[ARVADOS] updated: 1.3.0-2460-gb0205e1c5
Git user
git at public.arvados.org
Thu Apr 9 22:25:29 UTC 2020
Summary of changes:
CODE_OF_CONDUCT.md | 96 +++
CONTRIBUTING.md | 75 +++
COPYING | 4 +
README.md | 91 +--
apps/workbench/Gemfile.lock | 8 +-
apps/workbench/config/application.rb | 4 +
.../config/initializers/actionview_xss_fix.rb | 32 +
.../test/unit/helpers/javascript_helper_test.rb | 17 +
build/build-dev-docker-jobs-image.sh | 13 +-
build/package-build-dockerfiles/centos7/Dockerfile | 4 +-
.../package-build-dockerfiles/debian10/Dockerfile | 2 +-
build/package-build-dockerfiles/debian9/Dockerfile | 2 +-
.../ubuntu1604/Dockerfile | 4 +-
.../ubuntu1804/Dockerfile | 4 +-
build/package-test-dockerfiles/centos7/Dockerfile | 2 +-
build/package-test-dockerfiles/debian10/Dockerfile | 2 +-
build/package-test-dockerfiles/debian9/Dockerfile | 2 +-
.../package-test-dockerfiles/ubuntu1604/Dockerfile | 2 +-
.../package-test-dockerfiles/ubuntu1804/Dockerfile | 2 +-
build/run-build-packages.sh | 11 +-
build/run-tests.sh | 82 ++-
cmd/arvados-client/Makefile | 11 +
cmd/arvados-client/cmd.go | 3 +
.../ws => cmd/arvados-server}/arvados-ws.service | 1 +
cmd/arvados-server/cmd.go | 8 +-
doc/_config.yml | 1 +
doc/admin/metrics.html.textile.liquid | 2 +-
doc/admin/scoped-tokens.html.textile.liquid | 70 ++
doc/admin/upgrading.html.textile.liquid | 8 +-
doc/api/index.html.textile.liquid | 4 +
doc/api/methods.html.textile.liquid | 1 +
doc/api/tokens.html.textile.liquid | 6 +-
doc/examples/config/zzzzz.yml | 12 +
.../install-shell-server.html.textile.liquid | 2 +-
doc/sdk/python/cookbook.html.textile.liquid | 2 +-
go.mod | 11 +-
go.sum | 19 +-
lib/boot/cert.go | 64 ++
lib/boot/cmd.go | 108 ++++
lib/boot/nginx.go | 104 +++
lib/boot/passenger.go | 129 ++++
lib/boot/postgresql.go | 162 +++++
lib/boot/seed.go | 28 +
lib/boot/service.go | 100 +++
lib/boot/supervisor.go | 708 +++++++++++++++++++++
lib/config/config.default.yml | 25 +-
lib/config/export.go | 12 +-
lib/config/generated_config.go | 25 +-
lib/controller/federation/conn.go | 29 +-
lib/controller/federation/login_test.go | 3 +
lib/controller/handler.go | 5 +
lib/controller/integration_test.go | 225 +++++++
lib/controller/localdb/conn.go | 32 +-
lib/controller/localdb/login.go | 302 ++-------
.../localdb/{login.go => login_google.go} | 65 +-
.../{login_test.go => login_google_test.go} | 62 +-
lib/controller/localdb/login_pam.go | 109 ++++
lib/controller/localdb/login_pam_docker_test.go | 23 +
lib/controller/localdb/login_pam_docker_test.sh | 193 ++++++
lib/controller/localdb/login_pam_test.go | 84 +++
lib/controller/router/router.go | 29 +-
lib/controller/rpc/conn.go | 9 +-
lib/dispatchcloud/container/queue.go | 7 +-
lib/dispatchcloud/container/queue_test.go | 7 +
lib/dispatchcloud/dispatcher.go | 5 +
lib/dispatchcloud/worker/pool.go | 26 +-
lib/install/arvadostest_docker_build.sh | 38 ++
lib/install/arvadostest_docker_run.sh | 34 +
lib/install/deps.go | 417 ++++++++++++
lib/install/deps_test.go | 47 ++
lib/install/example_from_scratch.sh | 17 +
lib/mount/command.go | 86 +++
lib/mount/command_test.go | 81 +++
lib/mount/fs.go | 392 ++++++++++++
lib/mount/fs_test.go | 49 ++
lib/service/cmd.go | 18 +-
lib/service/cmd_test.go | 1 +
lib/service/error.go | 12 +
lib/service/log.go | 34 +
sdk/cli/arvados-cli.gemspec | 1 +
sdk/cwl/arvados_cwl/__init__.py | 37 --
sdk/cwl/arvados_cwl/arvworkflow.py | 29 +-
sdk/cwl/arvados_cwl/runner.py | 5 +-
sdk/cwl/setup.py | 11 +-
sdk/cwl/test_with_arvbox.sh | 26 +-
sdk/cwl/tests/test_container.py | 15 +-
sdk/cwl/tests/test_submit.py | 3 +-
sdk/cwl/tests/wf/scatter2_subwf.cwl | 15 +-
sdk/go/arvados/api.go | 9 +-
sdk/go/arvados/client.go | 2 +-
sdk/go/arvados/collection.go | 27 +
sdk/go/arvados/config.go | 42 +-
sdk/go/arvados/config_test.go | 26 +
sdk/go/arvados/container.go | 6 +-
sdk/go/arvados/login.go | 6 +-
sdk/go/arvadostest/api.go | 4 +
sdk/go/auth/auth.go | 4 +-
sdk/go/ctxlog/log.go | 6 +
sdk/go/health/aggregator.go | 12 +-
sdk/go/httpserver/logger.go | 14 +-
sdk/java-v2/build.gradle | 2 +-
.../arvados/client/api/client/LinksApiClient.java | 36 ++
.../java/org/arvados/client/api/model/Link.java | 62 ++
.../api/model/{UserList.java => LinkList.java} | 8 +-
sdk/python/arvados/commands/arv_copy.py | 294 +--------
sdk/python/arvados/util.py | 2 +-
sdk/python/setup.py | 2 +-
sdk/python/tests/nginx.conf | 38 +-
sdk/python/tests/run_test_server.py | 75 ++-
sdk/python/tests/test_keep_client.py | 8 +-
services/api/Gemfile.lock | 4 +-
.../controllers/arvados/v1/schema_controller.rb | 2 +-
.../app/controllers/arvados/v1/users_controller.rb | 5 +-
.../app/controllers/user_sessions_controller.rb | 3 +-
.../api/app/models/api_client_authorization.rb | 2 +-
services/api/app/models/user.rb | 8 +-
services/api/config/application.default.yml | 12 -
services/api/config/application.rb | 4 +
services/api/config/arvados_config.rb | 2 +-
services/api/lib/config_loader.rb | 11 +-
services/api/lib/record_filters.rb | 6 +-
services/api/test/fixtures/collections.yml | 49 +-
.../api/test/functional/arvados/v1/filters_test.rb | 7 +
services/api/test/integration/users_test.rb | 10 +-
services/keep-balance/server.go | 5 +
services/keepproxy/keepproxy.go | 2 +-
services/keepstore/command.go | 4 +
services/keepstore/unix_volume_test.go | 23 +-
services/login-sync/arvados-login-sync.gemspec | 1 +
services/ws/doc.go | 34 +-
services/ws/event.go | 8 +-
services/ws/event_source.go | 154 ++++-
services/ws/event_source_test.go | 10 +-
services/ws/event_test.go | 2 +-
services/ws/gocheck_test.go | 6 +-
services/ws/handler.go | 32 +-
services/ws/main.go | 77 ---
services/ws/permission.go | 10 +-
services/ws/permission_test.go | 12 +-
services/ws/router.go | 117 +---
services/ws/server.go | 88 ---
services/ws/service.go | 53 ++
services/ws/{server_test.go => service_test.go} | 144 +++--
services/ws/session.go | 2 +-
services/ws/session_v0.go | 7 +-
services/ws/session_v0_test.go | 24 +-
services/ws/session_v1.go | 2 +-
tools/arvbox/lib/arvbox/docker/Dockerfile.base | 4 +-
tools/arvbox/lib/arvbox/docker/common.sh | 4 +-
tools/arvbox/lib/arvbox/docker/service/nginx/run | 7 +-
.../lib/arvbox/docker/service/sdk/run-service | 6 +-
.../arvbox/docker/service/websockets/run-service | 26 +-
.../arvbox/docker/service/workbench2/run-service | 1 +
153 files changed, 4919 insertions(+), 1424 deletions(-)
create mode 100644 CODE_OF_CONDUCT.md
create mode 100644 CONTRIBUTING.md
create mode 100644 apps/workbench/config/initializers/actionview_xss_fix.rb
create mode 100644 apps/workbench/test/unit/helpers/javascript_helper_test.rb
create mode 100644 cmd/arvados-client/Makefile
rename {services/ws => cmd/arvados-server}/arvados-ws.service (94%)
create mode 100644 doc/admin/scoped-tokens.html.textile.liquid
create mode 100644 doc/examples/config/zzzzz.yml
create mode 100644 lib/boot/cert.go
create mode 100644 lib/boot/cmd.go
create mode 100644 lib/boot/nginx.go
create mode 100644 lib/boot/passenger.go
create mode 100644 lib/boot/postgresql.go
create mode 100644 lib/boot/seed.go
create mode 100644 lib/boot/service.go
create mode 100644 lib/boot/supervisor.go
create mode 100644 lib/controller/integration_test.go
copy lib/controller/localdb/{login.go => login_google.go} (78%)
rename lib/controller/localdb/{login_test.go => login_google_test.go} (93%)
create mode 100644 lib/controller/localdb/login_pam.go
create mode 100644 lib/controller/localdb/login_pam_docker_test.go
create mode 100755 lib/controller/localdb/login_pam_docker_test.sh
create mode 100644 lib/controller/localdb/login_pam_test.go
create mode 100755 lib/install/arvadostest_docker_build.sh
create mode 100755 lib/install/arvadostest_docker_run.sh
create mode 100644 lib/install/deps.go
create mode 100644 lib/install/deps_test.go
create mode 100644 lib/install/example_from_scratch.sh
create mode 100644 lib/mount/command.go
create mode 100644 lib/mount/command_test.go
create mode 100644 lib/mount/fs.go
create mode 100644 lib/mount/fs_test.go
create mode 100644 lib/service/log.go
create mode 100644 sdk/java-v2/src/main/java/org/arvados/client/api/client/LinksApiClient.java
create mode 100644 sdk/java-v2/src/main/java/org/arvados/client/api/model/Link.java
copy sdk/java-v2/src/main/java/org/arvados/client/api/model/{UserList.java => LinkList.java} (80%)
delete mode 100644 services/ws/main.go
delete mode 100644 services/ws/server.go
create mode 100644 services/ws/service.go
rename services/ws/{server_test.go => service_test.go} (55%)
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commit b0205e1c5e8bff315b475c6a2122bb23fbead70c
Author: Ward Vandewege <ward at jhvc.com>
Date: Thu Apr 9 17:53:31 2020 -0400
documentation: update descriptions for MaxKeepBlobBuffers and MaxConcurrentRequests
keepstore: MaxConcurrentRequests set to zero should mean no limit
refs #16326
Arvados-DCO-1.1-Signed-off-by: Ward Vandewege <ward at jhvc.com>
diff --git a/lib/config/config.default.yml b/lib/config/config.default.yml
index a4616d70b..fcccdd063 100644
--- a/lib/config/config.default.yml
+++ b/lib/config/config.default.yml
@@ -184,12 +184,21 @@ Clusters:
MaxItemsPerResponse: 1000
# Maximum number of concurrent requests to accept in a single
- # service process, or 0 for no limit. Currently supported only
- # by keepstore.
+ # service process, or 0 for no limit.
MaxConcurrentRequests: 0
- # Maximum number of 64MiB memory buffers per keepstore server
- # process, or 0 for no limit.
+ # Maximum number of 64MiB memory buffers per Keepstore server process, or
+ # 0 for no limit. When this limit is reached, up to
+ # (MaxConcurrentRequests - MaxKeepBlobBuffers) HTTP requests requiring
+ # buffers (like GET and PUT) will wait for buffer space to be released.
+ # Any HTTP requests beyond MaxConcurrentRequests will receive an
+ # immediate 503 response.
+ #
+ # MaxKeepBlobBuffers should be set such that (MaxKeepBlobBuffers * 64MiB
+ # * 1.1) fits comfortably in memory. On a host dedicated to running
+ # Keepstore, divide total memory by 88MiB to suggest a suitable value.
+ # For example, if grep MemTotal /proc/meminfo reports MemTotal: 7125440
+ # kB, compute 7125440 / (88 * 1024)=79 and configure MaxBuffers: 79
MaxKeepBlobBuffers: 128
# API methods to disable. Disabled methods are not listed in the
diff --git a/services/keepstore/command.go b/services/keepstore/command.go
index ea08cf977..0927b1870 100644
--- a/services/keepstore/command.go
+++ b/services/keepstore/command.go
@@ -157,10 +157,6 @@ func (h *handler) setup(ctx context.Context, cluster *arvados.Cluster, token str
}
bufs = newBufferPool(h.Logger, h.Cluster.API.MaxKeepBlobBuffers, BlockSize)
- if h.Cluster.API.MaxConcurrentRequests < 1 {
- h.Cluster.API.MaxConcurrentRequests = h.Cluster.API.MaxKeepBlobBuffers * 2
- h.Logger.Warnf("API.MaxConcurrentRequests <1 or not specified; defaulting to MaxKeepBlobBuffers * 2 == %d", h.Cluster.API.MaxConcurrentRequests)
- }
if h.Cluster.API.MaxConcurrentRequests > 0 && h.Cluster.API.MaxConcurrentRequests < h.Cluster.API.MaxKeepBlobBuffers {
h.Logger.Warnf("Possible configuration mistake: not useful to set API.MaxKeepBlobBuffers (%d) higher than API.MaxConcurrentRequests (%d)", h.Cluster.API.MaxKeepBlobBuffers, h.Cluster.API.MaxConcurrentRequests)
}
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