bash script for creating multiple files using forloop

Question

I am brand new at bash script. I want to write a script using forloop which will give me the following line and execute also these lines.

gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 1000 -e 10000 -skip 10 -o 1.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 2000 -e 20000 -skip 10 -o 2.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 3000 -e 30000 -skip 10 -o 3.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 4000 -e 40000 -skip 10 -o 4.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 5000 -e 50000 -skip 10 -o 5.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 6000 -e 60000 -skip 10 -o 6.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 7000 -e 70000 -skip 10 -o 7.out

....

Your question ins't really clear. Do you want a different script to execute each command and call that from within another script? Please clarify. — Difster
– Difster, Commented Jul 3, 2017 at 19:59
I want the script that will create the that command and execute that command — parash
– parash, Commented Jul 3, 2017 at 21:33

Mark Setchell · Accepted Answer · 2017-07-03 21:22:50Z

4

You can also save a couple of lines of typing and get them all done in parallel with GNU Parallel:

parallel gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b {}000 -e {}0000 -skip 10 -o {}.out ::: {1..7}

Use parallel --dry-run if you want to see what it would do but without actually doing anything.

answered Jul 3, 2017 at 21:22

Mark Setchell

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4 Comments

Mark Setchell Over a year ago

@DavidC.Rankin You know it makes sense - especially as CPUs continue to get wider (more cores) rather than taller (more GHz).... :-)

Ulysse BN Over a year ago

Very nice command! parallel isn't shipped with Ubuntu though

Ole Tange Over a year ago

@DavidC.Rankin May I suggest spending an hour on man parallel_tutorial?

David C. Rankin Over a year ago

Yes, will do. I can see it being beneficial in large builds for those packages that can be built in parallel (peripheral packages, etc.)

David C. Rankin · Accepted Answer · 2017-07-03 20:19:11Z

1

You can use a C-style loop as well, e.g.

for ((i = 1; i < 8; i++)); do
    echo "gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b $((i * 1000)) -e $((i * 10000)) -skip 10 -o $i.out"
done

Example Use/Output

$ for ((i = 1; i < 8; i++)); do
>     echo "gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b $((i * 1000)) -e $((i * 10000)) -skip 10 -o $i.out"
> done
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 1000 -e 10000 -skip 10 -o 1.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 2000 -e 20000 -skip 10 -o 2.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 3000 -e 30000 -skip 10 -o 3.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 4000 -e 40000 -skip 10 -o 4.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 5000 -e 50000 -skip 10 -o 5.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 6000 -e 60000 -skip 10 -o 6.out
gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b 7000 -e 70000 -skip 10 -o 7.out

answered Jul 3, 2017 at 20:19

David C. Rankin

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2 Comments

parash Over a year ago

Dear Sir, it gives me the Syntax error: Bad for loop variable

David C. Rankin Over a year ago

Hmm, are you using i somewhere else as a variable? That's the only thing I can think of. Obviously i is not a Bad for loop variable... Make sure you have no typo. (you can just copy/paste the code right into an xterm to run it -- it works -- no error... (make sure you copy the top code without the > (those are just terminal line continuation marks (actually your PS3 prompt) that the terminal outputs when entering multi-line input)

Ulysse BN · Accepted Answer · 2017-07-06 22:26:52Z

1

Using a basic bash for loop:

for i in {1..7}; do
  gmx trjconv -f md_0_1.xtc -s md_0_1.tpr -b ${i}000 -e ${i}0000 -skip 10 -o $i.out
done

edited Jul 6, 2017 at 22:26

answered Jul 3, 2017 at 20:01

Ulysse BN

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3 Comments

David C. Rankin Over a year ago

You need to multiply your -b and -e values by $i. (e.g. -b $((i * 1000)))

Ulysse BN Over a year ago

I didn't see that, thanks @DavidC.Rankin. You don't have to multiply though, ${i}000 does the trick :)

David C. Rankin Over a year ago

Sure, that's another creative way to solve the problem. I'll give you a vote on that one :)

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