Skip to content

Instantly share code, notes, and snippets.

@dsjoerg

dsjoerg/gist:9abc670bb0ef946a6c13192ab4af1294

Created April 24, 2020 01:56
Show Gist options
  • Star 0 You must be signed in to star a gist
  • Fork 0 You must be signed in to fork a gist
  • Save dsjoerg/9abc670bb0ef946a6c13192ab4af1294 to your computer and use it in GitHub Desktop.
Save dsjoerg/9abc670bb0ef946a6c13192ab4af1294 to your computer and use it in GitHub Desktop.
Download ZIP
Raw
gistfile1.txt
Last login: Fri Apr 24 01:06:37 2020 from 74.115.76.145
__| __|_ )
_| ( / Amazon Linux 2 AMI
___|\___|___|
https://aws.amazon.com/amazon-linux-2/
No packages needed for security; 4 packages available
Run "sudo yum update" to apply all updates.
[ec2-user@ip-172-31-6-36 ~]$ sudo yum update -y
Loaded plugins: extras_suggestions, langpacks, priorities, update-motd
Resolving Dependencies
--> Running transaction check
---> Package freetype.x86_64 0:2.4.11-15.amzn2.0.2 will be updated
---> Package freetype.x86_64 0:2.8-14.amzn2 will be an update
--> Processing Dependency: libpng15.so.15(PNG15_0)(64bit) for package: freetype-2.8-14.amzn2.x86_64
--> Processing Dependency: libpng15.so.15()(64bit) for package: freetype-2.8-14.amzn2.x86_64
---> Package gdisk.x86_64 0:0.8.6-5.amzn2.0.2 will be updated
---> Package gdisk.x86_64 0:0.8.10-3.amzn2 will be an update
---> Package glib2.x86_64 0:2.56.1-4.amzn2 will be updated
---> Package glib2.x86_64 0:2.56.1-5.amzn2.0.1 will be an update
---> Package libdrm.x86_64 0:2.4.83-2.amzn2.0.2 will be updated
---> Package libdrm.x86_64 0:2.4.97-2.amzn2 will be an update
--> Running transaction check
---> Package libpng.x86_64 2:1.5.13-7.amzn2.0.2 will be installed
--> Finished Dependency Resolution
Dependencies Resolved
==========================================================================
Package Arch Version Repository Size
==========================================================================
Updating:
freetype x86_64 2.8-14.amzn2 amzn2-core 373 k
gdisk x86_64 0.8.10-3.amzn2 amzn2-core 187 k
glib2 x86_64 2.56.1-5.amzn2.0.1 amzn2-core 2.4 M
libdrm x86_64 2.4.97-2.amzn2 amzn2-core 150 k
Installing for dependencies:
libpng x86_64 2:1.5.13-7.amzn2.0.2 amzn2-core 214 k
Transaction Summary
==========================================================================
Install ( 1 Dependent package)
Upgrade 4 Packages
Total download size: 3.3 M
Downloading packages:
Delta RPMs disabled because /usr/bin/applydeltarpm not installed.
(1/5): gdisk-0.8.10-3.amzn2.x86_64.rpm | 187 kB 00:00
(2/5): freetype-2.8-14.amzn2.x86_64.rpm | 373 kB 00:00
(3/5): libdrm-2.4.97-2.amzn2.x86_64.rpm | 150 kB 00:00
(4/5): libpng-1.5.13-7.amzn2.0.2.x86_64.rpm | 214 kB 00:00
(5/5): glib2-2.56.1-5.amzn2.0.1.x86_64.rpm | 2.4 MB 00:00
--------------------------------------------------------------------------
Total 19 MB/s | 3.3 MB 00:00
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
Installing : 2:libpng-1.5.13-7.amzn2.0.2.x86_64 1/9
Updating : freetype-2.8-14.amzn2.x86_64 2/9
Updating : gdisk-0.8.10-3.amzn2.x86_64 3/9
Updating : glib2-2.56.1-5.amzn2.0.1.x86_64 4/9
Updating : libdrm-2.4.97-2.amzn2.x86_64 5/9
Cleanup : freetype-2.4.11-15.amzn2.0.2.x86_64 6/9
Cleanup : gdisk-0.8.6-5.amzn2.0.2.x86_64 7/9
Cleanup : glib2-2.56.1-4.amzn2.x86_64 8/9
Cleanup : libdrm-2.4.83-2.amzn2.0.2.x86_64 9/9
Verifying : libdrm-2.4.97-2.amzn2.x86_64 1/9
Verifying : 2:libpng-1.5.13-7.amzn2.0.2.x86_64 2/9
Verifying : glib2-2.56.1-5.amzn2.0.1.x86_64 3/9
Verifying : gdisk-0.8.10-3.amzn2.x86_64 4/9
Verifying : freetype-2.8-14.amzn2.x86_64 5/9
Verifying : gdisk-0.8.6-5.amzn2.0.2.x86_64 6/9
Verifying : glib2-2.56.1-4.amzn2.x86_64 7/9
Verifying : freetype-2.4.11-15.amzn2.0.2.x86_64 8/9
Verifying : libdrm-2.4.83-2.amzn2.0.2.x86_64 9/9
Dependency Installed:
libpng.x86_64 2:1.5.13-7.amzn2.0.2
Updated:
freetype.x86_64 0:2.8-14.amzn2 gdisk.x86_64 0:0.8.10-3.amzn2
glib2.x86_64 0:2.56.1-5.amzn2.0.1 libdrm.x86_64 0:2.4.97-2.amzn2
Complete!
[ec2-user@ip-172-31-6-36 ~]$ sudo amazon-linux-extras install docker
NOTE: The livepatch extra is in public preview, not meant for production use
Installing docker
Loaded plugins: extras_suggestions, langpacks, priorities, update-motd
Cleaning repos: amzn2-core amzn2extra-docker
12 metadata files removed
4 sqlite files removed
0 metadata files removed
Loaded plugins: extras_suggestions, langpacks, priorities, update-motd
amzn2-core | 2.4 kB 00:00
amzn2extra-docker | 1.8 kB 00:00
(1/5): amzn2-core/2/x86_64/group_gz | 2.5 kB 00:00
(2/5): amzn2-core/2/x86_64/updateinfo | 203 kB 00:00
(3/5): amzn2extra-docker/2/x86_64/updateinfo | 69 B 00:00
(4/5): amzn2extra-docker/2/x86_64/primary_db | 65 kB 00:00
(5/5): amzn2-core/2/x86_64/primary_db | 40 MB 00:00
Resolving Dependencies
--> Running transaction check
---> Package docker.x86_64 0:19.03.6ce-2.amzn2 will be installed
--> Processing Dependency: runc >= 1.0.0 for package: docker-19.03.6ce-2.amzn2.x86_64
--> Processing Dependency: containerd >= 1.3.2 for package: docker-19.03.6ce-2.amzn2.x86_64
--> Processing Dependency: pigz for package: docker-19.03.6ce-2.amzn2.x86_64
--> Processing Dependency: libcgroup for package: docker-19.03.6ce-2.amzn2.x86_64
--> Running transaction check
---> Package containerd.x86_64 0:1.3.2-1.amzn2 will be installed
---> Package libcgroup.x86_64 0:0.41-21.amzn2 will be installed
---> Package pigz.x86_64 0:2.3.4-1.amzn2.0.1 will be installed
---> Package runc.x86_64 0:1.0.0-0.1.20200204.gitdc9208a.amzn2 will be installed
--> Finished Dependency Resolution
Dependencies Resolved
==========================================================================
Package Arch Version Repository Size
==========================================================================
Installing:
docker x86_64 19.03.6ce-2.amzn2 amzn2extra-docker 37 M
Installing for dependencies:
containerd x86_64 1.3.2-1.amzn2 amzn2extra-docker 24 M
libcgroup x86_64 0.41-21.amzn2 amzn2-core 66 k
pigz x86_64 2.3.4-1.amzn2.0.1 amzn2-core 81 k
runc x86_64 1.0.0-0.1.20200204.gitdc9208a.amzn2
amzn2extra-docker 2.6 M
Transaction Summary
==========================================================================
Install 1 Package (+4 Dependent packages)
Total download size: 65 M
Installed size: 271 M
Is this ok [y/d/N]: y
Downloading packages:
(1/5): libcgroup-0.41-21.amzn2.x86_64.rpm | 66 kB 00:00
(2/5): pigz-2.3.4-1.amzn2.0.1.x86_64.rpm | 81 kB 00:00
(3/5): containerd-1.3.2-1.amzn2.x86_64.rpm | 24 MB 00:00
(4/5): docker-19.03.6ce-2.amzn2.x86_64.rpm | 37 MB 00:00
(5/5): runc-1.0.0-0.1.20200204.gitdc9208a.amzn2.x86_ | 2.6 MB 00:00
--------------------------------------------------------------------------
Total 105 MB/s | 65 MB 00:00
Running transaction check
Running transaction test
Transaction test succeeded
Running transaction
Installing : runc-1.0.0-0.1.20200204.gitdc9208a.amzn2.x86_64 1/5
Installing : containerd-1.3.2-1.amzn2.x86_64 2/5
Installing : libcgroup-0.41-21.amzn2.x86_64 3/5
Installing : pigz-2.3.4-1.amzn2.0.1.x86_64 4/5
Installing : docker-19.03.6ce-2.amzn2.x86_64 5/5
Verifying : containerd-1.3.2-1.amzn2.x86_64 1/5
Verifying : docker-19.03.6ce-2.amzn2.x86_64 2/5
Verifying : pigz-2.3.4-1.amzn2.0.1.x86_64 3/5
Verifying : runc-1.0.0-0.1.20200204.gitdc9208a.amzn2.x86_64 4/5
Verifying : libcgroup-0.41-21.amzn2.x86_64 5/5
Installed:
docker.x86_64 0:19.03.6ce-2.amzn2
Dependency Installed:
containerd.x86_64 0:1.3.2-1.amzn2
libcgroup.x86_64 0:0.41-21.amzn2
pigz.x86_64 0:2.3.4-1.amzn2.0.1
runc.x86_64 0:1.0.0-0.1.20200204.gitdc9208a.amzn2
Complete!
NOTE: The livepatch extra is in public preview, not meant for production use
0 ansible2 available \
[ =2.4.2 =2.4.6 =2.8 =stable ]
2 httpd_modules available [ =1.0 =stable ]
3 memcached1.5 available \
[ =1.5.1 =1.5.16 =1.5.17 ]
5 postgresql9.6 available \
[ =9.6.6 =9.6.8 =stable ]
6 postgresql10 available [ =10 =stable ]
8 redis4.0 available \
[ =4.0.5 =4.0.10 =stable ]
9 R3.4 available [ =3.4.3 =stable ]
10 rust1 available \
[ =1.22.1 =1.26.0 =1.26.1 =1.27.2 =1.31.0 =1.38.0
=stable ]
11 vim available [ =8.0 =stable ]
13 ruby2.4 available \
[ =2.4.2 =2.4.4 =2.4.7 =stable ]
15 php7.2 available \
[ =7.2.0 =7.2.4 =7.2.5 =7.2.8 =7.2.11 =7.2.13 =7.2.14
=7.2.16 =7.2.17 =7.2.19 =7.2.21 =7.2.22 =7.2.23
=7.2.24 =7.2.26 =stable ]
17 lamp-mariadb10.2-php7.2 available \
[ =10.2.10_7.2.0 =10.2.10_7.2.4 =10.2.10_7.2.5
=10.2.10_7.2.8 =10.2.10_7.2.11 =10.2.10_7.2.13
=10.2.10_7.2.14 =10.2.10_7.2.16 =10.2.10_7.2.17
=10.2.10_7.2.19 =10.2.10_7.2.22 =10.2.10_7.2.23
=10.2.10_7.2.24 =stable ]
18 libreoffice available \
[ =5.0.6.2_15 =5.3.6.1 =stable ]
19 gimp available [ =2.8.22 ]
20 docker=latest enabled \
[ =17.12.1 =18.03.1 =18.06.1 =18.09.9 =stable ]
21 mate-desktop1.x available \
[ =1.19.0 =1.20.0 =stable ]
22 GraphicsMagick1.3 available \
[ =1.3.29 =1.3.32 =1.3.34 =stable ]
23 tomcat8.5 available \
[ =8.5.31 =8.5.32 =8.5.38 =8.5.40 =8.5.42 =8.5.50
=stable ]
24 epel available [ =7.11 =stable ]
25 testing available [ =1.0 =stable ]
26 ecs available [ =stable ]
27 corretto8 available \
[ =1.8.0_192 =1.8.0_202 =1.8.0_212 =1.8.0_222 =1.8.0_232
=1.8.0_242 =stable ]
28 firecracker available [ =0.11 =stable ]
29 golang1.11 available \
[ =1.11.3 =1.11.11 =1.11.13 =stable ]
30 squid4 available [ =4 =stable ]
31 php7.3 available \
[ =7.3.2 =7.3.3 =7.3.4 =7.3.6 =7.3.8 =7.3.9 =7.3.10
=7.3.11 =7.3.13 =stable ]
32 lustre2.10 available \
[ =2.10.5 =2.10.8 =stable ]
33 java-openjdk11 available [ =11 =stable ]
34 lynis available [ =stable ]
35 kernel-ng available [ =stable ]
36 BCC available [ =0.x =stable ]
37 mono available [ =5.x =stable ]
38 nginx1 available [ =stable ]
39 ruby2.6 available [ =2.6 =stable ]
40 mock available [ =stable ]
41 postgresql11 available [ =11 =stable ]
42 php7.4 available [ =stable ]
43 livepatch available [ =stable ]
[ec2-user@ip-172-31-6-36 ~]$ sudo service docker start
Redirecting to /bin/systemctl start docker.service
[ec2-user@ip-172-31-6-36 ~]$ sudo usermod -a -G docker ec2-user
[ec2-user@ip-172-31-6-36 ~]$ exit
logout
Connection to ec2-3-135-184-60.us-east-2.compute.amazonaws.com closed.
Fubars-MacBook-Pro:~ david$ !!
ssh -i ~/Dropbox/Daves_Docs/volunteering/COVID19/davidjoerg.pem ec2-user@ec2-3-135-184-60.us-east-2.compute.amazonaws.com
Last login: Fri Apr 24 01:06:58 2020 from 74.115.76.145
__| __|_ )
_| ( / Amazon Linux 2 AMI
___|\___|___|
https://aws.amazon.com/amazon-linux-2/
[ec2-user@ip-172-31-6-36 ~]$ docker info
Client:
Debug Mode: false
Server:
Containers: 0
Running: 0
Paused: 0
Stopped: 0
Images: 0
Server Version: 19.03.6-ce
Storage Driver: overlay2
Backing Filesystem: xfs
Supports d_type: true
Native Overlay Diff: true
Logging Driver: json-file
Cgroup Driver: cgroupfs
Plugins:
Volume: local
Network: bridge host ipvlan macvlan null overlay
Log: awslogs fluentd gcplogs gelf journald json-file local logentries splunk syslog
Swarm: inactive
Runtimes: runc
Default Runtime: runc
Init Binary: docker-init
containerd version: ff48f57fc83a8c44cf4ad5d672424a98ba37ded6
runc version: dc9208a3303feef5b3839f4323d9beb36df0a9dd
init version: fec3683
Security Options:
seccomp
Profile: default
Kernel Version: 4.14.173-137.229.amzn2.x86_64
Operating System: Amazon Linux 2
OSType: linux
Architecture: x86_64
CPUs: 2
Total Memory: 7.788GiB
Name: ip-172-31-6-36.us-east-2.compute.internal
ID: M7I2:4DXE:QU2B:X2WR:I54H:NBGU:SQYQ:YDSI:F6CW:IFT5:UYFY:Z7YD
Docker Root Dir: /var/lib/docker
Debug Mode: false
Registry: https://index.docker.io/v1/
Labels:
Experimental: false
Insecure Registries:
127.0.0.0/8
Live Restore Enabled: false
[ec2-user@ip-172-31-6-36 ~]$ docker run --rm -v $(pwd)/results:/var/model/results -v $(pwd)/figures:/var/model/figures harrisonzhu5080/covid19model:latest
Unable to find image 'harrisonzhu5080/covid19model:latest' locally
latest: Pulling from harrisonzhu5080/covid19model
1fcd5305bc72: Pull complete
d6dc70a850d4: Pull complete
8a97d6b476eb: Pull complete
b41b9c1207e0: Pull complete
507f4afa8390: Pull complete
69f93bb85877: Pull complete
db0e2f52d4b7: Pull complete
203e8bbc1654: Pull complete
7eb4bd7d335d: Pull complete
dbe93df6f9bd: Pull complete
248b63dc5e98: Pull complete
4bf524fb92f9: Pull complete
b333eb2ca80b: Pull complete
f17d18aee6bf: Pull complete
604bbbb7607f: Pull complete
b8165964f70f: Pull complete
90fb9781f462: Pull complete
ebe261b1136e: Pull complete
f62227e82bbe: Pull complete
f69771266bbf: Pull complete
089dc2b27abc: Pull complete
57ed4b066140: Pull complete
d4582926f815: Pull complete
Digest: sha256:fd0fd7ebc6e921b04f5efbec90420c1268c45803f90561b7fa72f5d5286614e0
Status: Downloaded newer image for harrisonzhu5080/covid19model:latest
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.19.3, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Attaching package: ‘lubridate’
The following objects are masked from ‘package:data.table’:
hour, isoweek, mday, minute, month, quarter, second, wday, week,
yday, year
The following objects are masked from ‘package:base’:
date, intersect, setdiff, union
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: ‘gdata’
The following objects are masked from ‘package:data.table’:
first, last
The following object is masked from ‘package:stats’:
nobs
The following object is masked from ‘package:utils’:
object.size
The following object is masked from ‘package:base’:
startsWith
Attaching package: ‘dplyr’
The following objects are masked from ‘package:gdata’:
combine, first, last
The following objects are masked from ‘package:lubridate’:
intersect, setdiff, union
The following objects are masked from ‘package:data.table’:
between, first, last
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Attaching package: ‘tidyr’
The following object is masked from ‘package:rstan’:
extract
Attaching package: ‘EnvStats’
The following objects are masked from ‘package:stats’:
predict, predict.lm
The following object is masked from ‘package:base’:
print.default
[1] "Running base"
[1] "First non-zero cases is on day 59, and 30 days before 10 deaths is day 53"
[1] "Denmark has 50 days of data"
[1] "First non-zero cases is on day 32, and 30 days before 10 deaths is day 28"
[1] "Italy has 75 days of data"
[1] "First non-zero cases is on day 29, and 30 days before 10 deaths is day 47"
[1] "Germany has 56 days of data"
[1] "First non-zero cases is on day 33, and 30 days before 10 deaths is day 41"
[1] "Spain has 62 days of data"
[1] "First non-zero cases is on day 32, and 30 days before 10 deaths is day 44"
[1] "United_Kingdom has 59 days of data"
[1] "First non-zero cases is on day 26, and 30 days before 10 deaths is day 39"
[1] "France has 64 days of data"
[1] "First non-zero cases is on day 59, and 30 days before 10 deaths is day 56"
[1] "Norway has 47 days of data"
[1] "First non-zero cases is on day 36, and 30 days before 10 deaths is day 50"
[1] "Belgium has 53 days of data"
[1] "First non-zero cases is on day 58, and 30 days before 10 deaths is day 54"
[1] "Austria has 49 days of data"
[1] "First non-zero cases is on day 33, and 30 days before 10 deaths is day 50"
[1] "Sweden has 53 days of data"
[1] "First non-zero cases is on day 58, and 30 days before 10 deaths is day 46"
[1] "Switzerland has 57 days of data"
[1] "First non-zero cases is on day 59, and 30 days before 10 deaths is day 51"
[1] "Greece has 50 days of data"
[1] "Portugal In padding"
[1] "First non-zero cases is on day 64, and 30 days before 10 deaths is day 53"
[1] "Portugal has 50 days of data"
[1] "First non-zero cases is on day 60, and 30 days before 10 deaths is day 46"
[1] "Netherlands has 57 days of data"
SAMPLING FOR MODEL 'base' NOW (CHAIN 1).
SAMPLING FOR MODEL 'base' NOW (CHAIN 2).
Chain 1:
Chain 1: Gradient evaluation took 0.026592 seconds
Chain 1: 1000 transitions using 10 leapfrog steps per transition would take 265.92 seconds.
Chain 1: Adjust your expectations accordingly!
Chain 1:
Chain 1:
Chain 1: WARNING: There aren't enough warmup iterations to fit the
Chain 1: three stages of adaptation as currently configured.
Chain 1: Reducing each adaptation stage to 15%/75%/10% of
Chain 1: the given number of warmup iterations:
Chain 1: init_buffer = 15
Chain 1: adapt_window = 75
Chain 1: term_buffer = 10
Chain 1:
Chain 2:
Chain 2: Gradient evaluation took 0.02715 seconds
Chain 2: 1000 transitions using 10 leapfrog steps per transition would take 271.5 seconds.
Chain 2: Adjust your expectations accordingly!
Chain 2:
Chain 2:
Chain 2: WARNING: There aren't enough warmup iterations to fit the
Chain 2: three stages of adaptation as currently configured.
Chain 2: Reducing each adaptation stage to 15%/75%/10% of
Chain 2: the given number of warmup iterations:
Chain 2: init_buffer = 15
Chain 2: adapt_window = 75
Chain 2: term_buffer = 10
Chain 2:
Chain 1: Iteration: 1 / 200 [ 0%] (Warmup)
Chain 2: Iteration: 1 / 200 [ 0%] (Warmup)
Chain 2: Iteration: 20 / 200 [ 10%] (Warmup)
Chain 1: Iteration: 20 / 200 [ 10%] (Warmup)
Chain 1: Iteration: 40 / 200 [ 20%] (Warmup)
Chain 2: Iteration: 40 / 200 [ 20%] (Warmup)
Chain 1: Iteration: 60 / 200 [ 30%] (Warmup)
Chain 1: Iteration: 80 / 200 [ 40%] (Warmup)
Chain 2: Iteration: 60 / 200 [ 30%] (Warmup)
Chain 1: Iteration: 100 / 200 [ 50%] (Warmup)
Chain 1: Iteration: 101 / 200 [ 50%] (Sampling)
Chain 2: Iteration: 80 / 200 [ 40%] (Warmup)
Chain 1: Iteration: 120 / 200 [ 60%] (Sampling)
Chain 2: Iteration: 100 / 200 [ 50%] (Warmup)
Chain 2: Iteration: 101 / 200 [ 50%] (Sampling)
Chain 1: Iteration: 140 / 200 [ 70%] (Sampling)
Chain 2: Iteration: 120 / 200 [ 60%] (Sampling)
Chain 2: Iteration: 140 / 200 [ 70%] (Sampling)
Chain 1: Iteration: 160 / 200 [ 80%] (Sampling)
Chain 2: Iteration: 160 / 200 [ 80%] (Sampling)
Chain 1: Iteration: 180 / 200 [ 90%] (Sampling)
Chain 2: Iteration: 180 / 200 [ 90%] (Sampling)
Chain 2: Iteration: 200 / 200 [100%] (Sampling)
Chain 1: Iteration: 200 / 200 [100%] (Sampling)
Chain 2:
Chain 2: Elapsed Time: 349.462 seconds (Warm-up)
Chain 2: 580.743 seconds (Sampling)
Chain 2: 930.205 seconds (Total)
Chain 2:
SAMPLING FOR MODEL 'base' NOW (CHAIN 3).
Chain 3:
Chain 3: Gradient evaluation took 0.02707 seconds
Chain 3: 1000 transitions using 10 leapfrog steps per transition would take 270.7 seconds.
Chain 3: Adjust your expectations accordingly!
Chain 3:
Chain 3:
Chain 3: WARNING: There aren't enough warmup iterations to fit the
Chain 3: three stages of adaptation as currently configured.
Chain 3: Reducing each adaptation stage to 15%/75%/10% of
Chain 3: the given number of warmup iterations:
Chain 3: init_buffer = 15
Chain 3: adapt_window = 75
Chain 3: term_buffer = 10
Chain 3:
Chain 3: Iteration: 1 / 200 [ 0%] (Warmup)
Chain 3: Iteration: 20 / 200 [ 10%] (Warmup)
Chain 1:
Chain 1: Elapsed Time: 164.59 seconds (Warm-up)
Chain 1: 772.119 seconds (Sampling)
Chain 1: 936.709 seconds (Total)
Chain 1:
SAMPLING FOR MODEL 'base' NOW (CHAIN 4).
Chain 4:
Chain 4: Gradient evaluation took 0.027106 seconds
Chain 4: 1000 transitions using 10 leapfrog steps per transition would take 271.06 seconds.
Chain 4: Adjust your expectations accordingly!
Chain 4:
Chain 4:
Chain 4: WARNING: There aren't enough warmup iterations to fit the
Chain 4: three stages of adaptation as currently configured.
Chain 4: Reducing each adaptation stage to 15%/75%/10% of
Chain 4: the given number of warmup iterations:
Chain 4: init_buffer = 15
Chain 4: adapt_window = 75
Chain 4: term_buffer = 10
Chain 4:
Chain 4: Iteration: 1 / 200 [ 0%] (Warmup)
Chain 4: Iteration: 20 / 200 [ 10%] (Warmup)
Chain 4: Iteration: 40 / 200 [ 20%] (Warmup)
Chain 4: Iteration: 60 / 200 [ 30%] (Warmup)
Chain 3: Iteration: 40 / 200 [ 20%] (Warmup)
Chain 4: Iteration: 80 / 200 [ 40%] (Warmup)
Chain 3: Iteration: 60 / 200 [ 30%] (Warmup)
Chain 4: Iteration: 100 / 200 [ 50%] (Warmup)
Chain 4: Iteration: 101 / 200 [ 50%] (Sampling)
Chain 3: Iteration: 80 / 200 [ 40%] (Warmup)
Chain 4: Iteration: 120 / 200 [ 60%] (Sampling)
Chain 3: Iteration: 100 / 200 [ 50%] (Warmup)
Chain 3: Iteration: 101 / 200 [ 50%] (Sampling)
Chain 4: Iteration: 140 / 200 [ 70%] (Sampling)
Chain 3: Iteration: 120 / 200 [ 60%] (Sampling)
Chain 4: Iteration: 160 / 200 [ 80%] (Sampling)
Chain 4: Iteration: 180 / 200 [ 90%] (Sampling)
Chain 3: Iteration: 140 / 200 [ 70%] (Sampling)
Chain 4: Iteration: 200 / 200 [100%] (Sampling)
Chain 4:
Chain 4: Elapsed Time: 280.749 seconds (Warm-up)
Chain 4: 649.495 seconds (Sampling)
Chain 4: 930.245 seconds (Total)
Chain 4:
Chain 3: Iteration: 160 / 200 [ 80%] (Sampling)
Chain 3: Iteration: 180 / 200 [ 90%] (Sampling)
Chain 3: Iteration: 200 / 200 [100%] (Sampling)
Chain 3:
Chain 3: Elapsed Time: 532.443 seconds (Warm-up)
Chain 3: 676.096 seconds (Sampling)
Chain 3: 1208.54 seconds (Total)
Chain 3:
Warning messages:
1: There were 51 transitions after warmup that exceeded the maximum treedepth. Increase max_treedepth above 10. See
http://mc-stan.org/misc/warnings.html#maximum-treedepth-exceeded
2: Examine the pairs() plot to diagnose sampling problems
3: The largest R-hat is 1.23, indicating chains have not mixed.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#r-hat
4: Bulk Effective Samples Size (ESS) is too low, indicating posterior means and medians may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#bulk-ess
5: Tail Effective Samples Size (ESS) is too low, indicating posterior variances and tail quantiles may be unreliable.
Running the chains for more iterations may help. See
http://mc-stan.org/misc/warnings.html#tail-ess
[1] "Jobid = 318697"
This is bayesplot version 1.7.1
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
* Does _not_ affect other ggplot2 plots
* See ?bayesplot_theme_set for details on theme setting
[1] "Generating covariate size effects plot"
Loading required package: magrittr
This is bayesplot version 1.7.1
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
* Does _not_ affect other ggplot2 plots
* See ?bayesplot_theme_set for details on theme setting
********************************************************
Note: As of version 1.0.0, cowplot does not change the
default ggplot2 theme anymore. To recover the previous
behavior, execute:
theme_set(theme_cowplot())
********************************************************
Attaching package: ‘cowplot’
The following object is masked from ‘package:ggpubr’:
get_legend
Warning message:
`prob_outer` (0.9) is less than `prob` (0.95)
... Swapping the values of `prob_outer` and `prob`
Warning message:
`prob_outer` (0.9) is less than `prob` (0.95)
... Swapping the values of `prob_outer` and `prob`
2.5% 97.5%
School Closure -0.01619184 0.8020856
Self Isolation -0.01625460 0.2018133
Public Events -0.01626263 0.2984186
Lockdown 0.52245240 1.6152294
Social distancing -0.01608366 0.3318881
Warning messages:
1: position_dodge requires non-overlapping x intervals
2: position_dodge requires non-overlapping x intervals
Warning messages:
1: position_dodge requires non-overlapping x intervals
2: position_dodge requires non-overlapping x intervals
Warning messages:
1: position_dodge requires non-overlapping x intervals
2: position_dodge requires non-overlapping x intervals
Warning messages:
1: position_dodge requires non-overlapping x intervals
2: position_dodge requires non-overlapping x intervals
[1] "Generate 3-panel plots"
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: StanHeaders
Loading required package: ggplot2
rstan (Version 2.19.3, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Attaching package: ‘rstan’
The following object is masked from ‘package:tidyr’:
extract
Attaching package: ‘data.table’
The following objects are masked from ‘package:dplyr’:
between, first, last
Attaching package: ‘lubridate’
The following objects are masked from ‘package:data.table’:
hour, isoweek, mday, minute, month, quarter, second, wday, week,
yday, year
The following objects are masked from ‘package:dplyr’:
intersect, setdiff, union
The following objects are masked from ‘package:base’:
date, intersect, setdiff, union
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: ‘gdata’
The following objects are masked from ‘package:data.table’:
first, last
The following objects are masked from ‘package:dplyr’:
combine, first, last
The following object is masked from ‘package:stats’:
nobs
The following object is masked from ‘package:utils’:
object.size
The following object is masked from ‘package:base’:
startsWith
Attaching package: ‘EnvStats’
The following objects are masked from ‘package:stats’:
predict, predict.lm
The following object is masked from ‘package:base’:
print.default
Attaching package: ‘matrixStats’
The following object is masked from ‘package:EnvStats’:
iqr
The following object is masked from ‘package:dplyr’:
count
Attaching package: ‘gridExtra’
The following object is masked from ‘package:gdata’:
combine
The following object is masked from ‘package:dplyr’:
combine
Loading required package: magrittr
Attaching package: ‘magrittr’
The following object is masked from ‘package:rstan’:
extract
The following object is masked from ‘package:tidyr’:
extract
This is bayesplot version 1.7.1
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
* Does _not_ affect other ggplot2 plots
* See ?bayesplot_theme_set for details on theme setting
********************************************************
Note: As of version 1.0.0, cowplot does not change the
default ggplot2 theme anymore. To recover the previous
behavior, execute:
theme_set(theme_cowplot())
********************************************************
Attaching package: ‘cowplot’
The following object is masked from ‘package:ggpubr’:
get_legend
The following object is masked from ‘package:lubridate’:
stamp
[1] "loading: results/base-318697-stanfit.Rdata"
[1] 1
[1] 2
[1] 3
[1] 4
[1] 5
[1] 6
[1] 7
[1] 8
[1] 9
[1] 10
[1] 11
[1] 12
[1] 13
[1] 14
Warning messages:
1: Removed 2 rows containing missing values (geom_segment).
2: Removed 2 rows containing missing values (geom_point).
3: Removed 2 rows containing missing values (geom_segment).
4: Removed 2 rows containing missing values (geom_point).
5: Removed 2 rows containing missing values (geom_segment).
6: Removed 2 rows containing missing values (geom_point).
7: Removed 2 rows containing missing values (geom_segment).
8: Removed 2 rows containing missing values (geom_point).
9: Removed 2 rows containing missing values (geom_segment).
10: Removed 2 rows containing missing values (geom_point).
[1] "Generate forecast plot"
Attaching package: ‘dplyr’
The following objects are masked from ‘package:stats’:
filter, lag
The following objects are masked from ‘package:base’:
intersect, setdiff, setequal, union
Loading required package: StanHeaders
rstan (Version 2.19.3, GitRev: 2e1f913d3ca3)
For execution on a local, multicore CPU with excess RAM we recommend calling
options(mc.cores = parallel::detectCores()).
To avoid recompilation of unchanged Stan programs, we recommend calling
rstan_options(auto_write = TRUE)
Attaching package: ‘rstan’
The following object is masked from ‘package:tidyr’:
extract
Attaching package: ‘data.table’
The following objects are masked from ‘package:dplyr’:
between, first, last
Attaching package: ‘lubridate’
The following objects are masked from ‘package:data.table’:
hour, isoweek, mday, minute, month, quarter, second, wday, week,
yday, year
The following objects are masked from ‘package:dplyr’:
intersect, setdiff, union
The following objects are masked from ‘package:base’:
date, intersect, setdiff, union
gdata: read.xls support for 'XLS' (Excel 97-2004) files ENABLED.
gdata: Unable to load perl libaries needed by read.xls()
gdata: to support 'XLSX' (Excel 2007+) files.
gdata: Run the function 'installXLSXsupport()'
gdata: to automatically download and install the perl
gdata: libaries needed to support Excel XLS and XLSX formats.
Attaching package: ‘gdata’
The following objects are masked from ‘package:data.table’:
first, last
The following objects are masked from ‘package:dplyr’:
combine, first, last
The following object is masked from ‘package:stats’:
nobs
The following object is masked from ‘package:utils’:
object.size
The following object is masked from ‘package:base’:
startsWith
Attaching package: ‘EnvStats’
The following objects are masked from ‘package:stats’:
predict, predict.lm
The following object is masked from ‘package:base’:
print.default
Attaching package: ‘matrixStats’
The following object is masked from ‘package:EnvStats’:
iqr
The following object is masked from ‘package:dplyr’:
count
Attaching package: ‘gridExtra’
The following object is masked from ‘package:gdata’:
combine
The following object is masked from ‘package:dplyr’:
combine
Loading required package: magrittr
Attaching package: ‘magrittr’
The following object is masked from ‘package:rstan’:
extract
The following object is masked from ‘package:tidyr’:
extract
This is bayesplot version 1.7.1
- Online documentation and vignettes at mc-stan.org/bayesplot
- bayesplot theme set to bayesplot::theme_default()
* Does _not_ affect other ggplot2 plots
* See ?bayesplot_theme_set for details on theme setting
********************************************************
Note: As of version 1.0.0, cowplot does not change the
default ggplot2 theme anymore. To recover the previous
behavior, execute:
theme_set(theme_cowplot())
********************************************************
Attaching package: ‘cowplot’
The following object is masked from ‘package:ggpubr’:
get_legend
The following object is masked from ‘package:lubridate’:
stamp
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
Saving 10 x 7 in image
There were 50 or more warnings (use warnings() to see the first 50)
[1] "Make forecast table"
[1] "Running results/base-318697-stanfit.Rdata"
Error in `$<-.data.frame`(`*tmp*`, value, value = character(0)) :
replacement has 0 rows, data has 14
Calls: $<- -> $<-.data.frame
Execution halted
Error: Generation of alpha covar table failed! Code: 1
Execution halted
[ec2-user@ip-172-31-6-36 ~]$ docker run --rm -v $(pwd)/results:/var/model/results -v $(pwd)/figures:/var/model/figures harrisonzhu5080/covid19model:latest
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment