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authorBonfaceKilz2021-06-17 10:09:38 +0300
committerzsloan2021-06-17 18:51:27 +0000
commit2f88a976ce4c732f2e8c06939dda325e80fb1f89 (patch)
tree858336bab6bec22d06430e53bc04f0fc8fe3e48f /doc
parent8521ba973ccf14b6918948a93cfde07d6cf1e27a (diff)
downloadgenenetwork2-2f88a976ce4c732f2e8c06939dda325e80fb1f89.tar.gz
doc: rpy2-performance: Replace begin_export with begin_src
Diffstat (limited to 'doc')
-rw-r--r--doc/rpy2-performance.org19
1 files changed, 11 insertions, 8 deletions
diff --git a/doc/rpy2-performance.org b/doc/rpy2-performance.org
index 29b99ba0..ddcac81a 100644
--- a/doc/rpy2-performance.org
+++ b/doc/rpy2-performance.org
@@ -21,7 +21,7 @@ server:
However, when loading the homepage, I occasionally ran into this trace:
-#+begin_export ascii
+#+begin_src
DEBUG:wqflask.views:.check_access_permissions: @app.before_request check_access_permissions
DEBUG:wqflask.views:.shutdown_session: remove db_session
WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: Error: ignoring SIGPIPE signal
@@ -58,7 +58,7 @@ Possible actions:
Selection:
-#+end_export
+#+end_src
This blocks the flask service. Seems to be related to: [[https://github.com/rpy2/rpy2/issues/769][rpy2-issue#769]]
and [[https://github.com/rpy2/rpy2/issues/809][rpy2-issue#809]]. I tried to reproduce this problem using some endpoint:
@@ -80,7 +80,7 @@ and [[https://github.com/rpy2/rpy2/issues/809][rpy2-issue#809]]. I tried to repr
which generates this trace:
-#+begin_export ascii
+#+begin_src
/home/bonface/opt/python3-genenetwork2/lib/python3.8/site-packages/rpy2/rinterface.py:955: UserWarning: R is not initialized by the main thread.
Its taking over SIGINT cannot be reversed here, and as a
consequence the embedded R cannot be interrupted with Ctrl-C.
@@ -89,7 +89,7 @@ which generates this trace:
warnings.warn(
DEBUG:wqflask.views:.shutdown_session: remove db_session
-#+end_export
+#+end_src
Modifying the endpoint to:
@@ -108,7 +108,7 @@ Modifying the endpoint to:
and refreshing the page a couple of times, I get:
-#+begin_export ascii
+#+begin_src
DEBUG:wqflask.views:.check_access_permissions: @app.before_request check_access_
permissions
Sleeping for 3 seconds
@@ -136,7 +136,7 @@ WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: library '/home/bonfa
ce/R/x86_64-unknown-linux-gnu-library/4.0' contains no packages
WARNING:rpy2.rinterface_lib.callbacks:R[write to console]:
-*** caught segfault ***
+\*** caught segfault ***
WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: address (nil), cause
'memory not mapped'
@@ -151,9 +151,11 @@ Possible actions:
Selection: [2021-06-16 13:11:00 +0300] [18657] [INFO] Handling signal: winch
[2021-06-16 13:11:00 +0300] [18657] [INFO] Handling signal: winch
[2021-06-16 13:13:02 +0300] [18657] [INFO] Handling signal: winch
-#+end_export
+#+end_src
-However, this seems to be non-deterministic, in the sense that I can't really pin what causes the above. I've tried to write a Locust Test that simulates users hitting that endpoint:
+However, this seems to be non-deterministic, in the sense that I can't
+really pin what causes the above. I've tried to write a Locust Test
+that simulates users hitting that endpoint:
#+begin_src python
"""Load test a single trait page"""
@@ -168,3 +170,4 @@ from locust import HttpUser, task, between
"""Fetch a single trait"""
self.client.get("/test")
#+end_src
+