Keck II System News and Updates

KeckII News

04/30/08 We will be switching our networking infrastructure today. This should result only in minimal (several seconds) network interruptions for each individual server. Sorry for the inconvenience. 04/04/08 The KeckII cluster frontend was rebooted around 1pm today. All running jobs were terminated. Sorry for the inconvenience. 03/06/08 All systems are up after a campus-wide power outage. 12/22/07 The KeckII cluster is back online. Please note that the cluster frontend erikson.ucsd.edu was moved to UCSD private network, its IP is now 172.23.128.50 and can be accessed only from within UCSD network. 12/13/07 The cluster frontend experienced a hard drive failure. The cluster will be inaccessible until the hard drive is replaced. Sorry for the inconvenience. 10/15/07 KeckII NIS server crashed this morning and this caused jobs to fail on the cluster. This problem has been fixed now. Sorry for the inconvenience. 10/10/07 New version of Gamess has been installed. See Keck2 software page for details. 07/02/07 A short power outage caused reboot of KeckII NFS servers early this morning and job interruption on the cluster. All systems are up and running now. Sorry for the inconvenience. 03/21/07 The KeckII stereo projector is fully functioning again. For information on how to use it with different applications please see Stereo Visualization How-To and Audio-Visual How-To. 03/20/07 11:53am We have experienced, together with a big part of the campus, a power outage which lasted 15 min. All Keck servers including the cluster are coming up, should be in production in the next 15 min. If you experience any problems please send email to keck-help. 02/14/07 Accelrys' software (InsightII, felix, etc.) is functional again although there is a limit on number of concurrent users. 07/31/06 A short power outage in the building forced reboot most of the cluster and termination of running jobs. Also most of the KeckII servers rebooted. Sorry for the inconvenience. 07/24/06 The Intel compilers have been upgraded to the latest version, 9.1. 06/12/06 Cambridge Structural Database has been updated to the latest version. 05/23/06 MGLTools version 1.4.1 package was installed (both sgi and linux versions). This contains AutoDock Tools for use with AutoDock. 04/19/06 cortez is back on-line. 04/18/06 cortez is down. The reason is being investigated, probably hardware failure. 02/16/06 The latest SUN development tools (Sun Studio 11) have been installed on cabot and cabrillo. For more detail see Compilers how-to. 02/16/06 10:40am A transient UPS failure brought down both NFS servers, all files should be accessible in 30 minutes. 02/14/06 We had two disk array failures today which could have caused login problems and job failures on the cluster. Sorry for the inconvenience. 12/01/05 A new linux workstation (serra) has been set up with stereo viewing capabilities. It allows to run, among others, InsightII and O applications in stereo mode. For more details please see stereo how-to page. 10/12/05 New version of NMRPipe has been installed. 09/28/05 New linux version of xmgrace has been installed in /soft/linux/pkg/grace. 08/15/05 9:55pm All systems are back on line. 08/12/05 All KeckII systems will be down for a scheduled maintenance on Monday Aug 15 starting at 8am. During this time failed drives in one of the KeckII arrays will be also replaced. This will take probably all day, maybe longer since it involves a large data transfer. You can check http://keck2.ucsd.edu during the day for updates on ETA. 07/20/05 The cluster has been upgraded to the latest Rocks 4.0.0. The scheduling system was also switched from PBS to SGE. For information on how to use SGE please see SGE how-to page. 07/18/05 The cluster upgrade which started today will extend until tomorrow. Please watch this space for updates. 06/17/05 The user directories are back on-line. Please send email to keck-help@keck2.ucsd.edu if you see any inconsistency in your data. 06/16/05 9:40am The NFS server is having a HW problem, not related to the disk array. The data transfer has been suspended until this is resolved. Please watch this space for updates. 06/15/05 9:55pm The data transfer from the backup is still undergoing. If everything goes well users should be able to access home directories early tomorrow (6/16/05). 06/13/05 12:11pm The replacement disks have been installed in the array and all data will be restored from the available backup. This will take several hours. 06/09/05 The replacement disks for the failed disk array have been ordered and should be here either tomorrow, on Friday or on Monday. 06/04/05 One of KeckII NFS disk arrays failed and some users won't be able to log in. We hope to have replacement disks here early next week. Sorry for the inconvenience. 05/17/05 Due to power shutdown in Urey Hall all Keck II computers including the cluster will be turned off late Friday (May 20, 2005). All servers should be back up on Saturday afternoon (May 21, 2005). 05/11/05 The latest version of pymol (0.97) has been installed on SGI's. To start it execute /soft/sgi/bin/pymol.com. 04/28/05 Keck II web server was moved from peary.ucsd.edu to livingstone.ucsd.edu. Mailing lists hosted on peary.ucsd.edu will follow shortly. If you observe any problems please send email to keck-help @ keck2.ucsd.edu 04/22/05 *** System PM Notice *** livingstone will be down for system upgrade on Monday (4/25/05) from 8am to 12pm. 03/31/05 *** System PM Notice *** Both NFS servers (cabrillo and cabot) will be down for preventive maintenance on Monday (4/4/05) from 8am to 12pm. All other systems will not be accessible during this time. 02/16/05 cabrillo, one of our NFS servers crashed and it is being rebooted. Some home directories may not be accessible at the moment. 01/10/05 Due to weather related power outage all servers were down from 8pm yesterday until 4am this morning. All systems are back up now. 09/21/04 The latest Intel compilers (icc/ifort) version 8.1 have been installed. See Compilers How-To page for more details. 07/08/04 The latest versions of CCP4 and CCP4i (version 5.0.1) have been installed on Linux and SGI's machines. For more details please see Keck II software page. 07/07/04 Crystallographic package Phaser version 1.2 has been installed on Linux and SGI's. For more details please see Keck II software page. 04/27/04 Matlab version 6.5.1 has been installed on all Unix workstation. For more details please see Keck II software page. 04/05/04 cabrillo - is back on line - thanks for your patience. 04/04/04 One of the NFS file servers - cabrillo - is experiencing hardware problems. This is being investigated. Some user home directories may not be accessible at this time. 03/31/04 cabrillo will be emergency rebooted today at 1pm. Some user directories won't be accessible during that period (5-10min). Sorry for any inconvenience. 03/29/04 Molden version 4.0 has been installed on all workstations in Keck II. Please see KeckII software page for more details. 03/26/04 Amber version 8 has been installed on the cluster. Please see Keck II software page for more details. 02/17/04 VMD has been upgraded to version 1.8.2 on SGI and Linux workstations. 01/25/04 New version of Intel C/C++/F77/F90 compilers (v8.0) has been installed on the cluster. For more information please see Compilers HOW-TO. 12/26/03 After a power failure in Urey Hall all systems are back on-line. All jobs running on the cluster at the time of the outage were purged. 11/25/03 New version of XPLOR-NIH (2.9.2) has been installed on SGI and Linux machines. 11/13/03 CCP4 has been updated to version 4.2.2 and the arp/warp interface has been fixed. 10/14/03 cabrillo crashed again this morning - it's back up now. 10/01/03 One of the NFS servers - cabrillo - and also the cluster frontend (erikson) crashed this morning. They will be up shortly. 09/29/03 The NIS server (peary) crashed early morning. This has been fixed and the server is up again. 09/14/03 One of the NFS servers (cabrillo) crashed today at 10am. It is back up but this downtime may have affected some jobs running on erikson. 08/04/03 ***** Scheduled KeckII System-wide Downtime ******* The two KeckII NFS servers will be down for system maintenance on Tuesday (8/5/03) from 8am to approx. 12pm. During this time user home directories will not be accessible. 07/24/03 One of the NFS servers (cabot) has been rebooted to fix an intermittent problem with a storage unit. 07/14/03 SGI chengho has been crashing in the last few days apparently due to a hardware failure. This is being investigated further. 05/28/03 BarcoReality 909 ultra-high resolution CRT projector has been installed in the KeckII room.This projector has both active and passive stereo projection capability. For more information please see A/V How-To.. 03/31/03 EPMR and sparky software suits have been installed. For more information please see keck2.ucsd/edu/software.html. 03/26/03 Newest version of XPLOR-NIH (2.0.6) has been installed. For more information please see keck2.ucsd/edu/software.html. 03/24/03 NOTICE: The two NFS servers - cabot and cabrillo - will be down for brief maintenance on Thursday (3/27/03) from 10am to 11am. During this time period some home directories will not be available. This also may interrupt some running jobs on the cluster. If you have any concerns or questions please contact keck-admin @ keck2.ucsd.edu. Thank you. 03/21/03 ARP/wARP - a software suite for improvement and objective interpretation of crystallographic electron density maps and automatic construction and refinement of macromolecular models - has been upgraded to version 6.0. 02/06/03 Intel compiler v.7.0 (icc/ifc) compiled GM version of MPICH library was installed in /soft/linux/share/mpich-gm.ifc. This should provide much better performance than the gcc/g77 version. Recompilation of your code which uses GM/MPICH with the new library is recommended. 01/08/03 Several different packages from Uppsala Software Factory have been installed. See http://keck2.ucsd.edu/software.html for more info. 12/19/02 SnB - a computer program based on Shake-and-Bake, a dual-space direct-methods procedure for determining crystal structures from X-ray diffraction data - has been installed on SGI's. 11/26/02 Intel compilers version 7.0 for Linux have been installed. Please see compilers howto for more information. 11/18/02 12:45pm cabrillo crashed again, it is being rebooted. 11/16/02 cabrillo has been fixed. 11/16/02 One of the NFS servers (cabrillo) crashed this morning so some user's home directories are not currently available. 10/31/02 Macromolecular crystallography package CCP4 was upgraded to version 4.2.1 Modeller - a program for homology or comparative modeling of protein three-dimensional structures - was installed on all three platforms. Please see software list for more details. 10/23/02 New version (0.2.4) of APBS has been installed in /soft/linux/share/apbs/bin (both serial and parallel executables). Please note that this is still beta version of the software. 04/23/02 Intel f77/f90 and c/c++ compilers version 6.0 for linux have been installed in /soft/linux/share/intel. Please see compilers howto for more information. 04/08/02 The NFS servers reboot will be done tomorrow (4/9/02) at 12pm instead of today. 04/08/02 The NFS servers (cabot and cabrillo) will be rebooted today around 2pm. 03/29/02 KeckII Center is featured in the NPACI and SDSC online news magazine. 03/28/02 4:45pm The data migration to the new storage units will still take another 5-8 hrs. All the KeckII systems except the cluster will be available tomorrow morning. 03/28/02 10:01am Due to unexpected delays in the upgrade process the KeckII systems are still unavailable. They are expected to be on-line by 8pm today. 03/25/02 Part of the storage RAID array failed today in the morning. Although there was no data lost the data recovery will take several hours. Until the reconstruction is completed users won't be able to access their home directories (note: that this effects only about 1/3 of users). 03/20/02 ***************************************************** ********** Scheduled System-wide Downtime *********** *** for Tuesday and Wednesday (3/26/02 - 3/27/02) *** ***************************************************** Due to a major upgrade of the storage facility at KeckII, all KeckII workstations including the cluster will be unavailable from Tuesday 3/26/02 starting at 12pm to Wednesday 3/27/02 until approx. 8pm. During this period SUN engineers will install two new T3 storage units (600GB each) and all home directories with user data will be transfered to the new T3 units. This upgrade should significantly improve NFS performance and expand available disk space. During this downtime period the clustering software on erikson will be upgraded to the latest Rocks version. It is anticipated that this upgrade will be finished also on Wednesday. The bottleneck of the upgrade process will be the transfer of the user data. Please, use this opportunity to clean up your home directories and back up all important and archive data to an off-site location. 02/07/02 Gaussian 98 and DL_POLY modeling packages have been installed. See the available software page for more details. 01/30/02 O, a macromolecular crystallographic modeling tool has been installed on all workstations. See the available software page for more details. 01/28/02 The Forte suite of SUN compilers (cc/CC/f77/f95) has been installed on cabot. For more information please see Compilers HOW-TO. 12/17/01 A high-end graphics system - SGI Onyx (serra.ucsd.edu) has been installed in the Center. This powerful system features 3 InfiniteReality graphics boards, 4 194MHz CPUs and 2 GB of memory. Currently, all users can access the onyx remotely, interactive logins will be enabled soon. 12/10/01 cook is back on-line. 11/13/01 cook is down, waiting for a replacement hardware part. 11/06/01 SSH has been upgraded on all workstations to OpenSSH_2.9.9p2 which supports both, 1.5 and 2.0 SSH protocols. If you have problems using it please see manual pages or use it in the version 1.0 compatibility mode: ssh -1. 11/02/01 CNS (crystallography and NMR software) has been upgraded to version 1.1 on SGI and SUN workstations and Linux version has been added. 10/08/01 cook is up but connected by fast ethernet only. Gigabit link will be up after the bad PCI cardcage is replaced. 10/02/01 StereoGraphics' CrystalEyes hardware has been installed on cortez. For more information on using CrystalEyes for stereo visualization please see Stereo how-to. 10/02/01 cook is down - a PCI bridge in the PCI cardcage went bad, will have to be replaced. 10/01/01 Condor has been upgraded to 6.2.1. 09/27/01 Failed hard drive has been replaced on mackenzie and mackenzie is back up. 09/20/01 One of the PCI slots in the PCI cardcage on cook has been diagnosed as bad. This has been fixed and cook is back up. 09/19/01 *** Scheduled Downtime for Thursday 9/27/01 from 8am to approx. 3pm *** A SUN engineer will be replacing failed memory on the NFS server (cabrillo) on Thursday morning. All users directories on the KeckII computers will be unavailable during this period, including the Linux cluster (erikson). All running jobs will most likely be terminated on Thursday (9/27/01) at 8am. This extended downtime will be also used for miscellaneous software and hardware upgrades. If you have any questions or concerns, please send email to keck-admin@keck2.ucsd.edu. Thank you. 09/17/01 cook is down - HW issues. 09/14/01 mackenzie (one of the SUN 80Ultra's) is down - HW problem. 08/29/01 PBS-HOWTO document has been added. Please read this carefully before submitting jobs on the cluster. 08/21/01 Several new crystallographic packages have been installed. Please see list of software for full list. 08/07/01 SGI binaries of Raster3D package have been installed. 08/06/01 3 dual CPU nodes have been re-added to the linux cluster after hardware maintenance. 07/15/01 ShelX Linux version has been installed and the SGI version updated. 07/09/01 ModelFree 4.10 and XtalView 4.1 software have been installed on SGIs. Please see software list for details. 07/05/01 Printing is now working on all Keck II computers. For usage please see printing HOW-TO page. 06/14/01 Jot users: Due to a GL bug in jot on our SGI's the jot editor has been replaced by 'nedit' (a symbolic link was made from /usr/sbin/jot to /usr/sbin/nedit - so when you call jot nedit will start up). Nedit is similar in functionality to jot. If you absolutely need to use jot - it is still available as //usr/sbin/jot.buggy - but bear in mind that you're risking crashing the system and you could loose your unsaved work. 06/14/01 The IP space reconfiguration in KeckII is finished. All systems including the cluster are up and running, printing is again functional from SGI's and Linux boxes. Please submit all non-interactive jobs on the cluster through PBS. 06/11/01 The linux cluster is down for system reconfiguration. It should be back up by tomorrow (6/12/01). 06/11/01 ***IP address change for Keck II computers *** Please note that we will be changing all IP addresses in Keck II this week. This change will be mostly transparent to the users (DNS records will be updated as well). However, you might experience problems when connecting to the computers this week - before all the changes are made permanent. In that case just use new numeric IP address. new address old address 132.239.16.130 132.239.16.194 cabot.ucsd.edu 132.239.16.131 132.239.16.195 cabrillo.ucsd.edu 132.239.16.132 132.239.16.196 mackenzie.ucsd.edu 132.239.16.133 132.239.16.197 peary.ucsd.edu 132.239.16.134 132.239.16.198 balboa.ucsd.edu 132.239.16.135 132.239.16.199 columbus.ucsd.edu 132.239.16.136 132.239.16.200 thompson.ucsd.edu 132.239.16.137 132.239.16.201 cortez.ucsd.edu 132.239.16.138 132.239.16.202 chengho.ucsd.edu 132.239.16.139 132.239.16.203 cook.ucsd.edu 132.239.16.140 132.239.16.204 polo.ucsd.edu 132.239.16.141 132.239.16.205 livingstone.ucsd.edu 132.239.16.142 132.239.16.206 erikson.ucsd.edu 06/04/01 The Linux cluster is fully functional now (with 33 dual nodes) including the PBS queuing system. Please submit all your jobs through PBS. If you need CPU time for interactive work - contact me. Please report any system irregularities or problems to keck-admin@keck2.ucsd.edu. 06/02/01 Due to unexpected problems the user logins are disabled on erikson. We will be enabling them again tomorrow or on Monday morning. 05/30/01 ** System Downtime Announcement ** The linux cluster (erikson) will be down on Friday, June 1st, from 7:30am to approx. 4:00pm for maintenance and system upgrade. We will be installing new Rocks cluster distribution and resolving some hardware issues. Sorry for any inconvenience this may cause. 05/29/01 7:15am Due to a power outage all computing nodes of the linux cluster are down. 2:30pm The cluster (except one node - compute-0-17) is back up. 05/24/01 We are currently in the process of reorganizing and consolidating the Keck II IP space. This should be finished the week of June 4th. There should not be any significant interruption of any services in Keck II with the exception of printing. Currently, the only way to print your documents is to do it from livingstone (linux workstation). If you notice any other unexpected behavior please report it to keck-help @ keck2.ucsd.edu. Thank you.