Difference between revisions of "Prometheus.uio.no"
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prometheus.uio.no is the front-end node for the NCMM cryoSPARC platform. | prometheus.uio.no is the front-end node for the NCMM cryoSPARC platform. | ||
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[https://cryosparc.com/ cryoSPARC] is a platform used for obtaining 3D structural information from single-particle cryoEM data | [https://cryosparc.com/ cryoSPARC] is a platform used for obtaining 3D structural information from single-particle cryoEM data | ||
| + | == Preparing the host == | ||
| + | |||
| + | (from jump-biotek) | ||
| + | ssh prometheus.uio.no | ||
| + | |||
| + | |||
| + | === Configuring the virsh serial port for the guest OS === | ||
| + | cp /etc/default/grub /etc/default/grub.orig | ||
| + | vi /etc/default/grub | ||
| + | insert the following lines for serial console: | ||
| + | GRUB_TIMEOUT=5 | ||
| + | GRUB_DISTRIBUTOR="$(sed 's, release .*$,,g' /etc/system-release)" | ||
| + | GRUB_DEFAULT=saved | ||
| + | GRUB_DISABLE_SUBMENU=true | ||
| + | GRUB_TERMINAL_OUTPUT="console serial" | ||
| + | GRUB_CMDLINE_LINUX="crashkernel=auto rd.lvm.lv=internvg/root rd.lvm.lv=internvg/swap rd.lvm.lv=internvg/usr console=tty1 console=ttyS0,115200" | ||
| + | GRUB_SERIAL_COMMAND="serial --speed=115200 --unit=0 --word=8 --parity=no --stop=1" | ||
| + | GRUB_DISABLE_RECOVERY="true" | ||
| + | |||
| + | cp /boot/grub2/grub.cfg /boot/grub2/grub.cfg.orig | ||
| + | grub2-mkconfig -o /boot/grub2/grub.cfg | ||
| + | systemctl reboot | ||
| + | |||
| + | === Installing base-line software and prerequisites === | ||
| + | |||
| + | yum install fail2ban* vim* etckeeper* git* collectd* lm_* ncdu bzip2 --skip-broken | ||
| + | |||
| + | |||
| + | === Allocating extra space for the /lsc partition | ||
| + | |||
| + | parted /dev/vdb | ||
| + | (parted) mklabel gtp | ||
| + | New disk label type? gpt | ||
| + | mkpart primary xfs 1 -1 | ||
| + | (parted) p | ||
| + | Model: Virtio Block Device (virtblk) | ||
| + | Disk /dev/vdb: 42.9GB | ||
| + | Sector size (logical/physical): 512B/512B | ||
| + | Partition Table: gpt | ||
| + | Disk Flags: | ||
| + | |||
| + | Number Start End Size File system Name Flags | ||
| + | 1 1049kB 42.9GB 42.9GB primary | ||
| + | |||
| + | (parted) quit | ||
| + | Information: You may need to update /etc/fstab. | ||
| + | quit | ||
| − | [[ | + | [root@prometheus ~]# mkfs.xfs /dev/vdb1 |
| + | meta-data=/dev/vdb1 isize=512 agcount=4, agsize=2621312 blks | ||
| + | = sectsz=512 attr=2, projid32bit=1 | ||
| + | = crc=1 finobt=0, sparse=0 | ||
| + | data = bsize=4096 blocks=10485248, imaxpct=25 | ||
| + | = sunit=0 swidth=0 blks | ||
| + | naming =version 2 bsize=4096 ascii-ci=0 ftype=1 | ||
| + | log =internal log bsize=4096 blocks=5119, version=2 | ||
| + | = sectsz=512 sunit=0 blks, lazy-count=1 | ||
| + | realtime =none extsz=4096 blocks=0, rtextents=0 | ||
| + | [root@prometheus ~]# blkid /dev/vdb1 | ||
| + | /dev/vdb1: UUID="450b41db-e9a4-49df-beb5-d4ccef7461a3" TYPE="xfs" PARTLABEL="primary" PARTUUID="d189b7ce-c419-4457-9281-13b9f988caa6" | ||
| − | + | === Mounting /lsc ==== | |
| − | |||
| − | |||
| − | |||
| − | + | #add an auxiliary space under /lsc | |
| − | + | vi /etc/fstab | |
| − | + | #RT 3485324 | |
| − | + | UUID=450b41db-e9a4-49df-beb5-d4ccef7461a3 /lsc xfs defaults 0 0 | |
| − | + | mount /dev/vdb1 /lsc | |
| − | + | df -h | |
| − | + | umount /lsc | |
| − | + | mount -a | |
| − | + | df -h | |
| − | |||
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Revision as of 16:09, 17 July 2019
prometheus.uio.no is the front-end node for the NCMM cryoSPARC platform.
cryoSPARC is a platform used for obtaining 3D structural information from single-particle cryoEM data
Contents
Preparing the host
(from jump-biotek) ssh prometheus.uio.no
Configuring the virsh serial port for the guest OS
cp /etc/default/grub /etc/default/grub.orig vi /etc/default/grub insert the following lines for serial console: GRUB_TIMEOUT=5 GRUB_DISTRIBUTOR="$(sed 's, release .*$,,g' /etc/system-release)" GRUB_DEFAULT=saved GRUB_DISABLE_SUBMENU=true GRUB_TERMINAL_OUTPUT="console serial" GRUB_CMDLINE_LINUX="crashkernel=auto rd.lvm.lv=internvg/root rd.lvm.lv=internvg/swap rd.lvm.lv=internvg/usr console=tty1 console=ttyS0,115200" GRUB_SERIAL_COMMAND="serial --speed=115200 --unit=0 --word=8 --parity=no --stop=1" GRUB_DISABLE_RECOVERY="true"
cp /boot/grub2/grub.cfg /boot/grub2/grub.cfg.orig grub2-mkconfig -o /boot/grub2/grub.cfg systemctl reboot
Installing base-line software and prerequisites
yum install fail2ban* vim* etckeeper* git* collectd* lm_* ncdu bzip2 --skip-broken
=== Allocating extra space for the /lsc partition
parted /dev/vdb (parted) mklabel gtp New disk label type? gpt mkpart primary xfs 1 -1 (parted) p Model: Virtio Block Device (virtblk) Disk /dev/vdb: 42.9GB Sector size (logical/physical): 512B/512B Partition Table: gpt Disk Flags:
Number Start End Size File system Name Flags 1 1049kB 42.9GB 42.9GB primary
(parted) quit Information: You may need to update /etc/fstab. quit
[root@prometheus ~]# mkfs.xfs /dev/vdb1 meta-data=/dev/vdb1 isize=512 agcount=4, agsize=2621312 blks = sectsz=512 attr=2, projid32bit=1 = crc=1 finobt=0, sparse=0 data = bsize=4096 blocks=10485248, imaxpct=25 = sunit=0 swidth=0 blks naming =version 2 bsize=4096 ascii-ci=0 ftype=1 log =internal log bsize=4096 blocks=5119, version=2 = sectsz=512 sunit=0 blks, lazy-count=1 realtime =none extsz=4096 blocks=0, rtextents=0 [root@prometheus ~]# blkid /dev/vdb1 /dev/vdb1: UUID="450b41db-e9a4-49df-beb5-d4ccef7461a3" TYPE="xfs" PARTLABEL="primary" PARTUUID="d189b7ce-c419-4457-9281-13b9f988caa6"
Mounting /lsc =
- add an auxiliary space under /lsc
vi /etc/fstab
- RT 3485324
UUID=450b41db-e9a4-49df-beb5-d4ccef7461a3 /lsc xfs defaults 0 0 mount /dev/vdb1 /lsc df -h umount /lsc mount -a df -h
