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amazon web services - how to clear Bus error (core dumped) on aws ec2 ubuntu s3 cli

I'm using aws ec2 ubuntu and have ssh connection.

All commands entered from ssh connection to s3 produces the error:

Bus error (core dumped)

Originally, I was trying to do a copy from mybucket to the server:

aws s3 cp s3://mybucket ./

but the result was the error. Even an ls command produces the error. I don't know how to fix this.

A few days ago, I expanded the system using these instructions for ebs volume.

The df -h command produces this:

Filesystem Size Used Avail Use% Mounted on
/dev/root 31G 13G 19G 40% /
devtmpfs 16G 0 16G 0% /dev
tmpfs 16G 8.0K 16G 1% /dev/shm
tmpfs 3.2G 940K 3.2G 1% /run
tmpfs 5.0M 0 5.0M 0% /run/lock
tmpfs 16G 0 16G 0% /sys/fs/cgroup
/dev/loop0 33M 33M 0 100% /snap/amazon-ssm-agent/2996
/dev/loop2 98M 98M 0 100% /snap/core/10577
/dev/loop3 98M 98M 0 100% /snap/core/10583
/dev/loop1 34M 34M 0 100% /snap/amazon-ssm-agent/3552
/dev/loop4 56M 56M 0 100% /snap/core18/1885
/dev/loop6 56M 56M 0 100% /snap/core18/1944
/dev/loop7 68M 68M 0 100% /snap/lxd/18150
tmpfs 3.2G 0 3.2G 0% /run/user/1000
tmpfs 10M 10M 0 100% /tmp
/dev/loop8 70M 70M 0 100% /snap/lxd/19032

and lsblk command produces this:

NAME    MAJ:MIN RM  SIZE RO TYPE MOUNTPOINT
loop0     7:0    0 32.3M  1 loop /snap/amazon-ssm-agent/2996
loop1     7:1    0 33.3M  1 loop /snap/amazon-ssm-agent/3552
loop2     7:2    0 97.9M  1 loop /snap/core/10577
loop3     7:3    0 97.9M  1 loop /snap/core/10583
loop4     7:4    0 55.3M  1 loop /snap/core18/1885
loop6     7:6    0 55.4M  1 loop /snap/core18/1944
loop7     7:7    0 67.8M  1 loop /snap/lxd/18150
loop8     7:8    0 69.8M  1 loop /snap/lxd/19032
xvda    202:0    0   32G  0 disk
└─xvda1 202:1    0   32G  0 part /

Today, work was proceeding as normal until I entered the command:

grep -vf MergedSamplesEdited.vcf ../resources/plink.GRCh37.autosome.map

The system Killed the process. I was then able do a few more grep / awk commands, including the one I should have done instead of the grep line above:

gawk -F$'' 'FNR == NR {a[$6]; next;} {if ($4 in a) {print $0 } }' oldfile.ibd ../resources/plink.GRCh37.autosome.map > newfile.ibd

Needing to copy files from s3 bucket, I tried the aws s3 command above and got the bus error.

I searched for a solution and found responses with the bus error, but those responses seemed highly specific and did not apply to my situation. For example, Git add . Gives me Bus error (core dumped).

Your help would be greatly appreciated.


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