接續(xù)上篇，安裝好虛擬機(jī)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)
安裝現(xiàn)有鏡像資源
- 從docker hub安裝已有的鏡像
singularity build trinityrna.sif docker://trinityrnaseq/trinityrnaseq - 從Cloud Library安裝已有的鏡像
singularity build ubuntu.sif library://ubuntu
image.png
修改臨時(shí)文件存儲(chǔ)位置到非home目錄后依舊報(bào)錯(cuò)
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
-
此問題是由虛擬機(jī)創(chuàng)建時(shí)默認(rèn)磁盤大小是20GB，Trinity比較大，超過20GB，故而不能繼續(xù)寫入
image.png 嘗試解決方案一，增加磁盤容量，編輯Vagrantfile文件
VAGRANT_EXPERIMENTAL="disks"
config.vm.disk :disk, size: "30GB", primary: true
(該方案還是未能解決，添加環(huán)境變量方式錯(cuò)誤)
@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
#擴(kuò)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、三修改為50GB后，再下載trinity.sif還是未能成功，說明修改未徹底。于是換方法
反復(fù)嘗試官方正解環(huán)境變量> 官方正解修改磁盤配置文件成功解決
分為2步
- 在
Vagrantfile配置文件中添加
config.vm.disk :disk, size: "50GB", primary: true
- 激活環(huán)境變量
export VAGRANT_EXPERIMENTAL="disks"并vagrant up
#激活環(huán)境變量成功
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.
成功配置磁盤為50GB后的樣子，注意還是原版的.vmdk文件，過程非常簡(jiǎn)潔
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
