macOS Big Sur使用Singularity build trinityrna.sif出现no space left on device不能写入问题

接续上篇，安装好虚拟机之后

Singularity is installed in your Vagrant Ubuntu VM! Now you can use Singularity as you would normally by logging into the VM directly

Remember that the VM is running in the background because we started it via the command vagrant up. You can shut the VM down using the command vagrant halt when you no longer need it.

vagrant ssh
Welcome to Ubuntu 18.04.5 LTS (GNU/Linux 4.15.0-55-generic x86_64)

安装现有镜像资源

• 从docker hub安装已有的镜像
  singularity build trinityrna.sif docker://trinityrnaseq/trinityrnaseq
• 从Cloud Library安装已有的镜像
  singularity build ubuntu.sif library://ubuntu
  
  image.png

修改临时文件存储位置到非home目录后依旧报错

export SINGULARITY_LOCALCACHEDIR=/fan_large/
export SINGULARITY_CACHEDIR=/fan_large/
export SINGULARITY_TMPDIR=/fan_large/

INFO:    Creating SIF file...
FATAL:   While performing build: while creating SIF: while creating container: writing data object for SIF file: copying data object file to SIF file: write /home/vagrant/fan_bin/trinityrna.sif: no space left on device

• 此问题是由虚拟机创建时默认磁盘大小是20GB，Trinity比较大，超过20GB，故而不能继续写入

  
  
  image.png

• 尝试解决方案一，增加磁盘容量，编辑Vagrantfile文件

VAGRANT_EXPERIMENTAL="disks"
config.vm.disk :disk, size: "30GB", primary: true

(该方案还是未能解决，添加环境变量方式错误)

• 尝试解决
  方案二参考A
  方案二参考B

@LaBelleVie:16:12:16 ~/VirtualBox VMs/vm-singularity_default_1617687821497_7397
$ VBoxManage clonehd "packer-virtualbox-iso-1606771518-disk001.vmdk" "packer-virtualbox-iso-1606771518-disk001.vdi" --format vdi
0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%
Clone medium created in format 'vdi'. UUID: 9ad0ca94-f812-4165-8e88-95350a929855

$ ll
total 10907296
drwx------  4 lifan  staff   128B  6 Apr 16:23 Logs/
-rw-------  1 lifan  staff   2.7G  6 Apr 16:31 packer-virtualbox-iso-1606771518-disk001.vdi
-rw-------  1 lifan  staff   2.4G  6 Apr 16:23 packer-virtualbox-iso-1606771518-disk001.vmdk
-rw-------  1 lifan  staff   4.6K  6 Apr 16:31 vm-singularity_default_1617687821497_7397.vbox
-rw-------  1 lifan  staff   4.6K  6 Apr 16:28 vm-singularity_default_1617687821497_7397.vbox-prev

#扩容到50GB
$ VBoxManage modifyhd "packer-virtualbox-iso-1606771518-disk001.vdi" --resize 51200
0%...10%...20%...30%...40%...50%...60%...70%...80%...90%...100%

vagrant@vagrant:~/large-bin$ df
'Filesystem                   1K-blocks      Used Available Use% Mounted on
udev                            474132         0    474132   0% /dev
tmpfs                           100912       536    100376   1% /run
/dev/mapper/vagrant--vg-root  19519312   6080388  12424348  33% /
tmpfs                           504544         0    504544   0% /dev/shm
tmpfs                             5120         0      5120   0% /run/lock
tmpfs                           504544         0    504544   0% /sys/fs/cgroup
vagrant                      244810132 167773692  77036440  69% /vagrant
tmpfs                           100908         0    100908   0% /run/user/900

用方案二、三修改为50GB后，再下载trinity.sif还是未能成功，说明修改未彻底。于是换方法

反复尝试官方正解环境变量> 官方正解修改磁盘配置文件成功解决

分为2步

1. 在Vagrantfile配置文件中添加

config.vm.disk :disk, size: "50GB", primary: true

2. 激活环境变量export VAGRANT_EXPERIMENTAL="disks" 并vagrant up

#激活环境变量成功
export VAGRANT_EXPERIMENTAL="disks" && \
> vagrant up
==> vagrant: You have requested to enabled the experimental flag with the following features:
==> vagrant:
==> vagrant: Features:  disks
==> vagrant:
==> vagrant: Please use with caution, as some of the features may not be fully
==> vagrant: functional yet.

成功配置磁盘为50GB后的样子，注意还是原版的.vmdk文件，过程非常简洁

image.png

vagrant@vagrant:/fan_large$ df -h
Filesystem                    Size  Used Avail Use% Mounted on
udev                          464M     0  464M   0% /dev
tmpfs                          99M  532K   99M   1% /run
/dev/mapper/vagrant--vg-root   19G  5.8G   12G  33% /
tmpfs                         493M     0  493M   0% /dev/shm
tmpfs                         5.0M     0  5.0M   0% /run/lock
tmpfs                         493M     0  493M   0% /sys/fs/cgroup
vagrant                       234G  160G   75G  69% /vagrant
tmpfs                          99M     0   99M   0% /run/user/900

#未成功
INFO:    Creating SIF file...
FATAL:   While performing build: while creating SIF: while creating container: writing data object for SIF file: copying data object file to SIF file: write /fan_large/trinityrna.sif: no space left on device

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