigate. + # GMP, MPFR: Something doesn't work when using a pre-installed + # FFTW library; need to investigate. - # LLVM: Julia works only with specific versions, and might require patches. - # Thus we let Julia install its own LLVM. + # LLVM: Julia works only with specific versions, and might require + # patches. Thus we let Julia install its own LLVM. # Other possible dependencies: # USE_SYSTEM_OPENLIBM=0 @@ -50,11 +62,21 @@ class Julia(Package): # USE_SYSTEM_UTF8PROC=0 # USE_SYSTEM_LIBGIT2=0 + # Run-time dependencies for Julia packages: + depends_on("hdf5") + depends_on("mpi") + def install(self, spec, prefix): - # Explicitly setting CC, CXX, or FC breaks building libuv, one of - # Julia's dependencies. This might be a Darwin-specific problem. Given - # how Spack sets up compilers, Julia should still use Spack's compilers, - # even if we don't specify them explicitly. + if '@master' in spec: + # Julia needs to know the offset from a specific commit + git = which('git') + git('fetch', '--unshallow') + + # Explicitly setting CC, CXX, or FC breaks building libuv, one + # of Julia's dependencies. This might be a Darwin-specific + # problem. Given how Spack sets up compilers, Julia should + # still use Spack's compilers, even if we don't specify them + # explicitly. options = [#"CC=cc", #"CXX=c++", #"FC=fc", -- cgit v1.2.3-70-g09d2 From 0ebb192b2f26cfd2bbadc9be72c36469c7493d89 Mon Sep 17 00:00:00 2001 From: Jim Galarowicz Date: Tue, 5 Apr 2016 10:36:20 -0700 Subject: Update the MRNet package with the latest source and patch related to the krell tools needs. Also, reorder the list of version to match with the spack standard: newest to oldest. --- .../repos/builtin/packages/mrnet/krell-5.0.1.patch | 154 +++++++++++++++++++++ var/spack/repos/builtin/packages/mrnet/package.py | 17 ++- 2 files changed, 167 insertions(+), 4 deletions(-) create mode 100644 var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch b/var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch new file mode 100644 index 0000000000..53294fbbc6 --- /dev/null +++ b/var/spack/repos/builtin/packages/mrnet/krell-5.0.1.patch @@ -0,0 +1,154 @@ +--- mrnet-3093918/include/mrnet/Types.h 2015-12-10 09:32:24.000000000 -0800 ++++ mrnet_top_of_tree/include/mrnet/Types.h 2016-03-16 12:29:33.986132302 -0700 +@@ -23,7 +23,7 @@ + #ifndef MRNET_VERSION_MAJOR + # define MRNET_VERSION_MAJOR 5 + # define MRNET_VERSION_MINOR 0 +-# define MRNET_VERSION_REV 0 ++# define MRNET_VERSION_REV 1 + #endif + + namespace MRN +--- mrnet-3093918/include/mrnet_lightweight/Types.h 2015-12-10 09:32:24.000000000 -0800 ++++ mrnet_top_of_tree/include/mrnet_lightweight/Types.h 2016-03-16 12:29:33.987132302 -0700 +@@ -30,7 +30,7 @@ + #ifndef MRNET_VERSION_MAJOR + #define MRNET_VERSION_MAJOR 5 + #define MRNET_VERSION_MINOR 0 +-#define MRNET_VERSION_REV 0 ++#define MRNET_VERSION_REV 1 + #endif + void get_Version(int* major, + int* minor, +--- mrnet-3093918/src/lightweight/SerialGraph.c 2015-12-10 09:32:24.000000000 -0800 ++++ mrnet_top_of_tree/src/lightweight/SerialGraph.c 2016-03-16 12:29:33.995132302 -0700 +@@ -59,7 +59,7 @@ + + mrn_dbg_func_begin(); + +- sprintf(hoststr, "[%s:%hu:%u:", ihostname, iport, irank); ++ sprintf(hoststr, "[%s:%05hu:%u:", ihostname, iport, irank); + mrn_dbg(5, mrn_printf(FLF, stderr, "looking for SubTreeRoot: '%s'\n", hoststr)); + + byte_array = sg->byte_array; +@@ -110,7 +110,7 @@ + + mrn_dbg_func_begin(); + +- len = (size_t) sprintf(hoststr, "[%s:%hu:%u:0]", ihostname, iport, irank); ++ len = (size_t) sprintf(hoststr, "[%s:%05hu:%u:0]", ihostname, iport, irank); + mrn_dbg(5, mrn_printf(FLF, stderr, "adding sub tree leaf: %s\n", hoststr)); + + len += strlen(sg->byte_array) + 1; +@@ -139,7 +139,7 @@ + + mrn_dbg_func_begin(); + +- len = (size_t) sprintf(hoststr, "[%s:%hu:%u:1", ihostname, iport, irank); ++ len = (size_t) sprintf(hoststr, "[%s:%05hu:%u:1", ihostname, iport, irank); + mrn_dbg(5, mrn_printf(FLF, stderr, "adding sub tree root: %s\n", hoststr)); + + len += strlen(sg->byte_array) + 1; +@@ -360,8 +360,8 @@ + char old_hoststr[256]; + char new_hoststr[256]; + +- sprintf(old_hoststr, "[%s:%hu:%u:", hostname, UnknownPort, irank); +- sprintf(new_hoststr, "[%s:%hu:%u:", hostname, port, irank); ++ sprintf(old_hoststr, "[%s:%05hu:%u:", hostname, UnknownPort, irank); ++ sprintf(new_hoststr, "[%s:%05hu:%u:", hostname, port, irank); + + old_byte_array = sg->byte_array; + new_byte_array = (char*) malloc( strlen(old_byte_array) + 10 ); +--- mrnet-3093918/xplat/src/lightweight/SocketUtils.c 2015-12-10 09:32:24.000000000 -0800 ++++ mrnet_top_of_tree/xplat/src/lightweight/SocketUtils.c 2016-03-16 12:29:34.006132303 -0700 +@@ -15,7 +15,7 @@ + #else + const XPlat_Socket InvalidSocket = INVALID_SOCKET; + #endif +-const XPlat_Port InvalidPort = (XPlat_Port)-1; ++const XPlat_Port InvalidPort = (XPlat_Port)0; + + static bool_t SetTcpNoDelay( XPlat_Socket sock ) + { +--- mrnet-3093918/conf/configure.in 2015-12-10 09:32:24.000000000 -0800 ++++ mrnet_top_of_tree/conf/configure.in 2016-03-16 12:45:54.573196781 -0700 +@@ -107,6 +107,18 @@ + AC_SUBST(PURIFY) + + ++AC_ARG_WITH(expat, ++ [AS_HELP_STRING([--with-expat=PATH], ++ [Absolute path to installation of EXPAT libraries (note: specify the path to the directory containing "include" and "lib" sub-directories)])], ++ [EXPAT_DIR="${withval}"], ++ [EXPAT_DIR=""]) ++ ++if test "x$EXPAT_DIR" = "x" ; then ++ EXPAT_LIB="" ++else ++ EXPAT_LIB="-L$EXPAT_DIR/lib" ++fi ++ + dnl === Checks for header files. + AC_CHECK_HEADERS([assert.h errno.h fcntl.h limits.h netdb.h signal.h stddef.h stdlib.h stdio.h string.h unistd.h arpa/inet.h netinet/in.h sys/ioctl.h sys/socket.h sys/sockio.h sys/time.h]) + AC_HEADER_STDBOOL +@@ -432,7 +444,7 @@ + CRAYXT_ATH_LIBS_SO="$CRAYXT_ATH_LIBS -lalps" + CRAYXT_ATH_LIBS="$CRAYXT_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc -Wl,-Bdynamic" + CRAYXE_ATH_LIBS_SO="$CRAYXE_ATH_LIBS -lalps" +- CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi -lexpat -Wl,-Bdynamic" ++ CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi $EXPAT_LIB -lexpat -Wl,-Bdynamic" + + AC_CHECK_LIB( [alps], [alps_launch_tool_helper], + [HAVE_ATH_LIBS="yes"; EXTRA_LIBS="$CRAYXT_ATH_LIBS $EXTRA_LIBS"; EXTRA_LIBS_SO="$CRAYXT_ATH_LIBS_SO $EXTRA_LIBS_SO"], +--- mrnet-3093918/configure 2015-12-10 09:32:24.000000000 -0800 ++++ mrnet_top_of_tree/configure 2016-03-16 13:47:20.386439143 -0700 +@@ -742,6 +742,7 @@ + enable_debug + enable_ltwt_threadsafe + with_purify ++with_expat + ' + ac_precious_vars='build_alias + host_alias +@@ -1399,6 +1400,9 @@ + containing "include" and "lib" sub-directories) + --with-launchmon=PATH Absolute path to installation of LaunchMON + --with-purify Use purify for memory debugging ++ --with-expat=PATH Absolute path to installation of EXPAT libraries ++ (note: specify the path to the directory containing ++ "include" and "lib" sub-directories) + + Some influential environment variables: + CC C compiler command +@@ -3541,6 +3545,21 @@ + + + ++# Check whether --with-expat was given. ++if test "${with_expat+set}" = set; then : ++ withval=$with_expat; EXPAT_DIR="${withval}" ++else ++ EXPAT_DIR="" ++fi ++ ++ ++if test "x$EXPAT_DIR" = "x" ; then ++ EXPAT_LIB="" ++else ++ EXPAT_LIB="-L$EXPAT_DIR/lib" ++fi ++ ++ + ac_ext=cpp + ac_cpp='$CXXCPP $CPPFLAGS' + ac_compile='$CXX -c $CXXFLAGS $CPPFLAGS conftest.$ac_ext >&5' +@@ -5473,7 +5492,7 @@ + CRAYXT_ATH_LIBS_SO="$CRAYXT_ATH_LIBS -lalps" + CRAYXT_ATH_LIBS="$CRAYXT_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc -Wl,-Bdynamic" + CRAYXE_ATH_LIBS_SO="$CRAYXE_ATH_LIBS -lalps" +- CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi -lexpat -Wl,-Bdynamic" ++ CRAYXE_ATH_LIBS="$CRAYXE_ATH_LIBS -Wl,-Bstatic -lalps -lxmlrpc-epi $EXPAT_LIB -lexpat -Wl,-Bdynamic" + + { $as_echo "$as_me:${as_lineno-$LINENO}: checking for alps_launch_tool_helper in -lalps" >&5 + $as_echo_n "checking for alps_launch_tool_helper in -lalps... " >&6; } diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py index fed944e45f..b8cbb7e8f9 100644 --- a/var/spack/repos/builtin/packages/mrnet/package.py +++ b/var/spack/repos/builtin/packages/mrnet/package.py @@ -3,16 +3,25 @@ from spack import * class Mrnet(Package): """The MRNet Multi-Cast Reduction Network.""" homepage = "http://paradyn.org/mrnet" - url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_4.0.0.tar.gz" + url = "ftp://ftp.cs.wisc.edu/paradyn/mrnet/mrnet_5.0.1.tar.gz" + list_url = "http://ftp.cs.wisc.edu/paradyn/mrnet" - version('4.0.0', 'd00301c078cba57ef68613be32ceea2f') - version('4.1.0', '5a248298b395b329e2371bf25366115c') version('5.0.1', '17f65738cf1b9f9b95647ff85f69ecdd') + version('4.1.0', '5a248298b395b329e2371bf25366115c') + version('4.0.0', 'd00301c078cba57ef68613be32ceea2f') + + # Add a patch that brings mrnet-5.0.1 up to date with the current development tree + # The development tree contains fixes needed for the krell based tools + variant('krellpatch', default=False, description="Build MRNet with krell openspeedshop based patch.") + patch('krell-5.0.1.patch', when='@5.0.1+krellpatch') + + variant('lwthreads', default=False, description="Also build the MRNet LW threadsafe libraries") parallel = False - depends_on("boost") + #depends_on("boost") + depends_on("boost@1.53.0") def install(self, spec, prefix): # Build the MRNet LW thread safe libraries when the krelloptions variant is present -- cgit v1.2.3-70-g09d2 From 7d19154e1852ad43af889505e19a36873d0e9c18 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Fri, 8 Apr 2016 12:01:28 -0400 Subject: pkg-config: use the internal glib glib requires pkg-config itself, so on machines without pkg-config, there's a bootstrapping problem. --- var/spack/repos/builtin/packages/pkg-config/package.py | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/pkg-config/package.py b/var/spack/repos/builtin/packages/pkg-config/package.py index 9964c6ce34..a803bc3f9b 100644 --- a/var/spack/repos/builtin/packages/pkg-config/package.py +++ b/var/spack/repos/builtin/packages/pkg-config/package.py @@ -10,7 +10,12 @@ class PkgConfig(Package): parallel = False def install(self, spec, prefix): - configure("--prefix=%s" %prefix, "--enable-shared") + configure("--prefix=%s" %prefix, + "--enable-shared", + "--with-internal-glib") # There's a bootstrapping problem here; + # glib uses pkg-config as well, so + # break the cycle by using the internal + # glib. make() make("install") -- cgit v1.2.3-70-g09d2 From 6c409d6b9238199370512ff8a8d30c6b2ff67769 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Fri, 8 Apr 2016 12:03:05 -0400 Subject: py-matplotlib: depend on pkg-config On OS X, freetype isn't found by default, but pkg-config can. --- var/spack/repos/builtin/packages/py-matplotlib/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 45e77dd631..19194c942e 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -26,6 +26,7 @@ class PyMatplotlib(Package): depends_on('py-pbr') depends_on('py-funcsigs') + depends_on('pkg-config') depends_on('freetype') depends_on('qt', when='+gui') depends_on('bzip2') -- cgit v1.2.3-70-g09d2 From dcd6b1934808e3700a3d1fc71e261087d9e71ae7 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Fri, 8 Apr 2016 12:03:36 -0400 Subject: py-setuptools: sort versions --- var/spack/repos/builtin/packages/py-setuptools/package.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index c6d9be1add..38158f4d27 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -5,11 +5,11 @@ class PySetuptools(Package): homepage = "https://pypi.python.org/pypi/setuptools" url = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz" - version('11.3.1', '01f69212e019a2420c1693fb43593930') - version('16.0', '0ace0b96233516fc5f7c857d086aa3ad') - version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06') - version('19.2', '78353b1f80375ca5e088f4b4627ffe03') version('20.5', 'fadc1e1123ddbe31006e5e43e927362b') + version('19.2', '78353b1f80375ca5e088f4b4627ffe03') + version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06') + version('16.0', '0ace0b96233516fc5f7c857d086aa3ad') + version('11.3.1', '01f69212e019a2420c1693fb43593930') extends('python') -- cgit v1.2.3-70-g09d2 From 9eaf735bcdba9f3fd8a51219d0eebb61f8b2f166 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Fri, 8 Apr 2016 12:03:45 -0400 Subject: py-setuptools: add 20.6.7 --- var/spack/repos/builtin/packages/py-setuptools/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 38158f4d27..bc3420a25e 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -5,6 +5,7 @@ class PySetuptools(Package): homepage = "https://pypi.python.org/pypi/setuptools" url = "https://pypi.python.org/packages/source/s/setuptools/setuptools-11.3.tar.gz" + version('20.6.7', '45d6110f3ec14924e44c33411db64fe6') version('20.5', 'fadc1e1123ddbe31006e5e43e927362b') version('19.2', '78353b1f80375ca5e088f4b4627ffe03') version('18.1', 'f72e87f34fbf07f299f6cb46256a0b06') -- cgit v1.2.3-70-g09d2 From f461b9972265df09e8ff9ac5c99a3f3d96783883 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Fri, 8 Apr 2016 14:31:40 -0400 Subject: Building OpenBLAS requires recent binutils --- var/spack/repos/builtin/packages/julia/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index b3a523bc45..75d13fda8f 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -20,6 +20,7 @@ class Julia(Package): # depends_on("pkg-config") # Combined build-time and run-time dependencies: + depends_on("binutils") depends_on("cmake @2.8:") depends_on("git") depends_on("openssl") -- cgit v1.2.3-70-g09d2 From 3a4aac0213f46ff233b6252be5db7c645501ab34 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Fri, 8 Apr 2016 15:08:09 -0400 Subject: paraview: use the right cmake variables --- var/spack/repos/builtin/packages/paraview/package.py | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index c16054816c..888add3033 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -75,13 +75,13 @@ class Paraview(Package): cmake('..', '-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix, '-DBUILD_TESTING:BOOL=OFF', - '-DVTK_USER_SYSTEM_FREETYPE:BOOL=ON', - '-DVTK_USER_SYSTEM_HDF5:BOOL=ON', - '-DVTK_USER_SYSTEM_JPEG:BOOL=ON', - '-DVTK_USER_SYSTEM_LIBXML2:BOOL=ON', - '-DVTK_USER_SYSTEM_NETCDF:BOOL=ON', - '-DVTK_USER_SYSTEM_TIFF:BOOL=ON', - '-DVTK_USER_SYSTEM_ZLIB:BOOL=ON', + '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON', + '-DVTK_USE_SYSTEM_HDF5:BOOL=ON', + '-DVTK_USE_SYSTEM_JPEG:BOOL=ON', + '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON', + '-DVTK_USE_SYSTEM_NETCDF:BOOL=ON', + '-DVTK_USE_SYSTEM_TIFF:BOOL=ON', + '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON', *feature_args) make() make('install') -- cgit v1.2.3-70-g09d2 From 6e56ba9f24df62ad205006a6b7bc13ae067a6623 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Fri, 8 Apr 2016 15:08:29 -0400 Subject: paraview: use internal netcdf VTK needs to learn to cope with netcdf being split like this. --- var/spack/repos/builtin/packages/paraview/package.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 888add3033..13cd076286 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -33,7 +33,8 @@ class Paraview(Package): depends_on('libpng') depends_on('libtiff') depends_on('libxml2') - depends_on('netcdf') + #depends_on('netcdf') + #depends_on('netcdf-cxx') #depends_on('protobuf') # version mismatches? #depends_on('sqlite') # external version not supported depends_on('zlib') @@ -79,7 +80,7 @@ class Paraview(Package): '-DVTK_USE_SYSTEM_HDF5:BOOL=ON', '-DVTK_USE_SYSTEM_JPEG:BOOL=ON', '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON', - '-DVTK_USE_SYSTEM_NETCDF:BOOL=ON', + '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF', '-DVTK_USE_SYSTEM_TIFF:BOOL=ON', '-DVTK_USE_SYSTEM_ZLIB:BOOL=ON', *feature_args) -- cgit v1.2.3-70-g09d2 From 20b9f34b5c650eefb23f4118bb52985c468a9098 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Fri, 8 Apr 2016 15:09:02 -0400 Subject: paraview: use internal hdf5 Spack's HDF5 is too new. Rather than forcing everything in a ParaView chain to use older HDF5, use the internal one until ParaView is patched properly. --- var/spack/repos/builtin/packages/paraview/package.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paraview/package.py b/var/spack/repos/builtin/packages/paraview/package.py index 13cd076286..60f8d3c243 100644 --- a/var/spack/repos/builtin/packages/paraview/package.py +++ b/var/spack/repos/builtin/packages/paraview/package.py @@ -27,8 +27,8 @@ class Paraview(Package): depends_on('bzip2') depends_on('freetype') - depends_on('hdf5+mpi', when='+mpi') - depends_on('hdf5~mpi', when='~mpi') + #depends_on('hdf5+mpi', when='+mpi') + #depends_on('hdf5~mpi', when='~mpi') depends_on('jpeg') depends_on('libpng') depends_on('libtiff') @@ -77,7 +77,7 @@ class Paraview(Package): '-DCMAKE_INSTALL_PREFIX:PATH=%s' % prefix, '-DBUILD_TESTING:BOOL=OFF', '-DVTK_USE_SYSTEM_FREETYPE:BOOL=ON', - '-DVTK_USE_SYSTEM_HDF5:BOOL=ON', + '-DVTK_USE_SYSTEM_HDF5:BOOL=OFF', '-DVTK_USE_SYSTEM_JPEG:BOOL=ON', '-DVTK_USE_SYSTEM_LIBXML2:BOOL=ON', '-DVTK_USE_SYSTEM_NETCDF:BOOL=OFF', -- cgit v1.2.3-70-g09d2 From df7e3f8635530574c5190d9501f2fdf1b0aa0aff Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Sat, 9 Apr 2016 09:58:48 -0400 Subject: Correct version dependency for OpenBLAS patch --- var/spack/repos/builtin/packages/julia/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/julia/package.py b/var/spack/repos/builtin/packages/julia/package.py index 75d13fda8f..25d782266b 100644 --- a/var/spack/repos/builtin/packages/julia/package.py +++ b/var/spack/repos/builtin/packages/julia/package.py @@ -11,8 +11,8 @@ class Julia(Package): version('0.4.5', '69141ff5aa6cee7c0ec8c85a34aa49a6') version('0.4.3', '8a4a59fd335b05090dd1ebefbbe5aaac') - patch('gc.patch', when='@:0.5') - patch('openblas.patch') + patch('gc.patch') + patch('openblas.patch', when='@0.4:0.4.5') # Build-time dependencies: # depends_on("awk") -- cgit v1.2.3-70-g09d2 From cb6c6fb3747aafbfb0fe81803eacf2807dde301f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Mon, 11 Apr 2016 16:28:30 -0500 Subject: Add elk package --- var/spack/repos/builtin/packages/elk/package.py | 116 +++++++++++++++++++++ var/spack/repos/builtin/packages/libxc/package.py | 18 ++++ .../repos/builtin/packages/openblas/package.py | 6 ++ 3 files changed, 140 insertions(+) create mode 100644 var/spack/repos/builtin/packages/elk/package.py create mode 100644 var/spack/repos/builtin/packages/libxc/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py new file mode 100644 index 0000000000..28ebb89db3 --- /dev/null +++ b/var/spack/repos/builtin/packages/elk/package.py @@ -0,0 +1,116 @@ +from spack import * +import spack + +class Elk(Package): + '''An all-electron full-potential linearised augmented-plane wave + (FP-LAPW) code with many advanced features.''' + + homepage = 'http://elk.sourceforge.net/' + url = 'https://sourceforge.net/projects/elk/files/elk-3.3.17.tgz' + + version('3.3.17', 'f57f6230d14f3b3b558e5c71f62f0592') + + # Elk provides these libraries, but allows you to specify your own + variant('blas', default=True, description='Build with custom BLAS library') + variant('lapack', default=True, description='Build with custom LAPACK library') + variant('fft', default=True, description='Build with custom FFT library') + + # Elk does not provide these libraries, but allows you to use them + variant('mpi', default=True, description='Enable MPI parallelism') + variant('openmp', default=True, description='Enable OpenMP support') + variant('libxc', default=True, description='Link to Libxc functional library') + + depends_on('blas', when='+blas') + depends_on('lapack', when='+lapack') + depends_on('fftw', when='+fft') + depends_on('mpi', when='+mpi') + depends_on('libxc', when='+libxc') + + # Cannot be built in parallel + parallel = False + + + def configure(self, spec): + # Dictionary of configuration options + config = { + 'MAKE': 'make', + 'F90': join_path(spack.build_env_path, 'f90'), + 'F77': join_path(spack.build_env_path, 'f77'), + 'AR': 'ar', + 'LIB_FFT': 'fftlib.a', + 'SRC_MPI': 'mpi_stub.f90', + 'SRC_OMP': 'omp_stub.f90', + 'SRC_libxc': 'libxcifc_stub.f90', + 'SRC_FFT': 'zfftifc.f90' + } + + # Compiler-specific flags + flags = '' + if self.compiler.name == 'intel': + flags = '-O3 -ip -unroll -no-prec-div -openmp' + elif self.compiler.name == 'gcc': + flags = '-O3 -ffast-math -funroll-loops -fopenmp' + elif self.compiler.name == 'pgi': + flags = '-O3 -mp -lpthread' + elif self.compiler.name == 'g95': + flags = '-O3 -fno-second-underscore' + elif self.compiler.name == 'nag': + flags = '-O4 -kind=byte -dusty -dcfuns' + elif self.compiler.name == 'xl': + flags = '-O3 -qsmp=omp' + config['F90_OPTS'] = flags + config['F77_OPTS'] = flags + + # BLAS/LAPACK support + blas = 'blas.a' + lapack = 'lapack.a' + if '+blas' in spec: + blas = join_path(spec['blas'].prefix.lib, 'libblas.so') + if '+lapack' in spec: + lapack = join_path(spec['lapack'].prefix.lib, 'liblapack.so') + config['LIB_LPK'] = ' '.join([lapack, blas]) # lapack must come before blas + + # FFT support + if '+fft' in spec: + config['LIB_FFT'] = join_path(spec['fftw'].prefix.lib, 'libfftw3.so') + config['SRC_FFT'] = 'zfftifc_fftw.f90' + + # MPI support + if '+mpi' in spec: + config.pop('SRC_MPI') + config['F90'] = join_path(spec['mpi'].prefix.bin, 'mpif90') + config['F77'] = join_path(spec['mpi'].prefix.bin, 'mpif77') + + # OpenMP support + if '+openmp' in spec: + config.pop('SRC_OMP') + + # Libxc support + if '+libxc' in spec: + config['LIB_libxc'] = ' '.join([ + join_path(spec['libxc'].prefix.lib, 'libxcf90.so'), + join_path(spec['libxc'].prefix.lib, 'libxc.so') + ]) + config['SRC_libxc'] = ' '.join([ + 'libxc_funcs.f90', + 'libxc.f90', + 'libxcifc.f90' + ]) + + # Write configuration options to include file + with open('make.inc', 'w') as inc: + for key in config: + inc.write('{0} = {1}\n'.format(key, config[key])) + + + def install(self, spec, prefix): + self.configure(spec) + + make() + make('test') + + mkdirp(prefix.bin) + + install('src/elk', prefix.bin) + install('src/eos/eos', prefix.bin) + install('src/spacegroup/spacegroup', prefix.bin) diff --git a/var/spack/repos/builtin/packages/libxc/package.py b/var/spack/repos/builtin/packages/libxc/package.py new file mode 100644 index 0000000000..010a5918c5 --- /dev/null +++ b/var/spack/repos/builtin/packages/libxc/package.py @@ -0,0 +1,18 @@ +from spack import * + +class Libxc(Package): + """Libxc is a library of exchange-correlation functionals for + density-functional theory.""" + + homepage = "http://www.tddft.org/programs/octopus/wiki/index.php/Libxc" + url = "http://www.tddft.org/programs/octopus/down.php?file=libxc/libxc-2.2.2.tar.gz" + + version('2.2.2', 'd9f90a0d6e36df6c1312b6422280f2ec') + + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix, + '--enable-shared') + + make() + make("install") diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 9f13d0690b..4522130ccc 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -12,6 +12,7 @@ class Openblas(Package): version('0.2.15', 'b1190f3d3471685f17cfd1ec1d252ac9') variant('shared', default=True, description="Build shared libraries as well as static libs.") + variant('openmp', default=True, description="Enable OpenMP support.") # virtual dependency provides('blas') @@ -37,6 +38,11 @@ class Openblas(Package): if spec.satisfies('@0.2.16'): make_defs += ['BUILD_LAPACK_DEPRECATED=1'] + # Add support for OpenMP + # Note: Make sure your compiler supports OpenMP + if '+openmp' in spec: + make_defs += ['USE_OPENMP=1'] + make_args = make_defs + make_targets make(*make_args) -- cgit v1.2.3-70-g09d2 From 01f2dd03d5fe092ae448ee1a234a197babf38613 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 12 Apr 2016 16:51:27 -0500 Subject: Also install examples directory --- var/spack/repos/builtin/packages/elk/package.py | 5 +++++ 1 file changed, 5 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py index 28ebb89db3..780c41f726 100644 --- a/var/spack/repos/builtin/packages/elk/package.py +++ b/var/spack/repos/builtin/packages/elk/package.py @@ -104,13 +104,18 @@ class Elk(Package): def install(self, spec, prefix): + # Elk only provides an interactive setup script self.configure(spec) make() make('test') + # The Elk Makefile does not provide an install target mkdirp(prefix.bin) install('src/elk', prefix.bin) install('src/eos/eos', prefix.bin) install('src/spacegroup/spacegroup', prefix.bin) + + install_tree('examples', join_path(prefix, 'examples')) + -- cgit v1.2.3-70-g09d2 From abe744c5a099fd988ff3fe5eb1d50cca7a633d74 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Tue, 12 Apr 2016 16:53:45 -0500 Subject: Add latest version of PnetCDF --- var/spack/repos/builtin/packages/parallel-netcdf/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/parallel-netcdf/package.py b/var/spack/repos/builtin/packages/parallel-netcdf/package.py index 62a8f7ca0b..e6f8cf026b 100644 --- a/var/spack/repos/builtin/packages/parallel-netcdf/package.py +++ b/var/spack/repos/builtin/packages/parallel-netcdf/package.py @@ -8,6 +8,7 @@ class ParallelNetcdf(Package): homepage = "https://trac.mcs.anl.gov/projects/parallel-netcdf" url = "http://cucis.ece.northwestern.edu/projects/PnetCDF/Release/parallel-netcdf-1.6.1.tar.gz" + version('1.7.0', '267eab7b6f9dc78c4d0e6def2def3aea4bc7c9f0') version('1.6.1', '62a094eb952f9d1e15f07d56e535052604f1ac34') depends_on("m4") -- cgit v1.2.3-70-g09d2 From 04392babca88089de114864cbe5ad419f6fc212b Mon Sep 17 00:00:00 2001 From: Tom Scogland Date: Tue, 12 Apr 2016 15:53:29 -0700 Subject: add setuptools version 20.7.0 --- var/spack/repos/builtin/packages/py-setuptools/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-setuptools/package.py b/var/spack/repos/builtin/packages/py-setuptools/package.py index 9338a5e157..2086d0b3fb 100644 --- a/var/spack/repos/builtin/packages/py-setuptools/package.py +++ b/var/spack/repos/builtin/packages/py-setuptools/package.py @@ -11,6 +11,7 @@ class PySetuptools(Package): version('19.2', '78353b1f80375ca5e088f4b4627ffe03') version('20.5', 'fadc1e1123ddbe31006e5e43e927362b') version('20.6.7', '45d6110f3ec14924e44c33411db64fe6') + version('20.7.0', '5d12b39bf3e75e80fdce54e44b255615') extends('python') -- cgit v1.2.3-70-g09d2 From 5717cb981e38979727a9340eb118e88166a9f7e3 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 13 Apr 2016 15:03:03 -0500 Subject: fortran2003 option has been removed from HDF5 --- var/spack/repos/builtin/packages/hdf5/package.py | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index f26e225b83..cce609eb29 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -101,10 +101,10 @@ class Hdf5(Package): extra_args.append('--enable-cxx') if '+fortran' in spec: - extra_args.extend([ - '--enable-fortran', - '--enable-fortran2003' - ]) + extra_args.append('--enable-fortran') + # '--enable-fortran2003' no longer exists as of version 1.10.0 + if spec.satisfies('@:1.8.16'): + extra_args.append('--enable-fortran2003') if '+mpi' in spec: # The HDF5 configure script warns if cxx and mpi are enabled -- cgit v1.2.3-70-g09d2 From 2cf9ebc62c18414ddafb44bdda2b2487f72a4ec5 Mon Sep 17 00:00:00 2001 From: Jim Galarowicz Date: Wed, 13 Apr 2016 15:00:45 -0700 Subject: Fix compile issues with new libpng versions and qt3 builds by using an older version of libpng. In libpng, make older versions available. --- var/spack/repos/builtin/packages/libpng/package.py | 3 +++ var/spack/repos/builtin/packages/qt/package.py | 5 ++++- 2 files changed, 7 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/libpng/package.py b/var/spack/repos/builtin/packages/libpng/package.py index 73c8c62341..9d5782896e 100644 --- a/var/spack/repos/builtin/packages/libpng/package.py +++ b/var/spack/repos/builtin/packages/libpng/package.py @@ -8,6 +8,9 @@ class Libpng(Package): version('1.6.16', '1a4ad377919ab15b54f6cb6a3ae2622d') version('1.6.15', '829a256f3de9307731d4f52dc071916d') version('1.6.14', '2101b3de1d5f348925990f9aa8405660') + version('1.5.26', '3ca98347a5541a2dad55cd6d07ee60a9') + version('1.4.19', '89bcbc4fc8b31f4a403906cf4f662330') + version('1.2.56', '9508fc59d10a1ffadd9aae35116c19ee') depends_on('zlib') diff --git a/var/spack/repos/builtin/packages/qt/package.py b/var/spack/repos/builtin/packages/qt/package.py index 8cb88e6c85..93688fb777 100644 --- a/var/spack/repos/builtin/packages/qt/package.py +++ b/var/spack/repos/builtin/packages/qt/package.py @@ -29,7 +29,8 @@ class Qt(Package): depends_on("zlib") depends_on("dbus", when='@4:') depends_on("libtiff") - depends_on("libpng") + depends_on("libpng@1.2.56", when='@3') + depends_on("libpng", when='@4:') depends_on("libmng") depends_on("jpeg") @@ -120,6 +121,8 @@ class Qt(Package): @when('@3') def configure(self): + # An user report that this was necessary to link Qt3 on ubuntu + os.environ['LD_LIBRARY_PATH'] = os.getcwd()+'/lib' configure('-prefix', self.prefix, '-v', '-thread', -- cgit v1.2.3-70-g09d2 From f9aafeee1e6a33a76dc1904e97f117194915f4d0 Mon Sep 17 00:00:00 2001 From: Jim Galarowicz Date: Wed, 13 Apr 2016 21:58:57 -0700 Subject: Loosen the boost requirement from a specific version that was specified in my initial commit. --- var/spack/repos/builtin/packages/mrnet/package.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mrnet/package.py b/var/spack/repos/builtin/packages/mrnet/package.py index b8cbb7e8f9..a3abb71285 100644 --- a/var/spack/repos/builtin/packages/mrnet/package.py +++ b/var/spack/repos/builtin/packages/mrnet/package.py @@ -15,13 +15,10 @@ class Mrnet(Package): variant('krellpatch', default=False, description="Build MRNet with krell openspeedshop based patch.") patch('krell-5.0.1.patch', when='@5.0.1+krellpatch') - - variant('lwthreads', default=False, description="Also build the MRNet LW threadsafe libraries") parallel = False - #depends_on("boost") - depends_on("boost@1.53.0") + depends_on("boost") def install(self, spec, prefix): # Build the MRNet LW thread safe libraries when the krelloptions variant is present -- cgit v1.2.3-70-g09d2 From 01fab24c156e82f2886b464a2474fe3474d5312a Mon Sep 17 00:00:00 2001 From: Todd Gamblin Date: Wed, 13 Apr 2016 14:02:25 +0200 Subject: binutils depends on flex, bison, and m4 --- var/spack/repos/builtin/packages/binutils/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/binutils/package.py b/var/spack/repos/builtin/packages/binutils/package.py index 897539a439..b8064093d2 100644 --- a/var/spack/repos/builtin/packages/binutils/package.py +++ b/var/spack/repos/builtin/packages/binutils/package.py @@ -12,6 +12,10 @@ class Binutils(Package): version('2.23.2', '4f8fa651e35ef262edc01d60fb45702e') version('2.20.1', '2b9dc8f2b7dbd5ec5992c6e29de0b764') + depends_on('m4') + depends_on('flex') + depends_on('bison') + # Add a patch that creates binutils libiberty_pic.a which is preferred by OpenSpeedShop and cbtf-krell variant('krellpatch', default=False, description="build with openspeedshop based patch.") variant('gold', default=True, description="build the gold linker") -- cgit v1.2.3-70-g09d2 From cf1914fc00bd98a1885edc4d4190f9c424b0588b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 14 Apr 2016 10:18:06 -0500 Subject: Also install species directory --- var/spack/repos/builtin/packages/elk/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/elk/package.py b/var/spack/repos/builtin/packages/elk/package.py index 780c41f726..1d9216fd1a 100644 --- a/var/spack/repos/builtin/packages/elk/package.py +++ b/var/spack/repos/builtin/packages/elk/package.py @@ -118,4 +118,5 @@ class Elk(Package): install('src/spacegroup/spacegroup', prefix.bin) install_tree('examples', join_path(prefix, 'examples')) + install_tree('species', join_path(prefix, 'species')) -- cgit v1.2.3-70-g09d2 From a25e33d96ecbd3db690cd8f0bc5119f506310dab Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Sun, 17 Apr 2016 00:50:15 -0400 Subject: Create lib directory --- var/spack/repos/builtin/packages/cereal/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cereal/package.py b/var/spack/repos/builtin/packages/cereal/package.py index a83927456f..6acbf666c8 100644 --- a/var/spack/repos/builtin/packages/cereal/package.py +++ b/var/spack/repos/builtin/packages/cereal/package.py @@ -1,4 +1,5 @@ from spack import * +import os import shutil class Cereal(Package): @@ -30,5 +31,8 @@ class Cereal(Package): # Install shutil.rmtree(join_path(prefix, 'doc'), ignore_errors=True) shutil.rmtree(join_path(prefix, 'include'), ignore_errors=True) + shutil.rmtree(join_path(prefix, 'lib'), ignore_errors=True) shutil.copytree('doc', join_path(prefix, 'doc'), symlinks=True) shutil.copytree('include', join_path(prefix, 'include'), symlinks=True) + # Create empty directory to avoid linker warnings later + os.mkdir(join_path(prefix, 'lib')) -- cgit v1.2.3-70-g09d2 From 523be30974c4630450e779a9814d685716dd312e Mon Sep 17 00:00:00 2001 From: Kelly Thompson Date: Sat, 16 Apr 2016 23:11:19 -0600 Subject: + Add CMake version 3.5.2. (#787) --- var/spack/repos/builtin/packages/cmake/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/cmake/package.py b/var/spack/repos/builtin/packages/cmake/package.py index 91a4e3b415..2493cf0a13 100644 --- a/var/spack/repos/builtin/packages/cmake/package.py +++ b/var/spack/repos/builtin/packages/cmake/package.py @@ -30,6 +30,7 @@ class Cmake(Package): homepage = 'https://www.cmake.org' url = 'https://cmake.org/files/v3.4/cmake-3.4.3.tar.gz' + version('3.5.2', '701386a1b5ec95f8d1075ecf96383e02') version('3.5.1', 'ca051f4a66375c89d1a524e726da0296') version('3.5.0', '33c5d09d4c33d4ffcc63578a6ba8777e') version('3.4.3', '4cb3ff35b2472aae70f542116d616e63') -- cgit v1.2.3-70-g09d2 From fb4f361cd0a8f12c606013b382d7e4fa5706dbfb Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Sun, 17 Apr 2016 01:12:52 -0400 Subject: Update to version 4.1.0 (#785) --- var/spack/repos/builtin/packages/jemalloc/package.py | 4 ++++ 1 file changed, 4 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/jemalloc/package.py b/var/spack/repos/builtin/packages/jemalloc/package.py index 8cec9ea75b..9cb0fd1f40 100644 --- a/var/spack/repos/builtin/packages/jemalloc/package.py +++ b/var/spack/repos/builtin/packages/jemalloc/package.py @@ -5,6 +5,7 @@ class Jemalloc(Package): homepage = "http://www.canonware.com/jemalloc/" url = "https://github.com/jemalloc/jemalloc/releases/download/4.0.4/jemalloc-4.0.4.tar.bz2" + version('4.1.0', 'c4e53c947905a533d5899e5cc3da1f94') version('4.0.4', '687c5cc53b9a7ab711ccd680351ff988') variant('stats', default=False, description='Enable heap statistics') @@ -20,5 +21,8 @@ class Jemalloc(Package): configure(*configure_args) + # Don't use -Werror + filter_file(r'-Werror=\S*', '', 'Makefile') + make() make("install") -- cgit v1.2.3-70-g09d2 From 375de085e271f2926ef2381a2e22f40bd5541177 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Sun, 17 Apr 2016 01:14:34 -0400 Subject: Make PAPI build on Darwin (#772) * Make PAPI build on Darwin - don't use - run install_name_tool * Use fix_darwin_install_name --- var/spack/repos/builtin/packages/papi/package.py | 31 +++++++++++++++++------- 1 file changed, 22 insertions(+), 9 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/papi/package.py b/var/spack/repos/builtin/packages/papi/package.py index 53d69e28d9..74b3ea9ef9 100644 --- a/var/spack/repos/builtin/packages/papi/package.py +++ b/var/spack/repos/builtin/packages/papi/package.py @@ -1,5 +1,8 @@ from spack import * +import glob import os +import sys +from llnl.util.filesystem import fix_darwin_install_name class Papi(Package): """PAPI provides the tool designer and application engineer with a @@ -18,17 +21,27 @@ class Papi(Package): version('5.3.0', '367961dd0ab426e5ae367c2713924ffb') def install(self, spec, prefix): - os.chdir("src/") + with working_dir("src"): - configure_args=["--prefix=%s" % prefix] + configure_args=["--prefix=%s" % prefix] - # PAPI uses MPI if MPI is present; since we don't require an - # MPI package, we ensure that all attempts to use MPI fail, so - # that PAPI does not get confused - configure_args.append('MPICC=:') + # PAPI uses MPI if MPI is present; since we don't require + # an MPI package, we ensure that all attempts to use MPI + # fail, so that PAPI does not get confused + configure_args.append('MPICC=:') - configure(*configure_args) + configure(*configure_args) - make() - make("install") + # Don't use + for level in [".", "*", "*/*"]: + files = glob.iglob(join_path(level, "*.[ch]")) + filter_file(r"\", "", *files) + make() + make("install") + + # The shared library is not installed correctly on Darwin + if sys.platform == 'darwin': + os.rename(join_path(prefix.lib, 'libpapi.so'), + join_path(prefix.lib, 'libpapi.dylib')) + fix_darwin_install_name(prefix.lib) -- cgit v1.2.3-70-g09d2 From 63bade7a0c7350681dd29ce877f2a9fad679d67d Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Sun, 17 Apr 2016 01:15:07 -0400 Subject: metis: fix OS X install (#764) Without this, the binaries use relative paths for loading which causes them to not be found when running binaries. Not sure why the existing hack wasn't working, but this fixes it the proper way. --- var/spack/repos/builtin/packages/metis/package.py | 5 +---- 1 file changed, 1 insertion(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/metis/package.py b/var/spack/repos/builtin/packages/metis/package.py index 41e3ebb429..b05f23a3dc 100644 --- a/var/spack/repos/builtin/packages/metis/package.py +++ b/var/spack/repos/builtin/packages/metis/package.py @@ -136,6 +136,7 @@ class Metis(Package): source_directory = self.stage.source_path options.append('-DGKLIB_PATH:PATH={metis_source}/GKlib'.format(metis_source=source_directory)) + options.append('-DCMAKE_INSTALL_NAME_DIR:PATH=%s/lib' % prefix) if '+shared' in spec: options.append('-DSHARED:BOOL=ON') @@ -184,7 +185,3 @@ class Metis(Package): fs = glob.glob(join_path(source_directory,'GKlib',"*.h")) for f in fs: install(f, GKlib_dist) - - # The shared library is not installed correctly on Darwin; correct this - if (sys.platform == 'darwin') and ('+shared' in spec): - fix_darwin_install_name(prefix.lib) -- cgit v1.2.3-70-g09d2 From dd84a575807636159d80809f59962cf799b83fd7 Mon Sep 17 00:00:00 2001 From: Kelly Thompson Date: Sat, 16 Apr 2016 23:15:48 -0600 Subject: + On some systems, Dia also requires intltool. (#768) --- var/spack/repos/builtin/packages/dia/package.py | 1 + var/spack/repos/builtin/packages/intltool/package.py | 19 +++++++++++++++++++ 2 files changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/intltool/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dia/package.py b/var/spack/repos/builtin/packages/dia/package.py index 1cb5910e46..25d5f08205 100644 --- a/var/spack/repos/builtin/packages/dia/package.py +++ b/var/spack/repos/builtin/packages/dia/package.py @@ -7,6 +7,7 @@ class Dia(Package): version('0.97.3', '0e744a0f6a6c4cb6a089e4d955392c3c') + depends_on('intltool') depends_on('gtkplus@2.6.0:') depends_on('cairo') #depends_on('libart') # optional dependency, not yet supported by spack. diff --git a/var/spack/repos/builtin/packages/intltool/package.py b/var/spack/repos/builtin/packages/intltool/package.py new file mode 100644 index 0000000000..9b3c095378 --- /dev/null +++ b/var/spack/repos/builtin/packages/intltool/package.py @@ -0,0 +1,19 @@ +from spack import * + +class Intltool(Package): + """intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files.""" + homepage = 'https://freedesktop.org/wiki/Software/intltool/' + + version('0.51.0', '12e517cac2b57a0121cda351570f1e63') + + def url_for_version(self, version): + """Handle version-based custom URLs.""" + return 'https://launchpad.net/intltool/trunk/%s/+download/intltool-%s.tar.gz' % (version, version) + + def install(self, spec, prefix): + + # configure, build, install: + options = ['--prefix=%s' % prefix ] + configure(*options) + make() + make('install') -- cgit v1.2.3-70-g09d2 From ef9347bcfb52e7f80aacb4ecb63d1536b8aaa3c0 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Fri, 22 Apr 2016 04:25:17 +0200 Subject: dealii: set DEAL_II_DIR when loading a module (#816) --- var/spack/repos/builtin/packages/dealii/package.py | 3 +++ 1 file changed, 3 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index b251d50ca1..6810e86868 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -251,3 +251,6 @@ class Dealii(Package): cmake('.') make('release') make('run',parallel=False) + + def setup_environment(self, spack_env, env): + env.set('DEAL_II_DIR', self.prefix) -- cgit v1.2.3-70-g09d2 From 5c4bb69af9cceca0b3c4380357ab6e74e7554067 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Thu, 21 Apr 2016 22:29:20 -0400 Subject: xerces-c: update to 3.1.3 (#811) The 3.1.2 tarball seems to have gone missing. Also switch to using bz2 rather than gz to reduce the download size. --- var/spack/repos/builtin/packages/xerces-c/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/xerces-c/package.py b/var/spack/repos/builtin/packages/xerces-c/package.py index b59ab178ae..e36fb936e0 100644 --- a/var/spack/repos/builtin/packages/xerces-c/package.py +++ b/var/spack/repos/builtin/packages/xerces-c/package.py @@ -24,8 +24,8 @@ class XercesC(Package): """ homepage = "https://xerces.apache.org/xerces-c" - url = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.2.tar.gz" - version('3.1.2', '9eb1048939e88d6a7232c67569b23985') + url = "https://www.apache.org/dist/xerces/c/3/sources/xerces-c-3.1.3.tar.bz2" + version('3.1.3', '5e333b55cb43e6b025ddf0e5d0f0fb0d') def install(self, spec, prefix): configure("--prefix=%s" % prefix, -- cgit v1.2.3-70-g09d2 From e7d2fa7084a63d73fe19607a442e47036a3f864b Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Fri, 22 Apr 2016 12:30:24 -0500 Subject: Add IOR benchmark package --- var/spack/repos/builtin/packages/ior/package.py | 38 +++++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ior/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py new file mode 100644 index 0000000000..3ede3d7e37 --- /dev/null +++ b/var/spack/repos/builtin/packages/ior/package.py @@ -0,0 +1,38 @@ +from spack import * +import os + +class Ior(Package): + """The IOR software is used for benchmarking parallel file systems + using POSIX, MPI-IO, or HDF5 interfaces.""" + + homepage = "http://www.nersc.gov/users/computational-systems/cori/nersc-8-procurement/trinity-nersc-8-rfp/nersc-8-trinity-benchmarks/ior/" + url = "https://github.com/LLNL/ior/archive/3.0.1.tar.gz" + + version('3.0.1', '71150025e0bb6ea1761150f48b553065') + + variant('hdf5', default=False, description='support IO with HDF5 backend') + variant('ncmpi', default=False, description='support IO with NCMPI backend') + + depends_on('mpi') + depends_on('hdf5+mpi', when='+hdf5') + depends_on('netcdf+mpi', when='+ncmpi') + + + def install(self, spec, prefix): + os.system('./bootstrap') + + config_args = [ + 'MPICC=%s' % spec['mpi'].prefix.bin + '/mpicc', + '--prefix=%s' % prefix, + ] + + if '+hdf5' in spec: + config_args.append('--with-hdf5') + + if '+ncmpi' in spec: + config_args.append('--with-ncmpi') + + configure(*config_args) + + make() + make('install') -- cgit v1.2.3-70-g09d2 From d701d2ccf344ff22fee463504dd85e1d0a5bfdc6 Mon Sep 17 00:00:00 2001 From: Joseph Ciurej Date: Sat, 23 Apr 2016 12:15:14 -0700 Subject: Updated the Swig package file to include versions for all of the popular Swig releases. (#790) --- var/spack/repos/builtin/packages/swig/package.py | 12 +++++++++--- 1 file changed, 9 insertions(+), 3 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/swig/package.py b/var/spack/repos/builtin/packages/swig/package.py index 8d46c4fe46..78a6c6bbae 100644 --- a/var/spack/repos/builtin/packages/swig/package.py +++ b/var/spack/repos/builtin/packages/swig/package.py @@ -22,6 +22,7 @@ # 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 Swig(Package): @@ -33,14 +34,19 @@ class Swig(Package): code. In addition, SWIG provides a variety of customization features that let you tailor the wrapping process to suit your application.""" + homepage = "http://www.swig.org" - url = "http://prdownloads.sourceforge.net/swig/swig-3.0.2.tar.gz" + url = "http://prdownloads.sourceforge.net/swig/swig-3.0.8.tar.gz" + version('3.0.8', 'c96a1d5ecb13d38604d7e92148c73c97') version('3.0.2', '62f9b0d010cef36a13a010dc530d0d41') + version('2.0.12', 'c3fb0b2d710cc82ed0154b91e43085a4') + version('2.0.2', 'eaf619a4169886923e5f828349504a29') + version('1.3.40', '2df766c9e03e02811b1ab4bba1c7b9cc') depends_on('pcre') def install(self, spec, prefix): - configure("--prefix=%s" % prefix) + configure('--prefix=%s' % prefix) make() - make("install") + make('install') -- cgit v1.2.3-70-g09d2 From 4e062d86b4213595e74510f9b8d91382ed4e1041 Mon Sep 17 00:00:00 2001 From: Erik Schnetter Date: Sat, 23 Apr 2016 15:15:32 -0400 Subject: Refine wget's OpenSSL configuration options (#786) --- var/spack/repos/builtin/packages/wget/package.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/wget/package.py b/var/spack/repos/builtin/packages/wget/package.py index 55728b0515..4b92659478 100644 --- a/var/spack/repos/builtin/packages/wget/package.py +++ b/var/spack/repos/builtin/packages/wget/package.py @@ -17,6 +17,8 @@ class Wget(Package): def install(self, spec, prefix): configure("--prefix=%s" % prefix, - "--with-ssl=openssl") + "--with-ssl=openssl", + "OPENSSL_CFLAGS=-I%s" % spec['openssl'].prefix.include, + "OPENSSL_LIBS=-L%s -lssl -lcrypto -lz" % spec['openssl'].prefix.lib) make() make("install") -- cgit v1.2.3-70-g09d2 From 248248c6b270e2c1707ea29e90de74813ea2debf Mon Sep 17 00:00:00 2001 From: Elizabeth Fischer Date: Sat, 23 Apr 2016 15:15:53 -0400 Subject: Added package: NCView (#791) * ncview: Added package * Removed FIXMEs --- var/spack/repos/builtin/packages/ncview/package.py | 20 ++++++++++++++++++++ 1 file changed, 20 insertions(+) create mode 100644 var/spack/repos/builtin/packages/ncview/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/ncview/package.py b/var/spack/repos/builtin/packages/ncview/package.py new file mode 100644 index 0000000000..1aa13e3f03 --- /dev/null +++ b/var/spack/repos/builtin/packages/ncview/package.py @@ -0,0 +1,20 @@ +from spack import * + +class Ncview(Package): + """Simple viewer for NetCDF files.""" + homepage = "http://meteora.ucsd.edu/~pierce/ncview_home_page.html" + url = "ftp://cirrus.ucsd.edu/pub/ncview/ncview-2.1.7.tar.gz" + + version('2.1.7', 'debd6ca61410aac3514e53122ab2ba07') + + depends_on("netcdf") + depends_on("udunits2") + + # OS Dependencies + # Ubuntu: apt-get install libxaw7-dev + # CentOS 7: yum install libXaw-devel + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + make() + make("install") -- cgit v1.2.3-70-g09d2 From e32416430c16a51af673a78fb79d47c68464fa98 Mon Sep 17 00:00:00 2001 From: Ben Boeckel Date: Sat, 23 Apr 2016 15:18:58 -0400 Subject: Update git (#819) * git: update to 2.8.0 final and add 2.8.1 * git: hard-depend on curl and expat HTTP-based cloning is very prevalent now. --- var/spack/repos/builtin/packages/git/package.py | 32 ++++++------------------- 1 file changed, 7 insertions(+), 25 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/git/package.py b/var/spack/repos/builtin/packages/git/package.py index 388f84aefd..77521fd658 100644 --- a/var/spack/repos/builtin/packages/git/package.py +++ b/var/spack/repos/builtin/packages/git/package.py @@ -7,7 +7,8 @@ class Git(Package): homepage = "http://git-scm.com" url = "https://github.com/git/git/tarball/v2.7.1" - version('2.8.0-rc2', 'c2cf9f2cc70e35f2fafbaf9258f82e4c') + version('2.8.1', '1308448d95afa41a4135903f22262fc8') + version('2.8.0', 'eca687e46e9750121638f258cff8317b') version('2.7.3', 'fa1c008b56618c355a32ba4a678305f6') version('2.7.1', 'bf0706b433a8dedd27a63a72f9a66060') @@ -23,18 +24,10 @@ class Git(Package): #version('2.2.1', 'ff41fdb094eed1ec430aed8ee9b9849c') - # Git compiles with curl support by default on but if your system - # does not have it you will not be able to clone https repos - variant("curl", default=False, description="Add the internal support of curl for https clone") - - # Git compiles with expat support by default on but if your system - # does not have it you will not be able to push https repos - variant("expat", default=False, description="Add the internal support of expat for https push") - depends_on("openssl") depends_on("autoconf") - depends_on("curl", when="+curl") - depends_on("expat", when="+expat") + depends_on("curl") + depends_on("expat") # Also depends_on gettext: apt-get install gettext (Ubuntu) @@ -49,23 +42,12 @@ class Git(Package): "--prefix=%s" % prefix, "--without-pcre", "--with-openssl=%s" % spec['openssl'].prefix, - "--with-zlib=%s" % spec['zlib'].prefix + "--with-zlib=%s" % spec['zlib'].prefix, + "--with-curl=%s" % spec['curl'].prefix, + "--with-expat=%s" % spec['expat'].prefix, ] - if '+curl' in spec: - configure_args.append("--with-curl=%s" % spec['curl'].prefix) - - if '+expat' in spec: - configure_args.append("--with-expat=%s" % spec['expat'].prefix) - which('autoreconf')('-i') configure(*configure_args) make() make("install") - - - - - - - -- cgit v1.2.3-70-g09d2 From 22e4ee560465a633f7dd8e84a2e7088d8dcf547f Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sat, 23 Apr 2016 15:29:47 -0500 Subject: Add OSU Micro-Benchmarks package (#822) * Add OSU Micro-Benchmarks package * Add workaround for GCC bug --- .../packages/osu-micro-benchmarks/package.py | 38 ++++++++++++++++++++++ 1 file changed, 38 insertions(+) create mode 100644 var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py new file mode 100644 index 0000000000..01054471a3 --- /dev/null +++ b/var/spack/repos/builtin/packages/osu-micro-benchmarks/package.py @@ -0,0 +1,38 @@ +from spack import * + +class OsuMicroBenchmarks(Package): + """The Ohio MicroBenchmark suite is a collection of independent MPI + message passing performance microbenchmarks developed and written at + The Ohio State University. It includes traditional benchmarks and + performance measures such as latency, bandwidth and host overhead + and can be used for both traditional and GPU-enhanced nodes.""" + + homepage = "http://mvapich.cse.ohio-state.edu/benchmarks/" + url = "http://mvapich.cse.ohio-state.edu/download/mvapich/osu-micro-benchmarks-5.3.tar.gz" + + version('5.3', '42e22b931d451e8bec31a7424e4adfc2') + + variant('cuda', default=False, description="Enable CUDA support") + + depends_on('mpi') + depends_on('cuda', when='+cuda') + + + def install(self, spec, prefix): + config_args = [ + 'CC=%s' % spec['mpi'].prefix.bin + '/mpicc', + 'CXX=%s' % spec['mpi'].prefix.bin + '/mpicxx', + 'LDFLAGS=-lrt', + '--prefix=%s' % prefix + ] + + if '+cuda' in spec: + config_args.extend([ + '--enable-cuda', + '--with-cuda=%s' % spec['cuda'].prefix, + ]) + + configure(*config_args) + + make() + make('install') -- cgit v1.2.3-70-g09d2 From a7ffffc336beff3ba2ef98a82ec16c35d65c7982 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Sun, 24 Apr 2016 17:14:33 -0500 Subject: Change homepage, explicitly disable --- var/spack/repos/builtin/packages/ior/package.py | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/ior/package.py b/var/spack/repos/builtin/packages/ior/package.py index 3ede3d7e37..c46650a674 100644 --- a/var/spack/repos/builtin/packages/ior/package.py +++ b/var/spack/repos/builtin/packages/ior/package.py @@ -5,7 +5,7 @@ class Ior(Package): """The IOR software is used for benchmarking parallel file systems using POSIX, MPI-IO, or HDF5 interfaces.""" - homepage = "http://www.nersc.gov/users/computational-systems/cori/nersc-8-procurement/trinity-nersc-8-rfp/nersc-8-trinity-benchmarks/ior/" + homepage = "https://github.com/LLNL/ior" url = "https://github.com/LLNL/ior/archive/3.0.1.tar.gz" version('3.0.1', '71150025e0bb6ea1761150f48b553065') @@ -28,9 +28,13 @@ class Ior(Package): if '+hdf5' in spec: config_args.append('--with-hdf5') + else: + config_args.append('--without-hdf5') if '+ncmpi' in spec: config_args.append('--with-ncmpi') + else: + config_args.append('--without-ncmpi') configure(*config_args) -- cgit v1.2.3-70-g09d2 From 797af2e80f0effddeca2b964283705940fa45df8 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Sun, 24 Apr 2016 17:39:49 -0500 Subject: Add py-csvkit package This adds the py-csvkit package and needed dependencies for working with csv files. --- .../builtin/packages/py-SQLAlchemy/package.py | 15 ++++++++++++++ .../repos/builtin/packages/py-csvkit/package.py | 23 ++++++++++++++++++++++ var/spack/repos/builtin/packages/py-dbf/package.py | 17 ++++++++++++++++ .../repos/builtin/packages/py-jdcal/package.py | 15 ++++++++++++++ .../repos/builtin/packages/py-openpyxl/package.py | 18 +++++++++++++++++ .../repos/builtin/packages/py-xlrd/package.py | 16 +++++++++++++++ 6 files changed, 104 insertions(+) create mode 100644 var/spack/repos/builtin/packages/py-SQLAlchemy/package.py create mode 100644 var/spack/repos/builtin/packages/py-csvkit/package.py create mode 100644 var/spack/repos/builtin/packages/py-dbf/package.py create mode 100644 var/spack/repos/builtin/packages/py-jdcal/package.py create mode 100644 var/spack/repos/builtin/packages/py-openpyxl/package.py create mode 100644 var/spack/repos/builtin/packages/py-xlrd/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py new file mode 100644 index 0000000000..ccb882f749 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PySqlalchemy(Package): + """ + The Python SQL Toolkit and Object Relational Mapper + """ + homepage = 'http://www.sqlalchemy.org/' + url = "https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-1.0.12.tar.gz" + + version('1.0.12', '6d19ef29883bbebdcac6613cf391cac4') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py new file mode 100644 index 0000000000..1ab848161d --- /dev/null +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -0,0 +1,23 @@ +from spack import * + +class PyCsvkit(Package): + """ + A library of utilities for working with CSV, the king of tabular file + formats + """ + homepage = 'http://csvkit.rtfd.org/' + url = "https://pypi.python.org/packages/source/c/csvkit/csvkit-0.9.1.tar.gz" + + version('0.9.1', '48d78920019d18846933ee969502fff6') + + extends('python') + + depends_on('py-dateutil') + depends_on('py-dbf') + depends_on('py-xlrd') + depends_on('py-SQLAlchemy') + depends_on('py-six') + depends_on('py-openpyxl') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py new file mode 100644 index 0000000000..75c32b2d61 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-dbf/package.py @@ -0,0 +1,17 @@ +from spack import * + +class PyDbf(Package): + """ + Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro + .dbf files (including memos). + """ + + homepage = 'https://pypi.python.org/pypi/dbf' + url = "https://pypi.python.org/packages/source/d/dbf/dbf-0.96.005.tar.gz" + + version('0.96.005', 'bce1a1ed8b454a30606e7e18dd2f8277') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py new file mode 100644 index 0000000000..a2fcbe119c --- /dev/null +++ b/var/spack/repos/builtin/packages/py-jdcal/package.py @@ -0,0 +1,15 @@ +from spack import * + +class PyJdcal(Package): + """ + Julian dates from proleptic Gregorian and Julian calendars + """ + homepage = 'http://github.com/phn/jdcal' + url = "https://pypi.python.org/packages/source/j/jdcal/jdcal-1.2.tar.gz" + + version('1.2', 'ab8d5ba300fd1eb01514f363d19b1eb9') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py new file mode 100644 index 0000000000..5954c4758a --- /dev/null +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -0,0 +1,18 @@ +from spack import * + +class PyOpenpyxl(Package): + """ + A Python library to read/write Excel 2007 xlsx/xlsm files + """ + homepage = 'http://openpyxl.readthedocs.org/' + url = "https://pypi.python.org/packages/source/o/openpyxl/openpyxl-2.4.0-a1.tar.gz" + + version('2.4.0-a1', 'e5ca6d23ceccb15115d45cdf26e736fc') + + extends('python') + + depends_on('py-jdcal') + depends_on('py-setuptools') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py new file mode 100644 index 0000000000..10ca8ce2a7 --- /dev/null +++ b/var/spack/repos/builtin/packages/py-xlrd/package.py @@ -0,0 +1,16 @@ +from spack import * + +class PyXlrd(Package): + """ + Library for developers to extract data from Microsoft Excel (tm) + spreadsheet files + """ + homepage = 'http://www.python-excel.org/' + url = "https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.4.tar.gz" + + version('0.9.4', '911839f534d29fe04525ef8cd88fe865') + + extends('python') + + def install(self, spec, prefix): + python('setup.py', 'install', '--prefix=%s' % prefix) -- cgit v1.2.3-70-g09d2 From 4e671c54ee69d2a335e2b057aada75c2257c3850 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Sun, 24 Apr 2016 18:06:51 -0500 Subject: Reformat the description. --- var/spack/repos/builtin/packages/py-SQLAlchemy/package.py | 5 ++--- var/spack/repos/builtin/packages/py-csvkit/package.py | 7 +++---- var/spack/repos/builtin/packages/py-dbf/package.py | 6 ++---- var/spack/repos/builtin/packages/py-jdcal/package.py | 5 ++--- var/spack/repos/builtin/packages/py-openpyxl/package.py | 5 ++--- var/spack/repos/builtin/packages/py-xlrd/package.py | 7 +++---- 6 files changed, 14 insertions(+), 21 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py index ccb882f749..9aecc95c63 100644 --- a/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py +++ b/var/spack/repos/builtin/packages/py-SQLAlchemy/package.py @@ -1,9 +1,8 @@ from spack import * class PySqlalchemy(Package): - """ - The Python SQL Toolkit and Object Relational Mapper - """ + """The Python SQL Toolkit and Object Relational Mapper""" + homepage = 'http://www.sqlalchemy.org/' url = "https://pypi.python.org/packages/source/S/SQLAlchemy/SQLAlchemy-1.0.12.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-csvkit/package.py b/var/spack/repos/builtin/packages/py-csvkit/package.py index 1ab848161d..def30457be 100644 --- a/var/spack/repos/builtin/packages/py-csvkit/package.py +++ b/var/spack/repos/builtin/packages/py-csvkit/package.py @@ -1,10 +1,9 @@ from spack import * class PyCsvkit(Package): - """ - A library of utilities for working with CSV, the king of tabular file - formats - """ + """A library of utilities for working with CSV, the king of tabular file + formats""" + homepage = 'http://csvkit.rtfd.org/' url = "https://pypi.python.org/packages/source/c/csvkit/csvkit-0.9.1.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-dbf/package.py b/var/spack/repos/builtin/packages/py-dbf/package.py index 75c32b2d61..698b221903 100644 --- a/var/spack/repos/builtin/packages/py-dbf/package.py +++ b/var/spack/repos/builtin/packages/py-dbf/package.py @@ -1,10 +1,8 @@ from spack import * class PyDbf(Package): - """ - Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro - .dbf files (including memos). - """ + """Pure python package for reading/writing dBase, FoxPro, and Visual FoxPro + .dbf files (including memos)""" homepage = 'https://pypi.python.org/pypi/dbf' url = "https://pypi.python.org/packages/source/d/dbf/dbf-0.96.005.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-jdcal/package.py b/var/spack/repos/builtin/packages/py-jdcal/package.py index a2fcbe119c..54169b2c21 100644 --- a/var/spack/repos/builtin/packages/py-jdcal/package.py +++ b/var/spack/repos/builtin/packages/py-jdcal/package.py @@ -1,9 +1,8 @@ from spack import * class PyJdcal(Package): - """ - Julian dates from proleptic Gregorian and Julian calendars - """ + """Julian dates from proleptic Gregorian and Julian calendars""" + homepage = 'http://github.com/phn/jdcal' url = "https://pypi.python.org/packages/source/j/jdcal/jdcal-1.2.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-openpyxl/package.py b/var/spack/repos/builtin/packages/py-openpyxl/package.py index 5954c4758a..87ff9f3521 100644 --- a/var/spack/repos/builtin/packages/py-openpyxl/package.py +++ b/var/spack/repos/builtin/packages/py-openpyxl/package.py @@ -1,9 +1,8 @@ from spack import * class PyOpenpyxl(Package): - """ - A Python library to read/write Excel 2007 xlsx/xlsm files - """ + """A Python library to read/write Excel 2007 xlsx/xlsm files""" + homepage = 'http://openpyxl.readthedocs.org/' url = "https://pypi.python.org/packages/source/o/openpyxl/openpyxl-2.4.0-a1.tar.gz" diff --git a/var/spack/repos/builtin/packages/py-xlrd/package.py b/var/spack/repos/builtin/packages/py-xlrd/package.py index 10ca8ce2a7..8f25c06aad 100644 --- a/var/spack/repos/builtin/packages/py-xlrd/package.py +++ b/var/spack/repos/builtin/packages/py-xlrd/package.py @@ -1,10 +1,9 @@ from spack import * class PyXlrd(Package): - """ - Library for developers to extract data from Microsoft Excel (tm) - spreadsheet files - """ + """Library for developers to extract data from Microsoft Excel (tm) + spreadsheet files""" + homepage = 'http://www.python-excel.org/' url = "https://pypi.python.org/packages/source/x/xlrd/xlrd-0.9.4.tar.gz" -- cgit v1.2.3-70-g09d2 From b81cb554f505c4075b9df79ab3db08be3d3b9e36 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 25 Apr 2016 09:57:48 +0200 Subject: openblas: a small unit test to make sure Lapack symbols are compiled --- .../repos/builtin/packages/openblas/package.py | 55 ++++++++++++++++++++++ 1 file changed, 55 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 4522130ccc..252f699652 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -1,6 +1,7 @@ from spack import * import sys import os +import shutil class Openblas(Package): """OpenBLAS: An optimized BLAS library""" @@ -64,6 +65,10 @@ class Openblas(Package): if '+shared' in spec: symlink('libopenblas.%s' % dso_suffix, 'liblapack.%s' % dso_suffix) + # Openblas may pass its own test but still fail to compile Lapack + # symbols. To make sure we get working Blas and Lapack, do a small test. + self.check_install(spec) + def setup_dependent_package(self, module, dspec): # This is WIP for a prototype interface for virtual packages. @@ -76,3 +81,53 @@ class Openblas(Package): if '+shared' in self.spec: self.spec.blas_shared_lib = join_path(libdir, 'libopenblas.%s' % dso_suffix) self.spec.lapack_shared_lib = self.spec.blas_shared_lib + + def check_install(self, spec): + "Build and run a small program to test that we have Lapack symbols" + print "Checking Openblas installation..." + checkdir = "spack-check" + with working_dir(checkdir, create=True): + source = r""" +#include +#include +int main(void) { +int i=0; +double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; +double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; +double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; +cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, + 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); +for (i = 0; i < 8; i++) + printf("%lf ", C[i]); +printf("%lf", C[8]); +return 0; +} +""" + expected = """\ +11.000000 -9.000000 5.000000 -9.000000 21.000000 -1.000000 5.000000 -1.000000 3.000000\ +""" + with open("check.c", 'w') as f: + f.write(source) + cc = which('cc') + # TODO: Automate these path and library settings + cc('-c', "-I%s" % join_path(spec.prefix, "include"), "check.c") + cc('-o', "check", "check.o", + "-L%s" % join_path(spec.prefix, "lib"), "-llapack", "-lblas") + try: + check = Executable('./check') + output = check(return_output=True) + except: + output = "" + success = output == expected + if not success: + print "Produced output does not match expected output." + print "Expected output:" + print '-'*80 + print expected + print '-'*80 + print "Produced output:" + print '-'*80 + print output + print '-'*80 + raise RuntimeError("Openblas install check failed") + shutil.rmtree(checkdir) -- cgit v1.2.3-70-g09d2 From 42be50d10b649a130e64f2a742fa4133ed5534b7 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 25 Apr 2016 13:53:41 +0200 Subject: add a test/output pair --- .../repos/builtin/packages/openblas/test_cblas_dgemm.c | 14 ++++++++++++++ .../builtin/packages/openblas/test_cblas_dgemm.output | 1 + 2 files changed, 15 insertions(+) create mode 100644 var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c create mode 100644 var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c new file mode 100644 index 0000000000..37785bf47f --- /dev/null +++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c @@ -0,0 +1,14 @@ +#include +#include +int main(void) { +int i=0; +double A[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; +double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; +double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; +cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, + 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); +for (i = 0; i < 8; i++) + printf("%lf ", C[i]); +printf("%lf", C[8]); +return 0; +} diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output new file mode 100644 index 0000000000..490905aca0 --- /dev/null +++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output @@ -0,0 +1 @@ +11.000000 -9.000000 5.000000 -9.000000 21.000000 -1.000000 5.000000 -1.000000 3.000000 \ No newline at end of file -- cgit v1.2.3-70-g09d2 From dd37959899d03fc33d59f725dbad4fe33b579725 Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Mon, 25 Apr 2016 16:21:19 +0200 Subject: output with new lines --- var/spack/repos/builtin/packages/openblas/package.py | 15 +++++++++++---- .../repos/builtin/packages/openblas/test_cblas_dgemm.c | 5 ++--- .../builtin/packages/openblas/test_cblas_dgemm.output | 10 +++++++++- 3 files changed, 22 insertions(+), 8 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 252f699652..61250fb310 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -97,14 +97,21 @@ double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); -for (i = 0; i < 8; i++) - printf("%lf ", C[i]); -printf("%lf", C[8]); +for (i = 0; i < 9; i++) + printf("%f\n", C[i]); return 0; } """ expected = """\ -11.000000 -9.000000 5.000000 -9.000000 21.000000 -1.000000 5.000000 -1.000000 3.000000\ +11.000000 +-9.000000 +5.000000 +-9.000000 +21.000000 +-1.000000 +5.000000 +-1.000000 +3.000000 """ with open("check.c", 'w') as f: f.write(source) diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c index 37785bf47f..634e99d20b 100644 --- a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c +++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.c @@ -7,8 +7,7 @@ double B[6] = {1.0, 2.0, 1.0, -3.0, 4.0, -1.0}; double C[9] = {.5, .5, .5, .5, .5, .5, .5, .5, .5}; cblas_dgemm(CblasColMajor, CblasNoTrans, CblasTrans, 3, 3, 2, 1, A, 3, B, 3, 2, C, 3); -for (i = 0; i < 8; i++) - printf("%lf ", C[i]); -printf("%lf", C[8]); +for (i = 0; i < 9; i++) + printf("%f\n", C[i]); return 0; } diff --git a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output index 490905aca0..b8316d7477 100644 --- a/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output +++ b/var/spack/repos/builtin/packages/openblas/test_cblas_dgemm.output @@ -1 +1,9 @@ -11.000000 -9.000000 5.000000 -9.000000 21.000000 -1.000000 5.000000 -1.000000 3.000000 \ No newline at end of file +11.000000 +-9.000000 +5.000000 +-9.000000 +21.000000 +-1.000000 +5.000000 +-1.000000 +3.000000 -- cgit v1.2.3-70-g09d2 From 17b73050868818f62af4f98a65b371f68a4e5e59 Mon Sep 17 00:00:00 2001 From: Jean-Paul Pelteret Date: Tue, 19 Apr 2016 21:09:54 +0200 Subject: Added package for Paradiseo. --- .../packages/paradiseo/enable_eoserial.patch | 14 +++++ .../packages/paradiseo/fix_osx_detection.patch | 13 +++++ .../builtin/packages/paradiseo/fix_tests.patch | 13 +++++ .../builtin/packages/paradiseo/fix_tutorials.patch | 13 +++++ .../repos/builtin/packages/paradiseo/package.py | 59 ++++++++++++++++++++++ 5 files changed, 112 insertions(+) create mode 100644 var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch create mode 100644 var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch create mode 100644 var/spack/repos/builtin/packages/paradiseo/fix_tests.patch create mode 100644 var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch create mode 100644 var/spack/repos/builtin/packages/paradiseo/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch b/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch new file mode 100644 index 0000000000..8b3ccfeb84 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/enable_eoserial.patch @@ -0,0 +1,14 @@ +diff --git a/eo/src/CMakeLists.txt b/eo/src/CMakeLists.txt +index b2b445a..d45ddc7 100644 +--- a/eo/src/CMakeLists.txt ++++ b/eo/src/CMakeLists.txt +@@ -47,7 +47,7 @@ install(DIRECTORY do es ga gp other utils + add_subdirectory(es) + add_subdirectory(ga) + add_subdirectory(utils) +-#add_subdirectory(serial) ++add_subdirectory(serial) # Required when including , which is need by + + if(ENABLE_PYEO) + add_subdirectory(pyeo) + \ No newline at end of file diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch b/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch new file mode 100644 index 0000000000..27b240f673 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/fix_osx_detection.patch @@ -0,0 +1,13 @@ +diff --git a/cmake/Config.cmake b/cmake/Config.cmake +index 02593ba..d198ca9 100644 +--- a/cmake/Config.cmake ++++ b/cmake/Config.cmake +@@ -6,7 +6,7 @@ if(${CMAKE_SYSTEM_NAME} MATCHES "Darwin") + + # detect OS X version. (use '/usr/bin/sw_vers -productVersion' to extract V from '10.V.x'.) + execute_process (COMMAND /usr/bin/sw_vers -productVersion OUTPUT_VARIABLE MACOSX_VERSION_RAW) +- string(REGEX REPLACE "10\\.([0-9]).*" "\\1" MACOSX_VERSION "${MACOSX_VERSION_RAW}") ++ string(REGEX REPLACE "10\\.([0-9]+).*" "\\1" MACOSX_VERSION "${MACOSX_VERSION_RAW}") + if(${MACOSX_VERSION} LESS 5) + message(FATAL_ERROR "Unsupported version of OS X : ${MACOSX_VERSION_RAW}") + return() diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch b/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch new file mode 100644 index 0000000000..607c5d5262 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/fix_tests.patch @@ -0,0 +1,13 @@ +diff --git a/moeo/test/t-moeo2DMinHypervolumeArchive.cpp b/moeo/test/t-moeo2DMinHypervolumeArchive.cpp +index 994a9a4..c4ba77b 100644 +--- a/moeo/test/t-moeo2DMinHypervolumeArchive.cpp ++++ b/moeo/test/t-moeo2DMinHypervolumeArchive.cpp +@@ -41,7 +41,7 @@ + #include + #include + +-#include ++#include + + //----------------------------------------------------------------------------- + diff --git a/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch b/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch new file mode 100644 index 0000000000..14cb5fed74 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/fix_tutorials.patch @@ -0,0 +1,13 @@ +diff --git a/eo/tutorial/Lesson3/exercise3.1.cpp b/eo/tutorial/Lesson3/exercise3.1.cpp +index dc37479..d178941 100644 +--- a/eo/tutorial/Lesson3/exercise3.1.cpp ++++ b/eo/tutorial/Lesson3/exercise3.1.cpp +@@ -289,7 +289,7 @@ void main_function(int argc, char **argv) + checkpoint.add(fdcStat); + + // The Stdout monitor will print parameters to the screen ... +- eoStdoutMonitor monitor(false); ++ eoStdoutMonitor monitor; + + // when called by the checkpoint (i.e. at every generation) + checkpoint.add(monitor); diff --git a/var/spack/repos/builtin/packages/paradiseo/package.py b/var/spack/repos/builtin/packages/paradiseo/package.py new file mode 100644 index 0000000000..c254234b32 --- /dev/null +++ b/var/spack/repos/builtin/packages/paradiseo/package.py @@ -0,0 +1,59 @@ +from spack import * +import sys + +class Paradiseo(Package): + """A C++ white-box object-oriented framework dedicated to the reusable design of metaheuristics.""" + homepage = "http://paradiseo.gforge.inria.fr/" + + # Installing from the development version is a better option at this + # point than using the very old supplied packages + version('head', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git') + # This is a version that the package formula author has tested successfully. + # However, the clone is very large (~1Gb git history). The history in the + # head version has been trimmed significantly. + version('dev-safe', git='https://gforge.inria.fr/git/paradiseo/paradiseo.git', + commit='dbb8fbe9a786efd4d1c26408ac1883442e7643a6') + + variant('mpi', default=True, description='Compile with parallel and distributed metaheuristics module') + variant('smp', default=True, description='Compile with symmetric multi-processing module ') + variant('edo', default=True, description='Compile with (Experimental) EDO module') + #variant('tests', default=False, description='Compile with build tests') + #variant('doc', default=False, description='Compile with documentation') + variant('debug', default=False, description='Builds a debug version of the libraries') + + # Required dependencies + depends_on ("cmake") + depends_on ("eigen") + + # Optional dependencies + depends_on ("mpi", when="+mpi") + depends_on ("doxygen", when='+doc') + + # Patches + patch('enable_eoserial.patch') + patch('fix_osx_detection.patch') + patch('fix_tests.patch') + patch('fix_tutorials.patch') + + def install(self, spec, prefix): + options = [] + options.extend(std_cmake_args) + + options.extend([ + '-DCMAKE_BUILD_TYPE:STRING=%s' % ('Debug' if '+debug' in spec else 'Release'), + '-DINSTALL_TYPE:STRING=MIN', + '-DMPI:BOOL=%s' % ('TRUE' if '+mpi' in spec else 'FALSE'), + '-DSMP:BOOL=%s' % ('TRUE' if '+smp' in spec else 'FALSE'), # Note: This requires a C++11 compatible compiler + '-DEDO:BOOL=%s' % ('TRUE' if '+edo' in spec else 'FALSE'), + '-DENABLE_CMAKE_TESTING:BOOL=%s' % ('TRUE' if '+tests' in spec else 'FALSE') + ]) + + with working_dir('spack-build', create=True): + # Configure + cmake('..', *options) + + # Build, test and install + make("VERBOSE=1") + if '+tests' in spec: + make("test") + make("install") -- cgit v1.2.3-70-g09d2 From 168f9c46ea7f249fba3769cf1429348ca218eeae Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 26 Apr 2016 09:18:39 +0200 Subject: astyle: fix installation of the binary --- var/spack/repos/builtin/packages/astyle/package.py | 1 + 1 file changed, 1 insertion(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/astyle/package.py b/var/spack/repos/builtin/packages/astyle/package.py index 7260fd74a1..5274fc018f 100644 --- a/var/spack/repos/builtin/packages/astyle/package.py +++ b/var/spack/repos/builtin/packages/astyle/package.py @@ -14,4 +14,5 @@ class Astyle(Package): make('-f', join_path(self.stage.source_path,'build','clang','Makefile'), parallel=False) + mkdirp(self.prefix.bin) install(join_path(self.stage.source_path, 'src','bin','astyle'), self.prefix.bin) -- cgit v1.2.3-70-g09d2 From 8a45aa41854fbc1824401662f93e08d078109f6e Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 26 Apr 2016 12:52:49 +0200 Subject: p4est: add missing dependencies --- var/spack/repos/builtin/packages/p4est/package.py | 13 ++++++++----- 1 file changed, 8 insertions(+), 5 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/p4est/package.py b/var/spack/repos/builtin/packages/p4est/package.py index 1e2969fe64..017c4e3fbf 100644 --- a/var/spack/repos/builtin/packages/p4est/package.py +++ b/var/spack/repos/builtin/packages/p4est/package.py @@ -7,10 +7,15 @@ class P4est(Package): version('1.1', '37ba7f4410958cfb38a2140339dbf64f') - # disable by default to make it work on frontend of clusters - variant('tests', default=False, description='Run small tests') + # build dependencies + depends_on('automake') + depends_on('autoconf') + depends_on('libtool@2.4.2:') + # other dependencies + depends_on('lua') # Needed for the submodule sc depends_on('mpi') + depends_on('zlib') def install(self, spec, prefix): options = ['--enable-mpi', @@ -28,7 +33,5 @@ class P4est(Package): configure('--prefix=%s' % prefix, *options) make() - if '+tests' in self.spec: - make("check") - + make("check") make("install") -- cgit v1.2.3-70-g09d2 From 0ff41206923dc9235b7f7341b514b4e2944d262d Mon Sep 17 00:00:00 2001 From: Denis Davydov Date: Tue, 26 Apr 2016 13:13:47 +0200 Subject: dealii: add missing dependencies --- var/spack/repos/builtin/packages/dealii/package.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/dealii/package.py b/var/spack/repos/builtin/packages/dealii/package.py index 6810e86868..674fe3150a 100644 --- a/var/spack/repos/builtin/packages/dealii/package.py +++ b/var/spack/repos/builtin/packages/dealii/package.py @@ -50,8 +50,8 @@ class Dealii(Package): depends_on ("trilinos", when='+trilinos+mpi') # developer dependnecies - #depends_on ("numdiff") #FIXME - #depends_on ("astyle") #FIXME + depends_on ("numdiff", when='@dev') + depends_on ("astyle@2.04", when='@dev') def install(self, spec, prefix): options = [] -- cgit v1.2.3-70-g09d2 From f70046e6b713f783288afac3359ccba6bfd8e233 Mon Sep 17 00:00:00 2001 From: Geoffrey Oxberry Date: Tue, 26 Apr 2016 10:00:24 -0700 Subject: MFEM version 3.1 (#749) MFEM is a free, lightweight, scalable C++ library for finite element methods. Includes lapack, hypre, metis, suite-sparse, mpi variants & tests for serial and parallel versions. --- var/spack/repos/builtin/packages/mfem/package.py | 125 +++++++++++++++++++++++ 1 file changed, 125 insertions(+) create mode 100644 var/spack/repos/builtin/packages/mfem/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/mfem/package.py b/var/spack/repos/builtin/packages/mfem/package.py new file mode 100644 index 0000000000..510e09c4e1 --- /dev/null +++ b/var/spack/repos/builtin/packages/mfem/package.py @@ -0,0 +1,125 @@ +from spack import * +import glob, string + +class Mfem(Package): + """Free, lightweight, scalable C++ library for finite element methods.""" + + homepage = 'http://www.mfem.org' + url = 'https://github.com/mfem/mfem' + +# version('3.1', git='https://github.com/mfem/mfem.git', +# commit='dbae60fe32e071989b52efaaf59d7d0eb2a3b574') + + version('3.1', '841ea5cf58de6fae4de0f553b0e01ebaab9cd9c67fa821e8a715666ecf18fc57', + url='http://goo.gl/xrScXn', expand=False) + + variant('metis', default=False, description='Activate support for metis') + variant('hypre', default=False, description='Activate support for hypre') + variant('suite-sparse', default=False, + description='Activate support for SuiteSparse') + variant('mpi', default=False, description='Activate support for MPI') + variant('lapack', default=False, description='Activate support for LAPACK') + variant('debug', default=False, description='Build debug version') + + depends_on('blas', when='+lapack') + depends_on('lapack', when='+lapack') + + depends_on('mpi', when='+mpi') + depends_on('metis', when='+mpi') + depends_on('hypre', when='+mpi') + + depends_on('hypre', when='+hypre') + + depends_on('metis@4:', when='+metis') + + depends_on('suite-sparse', when='+suite-sparse') + depends_on('blas', when='+suite-sparse') + depends_on('lapack', when='+suite-sparse') + depends_on('metis@5:', when='+suite-sparse ^suite-sparse@4.5:') + depends_on('cmake', when='^metis@5:') + + def check_variants(self, spec): + if '+mpi' in spec and ('+hypre' not in spec or '+metis' not in spec): + raise InstallError('mfem+mpi must be built with +hypre ' + + 'and +metis!') + if '+suite-sparse' in spec and ('+metis' not in spec or + '+lapack' not in spec): + raise InstallError('mfem+suite-sparse must be built with ' + + '+metis and +lapack!') + if 'metis@5:' in spec and '%clang' in spec and ('^cmake %gcc' not in spec): + raise InstallError('To work around CMake bug with clang, must ' + + 'build mfem with mfem[+variants] %clang ' + + '^cmake %gcc to force CMake to build with gcc') + return + + def install(self, spec, prefix): + self.check_variants(spec) + + options = ['PREFIX=%s' % prefix] + + if '+lapack' in spec: + lapack_lib = '-L{0} -llapack -L{1} -lblas'.format( + spec['lapack'].prefix.lib, spec['blas'].prefix.lib) + options.extend(['MFEM_USE_LAPACK=YES', + 'LAPACK_OPT=-I%s' % spec['lapack'].prefix.include, + 'LAPACK_LIB=%s' % lapack_lib]) + + if '+hypre' in spec: + options.extend(['HYPRE_DIR=%s' % spec['hypre'].prefix, + 'HYPRE_OPT=-I%s' % spec['hypre'].prefix.include, + 'HYPRE_LIB=-L%s' % spec['hypre'].prefix.lib + + ' -lHYPRE']) + + if '+metis' in spec: + metis_lib = '-L%s -lmetis' % spec['metis'].prefix.lib + if spec['metis'].satisfies('@5:'): + metis_str = 'MFEM_USE_METIS_5=YES' + else: + metis_str = 'MFEM_USE_METIS_5=NO' + options.extend([metis_str, + 'METIS_DIR=%s' % spec['metis'].prefix, + 'METIS_OPT=-I%s' % spec['metis'].prefix.include, + 'METIS_LIB=%s' % metis_lib]) + + if '+mpi' in spec: options.extend(['MFEM_USE_MPI=YES']) + + if '+suite-sparse' in spec: + ssp = spec['suite-sparse'].prefix + ss_lib = '-L%s' % ssp.lib + ss_lib += (' -lumfpack -lcholmod -lcolamd -lamd -lcamd' + + ' -lccolamd -lsuitesparseconfig') + + no_librt_archs = ['darwin-i686', 'darwin-x86_64'] + no_rt = any(map(lambda a: spec.satisfies('='+a), no_librt_archs)) + if not no_rt: ss_lib += ' -lrt' + ss_lib += (' ' + metis_lib + ' ' + lapack_lib) + + options.extend(['MFEM_USE_SUITESPARSE=YES', + 'SUITESPARSE_DIR=%s' % ssp, + 'SUITESPARSE_OPT=-I%s' % ssp.include, + 'SUITESPARSE_LIB=%s' % ss_lib]) + + if '+debug' in spec: options.extend(['MFEM_DEBUG=YES']) + + # Dirty hack to cope with URL redirect + tgz_file = string.split(self.url,'/')[-1] + tar = which('tar') + tar('xzvf', tgz_file) + cd(glob.glob('mfem*')[0]) + # End dirty hack to cope with URL redirect + + make('config', *options) + make('all') + + # Run a small test before installation + args = ['-m', join_path('data','star.mesh'), '--no-visualization'] + if '+mpi' in spec: + Executable(join_path(spec['mpi'].prefix.bin, + 'mpirun'))('-np', + '4', + join_path('examples','ex1p'), + *args) + else: + Executable(join_path('examples', 'ex1'))(*args) + + make('install') -- cgit v1.2.3-70-g09d2 From 8e227f603d0c158e9f71a0bc0a815d977415908c Mon Sep 17 00:00:00 2001 From: jppelteret Date: Tue, 26 Apr 2016 19:01:09 +0200 Subject: Fix: Add missing dependencies for gmp and eigen (#830) See https://groups.google.com/forum/#!topic/spack/9JMDwafjBUs --- var/spack/repos/builtin/packages/eigen/package.py | 1 + var/spack/repos/builtin/packages/gmp/package.py | 2 ++ 2 files changed, 3 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/eigen/package.py b/var/spack/repos/builtin/packages/eigen/package.py index 1501989812..6b38ab0261 100644 --- a/var/spack/repos/builtin/packages/eigen/package.py +++ b/var/spack/repos/builtin/packages/eigen/package.py @@ -45,6 +45,7 @@ class Eigen(Package): # TODO : dependency on googlehash, superlu, adolc missing + depends_on('cmake') depends_on('metis@5:', when='+metis') depends_on('scotch', when='+scotch') depends_on('fftw', when='+fftw') diff --git a/var/spack/repos/builtin/packages/gmp/package.py b/var/spack/repos/builtin/packages/gmp/package.py index fe13de3b95..85e9c237d6 100644 --- a/var/spack/repos/builtin/packages/gmp/package.py +++ b/var/spack/repos/builtin/packages/gmp/package.py @@ -35,6 +35,8 @@ class Gmp(Package): version('6.0.0a', 'b7ff2d88cae7f8085bd5006096eed470') version('6.0.0' , '6ef5869ae735db9995619135bd856b84') + depends_on("m4") + def install(self, spec, prefix): configure("--prefix=%s" % prefix) make() -- cgit v1.2.3-70-g09d2 From 8ec5e8118643223c00b3106fb4e4f1204821e380 Mon Sep 17 00:00:00 2001 From: Joseph Ciurej Date: Tue, 26 Apr 2016 10:24:36 -0700 Subject: Update Package : Zoltan (#833) * Added preliminary implementations for the debug and shared variants. * Fixed a few problems with the '+shared' variant of the Zoltan package. Added support for a few more important Zoltan package versions. * Fixed a minor compiler incompatibility issue with the '+shared+mpi' variants. --- var/spack/repos/builtin/packages/zoltan/package.py | 35 +++++++++++++++++++--- 1 file changed, 31 insertions(+), 4 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/zoltan/package.py b/var/spack/repos/builtin/packages/zoltan/package.py index e20ae81adb..738dfb508b 100644 --- a/var/spack/repos/builtin/packages/zoltan/package.py +++ b/var/spack/repos/builtin/packages/zoltan/package.py @@ -1,3 +1,4 @@ +import re, os, glob from spack import * class Zoltan(Package): @@ -12,8 +13,13 @@ class Zoltan(Package): base_url = "http://www.cs.sandia.gov/~kddevin/Zoltan_Distributions" version('3.83', '1ff1bc93f91e12f2c533ddb01f2c095f') + version('3.8', '9d8fba8a990896881b85351d4327c4a9') + version('3.6', '9cce794f7241ecd8dbea36c3d7a880f9') version('3.3', '5eb8f00bda634b25ceefa0122bd18d65') + variant('debug', default=False, description='Builds a debug version of the library') + variant('shared', default=True, description='Builds a shared version of the library') + variant('fortran', default=True, description='Enable Fortran support') variant('mpi', default=False, description='Enable MPI support') @@ -24,28 +30,49 @@ class Zoltan(Package): '--enable-f90interface' if '+fortan' in spec else '--disable-f90interface', '--enable-mpi' if '+mpi' in spec else '--disable-mpi', ] + config_cflags = [ + '-O0' if '+debug' in spec else '-O3', + '-g' if '+debug' in spec else '-g0', + ] + + if '+shared' in spec: + config_args.append('--with-ar=$(CXX) -shared $(LDFLAGS) -o') + config_args.append('RANLIB=echo') + config_cflags.append('-fPIC') if '+mpi' in spec: - config_args.append('--with-mpi=%s' % spec['mpi'].prefix) - config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin) config_args.append('CC=%s/mpicc' % spec['mpi'].prefix.bin) config_args.append('CXX=%s/mpicxx' % spec['mpi'].prefix.bin) + config_args.append('--with-mpi=%s' % spec['mpi'].prefix) + config_args.append('--with-mpi-compilers=%s' % spec['mpi'].prefix.bin) # NOTE: Early versions of Zoltan come packaged with a few embedded # library packages (e.g. ParMETIS, Scotch), which messes with Spack's # ability to descend directly into the package's source directory. - if spec.satisfies('@:3.3'): + if spec.satisfies('@:3.6'): cd('Zoltan_v%s' % self.version) mkdirp('build') cd('build') config_zoltan = Executable('../configure') - config_zoltan('--prefix=%s' % pwd(), *config_args) + config_zoltan( + '--prefix=%s' % pwd(), + '--with-cflags=%s' % ' '.join(config_cflags), + '--with-cxxflags=%s' % ' '.join(config_cflags), + *config_args) make() make('install') + # NOTE: Unfortunately, Zoltan doesn't provide any configuration options for + # the extension of the output library files, so this script must change these + # extensions as a post-processing step. + if '+shared' in spec: + for libpath in glob.glob('lib/*.a'): + libdir, libname = (os.path.dirname(libpath), os.path.basename(libpath)) + move(libpath, os.path.join(libdir, re.sub(r'\.a$', '.so', libname))) + mkdirp(prefix) move('include', prefix) move('lib', prefix) -- cgit v1.2.3-70-g09d2 From b56bfcea968fb6fb2a81a08804258300178c4b05 Mon Sep 17 00:00:00 2001 From: Glenn Johnson Date: Tue, 26 Apr 2016 12:31:48 -0500 Subject: Add the turbomole package. (#826) * Add the turbomole package. This package has three modes of operation that need to be selected independently. This is handled with spack vaiants. Turbomole has a builtin MPI implementation so it does not need to depend on an mpi provider when using the +mpi variant. * Whitespace cleanup. --- .../repos/builtin/packages/turbomole/package.py | 124 +++++++++++++++++++++ 1 file changed, 124 insertions(+) create mode 100644 var/spack/repos/builtin/packages/turbomole/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/turbomole/package.py b/var/spack/repos/builtin/packages/turbomole/package.py new file mode 100644 index 0000000000..acc95e3b10 --- /dev/null +++ b/var/spack/repos/builtin/packages/turbomole/package.py @@ -0,0 +1,124 @@ +from spack import * +import os +import subprocess + +class Turbomole(Package): + """TURBOMOLE: Program Package for ab initio Electronic Structure + Calculations. NB: Requires a license to download.""" + + # NOTE: Turbomole requires purchase of a license to download. Go to the + # NOTE: Turbomole home page, http://www.turbomole-gmbh.com, for details. + # NOTE: Spack will search the current directory for this file. It is + # NOTE: probably best to add this file to a Spack mirror so that it can be + # NOTE: found from anywhere. For information on setting up a Spack mirror + # NOTE: see http://software.llnl.gov/spack/mirrors.html + + homepage = "http://www.turbomole-gmbh.com/" + + version('7.0.2', '92b97e1e52e8dcf02a4d9ac0147c09d6', + url="file://%s/turbolinux702.tar.gz" % os.getcwd()) + + variant('mpi', default=False, description='Set up MPI environment') + variant('smp', default=False, description='Set up SMP environment') + + # Turbomole's install is odd. There are three variants + # - serial + # - parallel, MPI + # - parallel, SMP + # + # Only one of these can be active at a time. MPI and SMP are set as + # variants so there could be up to 3 installs per version. Switching + # between them would be accomplished with `module swap` commands. + + def do_fetch(self, mirror_only=True): + if '+mpi' in self.spec and '+smp' in self.spec: + raise InstallError('Can not have both SMP and MPI enabled in the same build.') + super(Turbomole, self).do_fetch(mirror_only) + + def get_tm_arch(self): + # For python-2.7 we could use `tm_arch = subprocess.check_output()` + # Use the following for compatibility with python 2.6 + if 'TURBOMOLE' in os.getcwd(): + tm_arch = subprocess.Popen(['sh', 'scripts/sysname'], + stdout=subprocess.PIPE).communicate()[0] + return tm_arch.rstrip('\n') + else: + return + + def install(self, spec, prefix): + if spec.satisfies('@:7.0.2'): + calculate_version = 'calculate_2.4_linux64' + molecontrol_version = 'MoleControl_2.5' + + tm_arch=self.get_tm_arch() + + tar = which('tar') + dst = join_path(prefix, 'TURBOMOLE') + + tar('-x', '-z', '-f', 'thermocalc.tar.gz') + with working_dir('thermocalc'): + cmd = 'sh install << Date: Tue, 26 Apr 2016 12:32:14 -0500 Subject: Put f2py of py-numpy in python ignore list. (#827) There are many python packages that depend on py-numpy. Each one of those will have a copy of f2py that will need to be put in the ignore list for activation. Thise PR adds f2py to the ignore list in the python package.py file so that it does not have to be done for each package that depends on py-numpy. This follows the model of what is done for py-setuptools. This PR also removes the f2py ignore expression for python packages that were using it as it is no longer needed in the individual packages. --- var/spack/repos/builtin/packages/py-bottleneck/package.py | 2 +- var/spack/repos/builtin/packages/py-matplotlib/package.py | 2 +- var/spack/repos/builtin/packages/py-numexpr/package.py | 2 +- var/spack/repos/builtin/packages/py-pandas/package.py | 2 +- var/spack/repos/builtin/packages/py-scikit-image/package.py | 2 +- var/spack/repos/builtin/packages/python/package.py | 2 ++ 6 files changed, 7 insertions(+), 5 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/py-bottleneck/package.py b/var/spack/repos/builtin/packages/py-bottleneck/package.py index 0aa4208b4d..d43308543b 100644 --- a/var/spack/repos/builtin/packages/py-bottleneck/package.py +++ b/var/spack/repos/builtin/packages/py-bottleneck/package.py @@ -7,7 +7,7 @@ class PyBottleneck(Package): version('1.0.0', '380fa6f275bd24f27e7cf0e0d752f5d2') - extends('python', ignore=r'bin/f2py$') + extends('python') depends_on('py-numpy') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-matplotlib/package.py b/var/spack/repos/builtin/packages/py-matplotlib/package.py index 19194c942e..1a190cc5f3 100644 --- a/var/spack/repos/builtin/packages/py-matplotlib/package.py +++ b/var/spack/repos/builtin/packages/py-matplotlib/package.py @@ -12,7 +12,7 @@ class PyMatplotlib(Package): variant('gui', default=False, description='Enable GUI') variant('ipython', default=False, description='Enable ipython support') - extends('python', ignore=r'bin/nosetests.*$|bin/pbr$|bin/f2py$') + extends('python', ignore=r'bin/nosetests.*$|bin/pbr$') depends_on('py-pyside', when='+gui') depends_on('py-ipython', when='+ipython') diff --git a/var/spack/repos/builtin/packages/py-numexpr/package.py b/var/spack/repos/builtin/packages/py-numexpr/package.py index 081a79dec6..0076aa456b 100644 --- a/var/spack/repos/builtin/packages/py-numexpr/package.py +++ b/var/spack/repos/builtin/packages/py-numexpr/package.py @@ -9,7 +9,7 @@ class PyNumexpr(Package): version('2.4.6', '17ac6fafc9ea1ce3eb970b9abccb4fbd') version('2.5', '84f66cced45ba3e30dcf77a937763aaa') - extends('python', ignore=r'bin/f2py$') + extends('python') depends_on('py-numpy') def install(self, spec, prefix): diff --git a/var/spack/repos/builtin/packages/py-pandas/package.py b/var/spack/repos/builtin/packages/py-pandas/package.py index 2320b1f92f..59d515eb5e 100644 --- a/var/spack/repos/builtin/packages/py-pandas/package.py +++ b/var/spack/repos/builtin/packages/py-pandas/package.py @@ -10,7 +10,7 @@ class PyPandas(Package): version('0.16.1', 'fac4f25748f9610a3e00e765474bdea8') version('0.18.0', 'f143762cd7a59815e348adf4308d2cf6') - extends('python', ignore=r'bin/f2py$') + extends('python') depends_on('py-dateutil') depends_on('py-numpy') depends_on('py-setuptools') diff --git a/var/spack/repos/builtin/packages/py-scikit-image/package.py b/var/spack/repos/builtin/packages/py-scikit-image/package.py index 22ce1f8374..d13339060e 100644 --- a/var/spack/repos/builtin/packages/py-scikit-image/package.py +++ b/var/spack/repos/builtin/packages/py-scikit-image/package.py @@ -7,7 +7,7 @@ class PyScikitImage(Package): version('0.12.3', '04ea833383e0b6ad5f65da21292c25e1') - extends('python', ignore=r'bin/.*\.py$|bin/f2py$') + extends('python', ignore=r'bin/.*\.py$') depends_on('py-dask') depends_on('py-pillow') diff --git a/var/spack/repos/builtin/packages/python/package.py b/var/spack/repos/builtin/packages/python/package.py index f5237c3b57..f7e1d94567 100644 --- a/var/spack/repos/builtin/packages/python/package.py +++ b/var/spack/repos/builtin/packages/python/package.py @@ -151,6 +151,8 @@ class Python(Package): patterns.append(r'setuptools\.pth') patterns.append(r'bin/easy_install[^/]*$') patterns.append(r'setuptools.*egg$') + if ext_pkg.name != 'py-numpy': + patterns.append(r'bin/f2py$') return match_predicate(ignore_arg, patterns) -- cgit v1.2.3-70-g09d2 From ee6a75c9b5bb072ef852b2fae80e2dc1f3944d53 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Wed, 27 Apr 2016 18:43:16 -0400 Subject: Added missing -lpthread to OpenBLAS check. See: https://github.com/xianyi/OpenBLAS/wiki/faq#static_link --- var/spack/repos/builtin/packages/openblas/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 61250fb310..52edd1a77a 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -119,7 +119,7 @@ return 0; # TODO: Automate these path and library settings cc('-c', "-I%s" % join_path(spec.prefix, "include"), "check.c") cc('-o', "check", "check.o", - "-L%s" % join_path(spec.prefix, "lib"), "-llapack", "-lblas") + "-L%s" % join_path(spec.prefix, "lib"), "-llapack", "-lblas", "-lpthread") try: check = Executable('./check') output = check(return_output=True) -- cgit v1.2.3-70-g09d2 From 62d806d51254c4b063c2e88b616526d1abb1e61e Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Wed, 27 Apr 2016 19:01:41 -0400 Subject: hdf5: Set preferred version, so as to not break NetCDF (for now). --- var/spack/repos/builtin/packages/hdf5/package.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/hdf5/package.py b/var/spack/repos/builtin/packages/hdf5/package.py index cce609eb29..470969832f 100644 --- a/var/spack/repos/builtin/packages/hdf5/package.py +++ b/var/spack/repos/builtin/packages/hdf5/package.py @@ -38,7 +38,7 @@ class Hdf5(Package): list_depth = 3 version('1.10.0', 'bdc935337ee8282579cd6bc4270ad199') - version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618') + version('1.8.16', 'b8ed9a36ae142317f88b0c7ef4b9c618', preferred=True) version('1.8.15', '03cccb5b33dbe975fdcd8ae9dc021f24') version('1.8.13', 'c03426e9e77d7766944654280b467289') -- cgit v1.2.3-70-g09d2 From 71ca837adad0e8c8149bdfd5be602ac7cc27c9a5 Mon Sep 17 00:00:00 2001 From: Elizabeth F Date: Wed, 27 Apr 2016 20:35:29 -0400 Subject: Add '+fpic' variant. --- var/spack/repos/builtin/packages/openblas/package.py | 3 +++ 1 file changed, 3 insertions(+) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openblas/package.py b/var/spack/repos/builtin/packages/openblas/package.py index 52edd1a77a..f5d656f659 100644 --- a/var/spack/repos/builtin/packages/openblas/package.py +++ b/var/spack/repos/builtin/packages/openblas/package.py @@ -14,6 +14,7 @@ class Openblas(Package): variant('shared', default=True, description="Build shared libraries as well as static libs.") variant('openmp', default=True, description="Enable OpenMP support.") + variant('fpic', default=True, description="Build position independent code") # virtual dependency provides('blas') @@ -33,6 +34,8 @@ class Openblas(Package): if '+shared' in spec: make_targets += ['shared'] else: + if '+fpic' in spec: + make_defs.extend(['CFLAGS=-fPIC', 'FFLAGS=-fPIC']) make_defs += ['NO_SHARED=1'] # fix missing _dggsvd_ and _sggsvd_ -- cgit v1.2.3-70-g09d2 From b99c8b641a6c370ddbe8cbf78bc8339dbb3d8598 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Wed, 20 Apr 2016 10:46:09 -0500 Subject: Add hydra package --- var/spack/repos/builtin/packages/hydra/package.py | 21 +++++++++++++++++++++ 1 file changed, 21 insertions(+) create mode 100644 var/spack/repos/builtin/packages/hydra/package.py (limited to 'var') diff --git a/var/spack/repos/builtin/packages/hydra/package.py b/var/spack/repos/builtin/packages/hydra/package.py new file mode 100644 index 0000000000..c1b8868276 --- /dev/null +++ b/var/spack/repos/builtin/packages/hydra/package.py @@ -0,0 +1,21 @@ +from spack import * + +class Hydra(Package): + """Hydra is a process management system for starting parallel jobs. + Hydra is designed to natively work with existing launcher daemons + (such as ssh, rsh, fork), as well as natively integrate with resource + management systems (such as slurm, pbs, sge).""" + + homepage = "http://www.mpich.org" + url = "http://www.mpich.org/static/downloads/3.2/hydra-3.2.tar.gz" + list_url = "http://www.mpich.org/static/downloads/" + list_depth = 2 + + version('3.2', '4d670916695bf7e3a869cc336a881b39') + + + def install(self, spec, prefix): + configure('--prefix=%s' % prefix) + + make() + make("install") -- cgit v1.2.3-70-g09d2 From c110865bf258b67d745b31a526dcb9b348fd9893 Mon Sep 17 00:00:00 2001 From: "Adam J. Stewart" Date: Thu, 21 Apr 2016 15:53:44 -0500 Subject: Remove OpenMPI dependency on hwloc --- var/spack/repos/builtin/packages/openmpi/package.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) (limited to 'var') diff --git a/var/spack/repos/builtin/packages/openmpi/package.py b/var/spack/repos/builtin/packages/openmpi/package.py index 9a127f1812..3cb9b0be21 100644 --- a/var/spack/repos/builtin/packages/openmpi/package.py +++ b/var/spack/repos/builtin/packages/openmpi/package.py @@ -1,7 +1,5 @@ -import os - from spack import * - +import os class Openmpi(Package): """Open MPI is a project combining technologies and resources from @@ -36,7 +34,6 @@ class Openmpi(Package): provides('mpi@:2.2', when='@1.6.5') provides('mpi@:3.0', when='@1.7.5:') - depends_on('hwloc') def url_for_version(self, version): return "http://www.open-mpi.org/software/ompi/v%s/downloads/openmpi-%s.tar.bz2" % (version.up_to(2), version) @@ -51,7 +48,6 @@ class Openmpi(Package): def install(self, spec, prefix): config_args = ["--prefix=%s" % prefix, - "--with-hwloc=%s" % spec['hwloc'].prefix, "--enable-shared", "--enable-static"] -- cgit v1.2.3-70-g09d2