Revise uwsgi defaults and display.

In https://github.com/galaxyproject/galaxy/issues/1530 we realized that buffer-size needs to be increased for Galaxy requests. Also mention thunder-lock since that should frequently be enabled - https://github.com/galaxyproject/ansible-galaxy-extras/pull/195.

config/galaxy.yml.sample

@@ -25,12 +25,13 @@ uwsgi:
 
   # By default uWSGI allocates a very small buffer (4096 bytes) for the
   # headers of each request. If you start receiving "invalid request
-  # block size" in your logs, it could mean you need a bigger buffer.
-  # Increase it up to 65535.
-  buffer-size: 4096
+  # block size" in your logs, it could mean you need a bigger buffer. We
+  # recommend at least 16384.
+  buffer-size: 16384
 
   # Number of web server (worker) processes to fork after the
-  # application has loaded.
+  # application has loaded. If this is set to greater than 1, thunder-
+  # lock likely should be enabled below.
   processes: 1
 
   # Number of threads for each web server process.
@@ -61,6 +62,10 @@ uwsgi:
   # Reports, etc.) that you are loading.
   module: galaxy.webapps.galaxy.buildapp:uwsgi_app()
 
+  # It is usually a good idea to set this to ``true`` if processes is
+  # greater than 1.
+  thunder-lock: false
+
   # Cause uWSGI to respect the traditional behavior of dying on SIGTERM
   # (its default is to brutally reload workers)
   die-on-term: true

config/reports.yml.sample

@@ -7,12 +7,13 @@ uwsgi:
 
   # By default uWSGI allocates a very small buffer (4096 bytes) for the
   # headers of each request. If you start receiving "invalid request
-  # block size" in your logs, it could mean you need a bigger buffer.
-  # Increase it up to 65535.
-  buffer-size: 4096
+  # block size" in your logs, it could mean you need a bigger buffer. We
+  # recommend at least 16384.
+  buffer-size: 16384
 
   # Number of web server (worker) processes to fork after the
-  # application has loaded.
+  # application has loaded. If this is set to greater than 1, thunder-
+  # lock likely should be enabled below.
   processes: 1
 
   # Number of threads for each web server process.
@@ -43,6 +44,10 @@ uwsgi:
   # Reports, etc.) that you are loading.
   module: galaxy.webapps.reports.buildapp:uwsgi_app()
 
+  # It is usually a good idea to set this to ``true`` if processes is
+  # greater than 1.
+  thunder-lock: false
+
   # Cause uWSGI to respect the traditional behavior of dying on SIGTERM
   # (its default is to brutally reload workers)
   die-on-term: true

config/tool_shed.yml.sample

@@ -7,12 +7,13 @@ uwsgi:
 
   # By default uWSGI allocates a very small buffer (4096 bytes) for the
   # headers of each request. If you start receiving "invalid request
-  # block size" in your logs, it could mean you need a bigger buffer.
-  # Increase it up to 65535.
-  buffer-size: 4096
+  # block size" in your logs, it could mean you need a bigger buffer. We
+  # recommend at least 16384.
+  buffer-size: 16384
 
   # Number of web server (worker) processes to fork after the
-  # application has loaded.
+  # application has loaded. If this is set to greater than 1, thunder-
+  # lock likely should be enabled below.
   processes: 1
 
   # Number of threads for each web server process.
@@ -43,6 +44,10 @@ uwsgi:
   # Reports, etc.) that you are loading.
   module: galaxy.webapps.tool_shed.buildapp:uwsgi_app()
 
+  # It is usually a good idea to set this to ``true`` if processes is
+  # greater than 1.
+  thunder-lock: false
+
   # Cause uWSGI to respect the traditional behavior of dying on SIGTERM
   # (its default is to brutally reload workers)
   die-on-term: true

doc/source/admin/galaxy_options.rst

@@ -3435,6 +3435,38 @@
 :Type: str
 
 
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``workflow_resource_params_file``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    Similar to the above parameter, workflows can describe parameters
+    used to influence scheduling of jobs within the workflow. This
+    requires both a description of the fields available (which
+    defaults to the definitions in job_resource_params_file if not
+    set).
+:Default: ``config/workflow_resource_params_conf.xml``
+:Type: str
+
+
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+``workflow_resource_params_mapper``
+~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
+
+:Description:
+    This parameter describes how to map users and workflows to a set
+    of workflow resource parameter to present (typically input IDs
+    from workflow_resource_params_file). If this this is a function
+    reference it will be passed various inputs (workflow model object
+    and user) and it should produce a list of input IDs. If it is a
+    path it is expected to an XML or YAML file describing how to map
+    group names to parameter descriptions (additional types of
+    mappings via these files could be implemented but haven't yet -
+    for instance using workflow tags to do the mapping).
+:Default: ``config/workflow_resource_mapper_conf.yml``
+:Type: str
+
+
 ~~~~~~~~~~~~~~~~~~~~~~~~
 ``cache_user_job_count``
 ~~~~~~~~~~~~~~~~~~~~~~~~

lib/galaxy/webapps/config_manage.py

@@ -54,12 +54,12 @@ UWSGI_OPTIONS = OrderedDict([
         'type': 'str',
     }),
     ('buffer-size', {
-        'desc': """By default uWSGI allocates a very small buffer (4096 bytes) for the headers of each request. If you start receiving "invalid request block size" in your logs, it could mean you need a bigger buffer. Increase it up to 65535.""",
-        'default': 4096,
+        'desc': """By default uWSGI allocates a very small buffer (4096 bytes) for the headers of each request. If you start receiving "invalid request block size" in your logs, it could mean you need a bigger buffer. We recommend at least 16384.""",
+        'default': 16384,
         'type': 'int',
     }),
     ('processes', {
-        'desc': """Number of web server (worker) processes to fork after the application has loaded.""",
+        'desc': """Number of web server (worker) processes to fork after the application has loaded. If this is set to greater than 1, thunder-lock likely should be enabled below.""",
         'default': 1,
         'type': 'int',
     }),
@@ -105,6 +105,11 @@ UWSGI_OPTIONS = OrderedDict([
         'default': '$uwsgi_module',
         'type': 'str',
     }),
+    ('thunder-lock', {
+        'desc': """It is usually a good idea to set this to ``true`` if processes is greater than 1.""",
+        'default': False,
+        'type': 'bool',
+    }),
     ('die-on-term', {
         'desc': """Cause uWSGI to respect the traditional behavior of dying on SIGTERM (its default is to brutally reload workers)""",
         'default': True,

scripts/get_uwsgi_args.py

@@ -23,7 +23,7 @@ ALIASES = {
     'module': ('mount',),   # mount is not actually an alias for module, but we don't want to set module if mount is set
 }
 DEFAULT_ARGS = {
-    '_all_': ('virtualenv', 'pythonpath', 'threads', 'http', 'static-map', 'die-on-term', 'hook-master-start', 'enable-threads'),
+    '_all_': ('virtualenv', 'pythonpath', 'threads', 'buffer-size', 'http', 'static-map', 'die-on-term', 'hook-master-start', 'enable-threads'),
     'galaxy': ('py-call-osafterfork',),
     'reports': (),
     'tool_shed': (),
@@ -89,6 +89,7 @@ def _get_uwsgi_args(cliargs, kwargs):
         'virtualenv': os.environ.get('VIRTUAL_ENV', './.venv'),
         'pythonpath': 'lib',
         'threads': '4',
+        'buffer-size': '16384',  # https://github.com/galaxyproject/galaxy/issues/1530
         'http': 'localhost:{port}'.format(port=DEFAULT_PORTS[cliargs.app]),
         'static-map': ('/static/style={here}/static/style/blue'.format(here=os.getcwd()),
                        '/static={here}/static'.format(here=os.getcwd())),