Merge branch 'add_jax' into 'master'

hxtorch will soon depend on jax

See merge request technical-coordination/project-internal/devops/platform/ebrains-spack-builds!258

packages.yaml

@@ -7,3 +7,5 @@ packages:
     py-torch:
         version: [1.11.0]
         variants: [~cuda~rocm~valgrind~mkldnn~mpi~gloo+tensorpipe~onnx_ml]
+    py-jax:
+        variants: [~cuda]

packages/bazel/add-include-limits-0.25.patch

+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"
+ 

packages/bazel/add-include-limits-zlib_client.patch

+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"
+ 

packages/bazel/bazelconfiguration-0.3.patch

+--- 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) {

packages/bazel/bazelruleclassprovider-0.14.patch

+--- 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.

packages/bazel/bazelruleclassprovider-0.25.patch

+--- 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
+@@ -181,6 +181,13 @@ 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.

packages/bazel/bazelruleclassprovider_fj-0.25.patch

+--- 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
+@@ -185,7 +185,7 @@ public class BazelRuleClassProvider {
+ 
+         Map<String, String> spackEnv = System.getenv();
+         for (String envName : spackEnv.keySet()) {
+-          if (envName.startsWith("SPACK_")) {
++          if ((envName.startsWith("SPACK_")) || (envName.equals("fcc_ENV")) || (envName.equals("FCC_ENV"))) {
+             env.put(envName, spackEnv.get(envName));
+           }
+         }

packages/bazel/blaze_util_posix-0.29.1.patch

+diff -Naur a/src/main/cpp/blaze_util_posix.cc b/src/main/cpp/blaze_util_posix.cc
+--- a/src/main/cpp/blaze_util_posix.cc	1980-01-01 00:00:00.000000000 -0800
++++ b/src/main/cpp/blaze_util_posix.cc	2022-06-30 23:34:08.000000000 -0700
+@@ -600,7 +600,7 @@
+   // Prefer OFD locks if available.  POSIX locks can be lost "accidentally"
+   // due to any close() on the lock file, and are not reliably preserved
+   // across execve() on Linux, which we need for --batch mode.
+-  if (fcntl(fd, F_OFD_SETLK, lock) == 0) return 0;
++  if (fcntl(fd, F_SETLK, lock) == 0) return 0;
+   if (errno != EINVAL) {
+     if (errno != EACCES && errno != EAGAIN) {
+       BAZEL_DIE(blaze_exit_code::LOCAL_ENVIRONMENTAL_ERROR)

packages/bazel/build-0.29.1.patch

+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)
+

packages/bazel/cc_configure-0.3.0.patch

+--- 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."""

packages/bazel/cc_configure-0.5.0.patch

+--- 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):

packages/bazel/cc_env.patch

+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"

packages/bazel/compile-0.13.patch

+--- 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"

packages/bazel/compile-0.16.patch

+--- 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"

packages/bazel/compile-0.21.patch

+--- 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 \

packages/bazel/compile-0.29.patch

+--- a/compile.sh
++++ b/compile.sh
+@@ -63,7 +63,7 @@
+ log "Building output/bazel"
+ # We set host and target platform directly because we are building for the local
+ # host.
+-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=@local_config_platform//:host \
+   --platforms=@local_config_platform//:host \

packages/bazel/compile-0.3.patch

+--- 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}"

packages/bazel/compile-0.4.patch

+--- a/compile.sh
++++ b/compile.sh
+@@ -124,7 +124,7 @@
+   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}" \
+     || fail "Could not build Bazel"
+   bazel_bin_path="$(get_bazel_bin_path)/src/bazel${EXE_EXT}"
+   [ -e "$bazel_bin_path" ] \

packages/bazel/compile-0.6.patch

+--- a/compile.sh
++++ b/compile.sh
+@@ -85,7 +85,7 @@
+ 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}" \
+   --experimental_host_platform=//tools/platforms:host_platform \
+   --experimental_platforms=//tools/platforms:target_platform \
+   || fail "Could not build Bazel"

packages/bazel/compile-0.9.patch

+--- 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"