I would like to set a job to run daily in the root crontab. But I would like it to execute it from a particular directory so it can find all the files it needs, since the application has a bunch of relative paths.
Anyway, can I tell crontab to run from a particular directory?
All jobs are executed by a shell, so start that shell snippet by a command to change the directory.
cd /path/to/directory && ./bin/myapp
Concerning the use of && instead of ;: normally it doesn't make a difference, but if the cd command fails (e.g. because the directory doesn't exist) with && the application isn't executed, whereas with ; it's executed (but not in the intended directory).
Reading man 5 crontab should tell you that there's a HOME variable set which can be redefined in the file. It becomes your working directory. You can set PATH for the command(s) too. Of course this affects all the cron schedule lines.
E.G.
Several environment variables are set up automatically by the cron(8)
daemon. SHELL is set to /bin/sh, and LOGNAME and HOME are set from
the /etc/passwd line of the crontab´s owner. HOME and SHELL can be
overridden by settings in the crontab; LOGNAME can not.
(Note: the LOGNAME variable is sometimes called USER on BSD systems
and is also automatically set).
Depending on your cron of course, but mine also has MAILTO, MAILFROM CONTENT_TYPE, CRON_TZ, RANDOM_DELAY, and MLS_LEVEL.
So for your hypothetical app I'd recommend a file name /etc/cron.d/hypothetical containing:
# Runs hypothetical app # 00:01Z in its local path for reading its config or something.
SHELL=/bin/sh
HOME=/where/the/app/is
PATH=/where/the/app/is:/bin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin
CRON_TZ=UTC
1 0 * * * theappuser hypothetical --with arguments
For example with docker-compose relying on the cwd docker-compose.yml:
SHELL=/bin/sh
HOME=/path/to/composed-app
5 5 * * * root docker-compose restart -t 10 service-name
Related
I'm using a wp-cli tool in order to optimize images:
$ wp image-optimize batch --limit=20
I've installed wpcli using composer so it's in an unusual location, but is in my $PATH:
/home/user/.config/composer/vendor/wp-cli/wp-cli/bin/wp
This works great. I'd like to run this command nightly. I've tried two different approaches to this. First, I tried running the command as a cronjob (set every minute for testing):
$ crontab -e
* * * * * cd /path/to/example.com && wp image-optimize batch --limit=20
I got no response. I wondered if the problem had something to do with passing arguments in a cronjob. So, I created a bash script nightly-image-optimize (also in path) hoping that this might get around it:
#!/bin/bash
echo "begin" >> /home/user/cronlog.log
cd /path/to/example.com
sh /home/user/.config/composer/vendor/wp-cli/wp-cli/bin/wp image-optimize batch --limit=2
echo "end" >> /home/user/cronlog.log
I then modified the cronjob to execute this file every minute as my username since cron runs as root:
* * * * * username /usr/local/bin/nightly-image-optimize
I know the cronjob is running because my cronlog.log file is created and is populated every minute with the echo begin and end statements above.
While in context this is a wp-cli problem, I don't believe that the issue has anything to do with wp-cli. I think I'm misunderstanding how to essentially 'tell' bash to run a process as if I had manually entered it in (maybe something to do with the interactivity of wp-cli?).
Any ideas?
Note:
I'm on AWS running Ubuntu 18.04.3 as a non-root user with sudo privileges
I have a shell script where I am calling the hana.scr script from within the main script. The hana.scr contains the below code.
chmod 777 /data/auto/SLT.out; rm -rf /data/auto/SLT.out; hdbsql -n plhesappr61 -i 00 -u USR -p $#^F#$GGG -o /data/auto/SLT.out "Select sum("ERPACC_RPPCLNT200"."VABD"."NETWR") FROM "ACC_CLNT"."VFKH" inner join "ACC_CLNT"."VNRO" on ("ACC_CLNT"."VNRO"."VBELN"="ACC_CLNT"."VFKH"."VBELN") where FKART in ('ZFP1','ZFP3') and FKDAT = (select ADD_DAYS (TO_DATE (current_date, 'YYYY-MM-DD'), -1) "add_days" from dummy) group by FKDAT";
When I run the main script manually, it calls this script fine and the SLT.out file is also generated.
But when I schedule it in cron, the main script executes just fine, except for this hana.scr which does not seem to execute because it does not does not even remove the old file as per the second command rm in the hana.scr.
The cron is the same user as the one I run the script manually with.
I read that if the cron does not get the same environment to run, these issues happen. I tried to import the UNIX profile of the user before executing as the hana.scr as well, but was not successful.
Below is the cron command which runs the main script which calls the hana.scr from within: Used absolute paths..
37 0,2,3,4,5,6 * * * /data/esb/auto/./main.sh R > /data/esb/auto/main.log
The hana.scr is executed in the below manner:
./hana.scr;
check6=$? ;
if [ $check6 = "1" ]
then
echo "***********HANA counts were not generated**********"
fi
After /data/esb/auto/./main.sh your current directory is not changed to /data/esb/auto/. I think you started main.sh from the commandline while your $PWD was the same as where hana.scr was.
Test it from the commandline with
cd /
/data/esb/auto/main.sh
How to fix?
The worst solution is changing the crontab line into
37 0,2,3,4,5,6 * * * cd /data/esb/auto; /data/esb/auto/main.sh R > /data/esb/auto/main.log
That is a workaround for the crontab but main.sh still fails when started from a different directory.
Slightly better is using the complete path in main.sh when you call hana.scr
myscriptdir=/data/esb/auto
..
${myscriptdir}/hana.scr
When you change the folders you need to edit the files and repair the settings.
You can try to use some config file with settings or let main.sh figure out what in which directory it is:
Getting the source directory of a Bash script from within
In an Amazon EC2 terminal, I type: `sudo nano crontab -e' to bring up the editor. I have the following (empty line at the end included):
#reboot echo "Running RMV scrape & R Shiny via: nano crontab -e"
#reboot nohup python /home/ec2-user/RMV/RMV_scrape.py &
#reboot nohup shiny-server &
#reboot service start httpd
#hourly cp -f /home/ec2-user/RMV/wait_times.csv /var/shiny-server/www/wait_times.csv
Here, I'm trying to run (a) my program, (b) apache, (c) R Shiny server and (d) a script that runs hourly to copy a file.
For some reason, this fails to run. pgrep chron does show chron runs upon startup. It shouldn't be a permissions issue because I ran crontab using sudo. I had one relative pathname in my .py script but I changed it to an absolute pathname.
I've consulted:
https://askubuntu.com/questions/23009/reasons-why-crontab-does-not-work
http://www.unix.com/answers-to-frequently-asked-questions/13527-cron-crontab.html
Any ideas why this may not be working?
I think your problems is with the command you used to edit the crontab sudo nano crontab -e does not edit the crontab you made a file named crontab in whatever directory you were working in, but crontab files are in /var and are not intended to be edited directly. For any given user crontab -e will edit the crontab using the editor specified in the environment variable EDITOR. So to edit root's crontab the command is sudo crontab -e.
That said adding entries to root's crontab is probably not what you want. You probably want to use the system crontab for some thing like this. In almost all cases the system crontab is /etc/crontab which can be edited using sudo nano /etc/crontab. Note that for the system crontab you need to add the user of the command between the time and command sections. e.g.
#reboot root echo "Running RMV scrape & R Shiny via: nano crontab -e"
Also note that crontab uses a very minimal PATH environment variable for security reasons. If a command you issue is not on the path it will not execute. Remember to either add the paths you need to the crontab PATH (specified in the particular crontab file) or use the full path to a given executable from the (filesystem) root directory.
I have RStudio server installed on a remote aws server (ubuntu) and want to run several projects at the same time (one of which takes lots of time to finish). On Windows there is a simple GUI solution like 'Open Project in New Window'. Is there something similar for rstudio server?
Simple question, but failed to find a solution except this related question for Macs, which offers
Run multiple rstudio sessions using projects
but how?
While running batch scripts is certainly a good option, it's not the only solution. Sometimes you may still want interactive use in different sessions rather than having to do everything as batch scripts.
Nothing stops you from running multiple instances of RStudio server on your Ubuntu server on different ports. (I find this particularly easy to do by launching RStudio through docker, as outlined here. Because an instance will keep running even when you close the browser window, you can easily launch several instances and switch between them. You'll just have to login again when you switch.
Unfortunately, RStudio-server still prevents you having multiple instances open in the browser at the same time (see the help forum). This is not a big issue as you just have to log in again, but you can work around it by using different browsers.
EDIT: Multiple instances are fine, as long as they are not on the same browser, same browser-user AND on the same IP address. e.g. a session on 127.0.0.1 and another on 0.0.0.0 would be fine. More importantly, the instances keep on running even if they are not 'open', so this really isn't a problem. The only thing to note about this is you would have to log back in to access the instance.
As for projects, you'll see you can switch between projects using the 'projects' button on the top right, but while this will preserve your other sessions I do not think the it actually supports simultaneous code execution. You need multiple instances of the R environment running to actually do that.
UPDATE 2020 Okay, it's now 2020 and there's lots of ways to do this.
For running scripts or functions in a new R environment, check out:
the callr package
The RStudio jobs panel
Run new R sessions or scripts from one or more terminal sessions in the RStudio terminal panel
Log out and log in to the RStudio-server as a different user (requires multiple users to be set up in the container, obviously not a good workflow for a single user but just noting that many different users can access the same RStudio server instance no problem.
Of course, spinning up multiple docker sessions on different ports is still a good option as well. Note that many of the ways listed above still do not allow you to restart the main R session, which prevents you from reloading installed packages, switching between projects, etc, which is clearly not ideal. I think it would be fantastic if switching between projects in an RStudio (server) session would allow jobs in the previously active project to keep running in the background, but have no idea if that's in the cards for the open source version.
Often you don't need several instances of Rstudio - in this case just save your code in .R file and launch it using ubuntu command prompt (maybe using screen)
Rscript script.R
That will launch a separate R session which will do the work without freezing your Rstudio. You can pass arguments too, for example
# script.R -
args <- commandArgs(trailingOnly = TRUE)
if (length(args) == 0) {
start = '2015-08-01'
} else {
start = args[1]
}
console -
Rscript script.R 2015-11-01
I think you need R Studio Server Pro to be able to log in with multiple users/sessions.
You can see the comparison table below for reference.
https://www.rstudio.com/products/rstudio-server-pro/
Installing another instance of rstudio server is less than ideal.
Linux server admins, fear not. You just need root access or a kind admin.
Create a group to use: groupadd Rwarrior
Create an additional user with same home directory as your primary Rstudio login:
useradd -d /home/user1 user2
Add primary and new user into Rwarrior group:
gpasswd -a user2 Rwarrior
gpasswd -a user1 Rwarrior
Take care of the permissions for your primary home directory:
cd /home
chown -R user1:Rwarrior /home/user1
chmod -R 770 /home/user1
chmod g+s /home/user1
Set password for the new user:
passwd user2
Open a new browser window in incognito/private browsing mode and login to Rstudio with the new user you created. Enjoy.
I run multiple RStudio servers by isolating them in Singularity instances. Download the Singularity image with the command singularity pull shub://nickjer/singularity-rstudio
I use two scripts:
run-rserver.sh:
Find a free port
#!/bin/env bash
set -ue
thisdir="$(dirname "${BASH_SOURCE[0]}")"
# Return 0 if the port $1 is free, else return 1
is_port_free(){
port="$1"
set +e
netstat -an |
grep --color=none "^tcp.*LISTEN\s*$" | \
awk '{gsub("^.*:","",$4);print $4}' | \
grep -q "^$port\$"
r="$?"
set -e
if [ "$r" = 0 ]; then return 1; else return 0; fi
}
# Find a free port
find_free_port(){
local lower_port="$1"
local upper_port="$2"
for ((port=lower_port; port <= upper_port; port++)); do
if is_port_free "$port"; then r=free; else r=used; fi
if [ "$r" = "used" -a "$port" = "$upper_port" ]; then
echo "Ports $lower_port to $upper_port are all in use" >&2
exit 1
fi
if [ "$r" = "free" ]; then break; fi
done
echo $port
}
port=$(find_free_port 8080 8200)
echo "Access RStudio Server on http://localhost:$port" >&2
"$thisdir/cexec" \
rserver \
--www-address 127.0.0.1 \
--www-port $port
cexec:
Create a dedicated config directory for each instance
Create a dedicated temporary directory for each instance
Use the singularity instance mechanism to avoid that forked R sessions are adopted by PID 1 and stay around after the rserver has shut down. Instead, they become children of the Singularity instance and are killed when that shuts down.
Map the current directory to the directory /data inside the container and set that as home folder (this step might not be nessecary if you don't care about reproducible paths on every machine)
#!/usr/bin/env bash
# Execute a command in the container
set -ue
if [ "${1-}" = "--help" ]; then
echo <<EOF
Usage: cexec command [args...]
Execute `command` in the container. This script starts the Singularity
container and executes the given command therein. The project root is mapped
to the folder `/data` inside the container. Moreover, a temporary directory
is provided at `/tmp` that is removed after the end of the script.
EOF
exit 0
fi
thisdir="$(dirname "${BASH_SOURCE[0]}")"
container="rserver_200403.sif"
# Create a temporary directory
tmpdir="$(mktemp -d -t cexec-XXXXXXXX)"
# We delete this directory afterwards, so its important that $tmpdir
# really has the path to an empty, temporary dir, and nothing else!
# (for example empty string or home dir)
if [[ ! "$tmpdir" || ! -d "$tmpdir" ]]; then
echo "Error: Could not create temp dir $tmpdir"
exit 1
fi
# check if temp dir is empty (this might be superfluous, see
# https://codereview.stackexchange.com/questions/238439)
tmpcontent="$(ls -A "$tmpdir")"
if [ ! -z "$tmpcontent" ]; then
echo "Error: Temp dir '$tmpdir' is not empty"
exit 1
fi
# Start Singularity instance
instancename="$(basename "$tmpdir")"
# Maybe also superfluous (like above)
rundir="$(readlink -f "$thisdir/.run/$instancename")"
if [ -e "$rundir" ]; then
echo "Error: Runtime directory '$rundir' exists already!" >&2
exit 1
fi
mkdir -p "$rundir"
singularity instance start \
--contain \
-W "$tmpdir" \
-H "$thisdir:/data" \
-B "$rundir:/data/.rstudio" \
-B "$thisdir/.rstudio/monitored/user-settings:/data/.rstudio/monitored/user-settings" \
"$container" \
"$instancename"
# Delete the temporary directory after the end of the script
trap "singularity instance stop '$instancename'; rm -rf '$tmpdir'; rm -rf '$rundir'" EXIT
singularity exec \
--pwd "/data" \
"instance://$instancename" \
"$#"
I'm quite new to cron and crontab.
I've edited the crontab file and I need to execute manually one of commands so I can try it and test it beforehand. How do I do that? If it fails, is there a mode that shows the errors?
Write a shell script that you can test.
Execute that shell script from the crontab.
Remember that cron provides barely any environment - so your script may have to fix that. In particular, your profile will not be used.
Do not get fancy with what you put in the crontab.
Build a debug mode into your shell script.
No, there isn't specifically a mode that shows errors. Usually, if the cron job witters, the output is emailed to you. That is, it sends standard output and standard error information to you if the executed command writes anything to either standard output or standard error.
On MacOS X (10.6.7), the environment I got was (via a crontab entry like 12 37 17 5 * env >/tmp/cron.env):
SHELL=/bin/sh
USER=jleffler
PATH=/usr/bin:/bin
PWD=/Users/jleffler
SHLVL=1
HOME=/Users/jleffler
LOGNAME=jleffler
_=/usr/bin/env
Of those, PWD, _ and SHLVL are handled by the shell. So, to test your script reliably in a cron-like environment, use:
(cd $HOME
env -i \
SHELL=/bin/sh \
USER=$USER \
PATH=/usr/bin:/bin \
HOME=$HOME \
LOGNAME=$LOGNAME \
/path/to/script/you/execute ...
)
The -i option to env means 'ignore all inherited enviroment'; the script will see exactly the five values specified plus anything the shell specifies automatically. With no arguments, env reports on the environment; with arguments, it adjusts the environment and executes a command.
To execute a script "manually" you first have to make it executable by doing:
$ chmod +x yourScriptName
Then do either
$ ./yourScriptName
if you execute it from its path or
$ /full/path/to/yourScriptName
from anywhere.