./create_atomgroup.sh: line 14: /home/center/opt/aarch64/apps/amber/19.0/bin/cpptraj: cannot execute binary file

[passive-radio]

Dear @flat35hd99

I faced an error when running 0structure/create_atomgroups.sh to generate files that are needed at step5 CURP calculation.

terminal says

./create_atomgroup.sh: line 14: /home/center/opt/aarch64/apps/amber/19.0/bin/cpptraj: cannot execute binary file

(the terminal output is long enough to cover a whole screen, so please refer terminal_output.txt attached for more detailed output.) terminal_output.txt

create_atomgroups.sh

#!/bin/sh -xeu
#PJM -L rscgrp=fx-debug
#PJM -L elapse=02:00:00
#PJM --mpi proc=1
#PJM -j

prefix=$PREFIX_7R98

source $prefix/util/load_amber
module load python/3.7.7

cd $prefix/0structure

cpptraj -i input/atominfo.cpptraj # <= line 14

python3 generate_atomgroup_sidechain.py \
    --sidechain-filename output/atomgroup_side.dat \
    --residue-filename output/atomgroup_residue.dat \
    --atominfo-filename output/atominfo.dat

input/atom_info.cpptraj

parm output/system.dry.prmtop
atominfo out output/atominfo.dat
quit

I looked in http://archive.ambermd.org/ and etc.. to find out the solution but failed. I hope that I can go thorough this step.

Thank you

[flat35hd99]

@passive-radio I'm surprised your high motivation ! The create_atomgroup.sh is job file for type 1 node. So, please login type 1 node (I assume that you can do that by ssh f1 on local ) then

cd 0structure/log
pjsub ../create_atomgroup.sh

Why the command failed?

Because the binary is suitable for aarch64, not x86. All login node and calculation node without type 1 has x86. Only calculation node of type 1 has aarch64. If you run source load_amber, then Amber for aarch64 is in PATH. So, the running failed.

[flat35hd99]

Unfortunately, you don't have enough time to get CURP calculation result. The calculation takes 1 or 2 days but the limit does not allow you to do that.

I recommend you to download all your calculation into local. If you don't have disk space, we have. Please let me know.

[passive-radio]

@flat35hd99 Thank you for your response. But I had tried running the scripts on type1 node and the error appeared🤔

Though I wouldn't manage to get the final result, I've learned a lot and I'll be sure to download all the outputs from the calculations.

Thank you!

@passive-radio I'm surprised your high motivation !

The create_atomgroup.sh is job file for type 1 node. So, please login type 1 node (I assume that you can do that by ssh f1 on local ) then

cd 0structure/log

pjsub ../create_atomgroup.sh

Why the command failed?

Because the binary is suitable for aarch64, not x86. All login node and calculation node without type 1 has x86. Only calculation node of type 1 has aarch64. If you run source load_amber, then Amber for aarch64 is in PATH. So, the running failed.

[flat35hd99]

メール見てね！！！ @passive-radio