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-rw-r--r--doc/README.org98
-rw-r--r--doc/database.org150
-rw-r--r--doc/docker-container.org15
-rw-r--r--doc/guix_profile_setup.org39
-rw-r--r--doc/heatmap-generation.org34
-rw-r--r--doc/images/gn2_header_collections.pngbin0 -> 7890 bytes
-rw-r--r--doc/images/heatmap_form.pngbin0 -> 9363 bytes
-rw-r--r--doc/images/heatmap_with_hover_tools.pngbin0 -> 42578 bytes
-rw-r--r--doc/rpy2-performance.org182
9 files changed, 495 insertions, 23 deletions
diff --git a/doc/README.org b/doc/README.org
index 43c92e3c..1236016e 100644
--- a/doc/README.org
+++ b/doc/README.org
@@ -2,7 +2,9 @@
* Table of Contents :TOC:
- [[#introduction][Introduction]]
- - [[#install][Install]]
+ - [[#check-list][Check list]]
+ - [[#installing-guix-packages][Installing Guix packages]]
+ - [[#creating-a-gnu-guix-profile][Creating a GNU Guix profile]]
- [[#running-gn2][Running GN2]]
- [[#run-gn-proxy][Run gn-proxy]]
- [[#run-redis][Run Redis]]
@@ -37,32 +39,106 @@ tree. Current supported versions can be found as the SHA values of
For a full view of runtime dependencies as defined by GNU Guix, see
an example of the [[#gn2-dependency-graph][GN2 Dependency Graph]].
-* Install
+* Check list
+
+To run GeneNetwork the following services need to function:
+
+1. [ ] GNU Guix with a guix profile for genenetwork2
+1. [ ] A path to the (static) genotype files
+1. [ ] Gn-proxy for authentication
+1. [ ] The genenetwork3 service
+1. [ ] Redis
+1. [ ] Mariadb
+
+* Installing Guix packages
Make sure to install GNU Guix using the binary download instructions
on the main website. Follow the instructions on
[[GUIX-Reproducible-from-source.org]] to download pre-built binaries. Note
-the download amounts to several GBs of data.
+the download amounts to several GBs of data. Debian-derived distros
+may support
+
+: apt-get install guix
+
+* Creating a GNU Guix profile
+
+We run a GNU Guix channel with packages at [[https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics][guix-bioinformatics]]. The
+README has instructions for hosting a channel, but typically we use
+the GUIX_PACKAGE_PATH instead. First upgrade to a recent guix with
+
+: mkdir ~/opt
+: guix pull -p ~/opt/guix-pull
+
+It should upgrade (ignore the locales warnings). You can optionally
+specify the specific git checkout of guix with
+
+: guix pull -p ~/opt/guix-pull --commit=f04883d
+
+which is useful when you ned to roll back to an earlier version
+(sometimes our channel goes out of sync). Next, we install
+GeneNetwork2 with
+
+: source ~/opt/guix-pull/etc/profile
+: git clone https://git.genenetwork.org/guix-bioinformatics/guix-bioinformatics.git ~/guix-bioinformatics
+: cd ~/guix-bioinformatics
+: git pull
+: env GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics guix package -i genenetwork2 -p ~/opt/genenetwork2
+
+you probably also need guix-past (the upstream channel for older packages):
+
+: git clone https://gitlab.inria.fr/guix-hpc/guix-past.git ~/guix-past
+: cd ~/guix-past
+: git pull
+: env GUIX_PACKAGE_PATH=$HOME/guix-bioinformatics:$HOME/guix-past/modules ~/opt/guix-pull/bin/guix package -i genenetwork2 -p ~/opt/genenetwork2
+
+ignore the warnings. Guix should install the software without trying
+to build everything. If you system insists on building all packages,
+try the `--dry-run` switch and fix the [[https://guix.gnu.org/manual/en/html_node/Substitute-Server-Authorization.html][substitutes]]. You may add the
+`--substitute-urls="http://guix.genenetwork.org https://ci.guix.gnu.org https://mirror.hydra.gnu.org"` switch.
+
+The guix.genenetwork.org has most of our packages pre-built(!). To use
+it on your own machine the public key is
+
+#+begin_src scheme
+(public-key
+ (ecc
+ (curve Ed25519)
+ (q #E50F005E6DA2F85749B9AA62C8E86BB551CE2B541DC578C4DBE613B39EC9E750#)))
+#+end_src
+
+Once we have a GNU Guix profile, a running database (see below) and the file storage,
+we should be ready to fire up GeneNetwork:
* Running GN2
-Default settings for GN2 are listed in a file called
-[[../etc/default_settings.py][default_settings.py]]. You can copy this file and pass it as a new
-parameter to the genenetwork2 command, e.g.
+Check out the source with git:
-: genenetwork2 mysettings.py
+: git clone git@github.com:genenetwork/genenetwork2.git
+: cd genenetwork2
-or you can set environment variables to override individual parameters, e.g.
+Run GN2 with above Guix profile
-: env SERVER_PORT=5004 SQL_URI=mysql://user:pwd@dbhostname/db_webqtl genenetwork2
+: export GN2_PROFILE=$HOME/opt/genenetwork2
+: env TMPDIR=$HOME/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG SERVER_PORT=5012 GENENETWORK_FILES=/export/data/genenetwork/genotype_files SQL_URI=mysql://webqtlout:webqtlout@localhost/db_webqtl ./bin/genenetwork2 etc/default_settings.py -gunicorn-dev
the debug and logging switches can be particularly useful when
-developing GN2.
+developing GN2. Location and files are the current ones for Penguin2.
+
+It may be useful to tunnel the web server to your local browser with
+an ssh tunnel:
+
+If you want to test a service running on the server on a certain
+port (say 8202) use
+
+ ssh -L 8202:127.0.0.1:8202 -f -N myname@penguin2.genenetwork.org
+
+And browse on your local machine to http://localhost:8202/
* Run gn-proxy
GeneNetwork requires a separate gn-proxy server which handles
-authorisation and access control. For instructions see the [[https://github.com/genenetwork/gn-proxy][README]].
+authorisation and access control. For instructions see the
+[[https://github.com/genenetwork/gn-proxy][README]]. Note it may already be running on our servers!
* Run Redis
diff --git a/doc/database.org b/doc/database.org
index 5107b660..d5462d4e 100644
--- a/doc/database.org
+++ b/doc/database.org
@@ -1339,7 +1339,8 @@ The SNP count info for the BXD is calculated like this
startMb += stepMb
#+end_src
-select * from BXDSnpPosition limit 5;
+: select * from BXDSnpPosition limit 5;
+
+------+-----------+-----------+----------+
| Chr | StrainId1 | StrainId2 | Mb |
+------+-----------+-----------+----------+
@@ -1368,3 +1369,150 @@ mysql> select * from SnpSource limit 5;
Empty set (0.00 sec)
Hmmm. This is the test database. Then there are the plink files and VCF files.
+
+* Optimize SQL?
+
+We were facing some issues with slow queries. A query
+was really slow on Penguin2:
+
+: time mysql -u webqtlout -pwebqtlout db_webqtl < ~/chunk.sql > /dev/null
+: real 0m13.082s
+: user 0m0.292s
+: sys 0m0.032s
+
+Runs in 1s on Tux01 and 13s on P2, why is that? The gist of it
+was increasing an InnoDB cache size(!)
+
+Interestingly, Penguin2 is running InnoDB on a much slower storage.
+It has more indices that Tux01(?!). Probably due to things we have
+been trying to make the datatables faster.
+
+Meanwhile the query is one with many joins:
+
+#+begin_src sql
+SELECT ProbeSet.Name,ProbeSetXRef.DataId, T4.value, T5.value, T6.value, T7.value, T8.value, T9.value, T10.value, T11.value, T12.value, T14.value, T15.value, T17.value, T18.value, T19.value, T20.value, T21.value, T22.value, T24.value, T25.value, T26.value, T28.value, T29.value, T30.value, T31.value, T35.value, T36.value, T37.value, T39.value, T98.value, T99.value, T100.value, T103.value, T487.value, T105.value, T106.value, T110.value FROM (ProbeSet, ProbeSetXRef, ProbeSetFreeze)
+ left join ProbeSetData as T4 on T4.Id = ProbeSetXRef.DataId
+ and T4.StrainId=4
+ (...)
+ left join ProbeSetData as T110 on T110.Id = ProbeSetXRef.DataId
+ and T110.StrainId=110
+ WHERE ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id
+ and ProbeSetFreeze.Name = 'HC_M2_0606_P'
+ and ProbeSet.Id = ProbeSetXRef.ProbeSetId
+ order by ProbeSet.Id
+#+end_src
+
+And is blazingly fast on Tux01 and (now) fast enough on Penguin2.
+
+First I checked the tables for indices and storage type. Next I
+checked the difference in configuration.
+
+** Check tables
+
+Tables (ProbeSetData, ProbeSet, ProbeSetXRef, ProbeSetFreeze)
+
+*** ProbeSetData
+
+Same on Tux01 and P2:
+
+: show indexes from ProbeSetData ;
+
+| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment |
+|--------------+------------+----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------|
+| ProbeSetData | 0 | DataId | 1 | Id | A | 47769944 | NULL | NULL | | BTREE | | |
+| ProbeSetData | 0 | DataId | 2 | StrainId | A | 5111384047 | NULL | NULL | | BTREE | | |
+
+*** ProbeSetFreeze
+
+Tux01 has less indexes than P2(!):
+
+| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment |
+|----------------+------------+-----------+--------------+-------------+-----------+-------------+----------+--------+------+------------+---------+---------------|
+| ProbeSetFreeze | 0 | PRIMARY | 1 | Id | A | 911 | NULL | NULL | | BTREE | | |
+| ProbeSetFreeze | 0 | FullName | 1 | FullName | A | 911 | NULL | NULL | | BTREE | | |
+| ProbeSetFreeze | 0 | Name | 1 | Name | A | 911 | NULL | NULL | YES | BTREE | | |
+| ProbeSetFreeze | 1 | NameIndex | 1 | Name2 | A | 911 | NULL | NULL | | BTREE | | |
+: 4 rows in set (0.000 sec)
+
+| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment |
+|----------------+------------+-----------------+--------------+-----------------+-----------+-------------+----------+--------+------+------------+---------+---------------|
+| ProbeSetFreeze | 0 | PRIMARY | 1 | Id | A | 883 | NULL | NULL | | BTREE | | |
+| ProbeSetFreeze | 0 | FullName | 1 | FullName | A | 883 | NULL | NULL | | BTREE | | |
+| ProbeSetFreeze | 0 | Name | 1 | Name | A | 883 | NULL | NULL | YES | BTREE | | |
+| ProbeSetFreeze | 1 | NameIndex | 1 | Name2 | A | 883 | NULL | NULL | | BTREE | | |
+| ProbeSetFreeze | 1 | ShortName | 1 | ShortName | A | 883 | NULL | NULL | | BTREE | | |
+| ProbeSetFreeze | 1 | ProbeFreezeId | 1 | ProbeFreezeId | A | 441 | NULL | NULL | | BTREE | | |
+| ProbeSetFreeze | 1 | conf_and_public | 1 | confidentiality | A | 3 | NULL | NULL | | BTREE | | |
+| ProbeSetFreeze | 1 | conf_and_public | 2 | public | A | 4 | NULL | NULL | | BTREE | | |
+: 8 rows in set (0.00 sec)
+
+*** ProbeSet
+
+Identical indexes
+
+*** ProbeSetXRef
+
+Tux01 has less indexes than P2(!):
+
+: MariaDB [db_webqtl]> show indexes from ProbeSetXRef ;
+| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment |
+|--------------+------------+------------+--------------+------------------+-----------+-------------+----------+--------+------+------------+---------+---------------|
+| ProbeSetXRef | 0 | ProbeSetId | 1 | ProbeSetFreezeId | A | 885 | NULL | NULL | | BTREE | | |
+| ProbeSetXRef | 0 | ProbeSetId | 2 | ProbeSetId | A | 47713039 | NULL | NULL | | BTREE | | |
+| ProbeSetXRef | 0 | DataId_IDX | 1 | DataId | A | 47713039 | NULL | NULL | | BTREE | | |
+| ProbeSetXRef | 1 | Locus_IDX | 1 | Locus | A | 15904346 | NULL | NULL | YES | BTREE | | |
+: 4 rows in set (0.000 sec)
+
+
+
+: MariaDB [db_webqtl]> show indexes from ProbeSetXRef ;
+| Table | Non_unique | Key_name | Seq_in_index | Column_name | Collation | Cardinality | Sub_part | Packed | Null | Index_type | Comment | Index_comment |
+|--------------+------------+-------------+--------------+------------------+-----------+-------------+----------+--------+------+------------+---------+---------------|
+| ProbeSetXRef | 0 | ProbeSetId | 1 | ProbeSetFreezeId | A | 856 | NULL | NULL | | BTREE | | |
+| ProbeSetXRef | 0 | ProbeSetId | 2 | ProbeSetId | A | 46412145 | NULL | NULL | | BTREE | | |
+| ProbeSetXRef | 0 | DataId_IDX | 1 | DataId | A | 46412145 | NULL | NULL | | BTREE | | |
+| ProbeSetXRef | 1 | ProbeSetId1 | 1 | ProbeSetId | A | 5156905 | NULL | NULL | | BTREE | | |
+| ProbeSetXRef | 1 | Locus | 1 | Locus | A | 23206072 | NULL | NULL | YES | BTREE | | |
+: 5 rows in set (0.00 sec)
+
+** Check storage
+
+The database in Tux01 is mounted on NVME. On Penguin2 it
+is slower SATA with RAID5.
+
+Also on Penguin2 the following tables are using InnoDB instead of
+MyISAM
+
+#+begin_src sh
+-rw-rw---- 1 mysql mysql 79691776 Oct 15 2019 AccessLog.ibd
+-rw-rw---- 1 mysql mysql 196608 Oct 24 2019 Docs.ibd
+-rw-rw---- 1 mysql mysql 63673729024 Jul 10 2020 GenoData.ibd
+-rw-rw---- 1 mysql mysql 34787557376 Jul 9 2020 ProbeData.ibd
+-rw-rw---- 1 mysql mysql 254690721792 Jul 10 2020 ProbeSetData.ibd
+-rw-rw---- 1 mysql mysql 32103202816 Jul 9 2020 SnpAll.ibd
+-rw-rw---- 1 mysql mysql 98304 May 6 2020 TraitMetadata.ibd
+#+end_src
+
+This [[https://www.liquidweb.com/kb/mysql-performance-myisam-vs-innodb/][article]] suggests that myISAM will be faster for our use case.
+
+** Configuration
+
+There was one setting on Tux01 missing on P2
+
+: +innodb_buffer_pool_size=1024M
+
+Running the same query twice (so you can see the warmup after
+a restart of MariaDB)
+
+#+begin_src sh
+penguin2:/etc$ time mysql -u webqtlout -pwebqtlout db_webqtl < ~/chunk.sql > ~/test.out
+real 0m4.253s
+user 0m0.276s
+sys 0m0.040s
+penguin2:/etc$ time mysql -u webqtlout -pwebqtlout db_webqtl < ~/chunk.sql > ~/test.out
+real 0m2.633s
+user 0m0.296s
+sys 0m0.028s
+#+end_src
+
+That is much better :)
diff --git a/doc/docker-container.org b/doc/docker-container.org
index ec91824a..79b8272f 100644
--- a/doc/docker-container.org
+++ b/doc/docker-container.org
@@ -28,17 +28,10 @@ which will be added to a base mariaDB image.
First create the gn2 tar archive by running:
#+begin_src sh
-# For the Python 2 version:
env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
./pre-inst-env guix pack --no-grafts\
-S /gn2-profile=/ \
screen genenetwork2
-
-# For the Python 3 version:
-env GUIX_PACKAGE_PATH="/home/bonface/projects/guix-bioinformatics:/home/bonface/projects/guix-past/modules" \
- ./pre-inst-env guix pack --no-grafts\
- -S /gn2-profile=/ \
- screen python3-genenetwork2
#+end_src
The output will look something similar to:
@@ -59,16 +52,16 @@ RUN tar -xzf /tmp/gn2.tar.gz -C / && rm -f /tmp/gn2.tar.gz && \
Build the image(Note the fullstop at the end):
-: sudo docker build -t python2-genenetwork2:latest -f Dockerfile .
+: sudo docker build -t genenetwork2:latest -f Dockerfile .
To load the image interactively you've just created:
-: docker run -ti "python2-genenetwork2:latest" bash
+: docker run -ti "genenetwork2:latest" bash
Assuming you have a docker instance running, you could always run
commands in it e.g:
-: docker run "python2-genenetwork2:latest" python --version
+: docker run "genenetwork2:latest" python --version
* Pushing to DockerHub
@@ -78,7 +71,7 @@ CI environment using Github Actions.
To push to dockerhub, first get the image name by running =docker
images=. Push to dockerhub using a command similar to:
-: docker push bonfacekilz/python2-genenetwork2:latest
+: docker push bonfacekilz/genenetwork2:latest
Right now, we have 2 images on DockerHub:
diff --git a/doc/guix_profile_setup.org b/doc/guix_profile_setup.org
new file mode 100644
index 00000000..c397377c
--- /dev/null
+++ b/doc/guix_profile_setup.org
@@ -0,0 +1,39 @@
+* Setting up GUIX profile for GN
+
+First create a guix profile with the latest packages:
+
+: ~/opt/guix/bin/guix pull
+
+This will create a profile with the latest packages under`~/.config/guix/current`
+
+Now you have the latest guix. Check: `$HOME/.config/guix/current/bin/guix --version`
+
+At this point, it's worth mentioning that installing
+python3-genenetwork using `$HOME/.config/guix/current/bin/guix` should
+work; but let's use the dev version(since that may come handy in
+time), and it's a nice thing to know.
+
+Next, we ensure that the appropriate GUILE<sub>PATHS</sub> are set:
+
+: export GUILE_LOAD_PATH=$HOME/.config/guix/current/share/guile/site/3.0/
+: export GUILE_LOAD_COMPILED_PATH=$HOME/.config/guix/current/lib/guile/3.0/site-ccache/
+
+Get into the container:
+
+: $HOME/.config/guix/current/bin/guix environment -C guix --ad-hoc bash gcc-toolchain
+: ./bootstrap
+: ./configure --localstatedir=/var --sysconfdir=/etc
+
+Check that everything works:
+
+: make check
+
+Clean up and build:
+
+: make clean-go
+: make -j 4
+: exit
+
+Install Python3 (substitute paths when necessary):
+
+: env GUIX_PACKAGE_PATH='/home/zas1024/guix-bioinformatics:/home/zas1024/guix-past/modules' $HOME/.config/guix/current/bin/guix install python3-genenetwork2 -p ~/opt/python3-genenetwork2 --substitute-urls="http://guix.genenetwork.org https://berlin.guixsd.org https://ci.guix.gnu.org https://mirror.hydra.gnu.org"
diff --git a/doc/heatmap-generation.org b/doc/heatmap-generation.org
new file mode 100644
index 00000000..a697c70b
--- /dev/null
+++ b/doc/heatmap-generation.org
@@ -0,0 +1,34 @@
+#+STARTUP: inlineimages
+#+TITLE: Heatmap Generation
+#+AUTHOR: Muriithi Frederick Muriuki
+
+* Generating Heatmaps
+
+Like a lot of other features, the heatmap generation requires an existing collection. If none exists, see [[][Creating a new collection]] for how to create a new collection.
+
+Once you have a collection, you can navigate to the collections page by clicking on the "Collections" link in the header
+
+
+[[./images/gn2_header_collections.png]]
+
+From that page, pick the collection that you want to work with by clicking on its name on the collections table.
+
+That takes you to that collection's page, where you can select the data that you want to use to generate the heatmap.
+
+** Selecting Orientation
+
+Once you have selected the data, select the orientation of the heatmap you want generated. You do this by selecting either *"vertical"* or *"horizontal"* in the heatmaps form:
+
+[[./images/heatmap_form.png]]
+
+Once you have selected the orientation, click on the "Generate Heatmap" button as in the image above.
+
+The heatmap generation might take a while, but once it is done, an image shows up above the data table.
+
+** Downloading the PNG copy of the Heatmap
+
+Once the heatmap image is shown, hovering over it, displays some tools to interact with the image.
+
+To download, hover over the heatmap image, and click on the "Download plot as png" icon as shown.
+
+[[./images/heatmap_with_hover_tools.png]]
diff --git a/doc/images/gn2_header_collections.png b/doc/images/gn2_header_collections.png
new file mode 100644
index 00000000..ac23f9c1
--- /dev/null
+++ b/doc/images/gn2_header_collections.png
Binary files differ
diff --git a/doc/images/heatmap_form.png b/doc/images/heatmap_form.png
new file mode 100644
index 00000000..163fbb60
--- /dev/null
+++ b/doc/images/heatmap_form.png
Binary files differ
diff --git a/doc/images/heatmap_with_hover_tools.png b/doc/images/heatmap_with_hover_tools.png
new file mode 100644
index 00000000..4ab79f99
--- /dev/null
+++ b/doc/images/heatmap_with_hover_tools.png
Binary files differ
diff --git a/doc/rpy2-performance.org b/doc/rpy2-performance.org
new file mode 100644
index 00000000..8f917ca0
--- /dev/null
+++ b/doc/rpy2-performance.org
@@ -0,0 +1,182 @@
+* Python-Rpy2 performance issues with genenetwork2
+
+At one point, genenetwork2 was down. A possible cause was that it
+wrote into the log file in an infinite loop due to rpy2(v3.4.4), so a
+solution was to empty it. Currently, as a work around, rpy2 is
+disabled by removing it's imports. This affects WGCNA/ CTL imports and
+commenting out Biweight Midcorrelation option in the trait page. See:
+
+- [[https://github.com/genenetwork/genenetwork2/commit/1baf5f7611909c651483208184c5fbf7d4a7a088][1baf5f7]]
+- [[https://github.com/genenetwork/genenetwork2/commit/afee4d625248565857df98d3510f680ae6204864][afee4d6]]
+- [[https://github.com/genenetwork/genenetwork2/commit/c458bf0ad731e5e5fd9cbd0686936b3a441bae63][c458bf0]]
+- [[https://github.com/genenetwork/genenetwork2/commit/d31f3f763471b19559ca74e73b52b3cb5e7153ce][d31f3f7]]
+
+** Reproducing the problem
+
+I went back to commit #b8408cea. With regards to logs, I never
+experienced any log issue. Perhaps it's because of how I start my
+server:
+
+: env SERVER_PORT=5004 TMPDIR=/home/bonface/tmp WEBSERVER_MODE=DEBUG LOG_LEVEL=DEBUG GENENETWORK_FILES=/home/bonface/data/genotype_files/ GN2_PROFILE=/home/bonface/opt/python3-genenetwork2 ./scripts/run_debug.sh
+
+However, when loading the homepage, I occasionally ran into this trace:
+
+#+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
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: In addition:
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: Warning messages:
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: 1:
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, :
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]:
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: library '/home/bonface/R/x86_64-unknown-linux-gnu-library/4.0' contains no packages
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: 2:
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: In (function (package, help, pos = 2, lib.loc = NULL, character.only = FALSE, :
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]:
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: library '/home/bonface/R/x86_64-unknown-linux-gnu-library/4.0' contains no packages
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: Fatal error: unable to initialize the JIT
+
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]:
+ *** caught segfault ***
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: address (nil), cause 'memory not mapped'
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]:
+Possible actions:
+1: abort (with core dump, if enabled)
+2: normal R exit
+3: exit R without saving workspace
+4: exit R saving workspace
+
+Selection:
+
+#+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:
+
+#+begin_src python
+@app.route("/test")
+ def test():
+ from rpy2 import robjects as ro
+ from rpy2 import rinterface
+ from threading import Thread
+
+ def rpy2_init_simple():
+ rinterface.initr_simple()
+
+ thread = Thread(target=rpy2_init_simple)
+ thread.start()
+ return "This is a test after importing rpy2"
+#+end_src
+
+which generates this trace:
+
+#+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.
+ Consider (re)setting the signal handler of your choice from
+ the main thread.
+warnings.warn(
+DEBUG:wqflask.views:.shutdown_session: remove db_session
+
+#+end_src
+
+Modifying the endpoint to:
+
+#+begin_src python
+@app.route("/test")
+ def test():
+ import wqflask.correlation.show_corr_results
+ import wqflask.ctl.ctl_analysis
+ import time
+ from wqflask.correlation.correlation_functions import cal_zero_order_corr_for_tiss
+
+ print("Sleeping for 3 seconds")
+ time.sleep(3)
+ return "This is a test after importing rpy2"
+#+end_src
+
+and refreshing the page a couple of times, I get:
+
+#+begin_src
+DEBUG:wqflask.views:.check_access_permissions: @app.before_request check_access_
+permissions
+Sleeping for 3 seconds
+DEBUG:wqflask.views:.shutdown_session: remove db_session
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: Error: ignoring SIGPI
+PE signal
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: In addition:
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: Warning messages:
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: 1:
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: In (function (package
+, help, pos = 2, lib.loc = NULL, character.only = FALSE, :
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]:
+
+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]: 2:
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: In (function (package
+, help, pos = 2, lib.loc = NULL, character.only = FALSE, :
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]:
+
+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 ***
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]: address (nil), cause
+'memory not mapped'
+
+WARNING:rpy2.rinterface_lib.callbacks:R[write to console]:
+Possible actions:
+1: abort (with core dump, if enabled)
+2: normal R exit
+3: exit R without saving workspace
+4: exit R saving workspace
+
+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_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:
+
+#+begin_src python
+"""Load test a single trait page"""
+from locust import HttpUser, task, between
+
+
+ class LoadTest(HttpUser):
+ wait_time = between(1, 2.5)
+
+ @task
+ def fetch_trait(self):
+ """Fetch a single trait"""
+ self.client.get("/test")
+#+end_src
+
+
+** A possible solution
+
+From this [[https://github.com/rpy2/rpy2/issues/809#issuecomment-845923975][comment]], a possible reason for the above traces, is that
+from Flask's end, a [[https://tldp.org/LDP/lpg/node20.html][SIGPIPE]] is somehow generated by our Python
+code. However, at this particular point, the R thread just happens to
+be running, and R can't handle this correctly. This seems to have been
+fixed in this [[https://github.com/rpy2/rpy2/pull/810][PR]] with a this [[https://github.com/rpy2/rpy2/issues/809#issuecomment-851618215][explanation]]. On our end, to have these
+changes, we have to update our python-rpy2 version.
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-24 11:19:42 +0000