Difference between revisions of "Prometheus.uio.no"
From medicin.ncmm.IT
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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. | ||
[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 | ||
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== Preparing the host == | == Preparing the host == | ||
| − | + | from jump-biotek, after | |
<pre>ssh prometheus.uio.no</pre> | <pre>ssh prometheus.uio.no</pre> | ||
=== Configuring the virsh serial port for the guest OS === | === Configuring the virsh serial port for the guest OS === | ||
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<pre> | <pre> | ||
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cp /etc/default/grub /etc/default/grub.orig | cp /etc/default/grub /etc/default/grub.orig | ||
vi /etc/default/grub | vi /etc/default/grub | ||
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systemctl reboot | systemctl reboot | ||
</pre> | </pre> | ||
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=== Installing base-line software and prerequisites === | === Installing base-line software and prerequisites === | ||
| − | yum install fail2ban* vim* etckeeper* git* collectd* lm_* ncdu bzip2 --skip-broken | + | <pre> |
| − | + | yum install -y fail2ban* vim* etckeeper* git* collectd* lm_* ncdu bzip2 lsof --skip-broken | |
| + | </pre> | ||
=== Allocating extra space for the /lsc partition === | === Allocating extra space for the /lsc partition === | ||
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parted /dev/vdb | parted /dev/vdb | ||
(parted) mklabel gtp | (parted) mklabel gtp | ||
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[root@prometheus ~]# blkid /dev/vdb1 | [root@prometheus ~]# blkid /dev/vdb1 | ||
/dev/vdb1: UUID="450b41db-e9a4-49df-beb5-d4ccef7461a3" TYPE="xfs" PARTLABEL="primary" PARTUUID="d189b7ce-c419-4457-9281-13b9f988caa6" | /dev/vdb1: UUID="450b41db-e9a4-49df-beb5-d4ccef7461a3" TYPE="xfs" PARTLABEL="primary" PARTUUID="d189b7ce-c419-4457-9281-13b9f988caa6" | ||
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Revision as of 16:19, 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, after
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 -y fail2ban* vim* etckeeper* git* collectd* lm_* ncdu bzip2 lsof --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"
