# Interactive app -Desktop : can not find command

**URL:** <https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111>\
**Category:** Get Help\
**Tags:** ondemand2, question\
**Created:** [June 10, 2022, 8:56am UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111 "2022-06-10T08:56:42Z")\
**Posts on this page:** 12\
**Page:** 1

<div class="post-metadata">

**Author:** ![SullivanJia](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/sullivanjia/32/1117_2.png) [@SullivanJia](https://discourse.openondemand.org/u/SullivanJia)\
**Post date:** [June 10, 2022, 8:56am UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/1 "2022-06-10T08:56:42Z")

</div>

After I submitted a desktop app to slurm by ood webportal , I got a error in output.log file:

```auto
/var/spool/slurmd/job00019/slurm_script: line 130: hostname: command not found
Setting VNC password...
/var/spool/slurmd/job00019/slurm_script: line 121: head: command not found
/var/spool/slurmd/job00019/slurm_script: line 121: head: command not found
Starting VNC server...
/var/spool/slurmd/job00019/slurm_script: line 165: seq: command not found
Cleaning up...
/var/spool/slurmd/job00019/slurm_script: line 26: awk: command not found
/usr/bin/env: perl: No such file or directory
/var/spool/slurmd/job00019/slurm_script: line 30: pkill: command not found

```

And when I try to ensure env by modifying template file , I could not find the template file under “/var/www/ood/apps/sys” path.  
So what should I do to solve this problem?

---

<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [June 10, 2022, 12:55pm UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/2 "2022-06-10T12:55:37Z")

</div>

There are a couple of different ways to set the environment during a job’s execution.

By default we use `--export=NONE` when we submit jobs. I wonder what the behaviour is for you when you submit jobs with `--export=NONE` from your shell? What is the `PATH` in either case?

One thing I’d ask is if you’re using `srun` or something like that because it’s usually only when we try to issue `srun` command that you see an error like this.

This configuration here will submit all your jobs with `--export=ALL`.

```nohighlight
# /etc/ood/config/clusters.d/my_cluster.yml
---
v2:
  metadata:
    title: "My Cluster"
  login:
    host: "my_cluster.my_center.edu"
  job:
    adapter: "slurm"
    copy_environment: true

```

Or you can try what we do, where we add the export `SLURM_EXPORT_ENV=ALL` in the before script itself.

> <https://github.com/OSC/osc-ood-config/blob/0af5195cd9185ed4104aa651c5cfa71059e66f55/ondemand.osc.edu/apps/bc_desktop/submit/vdi.yml.erb#L7-L15>

---

<div class="post-metadata">

**Author:** ![SullivanJia](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/sullivanjia/32/1117_2.png) [@SullivanJia](https://discourse.openondemand.org/u/SullivanJia)\
**Post date:** [June 10, 2022, 3:08pm UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/3 "2022-06-10T15:08:26Z")

</div>

> [@jeff.ohrstrom](#):
>
> add the export in the before script itself.`SLURM_EXPORT_ENV=ALL`

I had added it before I submitted bc\_desktop job.

```auto
# /etc/ood/config/apps/bc_desktop/submit/slurm-dev-submit.yml.erb
---
batch_connect:
  before_script: |
    # Export the module function if it exists
    [[$(type -t module) == "function"]] && export -f module

    # MATE acts strange in pitzer-exp and doesn't like /var/run/$(id -u)
    export XDG_RUNTIME_DIR="$TMPDIR/xdg_runtime"

    # reset SLURM_EXPORT_ENV so that things like srun & sbatch work out of the box
    export SLURM_EXPORT_ENV=ALL

    # set profile
    source /etc/profile

script:
  native:
    - "-N"
    - "<%= bc_num_slots.blank? ? 1 : bc_num_slots.to_i %>"

```

* * *

> [@jeff.ohrstrom](#):
>
> This configuration here will submit all your jobs with .`--export=ALL`

and follow this instruction, I updated my cluster configuration

```auto
# /etc/ood/config/clusters.d/my_cluster.yml
---
v2:
  metadata:
    title: "Cluster-DEV"
  login:
    host: "192.168.19.78."
  job:
    adapter: "slurm"
    bin: "/usr/bin/"
    conf: "/etc/slurm/slurm.conf"
    copy_environment: true // updated
  batch_connect:
    copy_environment: true //updated
    basic:
      script_wrapper: |
        module purge
        %s
    vnc:
      script_wrapper: |
        module purge
        source /etc/profile //updated
        source ~/.bash_profile //updated
        export PATH="/usr/local/turbovnc/bin:/opt/TurboVNC/bin"
        export WEBSOCKIFY_CMD="/usr/local/websockify/run"
        %s

```

but got more error when I had tried to submit a bc\_desktop job

```auto
/usr/libexec/grepconf.sh: line 5: grep: command not found
/usr/libexec/grepconf.sh: line 5: grep: command not found
/var/spool/slurmd/job00021/slurm_script: line 131: hostname: command not found
Setting VNC password...
/var/spool/slurmd/job00021/slurm_script: line 122: head: command not found
/var/spool/slurmd/job00021/slurm_script: line 122: head: command not found
Starting VNC server...
/var/spool/slurmd/job00021/slurm_script: line 166: seq: command not found
Cleaning up...
/var/spool/slurmd/job00021/slurm_script: line 27: awk: command not found
/usr/bin/env: perl: No such file or directory
/var/spool/slurmd/job00021/slurm_script: line 31: pkill: command not found

```

* * *

> [@jeff.ohrstrom](#):
>
> I wonder what the behaviour is for you when you submit jobs with from your shell?

Emmm, when I submit a normal shell job, it can be queued ,started,ran and completed successfully.  
I can use hostname/grep/awk and the other commands in nornal shell job.

---

<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [June 10, 2022, 3:27pm UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/4 "2022-06-10T15:27:50Z")

</div>

OK how about this. Are you a csh user with something csh specific in your `~/.profile`?

All our interactive apps use `/bin/bash` as the shell, so if you have something un-bash like in a common file like `~/.profile` (common to both bash and csh) then you could run into some oddities if your environment.

---

<div class="post-metadata">

**Author:** ![SullivanJia](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/sullivanjia/32/1117_2.png) [@SullivanJia](https://discourse.openondemand.org/u/SullivanJia)\
**Post date:** [June 10, 2022, 4:10pm UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/5 "2022-06-10T16:10:36Z")

</div>

> [@jeff.ohrstrom](#):
>
> Are you a csh user with something csh specific in your

No, I am not. I just use bash. and I add printenv command in script\_wrapper

```auto
SLURM_NODELIST=master
SLURM_JOB_NAME=sys/dashboard/sys/bc_desktop/form
XDG_SESSION_ID=c26
SLURMD_NODENAME=master
SLURM_TOPOLOGY_ADDR=master
HOSTNAME=master
SLURM_PRIO_PROCESS=0
SLURM_NODE_ALIASES=(null)
SLURM_EXPORT_ENV=NONE
SHELL=/bin/bash
SLURM_JOB_QOS=normal
HISTSIZE=1000
TMPDIR=/tmp
SLURM_TOPOLOGY_ADDR_PATTERN=node
SLURM_NNODES=1
USER=dev
SLURM_JOBID=29
SLURM_TASKS_PER_NODE=1
PATH=/usr/local/bin:/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/home/dev/.local/bin:/home/dev/bin
MAIL=/var/spool/mail/dev
SLURM_WORKING_CLUSTER=cluster:192.168.19.244:6817:9472:109
SLURM_CONF=/etc/slurm/slurm.conf
SLURM_JOB_ID=29
SLURM_JOB_USER=dev
PWD=/home/dev/ondemand/data/sys/dashboard/batch_connect/sys/bc_desktop/form/output/bf2e442b-969c-4293-ba24-ba6a283df3c2
LANG=en_US.UTF-8
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
SLURM_JOB_UID=1001
LOADEDMODULES=
SLURM_NODEID=0
SLURM_SUBMIT_DIR=/var/www/ood/apps/sys/dashboard
SLURM_TASK_PID=6824
SLURM_CPUS_ON_NODE=1
SLURM_PROCID=0
ENVIRONMENT=BATCH
HISTCONTROL=ignoredups
SLURM_JOB_NODELIST=master
HOME=/home/dev
SHLVL=2
SLURM_LOCALID=0
SLURM_GET_USER_ENV=1
SLURM_JOB_GID=1001
SLURM_JOB_CPUS_PER_NODE=1
SLURM_CLUSTER_NAME=cluster
SLURM_GTIDS=0
SLURM_SUBMIT_HOST=node02
SLURM_JOB_PARTITION=compute1
LOGNAME=dev
SLURM_JOB_NUM_NODES=1
MODULESHOME=/usr/share/Modules
LESSOPEN=||/usr/bin/lesspipe.sh %s
XDG_RUNTIME_DIR=/run/user/1001
BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`
}
_=/bin/printenv

```

Are there any problems?

---

<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [June 10, 2022, 5:31pm UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/6 "2022-06-10T17:31:38Z")

</div>

Let’s remove OOD from the situation because you seem to have a very small/new cluster.

Are you sure everything works as it should from the command line? what happens for something similar to this. Are you able to correctly submit a very simple script (with and without the `--export` flag) that has say `hostname`.

```bash
[johrstrom ~()] cat delme.sh 
#!/bin/bash

hostname
[johrstrom ~()] sbatch delme.sh 
Submitted batch job 19315661
[johrstrom ~()] cat slurm-19315661.out 
o0646.ten.osc.edu
[johrstrom ~()] sbatch --export=NONE delme.sh 
Submitted batch job 19315665
[johrstrom ~()] cat slurm-19315665.out 
o0646.ten.osc.edu

```

Also - `#` are comments in YAML. I don’t know if you added the `//updated` after the fact or what, but it’ll complain about that if you did.

---

<div class="post-metadata">

**Author:** ![SullivanJia](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/sullivanjia/32/1117_2.png) [@SullivanJia](https://discourse.openondemand.org/u/SullivanJia)\
**Post date:** [June 10, 2022, 6:00pm UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/7 "2022-06-10T18:00:25Z")

</div>

> [@jeff.ohrstrom](#):
>
> Are you sure everything works as it should from the command line?

I think I’ m sure .It really works.

```auto
[root@node02 dev]# cat myjob.sh
#!/bin/bash

hostname

ip addr |grep -v inet6 |grep inet |grep eth0

[root@node02 dev]# sbatch myjob.sh
Submitted batch job 33
[root@node02 dev]# cat slurm-33.out
master
    inet 192.168.19.244/24 brd 192.168.19.255 scope global noprefixroute eth0
[root@node02 dev]# sbatch --export=NONE myjob.sh
Submitted batch job 34
[root@node02 dev]# cat slurm-34.out
master
    inet 192.168.19.244/24 brd 192.168.19.255 scope global noprefixroute eth0
[root@node02 dev]# sbatch --export=ALL myjob.sh
Submitted batch job 35
[root@node02 dev]# cat slurm-35.out
master
    inet 192.168.19.244/24 brd 192.168.19.255 scope global noprefixroute eth0
[root@node02 dev]#

```

---

<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [June 10, 2022, 7:19pm UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/8 "2022-06-10T19:19:11Z")

</div>

OK I can see that node02 must be you’re web server and that you’ve submitted from the same node. So that’s all good.

I know I’m stuck on this export thing, but I would like to confirm that when you submit  
`sbatch --export=NONE myjob.sh` you don’t have any SLURM env variables defined that could override this, specifically `SLURM_EXPORT_ENV`.

I’ll keep digging on the slurm side.

---

<div class="post-metadata">

**Author:** ![SullivanJia](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/sullivanjia/32/1117_2.png) [@SullivanJia](https://discourse.openondemand.org/u/SullivanJia)\
**Post date:** [June 11, 2022, 7:29am UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/9 "2022-06-11T07:29:41Z")

</div>

> [@jeff.ohrstrom](#):
>
> SLURM env variables defined that could override this, specifically `SLURM_EXPORT_ENV`.

I think it could not be overrided.I modified myjob.sh and submited again, there are some resaults

```auto
[root@node02 dev]# cat myjob.sh
#!/bin/bash

#hostname

#ip addr |grep -v inet6 |grep inet |grep eth0

printenv

[root@node02 dev]# sbatch --export=NONE myjob.sh
Submitted batch job 39
[root@node02 dev]# sbatch myjob.sh
Submitted batch job 40
[root@node02 dev]# diff slurm-39.out slurm-40.out
3c3
< XDG_SESSION_ID=c30
---
> XDG_SESSION_ID=243
9d8
< SLURM_EXPORT_ENV=NONE
10a10
> TERM=xterm
14a15,16
> SSH_CLIENT=192.168.19.5 44014 22
> SSH_TTY=/dev/pts/0
17c19,20
< SLURM_JOBID=39
---
> LS_COLORS=rs=0:di=01;34:ln=01;36:mh=00:pi=40;33:so=01;35:do=01;35:bd=40;33;01:cd=40;33;01:or=40;31;01:mi=01;05;37;41:su=37;41:sg=30;43:ca=30;41:tw=30;42:ow=34;42:st=37;44:ex=01;32:*.tar=01;31:*.tgz=01;31:*.arc=01;31:*.arj=01;31:*.taz=01;31:*.lha=01;31:*.lz4=01;31:*.lzh=01;31:*.lzma=01;31:*.tlz=01;31:*.txz=01;31:*.tzo=01;31:*.t7z=01;31:*.zip=01;31:*.z=01;31:*.Z=01;31:*.dz=01;31:*.gz=01;31:*.lrz=01;31:*.lz=01;31:*.lzo=01;31:*.xz=01;31:*.bz2=01;31:*.bz=01;31:*.tbz=01;31:*.tbz2=01;31:*.tz=01;31:*.deb=01;31:*.rpm=01;31:*.jar=01;31:*.war=01;31:*.ear=01;31:*.sar=01;31:*.rar=01;31:*.alz=01;31:*.ace=01;31:*.zoo=01;31:*.cpio=01;31:*.7z=01;31:*.rz=01;31:*.cab=01;31:*.jpg=01;35:*.jpeg=01;35:*.gif=01;35:*.bmp=01;35:*.pbm=01;35:*.pgm=01;35:*.ppm=01;35:*.tga=01;35:*.xbm=01;35:*.xpm=01;35:*.tif=01;35:*.tiff=01;35:*.png=01;35:*.svg=01;35:*.svgz=01;35:*.mng=01;35:*.pcx=01;35:*.mov=01;35:*.mpg=01;35:*.mpeg=01;35:*.m2v=01;35:*.mkv=01;35:*.webm=01;35:*.ogm=01;35:*.mp4=01;35:*.m4v=01;35:*.mp4v=01;35:*.vob=01;35:*.qt=01;35:*.nuv=01;35:*.wmv=01;35:*.asf=01;35:*.rm=01;35:*.rmvb=01;35:*.flc=01;35:*.avi=01;35:*.fli=01;35:*.flv=01;35:*.gl=01;35:*.dl=01;35:*.xcf=01;35:*.xwd=01;35:*.yuv=01;35:*.cgm=01;35:*.emf=01;35:*.axv=01;35:*.anx=01;35:*.ogv=01;35:*.ogx=01;35:*.aac=01;36:*.au=01;36:*.flac=01;36:*.mid=01;36:*.midi=01;36:*.mka=01;36:*.mp3=01;36:*.mpc=01;36:*.ogg=01;36:*.ra=01;36:*.wav=01;36:*.axa=01;36:*.oga=01;36:*.spx=01;36:*.xspf=01;36:
> SLURM_JOBID=40
19c22
< PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin
---
> PATH=/home/ruby-3.0.0/bin:/home/node-v14.18.1-linux-x64/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/root/bin
23,24c26,27
< SLURM_JOB_ID=39
< _=/bin/printenv
---
> SLURM_JOB_ID=40
> _=/usr/bin/printenv
33c36
< SLURM_TASK_PID=9728
---
> SLURM_TASK_PID=9749
34a38
> RUBY_HOME=/home/ruby-3.0.0
42d45
< SLURM_GET_USER_ENV=1
50a54
> SSH_CONNECTION=192.168.19.5 44014 192.168.19.250 22
53a58
> DISPLAY=localhost:10.0
54a60
> NODE_HOME=/home/node-v14.18.1-linux-x64

```

and in slurm-39.out which set export=NONE ,I can see that `SLURM_EXPORT_ENV` is None.

```auto
SLURM_NODELIST=master
SLURM_JOB_NAME=myjob.sh
XDG_SESSION_ID=c30
SLURMD_NODENAME=master
SLURM_TOPOLOGY_ADDR=master
HOSTNAME=master
SLURM_PRIO_PROCESS=0
SLURM_NODE_ALIASES=(null)
SLURM_EXPORT_ENV=NONE
SHELL=/bin/bash
SLURM_JOB_QOS=normal
HISTSIZE=1000
TMPDIR=/tmp
SLURM_TOPOLOGY_ADDR_PATTERN=node
SLURM_NNODES=1
USER=root
SLURM_JOBID=39
SLURM_TASKS_PER_NODE=1
PATH=/usr/local/sbin:/usr/local/bin:/sbin:/bin:/usr/sbin:/usr/bin:/root/bin
MAIL=/var/spool/mail/root
SLURM_WORKING_CLUSTER=cluster:192.168.19.244:6817:9472:109
SLURM_CONF=/etc/slurm/slurm.conf
SLURM_JOB_ID=39
_=/bin/printenv
SLURM_JOB_USER=root
PWD=/home/dev
LANG=en_US.UTF-8
MODULEPATH=/usr/share/Modules/modulefiles:/etc/modulefiles
SLURM_JOB_UID=0
LOADEDMODULES=
SLURM_NODEID=0
SLURM_SUBMIT_DIR=/home/dev
SLURM_TASK_PID=9728
SLURM_CPUS_ON_NODE=1
SLURM_PROCID=0
ENVIRONMENT=BATCH
HISTCONTROL=ignoredups
SLURM_JOB_NODELIST=master
HOME=/root
SHLVL=2
SLURM_LOCALID=0
SLURM_GET_USER_ENV=1
SLURM_JOB_GID=0
SLURM_JOB_CPUS_PER_NODE=1
SLURM_CLUSTER_NAME=cluster
SLURM_GTIDS=0
SLURM_SUBMIT_HOST=node02
SLURM_JOB_PARTITION=compute1
LOGNAME=root
SLURM_JOB_ACCOUNT=root
SLURM_JOB_NUM_NODES=1
MODULESHOME=/usr/share/Modules
LESSOPEN=||/usr/bin/lesspipe.sh %s
XDG_RUNTIME_DIR=/run/user/0
BASH_FUNC_module()=() { eval `/usr/bin/modulecmd bash $*`
}

```

---

<div class="post-metadata">

**Author:** ![jeff.ohrstrom](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/jeff.ohrstrom/32/136_2.png) [@jeff.ohrstrom](https://discourse.openondemand.org/u/jeff.ohrstrom)\
**Post date:** [June 13, 2022, 1:52pm UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/10 "2022-06-13T13:52:43Z")

</div>

I mean to check the environment variables of the submitting user’s environment, not the jobs’.

You are testing the CLI parity as root. Can you submit jobs as your non-privileged regular user?

---

<div class="post-metadata">

**Author:** ![SullivanJia](https://sea1.discourse-cdn.com/flex015/user_avatar/discourse.openondemand.org/sullivanjia/32/1117_2.png) [@SullivanJia](https://discourse.openondemand.org/u/SullivanJia)\
**Post date:** [June 14, 2022, 7:39am UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/11 "2022-06-14T07:39:27Z")

</div>

> [@SullivanJia](#):
>
> `export PATH="/usr/local/turbovnc/bin:/opt/TurboVNC/bin"`

It’s my fault. I lost my system `$path`. It should be ` export PATH="/usr/local/turbovnc/bin:/opt/TurboVNC/bin:$PATH"`

---

<div class="post-metadata">

**Author:** ![system](https://us1.discourse-cdn.com/flex015/uploads/osc/original/2X/b/bae70bd0ed39a3ae769c2108155f4cb3e9da8385.png) [@system](https://discourse.openondemand.org/u/system)\
**Post date:** [December 11, 2022, 7:40am UTC](https://discourse.openondemand.org/t/interactive-app-desktop-can-not-find-command/2111/12 "2022-12-11T07:40:15Z")

</div>

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