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.
