Description
Hello,
I am a PhD student attempting to train a 2D model to segment Purkinje cells using the u-net Fiji plugin. I am running this on a Mac mini OS with an M1 chip, so I am running the CPU only code (because there is no NIVIDIA graphics card) and am using the Ubuntu 18.04 AMI and g4dn instance type. I am very new to this and am having difficulty getting past two errors: after about 8% into fine-tuning, the terminal displays client_loop: send disconnect: broken pipe; soon after the u-net job manager will send an SFTP Failure 4 and abort the job. I am not having issues connecting to my instance, so I think it might be an issue with my bashrc file.
This is the code I have been using to connect and set up my instance:
Ssh -i /Users/neuroanatomy/Desktop/LD_key.pem [email protected]
wget https://lmb.informatik.uni-freiburg.de/resources/opensource/unet/caffe_unet_package_18.04_cpu.tar.gz
tar xfvz caffe_unet_package_18.04_cpu.tar.gz
rm -rf u-net
mv caffe_unet_package_18.04_cpu u-net
echo "export PATH=$PATH:/home/ubuntu/u-net/bin" | cat - ~/.bashrc > tmp
echo "export LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/home/ubuntu/u-net/lib:/home/ubuntu/u-net/extlib" | cat - tmp > ~/.bashrc
I have been sourcing the bashrc file in the bash profile:
But I think my issue is that the bashrc file may not ensure that no output to standard output is being generated in non-interactive mode. I have been running into this issue when running the instance with the bashrc file as is, so I tried to edit it to address this problem, but am still running into the same issue:
Any insight into this issue will be greatly appreciated.
Thank you!