Changes in 74e8c8a: TK updates

				bch3-kirchhausen.md
			
          @@ -1,34 +1,44 @@

           <!-- --- title: BCH: Kirchhausen Lab  -->

           # Overview

          -SBGrid provides comprehensive system administration support for computers that are used for data collection and analysis with Lattice Light Sheet Microscopy (LLSM) in the Kirchhausen lab. 

          -All servers are on the HMS network and are are physically located in a BCH-IT managed network closet on the 3rd floor of CLSB. In case of an emergency, please notify BCH-IT so they can allow the SBGrid support team access to the room.

          +SBGrid provides comprehensive system administration support for computers that are used for data collection and analysis with Lattice Light Sheet Microscopy (LLSM) in the Kirchhausen lab. All servers are on the HMS network and are are physically located in a BCH managed network closet on the 3rd floor of CLSB. SBgrid also creates accounts on the Confocal data server on the BCH network.

          -Remote access to the file server is available to lab members upon approval. Please email the SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and CC your Lab Admin.

          +For access to the file servers is available to lab members upon approval. Please email the SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and CC your Lab Admin.

          -Lab workstations (OS X, Linux, Windows) are managed by lab members. Please contact your Lab Admin for help. There are 7 Linux workstations totalling 252 cores, 2 Mac Pros totalling 20 cores, and 3 Windows machines totalling 32 cores.

          +Lab workstations (OS X, Linux, Windows) are managed by lab members. Please contact your Lab Admin for help.

           [[_TOC_]]

           # Get Help

          -For general questions, email SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org)  and include your name and the name of your lab. Email questions about your software installation to [bugs@sbgrid.org](mailto:bugs@sbgrid.org).

          - 

          -New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.

          -In case of an emergency, BCH-IT should be notified to allow physical access to the SBGrid support team. Please contact [help@sbgrid.org](mailto:help@sbgrid.org) first if you have trouble accessing your data on the server.

          +For general questions and server conenction issues email SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org)  and include your name, your lab and workstation name.

          +

          +New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.

           # LLSM

          -The Lattice Light Sheet Microscopy (LLSM) setup consists of a 208-core compute workstation cluster located in the Warren Alpert Building, 

          -where the data is also acquired. This local cluster is connected via 80GB link aggregated fiber connections to the server infrastructure at the CLS building, where the data is stored and later archived to HMS storage.

          -A 41 TB capacity scratch fast SSD server is configured to allow temporary storage of the data being processed and is racked in the CLS building. It is also connected to a 261 TB capacity spinning disk data storage file server via 40GB copper links.

          +The Lattice Light Sheet Microscopy (LLSM) setup consists of a 208-core compute workstation cluster located in the Warren Alpert Building,

          +where the data is also acquired. This local cluster is connected via 80GB link aggregated fiber connections to the server infrastructure at the CLS building, where the data is stored and later archived to HMS storage. A 41 TB capacity scratch fast SSD server is configured to allow temporary storage of the data being processed and is racked in the CLS building. It is also connected to a 261 TB capacity spinning disk data storage file server via 40GB copper links.

          +

          +A new 348 CPU cluster is being provisioned. You can ssh with your labs account to tkv1.med.harvard.edu and submit your CPU job there. As the new Linux workstations are ser up in the lab jobs will be able to directly submit jobs from there.

          -# Data Backups

          -Full and incremental backups are made of SBGrid file servers, including your home and data directories. These backups are usually kept for three months. If you need a file restored, please contact us at [help@sbgrid.org](mailto:help@sbgrid.org).

          +# Data Storage

           Processed data copied to the **datasync2** directory and flagged to be archived are synced to HMS orchestra storage.

           On the main storage server, directories located at **/data1/home/tk/public/datasync2** must be flagged with a 'transfer.txt' file in order for the data to sync with Orchestra transfer node. Users must manually create the file. While transfering, a 'transfering.txt' file is created inside the directory. Once the transfer is done, a 'transfered.txt' file is created inside the same directory to indicate that it finished.

          +# Linux Systems mount points

          +

          +/tkstorage/data Current LLSM project folders

          +/tkstorage/data1expansion Current LLSM project folders

          +/tkstorage/home New cluster home folders

          +/tkstorage/sbgrid-share SBGrid use

          +/scratch SSD scratch Server

          +/vscratch New cluster NVME scratch storage

          +

           # Networking and General IT Support

          -For networking and general IT support, contact the Children’s help desk at (617) 919-4357 or at [help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu). HMS IT has access to the networking closets at the Warren Alpert Building.

          +

          +For networking and general IT support for lab system connected to the BCH network contact the Children’s help desk at (617) 919-4357 or at [help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu). HMS IT has access to the networking closets at the Warren Alpert Building.

          +

          +For compute workstations contact [help@sbgrid.org](mailto:help@sbgrid.org).

...	...	@@ -1,34 +1,44 @@
1	1	<!-- --- title: BCH: Kirchhausen Lab -->
2	2
3	3	# Overview
4		-SBGrid provides comprehensive system administration support for computers that are used for data collection and analysis with Lattice Light Sheet Microscopy (LLSM) in the Kirchhausen lab.
5	4
6		-All servers are on the HMS network and are are physically located in a BCH-IT managed network closet on the 3rd floor of CLSB. In case of an emergency, please notify BCH-IT so they can allow the SBGrid support team access to the room.
	5	+SBGrid provides comprehensive system administration support for computers that are used for data collection and analysis with Lattice Light Sheet Microscopy (LLSM) in the Kirchhausen lab. All servers are on the HMS network and are are physically located in a BCH managed network closet on the 3rd floor of CLSB. SBgrid also creates accounts on the Confocal data server on the BCH network.
7	6
8		-Remote access to the file server is available to lab members upon approval. Please email the SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and CC your Lab Admin.
	7	+For access to the file servers is available to lab members upon approval. Please email the SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and CC your Lab Admin.
9	8
10		-Lab workstations (OS X, Linux, Windows) are managed by lab members. Please contact your Lab Admin for help. There are 7 Linux workstations totalling 252 cores, 2 Mac Pros totalling 20 cores, and 3 Windows machines totalling 32 cores.
	9	+Lab workstations (OS X, Linux, Windows) are managed by lab members. Please contact your Lab Admin for help.
11	10
12	11	[[_TOC_]]
13	12
14	13	# Get Help
15		-For general questions, email SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and include your name and the name of your lab. Email questions about your software installation to [bugs@sbgrid.org](mailto:bugs@sbgrid.org).
16		-
17		-New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.
18	14
19		-In case of an emergency, BCH-IT should be notified to allow physical access to the SBGrid support team. Please contact [help@sbgrid.org](mailto:help@sbgrid.org) first if you have trouble accessing your data on the server.
	15	+For general questions and server conenction issues email SBGrid at [help@sbgrid.org](mailto:help@sbgrid.org) and include your name, your lab and workstation name.
	16	+
	17	+New lab members should contact [help@sbgrid.org](mailto:help@sbgrid.org) to complete their initial setup.
20	18
21	19	# LLSM
22		-The Lattice Light Sheet Microscopy (LLSM) setup consists of a 208-core compute workstation cluster located in the Warren Alpert Building,
23		-where the data is also acquired. This local cluster is connected via 80GB link aggregated fiber connections to the server infrastructure at the CLS building, where the data is stored and later archived to HMS storage.
24	20
25		-A 41 TB capacity scratch fast SSD server is configured to allow temporary storage of the data being processed and is racked in the CLS building. It is also connected to a 261 TB capacity spinning disk data storage file server via 40GB copper links.
	21	+The Lattice Light Sheet Microscopy (LLSM) setup consists of a 208-core compute workstation cluster located in the Warren Alpert Building,
	22	+where the data is also acquired. This local cluster is connected via 80GB link aggregated fiber connections to the server infrastructure at the CLS building, where the data is stored and later archived to HMS storage. A 41 TB capacity scratch fast SSD server is configured to allow temporary storage of the data being processed and is racked in the CLS building. It is also connected to a 261 TB capacity spinning disk data storage file server via 40GB copper links.
	23	+
	24	+A new 348 CPU cluster is being provisioned. You can ssh with your labs account to tkv1.med.harvard.edu and submit your CPU job there. As the new Linux workstations are ser up in the lab jobs will be able to directly submit jobs from there.
26	25
27		-# Data Backups
28		-Full and incremental backups are made of SBGrid file servers, including your home and data directories. These backups are usually kept for three months. If you need a file restored, please contact us at [help@sbgrid.org](mailto:help@sbgrid.org).
	26	+# Data Storage
29	27
30	28	Processed data copied to the datasync2 directory and flagged to be archived are synced to HMS orchestra storage.
31	29	On the main storage server, directories located at /data1/home/tk/public/datasync2 must be flagged with a 'transfer.txt' file in order for the data to sync with Orchestra transfer node. Users must manually create the file. While transfering, a 'transfering.txt' file is created inside the directory. Once the transfer is done, a 'transfered.txt' file is created inside the same directory to indicate that it finished.
32	30
	31	+# Linux Systems mount points
	32	+
	33	+/tkstorage/data Current LLSM project folders
	34	+/tkstorage/data1expansion Current LLSM project folders
	35	+/tkstorage/home New cluster home folders
	36	+/tkstorage/sbgrid-share SBGrid use
	37	+/scratch SSD scratch Server
	38	+/vscratch New cluster NVME scratch storage
	39	+
33	40	# Networking and General IT Support
34		-For networking and general IT support, contact the Children’s help desk at (617) 919-4357 or at [help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu). HMS IT has access to the networking closets at the Warren Alpert Building.
	41	+
	42	+For networking and general IT support for lab system connected to the BCH network contact the Children’s help desk at (617) 919-4357 or at [help.desk@childrens.harvard.edu](mailto:help.desk@childrens.harvard.edu). HMS IT has access to the networking closets at the Warren Alpert Building.
	43	+
	44	+For compute workstations contact [help@sbgrid.org](mailto:help@sbgrid.org).