Difference between revisions of "Upgrading Endeavour"

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**Pre-reqs: yum install -y libtool openssl-devel libxml2-devel boost-devel gcc gcc-c++
 
**Pre-reqs: yum install -y libtool openssl-devel libxml2-devel boost-devel gcc gcc-c++
 
**Install hwloc: yum install -y hwloc
 
**Install hwloc: yum install -y hwloc
−
** ./configure --with-server-name=endeavour
+
** ./configure --with-default-server=endeavour
 
** make -j 8
 
** make -j 8
 +
**
  
 
= Upgrade main system =
 
= Upgrade main system =

Revision as of 14:52, 24 August 2017

Upgrade Nodes to Centos 7

  • Starting with Node2, which would not boot anyway since it kernel panicked.
    • Use USB boot stick.
    • - Configure "Compute Node" with legacy libraries, and NFS.
    • Edit the /etc/sysconfig/networking-scripts/ifcfg-enp5s0f0 to the address 10.0.0.2 netmask=255.255.0.0 gateway=10.0.0.100
    • Startup network.
    • Copy the dir /etc/ssh for ssh-keys.
    • Setup up /etc/yum.conf to use 10.0.0.100 as proxy.
    • Setup up /etc/resolv.conf to use our name servers.
    • install emacs
    • Set the hostname in /etc/hostname
    • Copy (node10) /etc/hosts
    • Copy/set /etc/resolve.conf
    • Setup LDAP and SSS (see Upgrading to Centos 7 )


Install Torque

Upgrade main system

Started with a sideways migration to Centos 5. This worked except for the infiniband packages, which were skipped:

New system @ Centos 6.6:

  • Reconfigured RAID. All the 2TB drives are now in slots 1-9 and configured for a RAID6, 14TB raid.
    • Slots 10,11,12 will be hot-spare, and 2x passthrough.
      • The passthrough are for: slot11 - Can contain Home directory drive when Gourd is being upgraded. slot12 -- OldSys a 1TB drive with the old Centos 5.5 system.
    • There are 3 volumes on the RAID: "system" ~ 100GB, "system2" ~100GB, "data1"
    • Remaining 12 slots will be filled with high density new drives for another RAID6
  • Restarted web server.
  • Setup fail2ban

Installing new RPMs on Nodes

  • The Centos DVDs are installed at /net/data/node10/RHEL/Centos-6.6
  • This dir is added to the c6-media in /etc/yum.repos.d/CentOS-Media.repo
  • Install packages with: yum --disablerepo \* --enablerepo c6-media install package_name

More recently, Endeavour is now a proxy server and yum on the nodes is setup to make use of the proxy. Thus "yum update" simply works.

Upgrading Endeavour nodes

Upgrade to Centos 6 started March 17, 2015 with node2:

  • Reboot Node2 from a USB key with Centos6 distribution installed. Chose "minimal install"
    • Note: Should have added scp, i.e openssh-client stuff. Added this "by hand" by using from endeavour: cat openssh-client-... | ssh node2 "cat - > openssh-client.rpm" and then installing that rpm.
  • SSH into the system
  • Copy the Centos ISO to node2 with scp. Mount on /mnt/centos
  • Install packages with: yum --disablerepo \* --enablerepo c6-media install
  • List of old package installed are in ~root/new_packages.txt with the distribution and package version stripped already. From this list, the packages were filtered into "installed" and "available" with yum. From the resulting list of "available" only the x86_64 and noarch packages were installed.
  • A number of config tweaks needed.
  • Nodes @ Centos 6.6
    • nodes: 2,3,7, 11, 13

Done

Node Cloning Recipe -- Adopted for Centos 7 --

Caveat Empor -- do not follow these steps blindly. These are notes from the procedure in 2015.

Prepare drive:

  1. If there is no label, or a new drive, or you did "dd if=/dev/zero of=/dev/sdb bs=1M bs=1000" to wipe it:
 parted /dev/sdb mislabel gpt
  1. else remove the old partitions
 parted /dev/sdb rm 1
 parted /dev/sdb rm 2
  1. create new partitions:
 parted /dev/sdb mkpart primary 1049kb 251MB
 parted /dev/sdb mkpart primary 251MB 100%
 parted /dev/sdb toggle 1 boot
  1. Boot Drive:
 mkfs.ext4 /dev/sdb1
 e2label /dev/sdb1 boot
 test -r /mnt/boot || mkdir -p /mnt/tmp_boot
 mount /dev/sdb1 /mnt/tmp_boot
 rsync  -avxHAX --numeric-ids /boot/  /mnt/tmp_boot
  1. Check to make sure it is all there.
  2. Rename node stuff -- This is Centos 6 only.
 cd /mnt/tmp_boot/grub
 sed 's/node2/node3/g' grub.conf  > tmp.conf && mv grub.conf grub.conf.orig && mv tmp.conf grub.conf
 sed 's/node2/node3/g' menu.lst  > tmp.lst && mv menu.lst menu.lst.orig && mv tmp.lst menu.lst
 cd /
 umount /dev/sdb1
  1. Create Logical volume sets:
  2. Is this does not work, it can be that 'old' lvm partitions are recognized. Use ls -l /dev/mapper to find out which and then destroy them. You can delete all the links, and then finally use 'dmsetup remove <diskname>' to get rid of them.
  pvcreate /dev/sdb2     
  vgcreate centos_node3 /dev/sdb2
 lvcreate -L 16G  -n swap  centos_node3
 lvcreate -l 100%FREE  -n root  centos_node3
 mkswap -L swap /dev/centos_node3/swap 
 mkfs.ext4 -L root /dev/centos_node3/root
  1. Copy data:
 cd /
 test -r /mnt/tmp_root || mkdir -p /mnt/tmp_root
 mount /dev/centos_node3/root /mnt/tmp_root
 mkdir  /mnt/tmp_root/proc /mnt/tmp_root/dev /mnt/tmp_root/tmp
 chmod 1777 /mnt/tmp_root/tmp
 chmod  555 /mnt/tmp_root/proc
 mkdir   /mnt/tmp_root/net  /mnt/tmp_root/srv  /mnt/tmp_root/sys /mnt/tmp_root/boot /mnt/tmp_root/data
 rsync  -avxHAX --numeric-ids bin etc lib lib64 media opt root sbin usr var /mnt/tmp_root
  1. Prep BOOT for grubbing
 mount /dev/sdb1 /mnt/tmp_root/boot
 mount -o bind /dev /mnt/tmp_root/dev
 mount -o bind /proc /mnt/tmp_root/proc
 chroot /mnt/tmp_root
  1. grub-install --recheck /dev/sdb # === Should work but fails
 grub << EOF
 root (hd1,0)
 setup (hd1)
 quit
 EOF
  1. Exit chroot
 exit
  1. Fixup /etc
 cd /mnt/tmp_root/etc
 rm -f udev/rules.d/70-persistent-net.rule
  1. fixup mtab fstab sysconfig/network sysconfig/network-scripts
 sed 's/node2/node3/g;/vg_node3/d' mtab > tmp.tmp && mv mtab mtab.orig && mv tmp.tmp mtab
 sed 's/node2/node3/g;' fstab > tmp.tmp && mv fstab fstab.orig && mv tmp.tmp fstab
 cd sysconfig
 sed 's/node2/node3/g;' network > tmp.tmp && mv network network.orig && mv tmp.tmp network
 cd network-scripts
 sed 's/10.0.0.2/10.0.0.3/g;/HWADDR/d;/UUID/d' ifcfg-eth0 > tmp.tmp && mv ifcfg-eth0 xx_ifcfg-eth0.orig && mv tmp.tmp ifcfg-eth0
 sed 's/10.1.0.2/10.1.0.3/g;/HWADDR/d;/UUID/d' ifcfg-ib0 > tmp.tmp && mv ifcfg-ib0 xx_ifcfg-ib0.orig && mv tmp.tmp ifcfg-ib0
 cd /
 umount /mnt/tmp_root/boot
 umount /mnt/tmp_root/dev
 umount /mnt/tmp_root/proc
 umount /mnt/tmp_root
 echo “ALL DONE - Shutdown the mother node, take out the 2nd hard drive, put it in the destiny node and boot that node. Repeat for next node.”

To Do

  • Configure MPI
    • Later. I'm not sure anyone is using this right now.
  • Reconfigure Ganglia
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