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with 79 additions and 348 deletions
# Copyright 2013-2022 Lawrence Livermore National Security, LLC and other
# Copyright 2013-2024 Lawrence Livermore National Security, LLC and other
# Spack Project Developers. See the top-level COPYRIGHT file for details.
#
# SPDX-License-Identifier: (Apache-2.0 OR MIT)
......@@ -12,27 +12,38 @@ class Arbor(CMakePackage, CudaPackage):
homepage = "https://arbor-sim.org"
git = "https://github.com/arbor-sim/arbor.git"
url = "https://github.com/arbor-sim/arbor/releases/download/v0.8.1/arbor-v0.8.1-full.tar.gz"
maintainers = ["bcumming", "brenthuisman", "haampie", "schmitts"]
url = "https://github.com/arbor-sim/arbor/releases/download/v0.9.0/arbor-v0.9.0-full.tar.gz"
maintainers = ("thorstenhater", "ErbB4", "haampie")
version("master", branch="master", submodules=True)
version("develop", branch="master", submodules=True)
version(
"0.10.0",
sha256="72966b7a2f45ce259b8ba167ca3e4f5ab9f212136a300267aaac0c04ed3fe3fc",
url="https://github.com/arbor-sim/arbor/releases/download/v0.10.1/arbor-v0.10.0-full.tar.gz",
)
version(
"0.9.0",
sha256="5f9740955c821aca81e23298c17ad64f33f635756ad9b4a0c1444710f564306a",
url="https://github.com/arbor-sim/arbor/releases/download/v0.9.0/arbor-v0.9.0-full.tar.gz",
)
version(
"0.8.1",
sha256="caebf96676ace6a9c50436541c420ca4bb53f0639dcab825de6fa370aacf6baa",
url="https://github.com/arbor-sim/arbor/releases/download/v0.8.1/arbor-v0.8.1-full.tar.gz",
)
version(
"0.8",
"0.8.0",
sha256="18df5600308841616996a9de93b55a105be0f59692daa5febd3a65aae5bc2c5d",
url="https://github.com/arbor-sim/arbor/releases/download/v0.8/arbor-v0.8-full.tar.gz",
)
version(
"0.7",
"0.7.0",
sha256="c3a6b7193946aee882bb85f9c38beac74209842ee94e80840968997ba3b84543",
url="https://github.com/arbor-sim/arbor/releases/download/v0.7/arbor-v0.7-full.tar.gz",
)
version(
"0.6",
"0.6.0",
sha256="4cd333b18effc8833428ddc0b99e7dc976804771bc85da90034c272c7019e1e8",
url="https://github.com/arbor-sim/arbor/releases/download/v0.6/arbor-v0.6-full.tar.gz",
)
......@@ -69,35 +80,50 @@ class Arbor(CMakePackage, CudaPackage):
conflicts("%cce@:9.1")
conflicts("%intel")
depends_on("cmake@3.19:", type="build")
# begin EBRAINS (modified: added run dep)
depends_on("cmake@3.19:", type=("build", "run"))
# end EBRAINS
# misc dependencies
depends_on("fmt@7.1:", when="@0.5.3:") # required by the modcc compiler
depends_on("fmt@9.1:", when="@0.7.1:")
# begin EBRAINS (modified: relaxed (upstream gave no info about update))
# upstream adds: depends_on("fmt@10.1:", when="@0.9.1:")
depends_on("googletest@1.12.1:", when="@0.7.1:")
depends_on("pugixml@1.11:", when="@0.7.1:")
depends_on("nlohmann-json")
# upstream adds: depends_on("pugixml@1.13:", when="@0.9.1:")
depends_on("nlohmann-json@3.11.2:")
depends_on("random123")
#upstream adds: depends_on("random123@1.14.0:", when="@0.10:")
# end EBRAINS (modified)
with when("+cuda"):
depends_on("cuda@10:")
depends_on("cuda@11:", when="@0.7.1:")
depends_on("cuda@12:", when="@0.9.1:")
# mpi
depends_on("mpi", when="+mpi")
# begin EBRAINS (modified: added run dep)
depends_on("mpi", when="+mpi", type=("build", "run"))
# end EBRAINS (modified)
depends_on("py-mpi4py", when="+mpi+python", type=("build", "run"))
# python (bindings)
extends("python", when="+python")
depends_on("python@3.7:", when="+python", type=("build", "run"))
depends_on("py-numpy", when="+python", type=("build", "run"))
with when("+python"):
depends_on("py-pybind11@2.6:", type=("build"))
depends_on("py-pybind11@2.8.1:", when="@0.5.3:", type=("build"))
depends_on("py-pybind11@2.10.1:", when="@0.7.1:", type=("build"))
extends("python")
depends_on("python@3.7:", type=("build", "run"))
depends_on("python@3.9:", when="@0.9.1:", type=("build", "run"))
depends_on("py-numpy", type=("build", "run"))
depends_on("py-pybind11@2.6:", type="build")
depends_on("py-pybind11@2.8.1:", when="@0.5.3:", type="build")
depends_on("py-pybind11@2.10.1:", when="@0.7.1:", type="build")
depends_on("py-pandas", type="test")
depends_on("py-seaborn", type="test")
# sphinx based documentation
depends_on("python@3.7:", when="+doc", type="build")
depends_on("py-sphinx", when="+doc", type="build")
depends_on("py-svgwrite", when="+doc", type="build")
with when("+doc"):
depends_on("python@3.10:", type="build")
depends_on("py-sphinx", type="build")
depends_on("py-svgwrite", type="build")
@property
def build_targets(self):
......@@ -117,14 +143,19 @@ class Arbor(CMakePackage, CudaPackage):
# query spack for the architecture-specific compiler flags set by its wrapper
args.append("-DARB_ARCH=none")
opt_flags = self.spec.target.optimization_flags(
self.spec.compiler.name, self.spec.compiler.version
opt_flags = spack.build_environment.optimization_flags(
self.compiler, self.spec.target
)
args.append("-DARB_CXX_FLAGS_TARGET=" + opt_flags)
# Might return nothing
if opt_flags:
args.append("-DARB_CXX_FLAGS_TARGET=" + opt_flags)
# Needed, spack has no units package
args.append("-DARB_USE_BUNDLED_UNITS=ON")
return args
@run_after('install')
@run_after("install", when="+python")
@on_package_attributes(run_tests=True)
def install_test(self):
python('-c', 'import arbor')
python("-c", "import arbor")
python("python/example/single_cell_model.py")
diff -pur third_party/ijar/mapped_file_unix.cc third_party/ijar/mapped_file_unix.cc
--- third_party/ijar/mapped_file_unix.cc 2021-10-05 15:24:37.243946507 +0200
+++ third_party/ijar/mapped_file_unix.cc 2021-10-05 15:24:28.707823401 +0200
@@ -19,6 +19,7 @@
#include <sys/mman.h>
#include <algorithm>
+#include <limits>
#include "third_party/ijar/mapped_file.h"
diff -pur third_party/ijar/zlib_client.h third_party/ijar/zlib_client.h
--- third_party/ijar/zlib_client.h 2021-10-07 09:32:57.087301302 +0200
+++ third_party/ijar/zlib_client.h 1980-01-01 00:00:00.000000000 +0100
@@ -16,6 +16,7 @@
#define THIRD_PARTY_IJAR_ZLIB_CLIENT_H_
#include <limits.h>
+#include <limits>
#include "third_party/ijar/common.h"
--- a/third_party/zlib/gzguts.h 1980-01-01 00:00:00
+++ b/third_party/zlib/gzguts.h 2023-04-03 12:23:10
@@ -3,6 +3,10 @@
* For conditions of distribution and use, see copyright notice in zlib.h
*/
+#ifndef _WIN32
+ #include <unistd.h>
+#endif
+
#ifdef _LARGEFILE64_SOURCE
# ifndef _LARGEFILE_SOURCE
# define _LARGEFILE_SOURCE 1
--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelConfiguration.java
@@ -150,6 +150,13 @@
builder.put("PATH", null);
builder.put("LD_LIBRARY_PATH", null);
}
+
+ Map<String, String> spackEnv = System.getenv();
+ for (String envName : spackEnv.keySet()) {
+ if (envName.startsWith("SPACK_")) {
+ builder.put(envName, spackEnv.get(envName));
+ }
+ }
}
private static PathFragment determineShellExecutable(OS os, PathFragment fromOption) {
--- a/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
+++ b/src/main/java/com/google/devtools/build/lib/bazel/rules/BazelRuleClassProvider.java
@@ -168,6 +168,13 @@ public class BazelRuleClassProvider {
env.put("PATH", null);
}
+ Map<String, String> spackEnv = System.getenv();
+ for (String envName : spackEnv.keySet()) {
+ if (envName.startsWith("SPACK_")) {
+ env.put(envName, spackEnv.get(envName));
+ }
+ }
+
// Shell environment variables specified via options take precedence over the
// ones inherited from the fragments. In the long run, these fragments will
// be replaced by appropriate default rc files anyway.
From 9c9d27561780bc56d9f0867e325c7421a94ee1cb Mon Sep 17 00:00:00 2001
From: Harsh Bhatia <bhatia4@llnl.gov>
Date: Tue, 15 Dec 2020 15:56:10 -0800
Subject: [PATCH] https://github.com/bazelbuild/bazel/commit/ab62a6e097590dac5ec946ad7a796ea0e8593ae0
---
src/conditions/BUILD | 6 ++++++
third_party/BUILD | 8 ++++++--
2 files changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/conditions/BUILD b/src/conditions/BUILD
index 2b28e28057..faa41a439d 100644
--- a/src/conditions/BUILD
+++ b/src/conditions/BUILD
@@ -10,6 +10,12 @@ filegroup(
visibility = ["//src:__pkg__"],
)
+config_setting(
+ name = "linux_ppc",
+ values = {"cpu": "ppc"},
+ visibility = ["//visibility:public"],
+)
+
config_setting(
name = "linux_x86_64",
values = {"cpu": "k8"},
diff --git a/third_party/BUILD b/third_party/BUILD
index 159006d741..4fcae54c00 100644
--- a/third_party/BUILD
+++ b/third_party/BUILD
@@ -523,12 +523,13 @@ UNNECESSARY_DYNAMIC_LIBRARIES = select({
"//src/conditions:darwin": "*.so *.dll",
"//src/conditions:darwin_x86_64": "*.so *.dll",
"//src/conditions:linux_x86_64": "*.jnilib *.dll",
+ "//src/conditions:linux_ppc": "*.so *.jnilib *.dll",
# The .so file is an x86 one, so we can just remove it if the CPU is not x86
"//src/conditions:arm": "*.so *.jnilib *.dll",
"//src/conditions:linux_aarch64": "*.so *.jnilib *.dll",
# Play it safe -- better have a big binary than a slow binary
# zip -d does require an argument. Supply something bogus.
- "//conditions:default": "*.bogusextension",
+ "//conditions:default": "",
})
# Remove native libraries that are for a platform different from the one we are
@@ -537,7 +538,10 @@ genrule(
name = "filter_netty_dynamic_libs",
srcs = ["netty_tcnative/netty-tcnative-boringssl-static-2.0.24.Final.jar"],
outs = ["netty_tcnative/netty-tcnative-filtered.jar"],
- cmd = "cp $< $@ && zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES,
+ cmd = "cp $< $@ && " +
+ # End successfully if there is nothing to be deleted from the archive
+ "if [ -n '" + UNNECESSARY_DYNAMIC_LIBRARIES + "' ]; then " +
+ "zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES + "; fi",
)
java_import(
--
2.21.0 (Apple Git-122.2)
--- a/tools/cpp/cc_configure.bzl
+++ b/tools/cpp/cc_configure.bzl
@@ -173,8 +173,19 @@
else:
inc_dirs = result.stderr[index1 + 1:index2].strip()
- return [repository_ctx.path(_cxx_inc_convert(p))
- for p in inc_dirs.split("\n")]
+ default_inc_directories = [
+ repository_ctx.path(_cxx_inc_convert(p))
+ for p in inc_dirs.split("\n")
+ ]
+
+ env = repository_ctx.os.environ
+ if "SPACK_INCLUDE_DIRS" in env:
+ for path in env["SPACK_INCLUDE_DIRS"].split(":"):
+ default_inc_directories.append(
+ repository_ctx.path(_cxx_inc_convert(path))
+ )
+
+ return default_inc_directories
def _add_option_if_supported(repository_ctx, cc, option):
"""Checks that `option` is supported by the C compiler."""
--- a/tools/cpp/cc_configure.bzl
+++ b/tools/cpp/cc_configure.bzl
@@ -200,8 +200,19 @@
else:
inc_dirs = result.stderr[index1 + 1:index2].strip()
- return [_escape_string(repository_ctx.path(_cxx_inc_convert(p)))
- for p in inc_dirs.split("\n")]
+ default_inc_directories = [
+ _escape_string(repository_ctx.path(_cxx_inc_convert(p)))
+ for p in inc_dirs.split("\n")
+ ]
+
+ env = repository_ctx.os.environ
+ if "SPACK_INCLUDE_DIRS" in env:
+ for path in env["SPACK_INCLUDE_DIRS"].split(":"):
+ default_inc_directories.append(
+ repository_ctx.path(_cxx_inc_convert(path))
+ )
+
+ return default_inc_directories
def _add_option_if_supported(repository_ctx, cc, option):
diff --git a/compile.sh b/compile.sh
index ed506d2..a5474ac 100755
--- a/compile.sh
+++ b/compile.sh
@@ -92,7 +92,7 @@ display "."
log "Building output/bazel"
# We set host and target platform directly since the defaults in @bazel_tools
# have not yet been generated.
-bazel_build "src:bazel_nojdk${EXE_EXT}" \
+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \
--host_platform=@bazel_tools//platforms:host_platform \
--platforms=@bazel_tools//platforms:target_platform \
|| fail "Could not build Bazel"
--- a/compile.sh
+++ b/compile.sh
@@ -92,7 +92,7 @@
log "Building output/bazel"
# We set host and target platform directly since the defaults in @bazel_tools
# have not yet been generated.
-bazel_build "src:bazel${EXE_EXT}" \
+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \
--host_platform=@bazel_tools//platforms:host_platform \
--platforms=@bazel_tools//platforms:target_platform \
|| fail "Could not build Bazel"
--- a/compile.sh
+++ b/compile.sh
@@ -92,7 +92,7 @@ display "."
log "Building output/bazel"
# We set host and target platform directly since the defaults in @bazel_tools
# have not yet been generated.
-bazel_build "src:bazel_nojdk${EXE_EXT}" \
+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \
--host_platform=@bazel_tools//platforms:host_platform \
--platforms=@bazel_tools//platforms:target_platform \
|| fail "Could not build Bazel"
--- a/compile.sh
+++ b/compile.sh
@@ -92,7 +92,7 @@ display "."
log "Building output/bazel"
# We set host and target platform directly since the defaults in @bazel_tools
# have not yet been generated.
-bazel_build "src:bazel_nojdk${EXE_EXT}" \
+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel_nojdk${EXE_EXT}" \
--action_env=PATH \
--host_platform=@bazel_tools//platforms:host_platform \
--platforms=@bazel_tools//platforms:target_platform \
--- a/compile.sh
+++ b/compile.sh
@@ -99,7 +99,7 @@
new_step 'Building Bazel with Bazel'
display "."
log "Building output/bazel"
- bazel_build "src:bazel${EXE_EXT}"
+ CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}"
cp -f "bazel-bin/src/bazel${EXE_EXT}" "output/bazel${EXE_EXT}"
chmod 0755 "output/bazel${EXE_EXT}"
BAZEL="$(pwd)/output/bazel${EXE_EXT}"
--- a/compile.sh
+++ b/compile.sh
@@ -92,7 +92,7 @@
log "Building output/bazel"
# We set host and target platform directly since the defaults in @bazel_tools
# have not yet been generated.
-bazel_build "src:bazel${EXE_EXT}" \
+CC=$SPACK_CC CXX=$SPACK_CXX bazel_build "src:bazel${EXE_EXT}" \
--host_platform=//tools/platforms:host_platform \
--platforms=//tools/platforms:target_platform \
|| fail "Could not build Bazel"
--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java.orig 2020-06-08 13:42:14.035342560 -0400
+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java 2020-06-08 13:42:25.149375458 -0400
@@ -963,7 +963,7 @@
// are, it's probably due to a non-hermetic #include, & we should stop
// the build with an error.
if (execPath.startsWith(execRoot)) {
- execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
+ // execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
} else {
problems.add(execPathFragment.getPathString());
continue;
diff --color=auto --color=auto -Naur a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java
--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java 1980-01-01 00:00:00
+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java 2024-02-15 13:36:37
@@ -143,7 +143,7 @@
LabelConstants.EXPERIMENTAL_EXTERNAL_PATH_PREFIX.getRelative(
execPath.relativeTo(execRoot.getParentDirectory()));
} else {
- absolutePathProblems.add(execPathFragment.getPathString());
+ // absolutePathProblems.add(execPathFragment.getPathString());
continue;
}
}
--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java.orig 2020-03-25 08:54:37.914186251 -0400
+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/HeaderDiscovery.java 2020-03-25 08:55:01.356250657 -0400
@@ -148,7 +148,7 @@
if (execPath.startsWith(execRoot)) {
execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
} else {
- problems.add(execPathFragment.getPathString());
+ // problems.add(execPathFragment.getPathString());
continue;
}
}
--- a/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java.orig 2020-06-08 13:42:14.035342560 -0400
+++ b/src/main/java/com/google/devtools/build/lib/rules/cpp/CppCompileAction.java 2020-06-08 13:42:25.149375458 -0400
@@ -963,7 +963,7 @@
// are, it's probably due to a non-hermetic #include, & we should stop
// the build with an error.
if (execPath.startsWith(execRoot)) {
- execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
+ // execPathFragment = execPath.relativeTo(execRoot); // funky but tolerable path
} else {
problems.add(execPathFragment.getPathString());
continue;
From 9c9d27561780bc56d9f0867e325c7421a94ee1cb Mon Sep 17 00:00:00 2001
From: Harsh Bhatia <bhatia4@llnl.gov>
Date: Tue, 15 Dec 2020 15:56:10 -0800
Subject: [PATCH] https://github.com/bazelbuild/bazel/commit/ab62a6e097590dac5ec946ad7a796ea0e8593ae0
---
src/conditions/BUILD | 6 ++++++
third_party/BUILD | 8 ++++++--
2 files changed, 12 insertions(+), 2 deletions(-)
diff --git a/src/conditions/BUILD b/src/conditions/BUILD
index 2b28e28057..faa41a439d 100644
--- a/src/conditions/BUILD
+++ b/src/conditions/BUILD
@@ -10,6 +10,12 @@ filegroup(
visibility = ["//src:__pkg__"],
)
+config_setting(
+ name = "linux_ppc",
+ values = {"cpu": "ppc"},
+ visibility = ["//visibility:public"],
+)
+
config_setting(
name = "linux_x86_64",
values = {"cpu": "k8"},
diff --git a/third_party/BUILD b/third_party/BUILD
index 159006d741..4fcae54c00 100644
--- a/third_party/BUILD
+++ b/third_party/BUILD
@@ -523,12 +523,13 @@ UNNECESSARY_DYNAMIC_LIBRARIES = select({
"//src/conditions:darwin": "*.so *.dll",
"//src/conditions:darwin_x86_64": "*.so *.dll",
"//src/conditions:linux_x86_64": "*.jnilib *.dll",
+ "//src/conditions:linux_ppc": "*.so *.jnilib *.dll",
# The .so file is an x86 one, so we can just remove it if the CPU is not x86
"//src/conditions:arm": "*.so *.jnilib *.dll",
"//src/conditions:linux_aarch64": "*.so *.jnilib *.dll",
# Play it safe -- better have a big binary than a slow binary
# zip -d does require an argument. Supply something bogus.
- "//conditions:default": "*.bogusextension",
+ "//conditions:default": "",
})
# Remove native libraries that are for a platform different from the one we are
@@ -537,7 +538,10 @@ genrule(
name = "filter_netty_dynamic_libs",
srcs = ["netty_tcnative/netty-tcnative-boringssl-static-2.0.24.Final.jar"],
outs = ["netty_tcnative/netty-tcnative-filtered.jar"],
- cmd = "cp $< $@ && zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES,
+ cmd = "cp $< $@ && " +
+ # End successfully if there is nothing to be deleted from the archive
+ "if [ -n '" + UNNECESSARY_DYNAMIC_LIBRARIES + "' ]; then " +
+ "zip -qd $@ " + UNNECESSARY_DYNAMIC_LIBRARIES + "; fi",
)
java_import(
--
2.21.0 (Apple Git-122.2)