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April 24, 2020 01:56
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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) | |
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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 | |
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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 | |
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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: | |
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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’ | |
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between, first, last | |
Attaching package: ‘lubridate’ | |
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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 | |
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combine, first, last | |
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nobs | |
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object.size | |
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startsWith | |
Attaching package: ‘EnvStats’ | |
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predict, predict.lm | |
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print.default | |
Attaching package: ‘matrixStats’ | |
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iqr | |
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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" | |
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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 | |
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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 |
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