If Xen Administrator Console doesn't connect to XenServer or just hanged on than one needs to restart xenagentd daemon:
# service xenagentd restart
Friday, October 19, 2007
Wednesday, October 17, 2007
iRODS installation
Run under ordinary user, i.e. irodsmgr;
Create folder for irods and iRodsPostgress and change owner to irodsmgr;
Run install.pl and answer no on first question;
Edit irods/install/install.config:
set
$ADMIN_PW
$RESOURCE_NAME
variables
and uncomment $LOCALHOST="yes";
Run install.pl again.
Requirements for iRods and Postgress:
gcc and dependencies
gcc-c++ and dependencies
Create folder for irods and iRodsPostgress and change owner to irodsmgr;
Run install.pl and answer no on first question;
Edit irods/install/install.config:
set
$ADMIN_PW
$RESOURCE_NAME
variables
and uncomment $LOCALHOST="yes";
Run install.pl again.
Requirements for iRods and Postgress:
gcc and dependencies
gcc-c++ and dependencies
Xen P2V conversion
- Shutdown a VM
- Power off the VM
- Change HVM status to Enable and put XenServer.iso into CDROM
- Power on the VM
- Follow the conversion procedure
- Power off the old VM
- Rename the new VM
- Change MAC address
- Boot first time
- Switch off SELinux in /etc/selinux/config
- Reboot the VM
- Done.
Tuesday, September 4, 2007
Optimize MySQL table
For Sakai database the largest table is CONTENT_RESOURCE_BODY_BINARY.MYIOPTIMIZE TABLEshould be used if you have deleted a large part of a table or if you have made many changes to a table with variable-length rows (tables that haveVARCHAR,VARBINARY,BLOB, orTEXTcolumns).
It keeps all files uploaded to Resources Tool. After deleting some files from Resources this table might be fragmented. To optimize its internal structure it's possible to use a mysql command:
optimize table CONTENT_RESOURCE_BODY_BINARY;or mysql utility:
myisamchk -r --sort-index --analyze \Option -o (--safe-recover) instead of -r should be used if there is an error:
CONTENT_RESOURCE_BODY_BINARY.MYI
myisamchk: error: sort_buffer_size is to small
Tuesday, August 21, 2007
AIX: File too large
It happens when file size large then user's limit. To see limits use a command
# ulimit -a
Change limits:
/etc/security/limits
# ulimit -a
Change limits:
/etc/security/limits
Monday, August 6, 2007
Networking in XEN
During last startup of the Gateway server after last Saturday relocation I realized that network interfaces should be UP on boot.
network-bridges custom script:
This script calls original network-bridge.orig script from Xen installation. In such sequence all bridges started up correct and all interfaces work well. It is called from xend configuration file during xend loading.
network-bridges custom script:
#!/bin/sh
/etc/xen/scripts/network-bridge.orig $1 netdev=eth0 bridge=xenbr0 vifnum=0
/etc/xen/scripts/network-bridge.orig $1 netdev=eth1 bridge=xenbr1 vifnum=1
/etc/xen/scripts/network-bridge.orig $1 netdev=eth2 bridge=xenbr2 vifnum=2
/etc/xen/scripts/network-bridge.orig $1 netdev=eth3 bridge=xenbr3 vifnum=3
/etc/xen/scripts/network-bridge.orig $1 netdev=eth4 bridge=xenbr4 vifnum=4
/etc/xen/scripts/network-bridge.orig $1 netdev=eth5 bridge=xenbr5 vifnum=5
route add default gw 130.216.189.254
This script calls original network-bridge.orig script from Xen installation. In such sequence all bridges started up correct and all interfaces work well. It is called from xend configuration file during xend loading.
Friday, August 3, 2007
No space left on device /dev/null
If it's impossible to copy a file with a size more than a particular volume then very likely the reason of that that /dev/null has been overwritten by ordinary file:
# cat 1GB > /dev/null
cat: write error: No space left on device
A solution is to recreate /dev/null as a character file:
> rm -f /dev/null (get rid of the file I had put there)
> mknod /dev/null c 1 3 (some unix magic: char device, major #, minor #)
> chmod a+w /dev/null (permissions)
It works.
# cat 1GB > /dev/null
cat: write error: No space left on device
A solution is to recreate /dev/null as a character file:
> rm -f /dev/null (get rid of the file I had put there)
> mknod /dev/null c 1 3 (some unix magic: char device, major #, minor #)
> chmod a+w /dev/null (permissions)
It works.
Wednesday, August 1, 2007
BG2 - First Virtual Server
The specifications for the server are fairly minimal see below:…I suggest 1.5GB of RAM for the Windows 2003 Web/Nesstar server .
We should allow at least 2GB for all future servers.
Web/Nesstar server Hardware/Software Requirements:
Windows XP, 2000 or NT4.
Windows Server 2003
All Service Pack updates should be installed. (If you experience problems with the installation under NT4, check that the video drivers are up to date).
1GB of RAM (more is preferable)
1 GHz CPU or better. A biprocessor machine can be useful, especially during upgrading when the new and the old server might be running side-by-side.
Accessing WebView requires a web browser which is set to accept cookies and is
JavaScript enabled. Security and privacy settings should be set to accommodate this
requirement.
IIS (Internet Information Server) versions 5 or 6:
To install a Nesstar Server on a secondary IP address, please refer to the Nesstar
document on socket pooling.
We should allow at least 2GB for all future servers.
Web/Nesstar server Hardware/Software Requirements:
Windows XP, 2000 or NT4.
Windows Server 2003
All Service Pack updates should be installed. (If you experience problems with the installation under NT4, check that the video drivers are up to date).
1GB of RAM (more is preferable)
1 GHz CPU or better. A biprocessor machine can be useful, especially during upgrading when the new and the old server might be running side-by-side.
Accessing WebView requires a web browser which is set to accept cookies and is
JavaScript enabled. Security and privacy settings should be set to accommodate this
requirement.
IIS (Internet Information Server) versions 5 or 6:
To install a Nesstar Server on a secondary IP address, please refer to the Nesstar
document on socket pooling.
BeSTGRID Server 2
To configure and install appropriate software:
All done!
Download Xen EnterpriseAcquire a license for the ServerAcquire Windows Server 2003 distributiveApply for IP poolAcquire empty CDsBurn CDs with Xen imagesConfigure RAIDs on BeSTGRID2Install Xen Enterprise on BG2Install Admin Console on my PCInstall WinServer2003 on first VMCreate VMs for WAYF and OpenIdP
All done!
Monday, July 30, 2007
Start/Stop Samba
Now I've added Samba as a subsystem:
# mkssys -s smbd -p /opt/pware/samba/3.0.24/sbin/smbd -a "-D" -u 0
and on default it should start automatically during the system boot. If it isn't started try first:
# startsrc -s smbd
if unsuccessful try next:
# /opt/pware/samba/3.0.24/sbin/smbd -D
Other option is to use files:
/etc/rc.d/rc2.d/Ssmbd
/etc/rc.d/rc2.d/Ksmbd
Now they are in /home/akha103
# mkssys -s smbd -p /opt/pware/samba/3.0.24/sbin/smbd -a "-D" -u 0
and on default it should start automatically during the system boot. If it isn't started try first:
# startsrc -s smbd
if unsuccessful try next:
# /opt/pware/samba/3.0.24/sbin/smbd -D
Other option is to use files:
/etc/rc.d/rc2.d/Ssmbd
/etc/rc.d/rc2.d/Ksmbd
Now they are in /home/akha103
AVOIDING Disk Crashes
1. Rule One: don't let this stop your system
* RAID5 or mirror everything
2. Rule Two: monitor error logs
* Make sure you know when a disk failed
3. Rule Three: call hardware support
* That is what they are for
4. Rule Four: Don't meddle
* Only try, if you know what you are doing
5. Rule Five: Read and practise
* Get the Redbooks and try it safely
* RAID5 or mirror everything
2. Rule Two: monitor error logs
* Make sure you know when a disk failed
3. Rule Three: call hardware support
* That is what they are for
4. Rule Four: Don't meddle
* Only try, if you know what you are doing
5. Rule Five: Read and practise
* Get the Redbooks and try it safely
Formatted list of active Volume groups
for i in $(lsvg);do lsvg $i;done \
| awk ' BEGIN { printf("%10s\t%10s\t%10s\t%10s\t%10s\n","VG","Total(MB)","Free","USED","Disks") };/VOLUME GROUP:/ \
{ printf("%10s\t", $3) };/TOTAL PP/ { B=index($0,"(") + 1;E=index($0," megaby");D=E-B;printf("%10s\t", substr($0,B,D) );};/FREE PP/ \
{ B=index($0,"(") + 1;E=index($0," megaby");D=E-B;printf("%10s\t", substr($0,B,D) );};/USED PP/ \
{ B=index($0,"(") + 1;E=index($0," megaby");D=E-B;printf("%10s\t", substr($0,B,D) );};/ACTIVE PV/ { printf("%10s\t\n", $3) } '
| awk ' BEGIN { printf("%10s\t%10s\t%10s\t%10s\t%10s\n","VG","Total(MB)","Free","USED","Disks") };/VOLUME GROUP:/ \
{ printf("%10s\t", $3) };/TOTAL PP/ { B=index($0,"(") + 1;E=index($0," megaby");D=E-B;printf("%10s\t", substr($0,B,D) );};/FREE PP/ \
{ B=index($0,"(") + 1;E=index($0," megaby");D=E-B;printf("%10s\t", substr($0,B,D) );};/USED PP/ \
{ B=index($0,"(") + 1;E=index($0," megaby");D=E-B;printf("%10s\t", substr($0,B,D) );};/ACTIVE PV/ { printf("%10s\t\n", $3) } '
Friday, July 27, 2007
emails from NGData has root@bestgrid30.math.auckland.ac.nz in From:
All emails from NGData has root@bestgrid30.math.auckland.ac.nz in From: field.
The reason of that is I created CNAME ngdata.auckland.ac.nz for data.bestgrid.org (bestgrid30.math.auckland.ac.nz) long time ago. And in revers lookup mail server finds bestgrid30 as a sender domain.
I've applied to move ngdata.auckland.ac.nz from bg30 to bg4.
UPD: Fixed on 27.07.2007
The reason of that is I created CNAME ngdata.auckland.ac.nz for data.bestgrid.org (bestgrid30.math.auckland.ac.nz) long time ago. And in revers lookup mail server finds bestgrid30 as a sender domain.
I've applied to move ngdata.auckland.ac.nz from bg30 to bg4.
UPD: Fixed on 27.07.2007
Use correct CPU number
#!/bin/bash
#PBS -u user_name
#PBS -l nodes=1:ppn=8
#PBS -o $PBS_JOBNAME.out
#PBS -e $PBS_JOBNAME.err
#How many procs do I have?
NP=$(wc -l $PBS_NODEFILE | awk '{print $1}')
#cd into the directory where I typed qsub cd $PBS_O_WORKDIR
#run executable
mpiexec -np $NP executable
#PBS -u user_name
#PBS -l nodes=1:ppn=8
#PBS -o $PBS_JOBNAME.out
#PBS -e $PBS_JOBNAME.err
#How many procs do I have?
NP=$(wc -l $PBS_NODEFILE | awk '{print $1}')
#cd into the directory where I typed qsub cd $PBS_O_WORKDIR
#run executable
mpiexec -np $NP executable
Thursday, July 26, 2007
Pre-install of any APAC packages.
Pre-install of any APAC packages.
Edit to enable centosrepo:
# nano /etc/yum.repos.d/CentOS-Base.repo
# rpm --import http://mirror.centos.org/centos/4/os/i386/RPM-GPG-KEY-centos4
# cd /etc/yum.repos.d && wget http://www.grid.apac.edu.au/repository/dist/APAC-Grid.repo
# yum install Gpulse Gbuild
Check hostcert.*
openssl x509 -in hostcert.pem -noout -modulus
openssl rsa -in hostkey.pem -noout -modulus
Build NGData
/usr/local/sbin/BuildNgdataVdt161.sh
Edit to enable centosrepo:
# nano /etc/yum.repos.d/CentOS-Base.repo
# rpm --import http://mirror.centos.org/centos/4/os/i386/RPM-GPG-KEY-centos4
# cd /etc/yum.repos.d && wget http://www.grid.apac.edu.au/repository/dist/APAC-Grid.repo
# yum install Gpulse Gbuild
Check hostcert.*
openssl x509 -in hostcert.pem -noout -modulus
openssl rsa -in hostkey.pem -noout -modulus
Build NGData
/usr/local/sbin/BuildNgdataVdt161.sh
Wednesday, July 25, 2007
Current Disk Space Allocation on GateWay
XENHOST
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 9.7G 1.2G 8.0G 14% /
/dev/sda3 56G 5.1G 48G 10% /home
VMHOST
VG #PV #LV #SN Attr VSize VFree
VolumeGroup00 1 29 0 wz--n- 409.84G 326.43G
LV VG Attr LSize
GridSphereR VolumeGroup00 -wi-ao 2.00G
GridSphereS VolumeGroup00 -wi-ao 512.00M
LanguageR VolumeGroup00 -wi-ao 2.00G
LanguageS VolumeGroup00 -wi-ao 512.00M
NG2Root VolumeGroup00 -wi-ao 16.00G
NG2Swap VolumeGroup00 -wi-ao 512.00M
OpenIdpR VolumeGroup00 -wi-ao 2.00G
OpenIdpS VolumeGroup00 -wi-ao 512.00M
SRSData VolumeGroup00 -wi-ao 20.00G
SRSRoot VolumeGroup00 -wi-ao 1.50G
SRSSwap VolumeGroup00 -wi-ao 512.00M
SakaiR VolumeGroup00 -wi-ao 8.00G
SakaiS VolumeGroup00 -wi-ao 512.00M
SakaitR VolumeGroup00 -wi-a- 8.00G
SakaitS VolumeGroup00 -wi-a- 512.00M
ServicesR VolumeGroup00 -wi-ao 4.00G
ServicesS VolumeGroup00 -wi-ao 512.00M
SolverR VolumeGroup00 -wi-ao 1.49G
SolverS VolumeGroup00 -wi-ao 512.00M
SolverU VolumeGroup00 -wi-ao 1.50G
VreR VolumeGroup00 -wi-ao 2.00G
VreS VolumeGroup00 -wi-ao 512.00M
VreU VolumeGroup00 -wi-ao 1.50G
WayfR VolumeGroup00 -wi-ao 2.00G
WayfS VolumeGroup00 -wi-ao 512.00M
WikiProdR VolumeGroup00 -wi-ao 2.93G
WikiProdS VolumeGroup00 -wi-ao 512.00M
WikiR VolumeGroup00 -wi-ao 2.00G
WikiS VolumeGroup00 -wi-ao 512.00M
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 9.7G 1.2G 8.0G 14% /
/dev/sda3 56G 5.1G 48G 10% /home
VMHOST
VG #PV #LV #SN Attr VSize VFree
VolumeGroup00 1 29 0 wz--n- 409.84G 326.43G
LV VG Attr LSize
GridSphereR VolumeGroup00 -wi-ao 2.00G
GridSphereS VolumeGroup00 -wi-ao 512.00M
LanguageR VolumeGroup00 -wi-ao 2.00G
LanguageS VolumeGroup00 -wi-ao 512.00M
NG2Root VolumeGroup00 -wi-ao 16.00G
NG2Swap VolumeGroup00 -wi-ao 512.00M
OpenIdpR VolumeGroup00 -wi-ao 2.00G
OpenIdpS VolumeGroup00 -wi-ao 512.00M
SRSData VolumeGroup00 -wi-ao 20.00G
SRSRoot VolumeGroup00 -wi-ao 1.50G
SRSSwap VolumeGroup00 -wi-ao 512.00M
SakaiR VolumeGroup00 -wi-ao 8.00G
SakaiS VolumeGroup00 -wi-ao 512.00M
SakaitR VolumeGroup00 -wi-a- 8.00G
SakaitS VolumeGroup00 -wi-a- 512.00M
ServicesR VolumeGroup00 -wi-ao 4.00G
ServicesS VolumeGroup00 -wi-ao 512.00M
SolverR VolumeGroup00 -wi-ao 1.49G
SolverS VolumeGroup00 -wi-ao 512.00M
SolverU VolumeGroup00 -wi-ao 1.50G
VreR VolumeGroup00 -wi-ao 2.00G
VreS VolumeGroup00 -wi-ao 512.00M
VreU VolumeGroup00 -wi-ao 1.50G
WayfR VolumeGroup00 -wi-ao 2.00G
WayfS VolumeGroup00 -wi-ao 512.00M
WikiProdR VolumeGroup00 -wi-ao 2.93G
WikiProdS VolumeGroup00 -wi-ao 512.00M
WikiR VolumeGroup00 -wi-ao 2.00G
WikiS VolumeGroup00 -wi-ao 512.00M
Tuesday, July 24, 2007
Auckland is in APAC!!!
ng2.auckland.ac.nz is in APAC structure now!!!
It is in GOC database: http://goc.grid.apac.edu.au/
AUCKLAND site in APAC MDS/MIP database:
http://www.sapac.edu.au/webmds/webmds?info=indexinfo&xsl=apacgluexsl
Seek 'AUCKLAND' on the page.
Also ng2.auckland.ac.nz is visible in gcc GUI and even it's possible to submit jobs
for MrBayes calculation but they don't run good yet. I'm working on this.
It is in GOC database: http://goc.grid.apac.edu.au/
AUCKLAND site in APAC MDS/MIP database:
http://www.sapac.edu.au/webmds/webmds?info=indexinfo&xsl=apacgluexsl
Seek 'AUCKLAND' on the page.
Also ng2.auckland.ac.nz is visible in gcc GUI and even it's possible to submit jobs
for MrBayes calculation but they don't run good yet. I'm working on this.
Thursday, July 19, 2007
MrBayes Installation
To provide a service in Computation Grid I decided to install MrBayes.
The home of MrBayes is http://www.mrbayes.net/
The latest version is 3.1.2. In Linux environment this package should be compiled. First attempt to compile was unsuccessful with errors:
'apt-get install -f libreadline5-dev'
Then compilation of MrBayes performed well. Now I think I need to install lam-mpi package to make MrBayes mpi compatible. Currently no mpi packages are install on my head node.
The home of MrBayes is http://www.mrbayes.net/
The latest version is 3.1.2. In Linux environment this package should be compiled. First attempt to compile was unsuccessful with errors:
bayes.c:45:31: readline/readline.h: No such file or directory
bayes.c:46:30: readline/history.h: No such file or directory
MrBayes manual says:Depending on which platform/distribution the compilation is being performed on, it may be necessary to install relevent development libraries to enable compilation. Users of Ubuntu 5.10 (Breezy Badger), for instance, may need to install the either the libreadline4-dev or libreadline5-dev package to provide linking during compilation to GNU readline functionality.The first try to install libreadline5-dev requires to issue 'apt-get install -f' without any package to update system. After this command I could to install libreadline5-dev by:
'apt-get install -f libreadline5-dev'
Then compilation of MrBayes performed well. Now I think I need to install lam-mpi package to make MrBayes mpi compatible. Currently no mpi packages are install on my head node.
Tuesday, July 10, 2007
Yahoo! Test2 is running!
Final thing was a connecting between ng2:pbs-logmaker and bestgrid-02:pbs-telltail.
Because of bestgrid-02 is Debian box I had to modify startup file quite heavily. Modified lines are bolded:
I copied /usr/local/pbs-telltail/* from ng2 to bestgrid-02.
Copied pbs-telltail.RH to /etc/init.d/pbs-telltail
And modified as mentioned above. Than started this script.
Before a pbs job had stuck and displayed a message "Job Unsubmitted". After it goes further and display env variables as that specified in test2.rsl file (job description).
Because of bestgrid-02 is Debian box I had to modify startup file quite heavily. Modified lines are bolded:
stop and status options don't work. I will investigate this later.
#!/bin/sh
# pbs-telltail Starts/stops pbs-telltail daemon.
# Graham JenkinsNov. 2005. Modified: 20051220
#
# chkconfig: 2345 99 05
# description: pbs-telltail startup script
# Adjust as appropriate
REMOTES="ng2.auckland.ac.nz:2812"
[ -z "$PBS_HOME" ] && PBS_HOME=/opt/torque
[ -z "$TELLTAIL_HOME" ] && TELLTAIL_HOME=/usr/local/pbs-telltail
#. /etc/rc.d/init.d/functions
RETVAL=0
case "$1" in
start ) for Remote in $REMOTES ; do
Host=`echo $Remote | awk -F: '{print $1}'`
Port=`echo $Remote | awk -F: '{print $2}'`
echo -n "Starting pbs-telltail on host: $Host .. port: $Port .. "
$TELLTAIL_HOME/pbs-telltail $PBS_HOME/server_logs $Host $Port
RETVAL=$?; echo; [ $RETVAL -ne 0 ] && break
done
[ $RETVAL -eq 0 ] && touch /var/lock/subsys/pbs-telltail ;;
stop ) echo -n "Shutting down pbs-telltail .. "
killproc pbs-telltail
RETVAL=$?; echo
[ $RETVAL -eq 0 ] && rm -f /var/lock/subsys/pbs-telltail ;;
status) status pbs-telltail
RETVAL=$? ;;
* ) echo "Usage: $0 {start|stop|status}"; exit 1 ;;
esac
exit $RETVAL
I copied /usr/local/pbs-telltail/* from ng2 to bestgrid-02.
Copied pbs-telltail.RH to /etc/init.d/pbs-telltail
And modified as mentioned above. Than started this script.
Before a pbs job had stuck and displayed a message "Job Unsubmitted". After it goes further and display env variables as that specified in test2.rsl file (job description).
Submit PBS job from ng2
In my configuration there are 3 boxes: ng2, bestgrid-02 (pbs-server), bestgrid-01 (node). Submitting of PBS jobs requires following issues:
- All three boxes have to have common folder for user which has been used as a grid user. In my case it's grid-user. I've exported /home/grid-user from bestgrid-02 and mounted it to ng2 and bestgrid-01 into the same folder;
- Ideally that should be whole /home folder exported from another box (i.e. data.bestgrid.org) and mounted on all boxes in a chain ng2->pbs-server->nodes;
- grid-user has to have passwordless access between all boxes in the chain;
- In /home/grid-user/.ssh/known_hosts records for all boxes should be existed for short and long names;
- All boxes should be in /etc/hosts of each box.
Friday, July 6, 2007
One way password less SSH
For user who has to have password less SSH between two hosts, all files in .ssh folder of both hosts must have the same permission attributes:
-rw-r--r-- 1 grid-user grid-user 867 Jul 6 13:51 authorized_keysIn my case I could ssh from ng2 to bestgrid-02 but not back. After Anton's suggestion I found out that on ng2 file authorized_keys had -rw-rw-r-- permissions. After changing to -rw-r--r-- I could ssh from bestgrid to ng2 without password.
-rw------- 1 grid-user grid-user 668 Jun 27 15:27 id_dsa
-rw-r--r-- 1 grid-user grid-user 618 Jun 27 15:27 id_dsa.pub
-rw------- 1 grid-user grid-user 883 Jun 27 15:27 id_rsa
-rw-r--r-- 1 grid-user grid-user 238 Jun 27 15:27 id_rsa.pub
-rw------- 1 grid-user grid-user 554 Jun 27 15:27 identity
-rw-r--r-- 1 grid-user grid-user 358 Jun 27 15:27 identity.pub
-rw-r--r-- 1 grid-user grid-user 918 Jun 27 15:02 known_hosts
Thursday, June 28, 2007
qstat: cannot connect to server ... (errno=111)
I could pass this error only when commented lines
in ng2:auckland.ac.nz:/etc/services file.
I placed those line reading Vladimir's recommendations.
UPD: after some tests I've found out that it's enough to edit first line in this group. It should be pbs_server 15000/tcp and then pbs utilities can connect to pbs_server. Even if on the box where pbs_server is running this line should like that, otherwise pbs utilities don't see the pbs_server.
pbs 15000/tcp
pbs_dis 15001/tcp
pbs_dis 15001/udp
pbs_mom 15002/tcp
pbs_mom 15003/udp
pbs_mom 15003/tcp
pbs_sched 15004/tcp
in ng2:auckland.ac.nz:/etc/services file.
I placed those line reading Vladimir's recommendations.
UPD: after some tests I've found out that it's enough to edit first line in this group. It should be pbs_server 15000/tcp and then pbs utilities can connect to pbs_server. Even if on the box where pbs_server is running this line should like that, otherwise pbs utilities don't see the pbs_server.
unknown nfs status return value: -1
This error message might appear while mounting NFS share exported from AIX box.
That means an importer doesn't have a record in DNS database.
To solve just add an entry about the importer into /etc/hosts file.
Source...
That means an importer doesn't have a record in DNS database.
To solve just add an entry about the importer into /etc/hosts file.
Source...
Wednesday, June 20, 2007
Virtual File System Manager
Some things to remember while using Virtual File System Manager:
- It looks like in Windows environment VFSM requires domain name of remote host should be A record rather than CNAME; If domain name of a host is CNAME, VFSM can't connect to it with an error like this:
- In Linux environment VFSM can mount remote file system of a host with both kind of domain names (A record or CNAME);
- VFSM can copy files between remote file system and local file system and back and can't copy files between two remote file systems. If user copies files between two remote hosts then files aren't appeared on destination hosts but deleted from source host.
- To copy user needs to use shortcuts Ctrl+C and Ctrl+V instead of mouse drag-n-drop.
- If there was an attempt to get access to any folder but /tmp as Anonymous user then VFSM didn't give access even to /tmp folder. The best way I know is to restart VFSM.
- May be there are some more troubles but I didn't investigate them yet.
Tuesday, June 19, 2007
CRL has expired
That means Certificate Revocation List has been expired. This error may appear when create proxy with -verify option:
grid-proxy-init -verify -debug
It's a file in /etc/grid-sequrity/certificates/1e12d831.r0 (for APACGrid CA) Next Update is overdated. Current (for the date of this posting) CRL has inside:
It hasn't been updated on my bestgrid-02 machine automatically because on unknown reason a line to call fetch-crl.cron script disappeared from crontab file.
To update APACGrid CA CRL use link http://ca.apac.edu.au/pub/crl/cacrl.txt
and place this file as /etc/grid-sequrity/certificates/1e12d831.r0. Also to automatic updates it's a good idea to create cron task for daily or even hourly updates of CRL:
grid-proxy-init -verify -debug
It's a file in /etc/grid-sequrity/certificates/1e12d831.r0 (for APACGrid CA) Next Update is overdated. Current (for the date of this posting) CRL has inside:
Version 1 (0x0)
Signature Algorithm: md5WithRSAEncryption
Issuer: /C=AU/O=APACGrid/OU=CA/CN=APACGrid/emailAddress=camanager@vpac.org
Last Update: Jun 18 23:50:25 2007 GMT
Next Update: Jul 18 23:50:25 2007 GMT
It hasn't been updated on my bestgrid-02 machine automatically because on unknown reason a line to call fetch-crl.cron script disappeared from crontab file.
To update APACGrid CA CRL use link http://ca.apac.edu.au/pub/crl/cacrl.txt
and place this file as /etc/grid-sequrity/certificates/1e12d831.r0. Also to automatic updates it's a good idea to create cron task for daily or even hourly updates of CRL:
#!/bin/bash
# /opt/vdt/fetch-crl/share/doc/fetch-crl-2.6.2/fetch-crl.cron
# in crontab:
# 12 2 * * * /opt/vdt/fetch-crl/share/doc/fetch-crl-2.6.2/fetch-crl.cron
# Designed to be ran once a day.
if [ -f /etc/sysconfig/fetch-crl ] ; then
. /etc/sysconfig/fetch-crl
fi
CRLDIR=${CRLDIR:-/opt/vdt/globus/TRUSTED_CA/}
QUIET=${QUIET:-yes}
if [ $QUIET = "yes" ] ; then
/opt/vdt/fetch-crl/sbin/fetch-crl --loc $CRLDIR -out $CRLDIR -a 24 --quiet
else
/opt/vdt/fetch-crl/sbin/fetch-crl --loc $CRLDIR -out $CRLDIR
fi
Monday, June 18, 2007
Submitting Job to Run in Canterbury
To submit job on ng2.canterbury.ac.nz I needed to run ggc (https://www.seegrid.csiro.au/twiki/bin/view/Compsrvices/GenericGridGUI) and fill fields like that.
It's possible to see a new folder with output files using Virtual File System Manager (http://www.vpac.org/twiki/bin/view/Sandbox/UsingVFSManager).
More detailed description is in http://www.bestgrid.org/index.php/Getting_Started_with_BeSTGRIDs_Computational_GRID
Thursday, June 14, 2007
Transport e-mails to Sakai
Sakai has own SMTP server - James. To receive messages in Sakai mailhost.auckland.ac.nz should forward messages to sakai.bestgrid.org. Now MailHost forwards messageg to services.bestgrid.org. It's a unneeded chain ring.
In sakai.properties set parameters for e-mails and use any dns IPs.
ToDo - ask Service Desk to redirect messages for *.bestgrid.org to sakai machine.
In sakai.properties set parameters for e-mails and use any dns IPs.
ToDo - ask Service Desk to redirect messages for *.bestgrid.org to sakai machine.
Friday, June 8, 2007
Adding user to Samba on AIX
edit file
/opt/pware/samba/3.0.24/lib/smb.conf
for each user add something like that
# A private directory, usable only by fred. Note that fred requires write
# access to the directory.
;[fredsdir]
; comment = Fred's Service
; path = /usr/somewhere/private
; valid users = fred
; public = no
; writable = yes
; printable = no
Create user account and set password:
/opt/pware/samba/3.0.24/bin/smbpasswd -a userupi
/opt/pware/samba/3.0.24/lib/smb.conf
for each user add something like that
# A private directory, usable only by fred. Note that fred requires write
# access to the directory.
;[fredsdir]
; comment = Fred's Service
; path = /usr/somewhere/private
; valid users = fred
; public = no
; writable = yes
; printable = no
Create user account and set password:
/opt/pware/samba/3.0.24/bin/smbpasswd -a userupi
Tuesday, June 5, 2007
Job submission (globusrun-ws)
- copy usercert.pem into ~/.globus folder
- copy userkey.pem into ~/.globus folder and change permissions to 600
- run grid-proxy-init -debug
- run globusrun-ws -Ft PBS -submit -S -c /bin/date
ng2 machine should be in acl_hosts list of PBS server (qmgr -c 'l s') and in /etc/hosts.equiv file
- copy userkey.pem into ~/.globus folder and change permissions to 600
- run grid-proxy-init -debug
- run globusrun-ws -Ft PBS -submit -S -c /bin/date
ng2 machine should be in acl_hosts list of PBS server (qmgr -c 'l s') and in /etc/hosts.equiv file
Friday, June 1, 2007
Xen error: Link veth4 is missing
On default Xen has four veths to communicate between bridges and real eths. If one uses a command:
to create bridge xenbr4 and connect it to eth4 then he receives a message with
Link veth4 is missing at the beginning. To fix that situation gateway.auckland.ac.nz:/boot/grup/grub.conf should be changed like this:
A number in netloop.nloopbacks parameter is equal to amount of real NICs. Real gateway server shoud be rebooted.
/etc/xen/scripts/network-bridge start netdev=eth4 bridge=xenbr4 vifnum=4
to create bridge xenbr4 and connect it to eth4 then he receives a message with
Link veth4 is missing at the beginning. To fix that situation gateway.auckland.ac.nz:/boot/grup/grub.conf should be changed like this:
kernel /boot/xen-3.gz dom0_mem=262144
module /boot/vmlinuz-2.6.16.33-xen ro root=LABEL=/ netloop.nloopbacks=8
module /boot/initrd.img-2.6.16.33-xen
A number in netloop.nloopbacks parameter is equal to amount of real NICs. Real gateway server shoud be rebooted.
Automate VM creation
To automate creation of VMs I developed a script based on VPAC recomendations:
Tar-ball 'vm-image-0.0.1.tar.bz2' is an image of fresh installed CentOS 4.0 on VM.
Both files reside in gateway.bestgrid.org:/etc/xen
#!/bin/sh
#Create a VM:
# allocate logical volumes for root and swap filesystems
# make swap and root filesystems
# untar VM image
# call editor to edit network configuration files
# copy and edit xen template
# create VM
#
#Parameters:
# $1 - Size for root filesystem
# $2 - Name of VM
#
#Author: Andrey Kharuk, 01/06/2007
#
if [ -z "$1" ]; then
echo " " >&2
echo "Usage: `basename $0` disksize(in Mb) VMname" >&2; exit 2
echo " " >&2
echo " " >&2
fi
lvcreate -L $1M -n $2R VolumeGroup00 ;
lvcreate -L 512M -n $2S VolumeGroup00 ;
mkswap /dev/VolumeGroup00/$2S ;
mkfs -t ext3 /dev/VolumeGroup00/$2R ;
mkdir /srv/$2 ;
mount -t ext3 /dev/VolumeGroup00/$2R /srv/$2 ;
cd /srv/$2 ;
tar xjpf /etc/xen/vm-image-0.0.1.tar.bz2 ;
nano /srv/$2/etc/sysconfig/network ;
nano /srv/$2/etc/sysconfig/network-scripts/ifcfg-eth0 ;
cp /etc/xen/template /etc/xen/$2 ;
nano /etc/xen/$2 ;
cd ..
umount /srv/$2 ;
xm create -c $2
Tar-ball 'vm-image-0.0.1.tar.bz2' is an image of fresh installed CentOS 4.0 on VM.
Both files reside in gateway.bestgrid.org:/etc/xen
Monday, May 21, 2007
globus-ws is on now (ng2.auckland.ac.nz)
To install hostcert I used a procedure from:
http://www.vpac.org/twiki/bin/view/APACgrid/HostCertRequestAPAC
globus-ws requires /etc/grid-cequirity/containercert.pem
I've created copies:
cp /etc/grid-cequirity/hostcert.pem /etc/grid-cequirity/containercert.pem
cp /etc/grid-cequirity/hostcert_request.pem /etc/grid-cequirity/containercert_request.pem
cp /etc/grid-cequirity/hostkey.pem /etc/grid-cequirity/containerkey.pem
Owner of those files is daemon:
-rw-r--r-- 1 daemon daemon 2630 May 21 00:02 containercert.pem
-rw-r--r-- 1 daemon daemon 1770 May 21 00:03 containercert_request.pem
-r-------- 1 daemon daemon 1679 May 21 00:03 containerkey.pem
To check the certificate use a command:
openssl verify -CApath /etc/grid-security/certificates /etc/grid-security/containercert.pem
http://www.vpac.org/twiki/bin/view/APACgrid/HostCertRequestAPAC
globus-ws requires /etc/grid-cequirity/containercert.pem
I've created copies:
cp /etc/grid-cequirity/hostcert.pem /etc/grid-cequirity/containercert.pem
cp /etc/grid-cequirity/hostcert_request.pem /etc/grid-cequirity/containercert_request.pem
cp /etc/grid-cequirity/hostkey.pem /etc/grid-cequirity/containerkey.pem
Owner of those files is daemon:
-rw-r--r-- 1 daemon daemon 2630 May 21 00:02 containercert.pem
-rw-r--r-- 1 daemon daemon 1770 May 21 00:03 containercert_request.pem
-r-------- 1 daemon daemon 1679 May 21 00:03 containerkey.pem
To check the certificate use a command:
openssl verify -CApath /etc/grid-security/certificates /etc/grid-security/containercert.pem
Tuesday, May 15, 2007
services.bestgrid.org
Established services on this host are:
- rsync
- mail server (under construction)
- Subversion server
tar: Removing leading '/' from member names
To eliminate this message while creating an archive file with tar use the following syntax:
> tar cj -C / var/www > backup.tar.bz2
instead of
> tar cjf backup.tar.bz2 /var/www
> tar cj -C / var/www > backup.tar.bz2
instead of
> tar cjf backup.tar.bz2 /var/www
Friday, May 11, 2007
Current Disk Space Allocation on GateWay
XENHOST
Filesystem Size Used Avail Use% Mounted on
/dev/sda1 9.7G 965M 8.2G 11% /
/dev/sda3 56G 4.3G 49G 8% /home
VMHOST
VG #PV #LV #SN Attr VSize VFree
VolumeGroup00 1 17 0 wz--n- 409.84G 342.86G
LV VG Attr LSize
GridSphereR VolumeGroup00 -wi-ao 2.00G
GridSphereS VolumeGroup00 -wi-ao 512.00M
LanguageR VolumeGroup00 -wi-ao 2.00G
LanguageS VolumeGroup00 -wi-ao 512.00M
NG2Root VolumeGroup00 -wi-ao 16.00G
NG2Swap VolumeGroup00 -wi-ao 512.00M
SRSData VolumeGroup00 -wi-ao 20.00G
SRSRoot VolumeGroup00 -wi-ao 1.50G
SRSSwap VolumeGroup00 -wi-ao 512.00M
SakaiR VolumeGroup00 -wi-ao 8.00G
SakaiS VolumeGroup00 -wi-ao 512.00M
SakaitR VolumeGroup00 -wi-a- 8.00G
SakaitS VolumeGroup00 -wi-a- 512.00M
ServicesR VolumeGroup00 -wi-ao 4.00G
ServicesS VolumeGroup00 -wi-ao 512.00M
SolverR VolumeGroup00 -wi-ao 1.49G
SolverS VolumeGroup00 -wi-ao 512.00M
Xen's VMs and IPs
In case to provide separate physical network interfaces for each BestGrid VM we need two IPs for each VM. One IP is for a bridge between NIC and VM and another one is for VM itself.
So to provide low IPs (189.2,3,4,5,6) for BeSTGrid GateWay VMs I need to swap NIC IPs to 189.38-42 range.
Unfortunately I have to state that our IP pool is over now. There are only two spare IPs - 189.37 and 189.43.
I'm going to start swap today after lunch.
So to provide low IPs (189.2,3,4,5,6) for BeSTGrid GateWay VMs I need to swap NIC IPs to 189.38-42 range.
Unfortunately I have to state that our IP pool is over now. There are only two spare IPs - 189.37 and 189.43.
I'm going to start swap today after lunch.
Thursday, May 10, 2007
Is it better than paper and simple notebook?
I try to follow my colleague Anton Gerdelan to keep a blog about my problems and achievements instead of to write then into a paper notebook. May be it's better... The bad thing is I can't keep here passwords for my stuff :)
But it's possible to keep it private... Hm... Anyway that's unsecured way to keep passwords here even in a private blog.
But it's possible to keep it private... Hm... Anyway that's unsecured way to keep passwords here even in a private blog.
Subscribe to:
Posts (Atom)