Windows file
Text files on Microsoft Windows and Linux (Hoffman2 cluster) use different end of line characters. While Linux uses \n, Windows uses \n\r. This may cause issues if the job script file is edited on a “naive” editor (such as “notepad”) on Windows and then transferred directly to Hoffman2 Cluster. A carefully configured text editor (such as VS Code) on Windows can avoid such situation.
Symptoms: a strange “bad interpreter” error message when the file appears to be ok.
Consider the file windows.sh. The file looks normal using the cat command:
$ cat windows.sh
#!/bin/bash
#$ -cwd
#$ -N windows
#$ -l h_rt=1:00:00,h_data=2G
But the “Windows” characters (^M) are visible if the -v option is added to the cat command:
$ cat -v windows.sh
#!/bin/bash^M
^M
#$ -cwd^M
#$ -N windows^M
#$ -l h_rt=1:00:00,h_data=2G^M
^M
The problem is easily fixed by running the utility program dos2unix on the file windows.sh:
dos2unix windows.sh
The ^M characters are now gone:
$ cat -v windows.sh
#!/bin/bash
#$ -cwd
#$ -N windows
#$ -l h_rt=1:00:00,h_data=2G