# How to start the PBS Job script in the directory that it was submitted from **URL:** \ **Category:** Users/Site Administrators\ **Created:** [January 23, 2020, 12:17am UTC](https://community.openpbs.org/t/how-to-start-the-pbs-job-script-in-the-directory-that-it-was-submitted-from/1967 "2020-01-23T00:17:38Z")\ **Posts on this page:** 7\ **Page:** 1
**Author:** ![jon](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.openpbs.org/jon/32/23_2.png) [@jon](https://community.openpbs.org/u/jon)\ **Post date:** [January 23, 2020, 12:17am UTC](https://community.openpbs.org/t/how-to-start-the-pbs-job-script-in-the-directory-that-it-was-submitted-from/1967/1 "2020-01-23T00:17:38Z")
I would like to submit a job from an application that calls its own program like qsub -q workq -l select=2:ncpus=1,place=scatter:excl – -i file.in option2 option3 The application fails since it can’t find the file. I could put the full path to the file.in but I don’t want to hard code the path since I would like to submit from various directories and I don’t want all of the stdout and stderr files in my home dir. I also tried to add this line in my ~/.bash\_profile if [! -z ${PBS\_O\_WORKDIR}]; then cd $PBS\_O\_WORKDIR;fi This works if I run the job interactively but not in batch. Is there a submission flag I can use when submitting my job to start it in the right directory or is there a way that I can get it to load my ~/.bash\_profile before the script is launched. ---
**Author:** ![adarsh](https://avatars.discourse-cdn.com/v4/letter/a/f07891/32.png) [@adarsh](https://community.openpbs.org/u/adarsh)\ **Post date:** [January 23, 2020, 10:55pm UTC](https://community.openpbs.org/t/how-to-start-the-pbs-job-script-in-the-directory-that-it-was-submitted-from/1967/2 "2020-01-23T22:55:56Z")
> [@jon](#): > > I also tried to add this line in my ~/.bash\_profile > > if [! -z ${PBS\_O\_WORKDIR}]; then cd $PBS\_O\_WORKDIR;fi I have not tested this , but just checking Would adding above line to /etc/profile.d/pbs\_work\_dir.sh would work ? ---
**Author:** ![jon](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.openpbs.org/jon/32/23_2.png) [@jon](https://community.openpbs.org/u/jon)\ **Post date:** [January 24, 2020, 2:03am UTC](https://community.openpbs.org/t/how-to-start-the-pbs-job-script-in-the-directory-that-it-was-submitted-from/1967/3 "2020-01-24T02:03:06Z")
Looks like I found my answer in the user guide ;( Does anyone know the non easy way or is the answer to write a hook for this? **2.3.4 Submitting Jobs by Specifying Executable on Command Line** You can run a PBS job by specifying an executable and its arguments instead of a job script. When you run qsub this way, it runs the executable directly. It does not start a shell, so no shell initialization scripts are run, and execution paths and other environment variables are not set. **There is not an easy way to run your command in a different directory.** You should make sure that environment variables are set correctly, and you will usually have to specify the full path to the command. To submit a job directly, you specify the executable on the command line: For example, to run myprog with the arguments a and b: To run myprog with the arguments a and b, naming the job JobA, To use environment variables you define earlier: _qsub [] – []_ **qsub – myprog a b qsub -N JobA – myprog a b** **export INFILE=/tmp/myinfile export INDATA=/tmp/mydata qsub – a.out $INFILE $INDATA** ---
**Author:** ![jon](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.openpbs.org/jon/32/23_2.png) [@jon](https://community.openpbs.org/u/jon)\ **Post date:** [January 24, 2020, 4:06am UTC](https://community.openpbs.org/t/how-to-start-the-pbs-job-script-in-the-directory-that-it-was-submitted-from/1967/4 "2020-01-24T04:06:12Z")
Well I found a solution I think. I wrote a wrapper script for bash called pbs\_bash that contains the following #!/bin/bash # Get the aliases and functions if [-f ~/.bashrc]; then . ~/.bashrc fi if [! -z ${PBS\_O\_WORKDIR}]; then cd $PBS\_O\_WORKDIR;fi “$@” I then do qsub – /full/path/to/pbs\_bash program arg1 arg2 … and it seems to work as expected. I would be nice to have an option in PBS to start the job in the current working directory. ---
**Author:** ![arwild01](https://avatars.discourse-cdn.com/v4/letter/a/8c91f0/32.png) [@arwild01](https://community.openpbs.org/u/arwild01)\ **Post date:** [January 24, 2020, 6:19am UTC](https://community.openpbs.org/t/how-to-start-the-pbs-job-script-in-the-directory-that-it-was-submitted-from/1967/5 "2020-01-24T06:19:46Z")
I wish PBSPro would steal an idea from torque. Torque’s qsub had a flag (-d) which would set the variable PBS\_O\_INITDIR. If -d wasn’t passed PBS\_O\_INITDIR defaulted to the user’s home directory. Torque would always chdir() to $PBS\_O\_INITDIR immediately prior to invoking the jobscript. This was true for both interactive and batch jobs, If PBSPro’s qsub had such an option you could have done: qsub … -d $PWD – program arg1 arg2 ---
**Author:** ![dtalcott](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.openpbs.org/dtalcott/32/410_2.png) [@dtalcott](https://community.openpbs.org/u/dtalcott)\ **Post date:** [January 28, 2020, 9:29pm UTC](https://community.openpbs.org/t/how-to-start-the-pbs-job-script-in-the-directory-that-it-was-submitted-from/1967/6 "2020-01-28T21:29:37Z")
Minor bug, but the last line should be `"$@"` rather than just `$@` Otherwise, any command line arguments with spaces or other special characters will get broken up. ---
**Author:** ![jon](https://yyz2.discourse-cdn.com/flex030/user_avatar/community.openpbs.org/jon/32/23_2.png) [@jon](https://community.openpbs.org/u/jon)\ **Post date:** [February 6, 2020, 6:06pm UTC](https://community.openpbs.org/t/how-to-start-the-pbs-job-script-in-the-directory-that-it-was-submitted-from/1967/7 "2020-02-06T18:06:40Z")
Thanks for the pointer @dtalcott. I have made the update.